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Sample records for cyclobutane thymine dimers

  1. Temperature-sensitive photoreactivation of cyclobutane thymine dimer in soybean.

    Science.gov (United States)

    Yamamoto, Ayumi; Tanbir, Najrana; Hirouchi, Tokuhisa; Teranishi, Mika; Hidema, Jun; Morioka, Hiroshi; Yamamoto, Kazuo

    2008-03-01

    UV radiation induces the formation of two classes of photoproducts in DNA, the cyclobutane pyrimidine dimer (CPD) and the pyrimidine 6-4 pyrimidone photoproduct. CPDs in plants are repaired by class II CPD photolyase via a UV-A/blue light-dependent mechanism. The genes for the class II CPD photolyase have been cloned from higher plants such as Arabidopsis, Cucumis sativus (cucumber), Oryza sativa (rice) and Spinacia oleracea (spinach). Flavin adenine dinucleotide (FAD) has been identified as a cofactor. Here we report the isolation and characterization of the CPD photolyase cDNA from soybean (Glycin max). The sequence of amino acids predicted from the cDNA sequence was highly homologous to sequences of higher plant class II CPD photolyases. When the cDNA was expressed in a photolyase-deficient Escherichia coli, photoreactivation activity was partially restored by illumination with a fluorescent light. The purified enzyme showed CPD binding and light-dependent photoreactivation activities in vitro. When soybean CPD photolyase was heat-treated in vitro from 25 degrees C to 45 degrees C for 3 min, thymine dimer-binding activity and photoreactivation activity were decreased, and FAD was released from the enzyme. On the other hand, when the enzyme-CPD complex was heat-treated, photoreactivation activity was stable. We argue that FAD in the soybean CPD photolyase is labile for temperature, but once the enzyme-CPD complex has formed, FAD becomes tightly bound to the enzyme or complex.

  2. Ring opening of the cyclobutane in a thymine dimer radical anion.

    Science.gov (United States)

    Chatgilialoglu, Chryssostomos; Guerra, Maurizio; Kaloudis, Panagiotis; Houée-Lévin, Chantal; Marignier, Jean-Louis; Swaminathan, Vijay N; Carell, Thomas

    2007-01-01

    The reactions of hydrated electrons (e(aq) (-)) with thymine dimer 2 and thymidine have been investigated by radiolytic methods coupled with product studies, and addressed computationally by means of BB1K-HMDFT calculations. Pulse radiolysis revealed that one-electron reduction of the thymine dimer 2 affords the radical anion of thymidine (5) with t(1/2)thymine rings, undergoes a fast partially ionic splitting of the cyclobutane with a half-life of a few ps. This model fits with the in vivo observation of thymine dimer repair in DNA by photolyase. gamma-Radiolysis of thymine dimer 2 demonstrates that the one-electron reduction and the subsequent cleavage of the cyclobutane ring does not proceed by means of a radical chain mechanism, that is, in this model reaction the T(-)* is unable to transfer an electron to the thymine dimer 2.

  3. Chemical synthesis and translesion replication of a cis-syn cyclobutane thymine-uracil dimer.

    Science.gov (United States)

    Takasawa, Kohei; Masutani, Chikahide; Hanaoka, Fumio; Iwai, Shigenori

    2004-01-01

    The cytosine base in DNA undergoes hydrolytic deamination at a considerable rate when UV radiation induces formation of a cyclobutane pyrimidine dimer (CPD) with an adjacent pyrimidine base. We have synthesized a phosphoramidite building block of a cis-syn cyclobutane thymine-uracil dimer (T[]U), which is the deaminated form of the CPD at a TC site, and incorporated it into oligodeoxyribonucleotides. The previously reported method for synthesis of the thymine dimer (T[]T) was applied, using partially protected thymidylyl-(3'-5')-2'-deoxyuridine as the starting material, and after triplet- sensitized irradiation, the configuration of the base moiety in the major product was determined by NMR spectroscopy. Presence of the cis-syn cyclobutane dimer in the obtained oligonucleotides was confirmed by UV photoreversal and reaction with T4 endonuclease V. Using a 30mer containing T[]U, translesion synthesis by human DNA polymerase eta was analyzed. There was no difference in the results between the templates containing T[]T and T[]U and pol eta bypassed both lesions with the same efficiency, incorporating two adenylates. This enzyme showed fidelity to base pair formation, but this replication causes a C-->T transition because the original sequence is TC.

  4. Base pair opening in a deoxynucleotide duplex containing a cis-syn thymine cyclobutane dimer lesion.

    Science.gov (United States)

    Wenke, Belinda B; Huiting, Leah N; Frankel, Elisa B; Lane, Benjamin F; Núñez, Megan E

    2013-12-23

    The cis-syn thymine cyclobutane dimer is a DNA photoproduct implicated in skin cancer. We compared the stability of individual base pairs in thymine dimer-containing duplexes to undamaged parent 10-mer duplexes. UV melting thermodynamic measurements, CD spectroscopy, and 2D NOESY NMR spectroscopy confirm that the thymine dimer lesion is locally and moderately destabilizing within an overall B-form duplex conformation. We measured the rates of exchange of individual imino protons by NMR using magnetization transfer from water and determined the equilibrium constant for the opening of each base pair K(op). In the normal duplex K(op) decreases from the frayed ends of the duplex toward the center, such that the central TA pair is the most stable with a K(op) of 8 × 10⁻⁷. In contrast, base pair opening at the 5'T of the thymine dimer is facile. The 5'T of the dimer has the largest equilibrium constant (K(op) = 3 × 10⁻⁴) in its duplex, considerably larger than even the frayed penultimate base pairs. Notably, base pairing by the 3'T of the dimer is much more stable than by the 5'T, indicating that the predominant opening mechanism for the thymine dimer lesion is not likely to be flipping out into solution as a single unit. The dimer asymmetrically affects the stability of the duplex in its vicinity, destabilizing base pairing on its 5' side more than on the 3' side. The striking differences in base pair opening between parent and dimer duplexes occur independently of the duplex-single strand melting transitions.

  5. Kinetics of cyclobutane thymine dimer splitting by DNA photolyase directly monitored in the UV.

    Science.gov (United States)

    Thiagarajan, Viruthachalam; Byrdin, Martin; Eker, André P M; Müller, Pavel; Brettel, Klaus

    2011-06-07

    CPD photolyase uses light to repair cyclobutane pyrimidine dimers (CPDs) formed between adjacent pyrimidines in UV-irradiated DNA. The enzyme harbors an FAD cofactor in fully reduced state (FADH(-)). The CPD repair mechanism involves electron transfer from photoexcited FADH(-) to the CPD, splitting of its intradimer bonds, and electron return to restore catalytically active FADH(-). The two electron transfer processes occur on time scales of 10(-10) and 10(-9) s, respectively. Until now, CPD splitting itself has only been poorly characterized by experiments. Using a previously unreported transient absorption setup, we succeeded in monitoring cyclobutane thymine dimer repair in the main UV absorption band of intact thymine at 266 nm. Flavin transitions that overlay DNA-based absorption changes at 266 nm were monitored independently in the visible and subtracted to obtain the true repair kinetics. Restoration of intact thymine showed a short lag and a biexponential rise with time constants of 0.2 and 1.5 ns. We assign these two time constants to splitting of the intradimer bonds (creating one intact thymine and one thymine anion radical T(∘-)) and electron return from T(∘-) to the FAD cofactor with recovery of the second thymine, respectively. Previous model studies and computer simulations yielded various CPD splitting times between < 1 ps and < 100 ns. Our experimental results should serve as a benchmark for future efforts to model enzymatic photorepair. The technique and methods developed here may be applied to monitor other photoreactions involving DNA.

  6. Production of cis-syn thymine-thymine cyclobutane dimer oligonucleotide in the presence of acetone photosensitizer.

    Science.gov (United States)

    Mu, Wanmeng; Han, Qingkai; Luo, Zhaofeng; Wang, Yuzhen

    2006-06-01

    cis-syn Cyclobutane pyrimidine dimer (CPD) oligonucleotide was produced by UV irradiation in the presence of acetone photosensitizer. Acetone could enhance the productivity but evidently induced the photocleavage of oligonucleotide under a long time irradiation. A statistical approach of orthogonal design was applied to optimize the preparation condition for the production of the modified oligonucleotide. Optimal conditions for maximal cis-syn CPD oligonucleotide productivity were determined based on three factors: acetone concentration, initial oligonucleotide concentration, and irradiation time at several different levels. The optimal modified oligonucleotide that this optimization could produce was 32.7%. Through analysis of 20% polyacrylamide gel electrophoresis, it was found that modified oligonucleotide migrated slightly more slowly than the parent oligonucleotide. The photoreactivation of cis-syn thymine-thymine dimer oligonucleotide displayed the selectivity of the substrate specificity of DNA photolyase with high-performance liquid chromatography (HPLC) analysis.

  7. Femtosecond stimulated Raman spectroscopy of the cyclobutane thymine dimer repair mechanism: a computational study.

    Science.gov (United States)

    Ando, Hideo; Fingerhut, Benjamin P; Dorfman, Konstantin E; Biggs, Jason D; Mukamel, Shaul

    2014-10-22

    Cyclobutane thymine dimer, one of the major lesions in DNA formed by exposure to UV sunlight, is repaired in a photoreactivation process, which is essential to maintain life. The molecular mechanism of the central step, i.e., intradimer C-C bond splitting, still remains an open question. In a simulation study, we demonstrate how the time evolution of characteristic marker bands (C═O and C═C/C-C stretch vibrations) of cyclobutane thymine dimer and thymine dinucleotide radical anion, thymidylyl(3'→5')thymidine, can be directly probed with femtosecond stimulated Raman spectroscopy (FSRS). We construct a DFT(M05-2X) potential energy surface with two minor barriers for the intradimer C₅-C₅' splitting and a main barrier for the C₆-C₆' splitting, and identify the appearance of two C₅═C₆ stretch vibrations due to the C₆-C₆' splitting as a spectroscopic signature of the underlying bond splitting mechanism. The sequential mechanism shows only absorptive features in the simulated FSRS signals, whereas the fast concerted mechanism shows characteristic dispersive line shapes.

  8. Photocrosslinking of human telomeric G-quadruplex loops by anti cyclobutane thymine dimer formation

    National Research Council Canada - National Science Library

    Dian G. T. Su; Huafeng Fang; Michael L. Gross; John-Stephen A. Taylor

    2009-01-01

    .... UVB irradiation of d[AGGG(TTAGGG) 3 ] in the presence of Na + results in a cis,syn thymine dimer between two adjacent Ts in a TTA loop and a mixture of nonadjacent anti thymine dimers between various loops...

  9. Essential dynamics of DNA containing a cis.syn cyclobutane thymine dimer lesion.

    Science.gov (United States)

    Yamaguchi, H; van Aalten, D M; Pinak, M; Furukawa, A; Osman, R

    1998-01-01

    Conformational properties of a UV-damaged DNA decamer containing a cis.syn cyclobutane thymine dimer (PD) have been investigated by molecular dynamics (MD) simulations. Results from MD simulations of the damaged decamer DNA show a kink of approximately 21.7 degrees at the PD damaged site and a disruption of H bonding between the 5'-thymine of the PD and its complementary adenine. However, no extra-helical flipping of the 3'-adenine complementary to the PD was observed. Comparison to two undamaged DNA decamers, one with the same sequence and the other with an AT replacing the TT sequence, indicates that these properties are specific to the damaged DNA. Essential dynamics (ED) derived from the MD trajectories of the three DNAs show that the backbone phosphate between the two adenines complementary to the PD of the damaged DNA has considerably larger mobility than the rest of the molecule and occurs only in the damaged DNA. As observed in the crystal structure of T4 endonuclease V in a complex with the damaged DNA, the interaction of the enzyme with the damaged DNA can lead to bending along the flexible joint and to induction of adenine flipping into an extra-helical position. Such motions may play an important role in damage recognition by repair enzymes. PMID:9518486

  10. Triplet excited fluoroquinolones as mediators for thymine cyclobutane dimer formation in DNA.

    Science.gov (United States)

    Lhiaubet-Vallet, Virginie; Cuquerella, M Consuelo; Castell, Jose V; Bosca, Francisco; Miranda, Miguel A

    2007-06-28

    A series of fluoroquinolones (FQs), including enoxacin (ENX), pefloxacin (PFX), norfloxacin (NFX), its N(4')-acetyl derivative (ANFX), ofloxacin (OFX), and rufloxacin (RFX) have been investigated to determine their potential as DNA photosensitizers via thymine cyclobutane dimer (TT) formation in DNA. At fluoroquinolone concentrations and light doses insufficient to produce direct single strand breaks, ENX, PFX, and NFX were able to produce TT dimers in DNA, revealed by enzymatic treatment with T4 endonuclease V. By contrast, ANFX, OFX, and RFX were inefficient in this assay. The absolute values of the triplet energies of ENX, PFX, NFX, ANFX, OFX, and RFX were estimated by means of laser flash photolysis, using flurbiprofen, 4-biphenylcarboxylic acid, and naproxen as energy acceptors. They were found to be 273, 269, 269, 265, 262, and 253 kJ/mol, respectively. Other triplet excited state properties of the FQs, including quantum yields and lifetimes, were also studied. All the results indicate that the threshold ET value required for a given compound to become a potential DNA photosensitizer via TT formation is in the range defined by the triplet energies of NFX and ANFX (265-269 kJ/mol). This provides the basis for an alert rule: any chemical (drugs, cosmetics, pesticides, etc.) with higher ET has to be considered with regard to its potential photogenotoxicity.

  11. UV induction of cyclobutane thymine dimers in the DNA of cultured melanocytes from foreskin, common melanocytic nevi and dysplastic nevi

    Energy Technology Data Exchange (ETDEWEB)

    Noz, K.C.; Bergman, W.; Schothorst, A.A. (Univ. Hospital Leiden (Netherlands). Dept. of Dermatology); Roza, L. (TNO Medical Biological Lab., Rijswijk (Netherlands)); Darroudi, F. (Rijksuniversiteit Leiden (Netherlands). Lab. voor Stralengenetica en Chemische Mutagenese)

    1994-05-01

    We compared the induction of cyclobutane thymine dimers after exposure to 302 nm UV in foreskin-derived melanocytes and melanocytes from nevocellular nevi, as well as in melanocytes cultured from dysplastic nevi, precursor lesions of melanoma, derived from four, three and four individuals, respectively. Cyclobutane thymine dimers were quantified in situ by means of an immunofluorescence assay with a specific monoclonal antibody. A method was developed to compare separately performed experiments in a standardized manner. For melanocytes from each source, we demonstrated a linear relationship between UV dose and immunofluorescence. In nevocellular and dysplastic nevi, two subpopulations could be detected, distinguished by their nuclear size. Large nucleated nevocellular nevus cells were most susceptible to the induction of thymine dimers (49% higher induction compared to induction in foreskin melanocytes), while in normal-sized nuclei of these nevus cells the same induction of thymine dimers was found as in nuclei from foreskin melanocytes. In contrast, large nucleated dysplastic nevus melanocytes did not differ from the foreskin melanocytes, while normal-sized nuclei of dysplastic nevus cells showed a lower induction (32% lower induction than in foreskin melanocytes). (Author).

  12. Photocrosslinking of Human Telomeric G-Quadruplex Loops by "Anti" Cyclobutane Thymine Dimer Formation

    National Research Council Canada - National Science Library

    Dian G. T. Su; Huafeng Fang; Michael L. Gross; John-Stephen A. Taylor; Philip C. Hanawalt

    2009-01-01

    .... UVB irradiation of d[AGGG(TTAGGG)₃] in the presence of Na⁺ results in a cis, syn thymine dimer between two adjacent Ts in a TTA loop and a mixture of nonadjacent anti thymine dimers between various loops...

  13. Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Cyclobutane Dimers Formed via Photoreaction between a Thymine and a Toluene Residue in the Dinucleotide Framework

    Science.gov (United States)

    Liu, Degang; Zhou, Yan

    2012-01-01

    Substituted toluenyl groups are considered as close isosteres of the thymine residue. They can be recognized by DNA polymerases as if they were thymine. These toluene derivatives are generally inert toward radical additions, including the [2+2] photo-cycloadditions, due to the stable structure of the aromatic ring and are usually used as solvents for radical reactions. Surprisingly, after incorporating toluene into the dinucleotide framework, we found that the UV excited thymine residue readily dimerizes with the toluenyl moiety through a [2+2] photo-addition reaction. Furthermore, the reaction site on the toluenyl moiety is not the C5=C6 bond, as commonly observed in cyclobutane pyrimidine dimers, but the C4=C5 or C3=C4 instead. Such a reaction pattern suggests that in the stacked structure, it is one of these bonds, not the C5=C6, that is close to the thymine C5=C6 bond. A similar structural feature is found in DNA duplex with a thymine replaced by a 2,4-difluorotoluene. Our results argue that although the substituted toluenyl moieties closely mimic the size and shape of the thymine residue, their more hydrophobic nature determines that they stack on DNA bases differently from the natural thymine residue and likely cause local conformational changes in duplex DNA. PMID:22588824

  14. Unusual conformation of (dA)n.(dT)n-tracts as revealed by cyclobutane thymine-thymine dimer formation.

    OpenAIRE

    Lyamichev, V

    1991-01-01

    Cyclobutane dimer formation has been used to probe conformation of (dA)n.(dT)n-tracts cloned in plasmid DNA. The observed dimer probability patterns for (dA)n.(dT)n-tracts with n greater than or equal to 4 exhibit maximum intensity at the 3'-terminal TT site of Tn-tract, whereas photoreactivity at all the other TT sites is inhibited. Both the temperature and dimethyl sulfoxide increase dimer formation within Tn-tracts and result in an even dimer pattern. The data obtained have been interprete...

  15. Photoinduced dissociation of cyclobutane thymine dimer studied by semiclassical dynamics simulation.

    Science.gov (United States)

    Dou, Yusheng; Xiong, Shanshan; Wu, Weifeng; Yuan, Shuai; Tang, Hong

    2010-10-05

    Photoinduced dissociation of the thymine dimer is studied in a semiclassical dynamics simulation. The simulation follows excitation of an isolated thymine dimer by a 25 fs fwhm laser pulse, and finds that dissociation proceeds via an asynchronously concerted mechanism, in which the C(5)-C(5)' bond breaks soon after application of the laser pulse, followed by cleavage of the C(6)-C(6)' bond. The dissociation results in two thymine monomers, one in an electronically excited state and the other in the ground state. The former decays to the electronic ground state through an avoided crossing induced by deformation of the pyrimidine ring at the C(5)' and C(6)' sites. Copyright 2010 Elsevier B.V. All rights reserved.

  16. Human Mitochondrial DNA Polymerase γ Exhibits Potential for Bypass and Mutagenesis at UV-induced Cyclobutane Thymine Dimers*

    Science.gov (United States)

    Kasiviswanathan, Rajesh; Gustafson, Margaret A.; Copeland, William C.; Meyer, Joel N.

    2012-01-01

    Cyclobutane thymine dimers (T-T) comprise the majority of DNA damage caused by short wavelength ultraviolet radiation. These lesions generally block replicative DNA polymerases and are repaired by nucleotide excision repair or bypassed by translesion polymerases in the nucleus. Mitochondria lack nucleotide excision repair, and therefore, it is important to understand how the sole mitochondrial DNA polymerase, pol γ, interacts with irreparable lesions such as T-T. We performed in vitro DNA polymerization assays to measure the kinetics of incorporation opposite the lesion and bypass of the lesion by pol γ with a dimer-containing template. Exonuclease-deficient pol γ bypassed thymine dimers with low relative efficiency; bypass was attenuated but still detectable when using exonuclease-proficient pol γ. When bypass did occur, pol γ misincorporated a guanine residue opposite the 3′-thymine of the dimer only 4-fold less efficiently than it incorporated an adenine. Surprisingly, the pol γ exonuclease-proficient enzyme excised the incorrectly incorporated guanine at similar rates irrespective of the nature of the thymines in the template. In the presence of all four dNTPs, pol γ extended the primer after incorporation of two adenines opposite the lesion with relatively higher efficiency compared with extension past either an adenine or a guanine incorporated opposite the 3′-thymine of the T-T. Our results suggest that T-T usually stalls mitochondrial DNA replication but also suggest a mechanism for the introduction of point mutations and deletions in the mitochondrial genomes of chronically UV-exposed cells. PMID:22194617

  17. Human mitochondrial DNA polymerase γ exhibits potential for bypass and mutagenesis at UV-induced cyclobutane thymine dimers.

    Science.gov (United States)

    Kasiviswanathan, Rajesh; Gustafson, Margaret A; Copeland, William C; Meyer, Joel N

    2012-03-16

    Cyclobutane thymine dimers (T-T) comprise the majority of DNA damage caused by short wavelength ultraviolet radiation. These lesions generally block replicative DNA polymerases and are repaired by nucleotide excision repair or bypassed by translesion polymerases in the nucleus. Mitochondria lack nucleotide excision repair, and therefore, it is important to understand how the sole mitochondrial DNA polymerase, pol γ, interacts with irreparable lesions such as T-T. We performed in vitro DNA polymerization assays to measure the kinetics of incorporation opposite the lesion and bypass of the lesion by pol γ with a dimer-containing template. Exonuclease-deficient pol γ bypassed thymine dimers with low relative efficiency; bypass was attenuated but still detectable when using exonuclease-proficient pol γ. When bypass did occur, pol γ misincorporated a guanine residue opposite the 3'-thymine of the dimer only 4-fold less efficiently than it incorporated an adenine. Surprisingly, the pol γ exonuclease-proficient enzyme excised the incorrectly incorporated guanine at similar rates irrespective of the nature of the thymines in the template. In the presence of all four dNTPs, pol γ extended the primer after incorporation of two adenines opposite the lesion with relatively higher efficiency compared with extension past either an adenine or a guanine incorporated opposite the 3'-thymine of the T-T. Our results suggest that T-T usually stalls mitochondrial DNA replication but also suggest a mechanism for the introduction of point mutations and deletions in the mitochondrial genomes of chronically UV-exposed cells.

  18. Recognition and repair of the cyclobutane thymine dimer, a major cause of skin cancers, by the human excision nuclease.

    Science.gov (United States)

    Reardon, Joyce T; Sancar, Aziz

    2003-10-15

    The cyclobutane thymine dimer is the major DNA lesion induced in human skin by sunlight and is a primary cause of skin cancer, the most prevalent form of cancer in the Northern Hemisphere. In humans, the only known cellular repair mechanism for eliminating the dimer from DNA is nucleotide excision repair. Yet the mechanism by which the dimer is recognized and removed by this repair system is not known. Here we demonstrate that the six-factor human excision nuclease recognizes and removes the dimer at a rate consistent with the in vivo rate of removal of this lesion, even though none of the six factors alone is capable of efficiently discriminating the dimer from undamaged DNA. We propose a recognition mechanism by which the low-specificity recognition factors, RPA, XPA, and XPC, act in a cooperative manner to locate the lesion and, aided by the kinetic proofreading provided by TFIIH, form a high-specificity complex at the damage site that initiates removal of thymine dimers at a physiologically relevant rate and specificity.

  19. Accumulation of the Cyclobutane Thymine Dimer in Defined Sequences of Free and Nucleosomal DNA

    Science.gov (United States)

    2013-08-01

    date. Introduction Covalent dimerization of adjacent thymines through a photo- chemical [2 + 2] reaction was first described over 50 years ago.1 The...endonuclease V after irradiation, polyacrylamide gel electrophoresis (8%) and phosphoimage analysis. The radio - labeled 5S gene as the free duplex and

  20. Photocrosslinking of human telomeric G-quadruplex loops by anti cyclobutane thymine dimer formation.

    Science.gov (United States)

    Su, Dian G T; Fang, Huafeng; Gross, Michael L; Taylor, John-Stephen A

    2009-08-04

    The unusual structural forms of telomere DNA, which protect the ends of chromosomes during replication, may render it vulnerable to unprecedented photodamage, possibly involving nonadjacent bases that are made proximate by folding. The G-quadruplex for the human telomere sequence consisting of a repeating d(TTAGGG) is one unusual form. Tel22, d[AGGG(TTAGGG)(3)], forms a basket structure in the presence of Na(+) and may form multiple equilibrating structures in the presence of K(+) with hybrid-type structures predominating. UVB irradiation of d[AGGG(TTAGGG)(3)] in the presence of Na(+) results in a cis,syn thymine dimer between two adjacent Ts in a TTA loop and a mixture of nonadjacent anti thymine dimers between various loops. Irradiation in the presence of K(+), however, produces, in addition to these same products, a large amount of specific anti thymine dimers formed between either T in loop 1 and the central T in loop 3. These latter species were not observed in the presence of Na(+). Interloop-specific anti thymine dimers are incompatible with hybrid-type structures, but could arise from a chair or basket-type structure or from triplex intermediates involved in interconverting these structures. If these unique nonadjacent anti thymine dimer photoproducts also form in vivo, they would constitute a previously unrecognized type of DNA photodamage that may interfere with telomere replication and present a unique challenge to DNA repair. Furthermore, these unusual anti photoproducts may be used to establish the presence of G-quadruplex or quadruplex-like structures in vivo.

  1. Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer.

    Science.gov (United States)

    Mendieta-Moreno, Jesús I; Trabada, Daniel G; Mendieta, Jesús; Lewis, James P; Gómez-Puertas, Paulino; Ortega, José

    2016-11-03

    The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

  2. Conical intersections S0/S1 of thymine mediating the non-radiative photodestruction of cyclobutane dimers: a CASSCF level study

    Science.gov (United States)

    Kancheva, P. B.; Delchev, V. B.

    2016-01-01

    Three new conical intersections S0/S1 (cis-anti, trans-syn and trans-anti) were fond which mediate the processes of photo-induced formation of cyclobutane thymine dimers. Their structures were optimized at the CASSCF(2,2) (Complete Active Space Self Consistent Field method) level of theory with the minimal bases set STO-3G*. The geometries were explored with respect to their structural and electron features. The found conical intersections S0/S1 give a clear indication that they could be included in the internal conversions of the 1ππ* excited states of the stacked dimers to cyclobutane photodimers and vice versa.

  3. Substituent effects on photosensitized splitting of thymine cyclobutane dimer by an attached indole.

    Science.gov (United States)

    Tang, Wenjian; Zhou, Hongmei; Wang, Jing; Pan, Chunxiao; Shi, Jingbo; Song, Qinhua

    2012-12-21

    In chromophore-containing cyclobutane pyrimidine dimer (CPD) model systems, solvent effects on the splitting efficiency may depend on the length of the linker, the molecular conformation, and the oxidation potential of the donor. To further explore the relationship between chromophore structure and splitting efficiency, we prepared a series of substituted indole-TT model compounds 2 a-2 g and measured their splitting quantum yields in various solvents. Two reverse solvent effects were observed: an increase in splitting efficiency in solvents of lower polarity for models 2 a-2 d with an electron-donating group (EDG), and vice versa for models 2 e-2 g with an electron-withdrawing group (EWG). According to the Hammett equation, the negative value of the slope of the Hammett plot indicates that the indole moiety during the TT-splitting reaction loses negative charge, and the larger negative value implies that the repair reaction is more sensitive to substituent effects in low-polarity solvents. The EDGs of the models 2 a-2 d can delocalize the charge-separated state, and low-polarity solvents make it more stable, which leads to higher splitting efficiency in low-polarity solvents. Conversely, the EWGs of models 2 e-2 g favor destabilization of the charge-separated state, and high-polarity solvents decrease the destabilization and hence lead to more efficient splitting in high-polarity solvents. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. DNA Repair by DNA: The UV1C DNAzyme Catalyzes Photoreactivation of Cyclobutane Thymine Dimers in DNA More Effectively than Their de Novo Formation.

    Science.gov (United States)

    Barlev, Adam; Sekhon, Gurpreet S; Bennet, Andrew J; Sen, Dipankar

    2016-11-01

    UV1C, a 42-nt DNA oligonucleotide, is a deoxyribozyme (DNAzyme) that optimally uses 305 nm wavelength light to catalyze photoreactivation of a cyclobutane thymine dimer placed within a gapped, unnatural DNA substrate, TDP. Herein we show that UV1C is also capable of photoreactivating thymine dimers within an authentic single-stranded DNA substrate, LDP. This bona fide UV1C substrate enables, for the first time, investigation of whether UV1C catalyzes only photoreactivation or also the de novo formation of thymine dimers. Single-turnover experiments carried out with LDP and UV1C, relative to control experiments with LDP alone in single-stranded and double-stranded contexts, show that while UV1C does modestly promote thymine dimer formation, its major activity is indeed photoreactivation. Distinct photostationary states are reached for LDP in its three contexts: as a single strand, as a constituent of a double-helix, and as a 1:1 complex with UV1C. The above results on the cofactor-independent photoreactivation capabilities of a catalytic DNA reinforce a series of recent, unexpected reports that purely nucleotide-based photoreactivation is also operational within conventional double-helical DNA.

  5. Calculated distortions of duplex DNA by a cis, syn cyclobutane thymine dimer are unaffected by a 3' TpA step.

    Science.gov (United States)

    Cooney, M G; Miller, J H

    1997-01-01

    Molecular dynamics simulations were performed on the duplex DNA dodecamers d(CGCGAA TT CGCG): d(CGCGAATTCGCG) and d(GCACGAA TT AAG): d(CTTAATTCGTGC), where TT denotes a cis, syn cyclobutane thymine dimer. The constant temperature and pressure algorithm of the AMBER 4.1 molecular-modeling package was used with explicit water and counterions, periodic boundary conditions and electrostatic interactions evaluated by the particle-mesh Ewald method. Results were analyzed by the CURVES algorithm and its implementation in DIALS and WINDOWS. Calculated distortions of DNA structure by the thymine dimer were qualitatively and quantitatively similar for the two sequences. Despite the enhanced flexibility of the native TpA dinucleotide step, major deviations from the B-DNA values of helicoidal parameters were found only at the Ap and p dinucleotide steps in both sequences. Only the AT base pairs of the two sequences that contain the 5' thymine of the dimers exhibited weakened Watson-Crick hydrogen bonds and anomalous stretching. Hence, we conclude that the pattern of structural perturbations responsible for recognition of cis, syn thymine dimers by repair enzymes is not sensitive to their sequence context. PMID:9060440

  6. 50 years thymine dimer.

    Science.gov (United States)

    Beukers, Rob; Eker, André P M; Lohman, Paul H M

    2008-03-01

    Fifty years ago thymine dimer was discovered in the Biochemical and Biophysical Laboratory of Delft Technological University, The Netherlands, by one of the authors of this review (Beukers) as the first environmentally induced DNA lesion. It is one of the photoproducts formed between adjacent pyrimidine bases in DNA by UV irradiation, currently known as cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts. Major lesions found in DNA after in vitro or in vivo UV irradiation are the cis-syn cyclobutane thymine dimer and the thymine-cytosine (6-4) photoproduct. Even after 50 years the study of photo-induced DNA lesions is still going on as is illustrated by the hundreds of papers published every year and the millions hits when browsing the internet for dimer-related information. Living organisms possess efficient and different mechanisms to repair detrimental lesions in their DNA. A unique mechanism to repair CPDs is reversion by either direct interaction with light of short wavelength or by enzymatic photoreactivation. Photophysical mechanisms that induce and reverse molecular bonds in biological macromolecules have been a main focus of research of the group in Delft in the middle of the last century. This review describes the break-through results of these studies which were the result of intense interactions between scientists in the fields of physics, organic chemistry and biochemistry. Philosophically, the "view" of the group in Delft was very appealing: since in nature photolesions are induced in DNA by the sun, how is it possible that repair of these lesions could be accomplished by the same energy source. Evolutionary, it is hardly possible to think of a more efficient repair mechanism.

  7. Cyclobutane Thymine Photodimerization Mechanism Revealed by Nonadiabatic Molecular Dynamics.

    Science.gov (United States)

    Rauer, Clemens; Nogueira, Juan J; Marquetand, Philipp; González, Leticia

    2016-12-14

    The formation of cyclobutane thymine dimers is one of the most important DNA carcinogenic photolesions induced by ultraviolet irradiation. The long debated question whether thymine dimerization after direct light excitation involves singlet or triplet states is investigated here for the first time using nonadiabatic molecular dynamics simulations. We find that the precursor of this [2 + 2] cycloaddition reaction is the singlet doubly π(2)π*(2) excited state, which is spectroscopically rather dark. Excitation to the bright (1)ππ* or dark (1)nπ* excited states does not lead to thymine dimer formation. In all cases, intersystem crossing to the triplet states is not observed during the simulated time, indicating that ultrafast dimerization occurs in the singlet manifold. The dynamics simulations also show that dimerization takes place only when conformational control happens in the doubly excited state.

  8. Solution-state Structure of a DNA Dodecamer Duplex Containing a Cis-syn Thymine Cyclobutane Dimer, the Major UV Photoproduct of DNA.

    Energy Technology Data Exchange (ETDEWEB)

    McAteer, Kathleen; Jing, Y; Kao, J; Taylor, J S.; Kennedy, Michael A.

    1998-10-09

    The solution structures of a duplex DNA dodecamer containing a cis-syn cyclobutane thymine dimer d(GCACGAAT[cs]TAAG).d(CTTAATTCG TGC) and its native parent sequence were determined using NMR data collected at 750 MHz. The dodecamer sequence corresponds to the section of a site-specific cis-syn dimer containing 49-mer that was found to be the binding site for the dimer-specific T4 denV endonuclease V repair enzyme by chemical and enzymatic footprinting experiments. Structures of both sequences were derived from NOE restrained molecular dynamics/simulated annealing calculations using a fixed outer layer of water and an inner dynamic layer of water with sodium counterions. The resulting structures reveal a subtle distortion to the phosphodiester backbone in the dimer-containing sequence which includes a BII phosphate at the T9pA10 junction immediately 3' to the dimer. The BII phosphate, established experimentally by analysis of the 31P chemical shifts and interpretation of the 3JP-H3' values using an optimized Karplus relationship, enables the DNA helix to accommodate the dimer by destacking the base 3' to the dimer. Furthermore, the structures provide explanations for the unusually shifted T8-N3H imino, A16-H2 and T8-Me proton resonances and T9pA10 (31)P NMR resonance and are consistent with bending, unwinding, and thermodynamic data.

  9. Structure determination of an interstrand-type cis-anti cyclobutane thymine dimer produced in high yield by UVB light in an oligodeoxynucleotide at acidic pH.

    Science.gov (United States)

    Su, Dian G T; Kao, Jeffrey L-F; Gross, Michael L; Taylor, John-Stephen A

    2008-08-27

    UVB irradiation of DNA produces photodimers in adjacent DNA bases and on rare occasions in nonadjacent bases. UVB irradiation (312 nm) of d(GTATCATGAGGTGC) gave rise to an unknown DNA photoproduct in approximately 40% yield at acidic pH of about 5. This product has a much shorter retention time in reverse phase HPLC compared to known dipyrimidine photoproducts of this sequence. A large upfield shift of two thymine H6 NMR signals and photoreversion to the parent ODN upon irradiation with 254 nm light indicates that the photoproduct is a cyclobutane thymine dimer. Exonuclease-coupled MS assay establishes that the photodimer forms between T2 and T7, which was confirmed by tandem mass spectrometric MS/MS identification of the endonuclease P1 digestion product pd(T2[A3])=pd(T7[G8]). Acidic hydrolysis of the photoproduct gave a product with the same retention time on reverse phase HPLC and the same MS/MS fragmentation pattern as authentic Thy[ c,a]Thy. 2D NOE NMR data are consistent with a cis-anti cyclobutane dimer between the 3'-sides of T2 and T7 in anti glycosyl conformations that had to have arisen from an interstand type reaction. In addition to pH dependency, the photoproduct yield is highly sequence specific and concentration dependent, indicating that it results from a higher order folded structure. The efficient formation of this interstrand-type photoproduct suggests the existence of a new type of folding motif and the possibility that this type of photoproduct might also form in other folded structures, such as G-quadruplexes and i-motif structures which can be now studied by the methods described.

  10. Thymine Dimer Formation probed by Time-Resolved Vibrational Spectroscopy

    Science.gov (United States)

    Schreier, Wolfgang J.; Schrader, Tobias E.; Roller, Florian O.; Gilch, Peter; Zinth, Wolfgang; Kohler, Bern

    Cyclobutane pyrimidine dimers are the major photoproducts formed when DNA is exposed to UV light. Femtosecond time-resolved vibrational spectroscopy reveals that thymine dimers are formed in thymidine oligonucleotides in an ultrafast photoreaction.

  11. Solution-state structure of a DNA dodecamer duplex containing a Cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA.

    Science.gov (United States)

    McAteer, K; Jing, Y; Kao, J; Taylor, J S; Kennedy, M A

    1998-10-09

    The solution structures of a duplex DNA dodecamer containing a cis-syn cyclobutane thymine dimer d(GCACGAAT[cs]TAAG).d(CTTAATTCG TGC) and its native parent sequence were determined using NMR data collected at 750 MHz. The dodecamer sequence corresponds to the section of a site-specific cis-syn dimer containing 49-mer that was found to be the binding site for the dimer-specific T4 denV endonuclease V repair enzyme by chemical and enzymatic footprinting experiments. Structures of both sequences were derived from NOE restrained molecular dynamics/simulated annealing calculations using a fixed outer layer of water and an inner dynamic layer of water with sodium counterions. The resulting structures reveal a subtle distortion to the phosphodiester backbone in the dimer-containing sequence which includes a BII phosphate at the T9pA10 junction immediately 3' to the dimer. The BII phosphate, established experimentally by analysis of the 31P chemical shifts and interpretation of the 3JP-H3' values using an optimized Karplus relationship, enables the DNA helix to accommodate the dimer by destacking the base 3' to the dimer. Furthermore, the structures provide explanations for the unusually shifted T8-N3H imino, A16-H2 and T8-Me proton resonances and T9pA10 (31)P NMR resonance and are consistent with bending, unwinding, and thermodynamic data. The implications of the structural data for the mechanism by which cis-syn dimers are recognized by repair enzymes and bypassed by DNA polymerases are also discussed. Copyright 1998 Academic Press.

  12. A cyclobutane thymine-N4-methylcytosine dimer is resistant to hydrolysis but strongly blocks DNA synthesis.

    Science.gov (United States)

    Yamamoto, Junpei; Oyama, Tomoko; Kunishi, Tomohiro; Masutani, Chikahide; Hanaoka, Fumio; Iwai, Shigenori

    2014-02-01

    Exposure of DNA to ultraviolet light produces harmful crosslinks between adjacent pyrimidine bases, to form cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts. The CPD is frequently formed, and its repair mechanisms have been exclusively studied by using a CPD formed at a TT site. On the other hand, biochemical analyses using CPDs formed within cytosine-containing sequence contexts are practically difficult, because saturated cytosine easily undergoes hydrolytic deamination. Here, we found that N-alkylation of the exocyclic amino group of 2'-deoxycytidine prevents hydrolysis in CPD formation, and an N-methylated cytosine-containing CPD was stable enough to be derivatized into its phosphoramidite building block and incorporated into oligonucleotides. Kinetic studies of the CPD-containing oligonucleotide indicated that its lifetime under physiological conditions is relatively long (∼ 7 days). In biochemical analyses using human DNA polymerase η, incorporation of TMP opposite the N-methylcytosine moiety of the CPD was clearly detected, in addition to dGMP incorporation, and the incorrect TMP incorporation blocked DNA synthesis. The thermodynamic parameters confirmed the formation of this unusual base pair.

  13. Multiple Electronic and Structural Factors Control Cyclobutane Pyrimidine Dimer and 6-4 Thymine-Thymine Photodimerization in a DNA Duplex.

    Science.gov (United States)

    Conti, Irene; Martínez-Fernández, Lara; Esposito, Luciana; Hofinger, Siegfried; Nenov, Artur; Garavelli, Marco; Improta, Roberto

    2017-10-26

    The T-T photodimerization paths leading to the formation of cyclobutane pyrimidine dimer (CPD) and 6-4 pyrimidine pyrimidone (64-PP), the two main DNA photolesions, have been resolved for a T-T step in a DNA duplex by two complementary state-of-the-art quantum mechanical approaches: QM(CASPT2//CASSCF)/MM and TD-DFT/PCM. Based on the analysis of several different representative structures, we define a new-ensemble of cooperating geometrical and electronic factors (besides the distance between the reacting bonds) ruling T-T photodimerization in DNA. CPD is formed by a barrierless path on an exciton state delocalized over the two bases. Large interbase stacking and shift values, together with a small pseudorotation phase angle for T at the 3'-end, favor this reaction. The oxetane intermediate, leading to a 64-PP adduct, is formed on a singlet T→T charge-transfer state and is favored by a large interbase angle and slide values. A small energy barrier (<0.3 eV) is associated to this path, likely contributing to the smaller quantum yield observed for this process. Eventually, a clear directionality is always shown by the electronic excitation characterizing the singlet photoactive state driving the photodimerization process: an exciton that is more localized on T(3) and a 5'-T→3'-T charge transfer for CPD and oxetane formation, respectively, thus calling for specific electronic constraints. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Preparation and characterization of DNA containing a site-specific nonadjacent cyclobutane thymine dimer of the type implicated in UV-induced -1 frameshift mutagenesis.

    Science.gov (United States)

    Lingbeck, J M; Taylor, J S

    1999-10-12

    One mechanism for the origin of UV-induced -1 deletion mutations involves the bypass of a nonadjacent cis-syn cyclobutane pyrimidine dimer containing a single intervening nucleotide. To begin to investigate this mechanism, we required a method for obtaining a single, site-specific, nonadjacent dimer. One approach to the preparation of a nonadjacent dimer is to irradiate a DNA duplex containing a centrally located TNT sequence in which the two T's are paired to an AA sequence in an otherwise fully complementary strand. Triplet-sensitized irradiation of the duplex formed between the 13-mer d(GAGTATCTATGAG) and the 12-mer d(CTCATAATACTC) on ice gave a major product that could be reverted to the parent 13-mer by 254 nm irradiation. Proton NMR experiments established the major product to be the nonadjacent cis-syn cyclobutane dimer formed between the two T's of the TCT sequence. Melting temperature studies show that the nonadjacent dimer is more destabilizing to DNA duplex structure than a normal cis-syn dimer and is as stable as the parental bulged DNA duplex. The nonadjacent dimer-containing 13-mer was ligated into a 51-mer and used as a template for primer-extension studies by DNA polymerases. The nonadjacent dimer could not be bypassed by Sequenase Version 2.0 and terminated synthesis primarily prior to and opposite the 3'-T of the dimer. In contrast, approximately 30% of the dimer was bypassed by an exonuclease-deficient (exo-) Klenow fragment, and termination occurred primarily opposite the 3'- and 5'-T's of the dimer. Bypass of the nonadjacent dimer by exo(-) Klenow fragment led primarily to a single-nucleotide deletion mutation as well as small amounts of a full-length product and a four-nucleotide deletion that could be explained by a primer misalignment mechanism.

  15. Insulin-like growth factor-1-mediated AKT activation postpones the onset of ultraviolet B-induced apoptosis, providing more time for cyclobutane thymine dimer removal in primary human keratinocytes.

    Science.gov (United States)

    Decraene, David; Agostinis, Patrizia; Bouillon, Roger; Degreef, Hugo; Garmyn, Marjan

    2002-09-06

    Insulin-like growth factor-1 (IGF-1) acts as a potent survival factor in numerous cell lines, primarily through activation of the AKT signaling pathway. Although some targets of this pathway have known anti-apoptotic functions, its relationship with the improved survival of cells after exposure to environmental stresses, including UVB, remains largely unclear. We report that in growth factor-deprived keratinocytes, IGF-1 significantly and consistently delayed the onset of UVB-induced apoptosis by >7 h. This delay allowed IGF-1-supplemented keratinocytes to repair significantly more cyclobutane thymine dimers than their growth factor-deprived counterparts. This increase in cyclobutane thymine removal resulted in enhanced survival if the amount of DNA damage was not too high. To increase cell survival after UVB irradiation, IGF-1 supplementation was required only during this initial time period in which extra repair was executed. Finally, we show that IGF-1 mediated this delay in the onset of UVB-induced apoptosis through activation of the AKT signaling pathway. We therefore believe that the AKT signaling pathway increases cell survival after a genotoxic insult such as UVB irradiation not by inhibiting the apoptotic stimulus, but only by postponing the induction of apoptosis, giving the DNA repair mechanism more time to work.

  16. Chemical synthesis and translesion replication of a cis–syn cyclobutane thymine–uracil dimer

    OpenAIRE

    Takasawa, Kohei; Masutani, Chikahide; Hanaoka, Fumio; Iwai, Shigenori

    2004-01-01

    The cytosine base in DNA undergoes hydrolytic deamination at a considerable rate when UV radiation induces formation of a cyclobutane pyrimidine dimer (CPD) with an adjacent pyrimidine base. We have synthesized a phosphoramidite building block of a cis–syn cyclobutane thymine–uracil dimer (T[]U), which is the deaminated form of the CPD at a TC site, and incorporated it into oligodeoxyribonucleotides. The previously reported method for synthesis of the thymine dimer (T[]T) was applied, using p...

  17. Transient expression of a plasmid gene, a tool to study DNA repair in human cells: defect of DNA repair in Cockayne syndrome; one thymine cyclobutane dimer is sufficient to block transcription.

    Science.gov (United States)

    Klocker, H; Schneider, R; Burtscher, H J; Auer, B; Hirsch-Kauffmann, M; Schweiger, M

    1986-01-01

    Transfected recombinant DNA with regulatory elements such as eukaryotic promoter and termination sites is transiently expressed in human fibroblast cells. Utilizing an expression vector containing the simian virus 40 (SV 40) early control region followed by the E. coli chloramphenicol acetyltransferase (CAT) gene, we investigated the ability of normal, Xeroderma pigmentosum and Cockayne Syndrome cells to repair UV lesions in transfected DNA. Fibroblasts from Xeroderma pigmentosum patients which cannot excise pyrimidine cyclobutane dimers were unable to restore expression of UV irradiated CAT gene. An UV dose inducing one thymine cyclobutane dimer in the transcribed strand of the CAT gene blocked its transcription in these repair deficient cells. Normal cell were able to repair the lesions in transfected DNA during an incubation period of about 40 h and in this way could overcome the UV block. In several fibroblast cell lines from patients suffering from Cockayne Syndrome expression of UV damaged CAT gene was restored significantly less than in normal fibroblasts, indicating that Cockayne Syndrome is associated with a UV repair defect.

  18. Time-resolved study of thymine dimer formation

    OpenAIRE

    Marguet, Sylvie; Markovitsi, Dimitra

    2005-01-01

    The formation of thymine dimers in the single-stranded oligonucleotide, (dT)20, is studied at room temperature by laser flash photolysis using 266 nm excitation. It is shown that the (6-4) adduct is formed within 4 ms via a reactive intermediate. The formation of cyclobutane dimers is faster than 200 ns. The overall quantum yield for the (6-4) formation is (3.7 ± 0.3) × 10-3, and that of the cyclobutane dimers is (2.8 ± 0.2) × 10-2. No triplet absorption is detected, showing that either the i...

  19. Thymine Dimerization in DNA is an Ultrafast Photoreaction

    OpenAIRE

    Schreier, Wolfgang J.; Schrader, Tobias E.; Koller, Florian O.; Gilch, Peter; Crespo-Hernández, Carlos E.; Swaminathan, Vijay N.; Carell, Thomas; Zinth, Wolfgang; Kohler, Bern

    2007-01-01

    Femtosecond time-resolved infrared spectroscopy is used to study the formation of cyclobutane dimers in the all-thymine oligonucleotide (dT)18 by ultraviolet light at 272 nanometers. The appearance of marker bands in time-resolved spectra indicate that dimers are fully formed ∼1 picosecond after ultraviolet excitation. The ultrafast appearance of this mutagenic photolesion points to an approximately barrierless excited-state reaction for bases that are properly oriented at the instant of ligh...

  20. Predicting thymine dimerization yields from molecular dynamics simulations.

    Science.gov (United States)

    Law, Yu Kay; Azadi, Javad; Crespo-Hernández, Carlos E; Olmon, Eric; Kohler, Bern

    2008-05-01

    It was recently shown that thymine dimers in the all-thymine oligonucleotide (dT)(18) are fully formed in dimers in DNA. Conformations obtained from simulations of thymidylyl-(3'-5')-thymidine in various cosolvents were classified as dimerizable or nondimerizable depending on the distance between the C5-C6 double bonds of the adjacent thymine bases and the torsion angle between them. The quantum yield of cyclobutane pyrimidine dimer formation was calculated as the number of dimerizable conformations divided by the total number of conformations. The experimental quantum yields measured in the different solvents were satisfactorily reproduced using physically reasonable values for the two parameters. The mean dimerizable structure computed by averaging all of the dimerizable cis-syn conformations is structurally similar to the actual cis-syn dimer. Compared to the canonical B-form TT step, the most important structural property of a dimerizable conformation is its reduced helical twist angle of 22 degrees.

  1. Blocking cyclobutane pyrimidine dimer formation by steric hindrance.

    Science.gov (United States)

    Vendrell-Criado, Victoria; Lhiaubet-Vallet, Virginie; Yamaji, Minoru; Cuquerella, M Consuelo; Miranda, Miguel A

    2016-04-26

    The efficiency of thymine (Thy) and uracil (Ura) to form cyclobutane pyrimidine dimers (CPDs) in solution, upon UV irradiation differs by one order of magnitude. This could to be partially related to the steric hindrance induced by the methyl at C5 in thymine. The aim of the present work is to establish the influence of a bulky moiety at this position on the photoreactivity of pyrimidines. With this purpose, photosensitization with benzophenone and acetone of a 5-tert-butyl uracil derivative () and the equivalent Thy () has been compared. Introduction of the tert-butyl group completely blocks CPD formation. Moreover, the mechanistic insight obtained by laser flash photolysis is in accordance with the observed photoreactivity.

  2. Time-resolved study of thymine dimer formation.

    Science.gov (United States)

    Marguet, Sylvie; Markovitsi, Dimitra

    2005-04-27

    The formation of thymine dimers in the single-stranded oligonucleotide, (dT)20, is studied at room temperature by laser flash photolysis using 266 nm excitation. It is shown that the (6-4) adduct is formed within 4 ms via a reactive intermediate. The formation of cyclobutane dimers is faster than 200 ns. The overall quantum yield for the (6-4) formation is (3.7 +/- 0.3) x 10-3, and that of the cyclobutane dimers is (2.8 +/- 0.2) x 10-2. No triplet absorption is detected, showing that either the intersystem crossing yield decreases by 1 order of magnitude upon oligomerization (dimers.

  3. Sequence-Dependent Thymine Dimer Formation and Photoreversal Rates in Double-Stranded DNA

    OpenAIRE

    Law, Yu Kay; Forties, Robert A.; Liu, Xin; Poirier, Michael G.; Kohler, Bern

    2013-01-01

    The kinetics of thymine-thymine cyclobutane pyrimidine dimer (TT-CPD) formation was studied at 23 thymine-thymine base steps in two 247-base pair DNA sequences irradiated at 254 nm. Damage was assayed site-specifically and simultaneously on both the forward and reverse strands by detecting emission from distinguishable fluorescent labels at the 5’-termini of fragments cleaved at CPD sites by T4 pyrimidine dimer glycosylase and separated by gel electrophoresis. The total DNA strand length of n...

  4. A deoxyribozyme that harnesses light to repair thymine dimers in DNA

    OpenAIRE

    Chinnapen, Daniel J.-F.; Sen, Dipankar

    2003-01-01

    In vitro selection was used to investigate whether nucleic acid enzymes are capable of catalyzing photochemical reactions. The reaction chosen was photoreactivation of thymine cyclobutane dimers in DNA by using serotonin as cofactor and light of wavelengths longer than the absorption spectrum of DNA. Curiously, the dominant single-stranded DNA sequence selected, UV1A, was found to repair its internal thymine dimer substrate efficiently even in the absence of serotonin or any other cofactor. U...

  5. Thymine dimer splitting in the TT-G trinucleotide model system: a semiclassical dynamics and TD-DFT study.

    Science.gov (United States)

    Yuan, Shuai; Shen, Zhi; Zhang, Wenying; Dou, Yusheng; Lo, Glenn V

    2014-05-01

    The mechanism leading to bond cleavage of a thymine-thymine cyclobutane dimer (TT) in a model system consisting of the dimer flanked by guanine trinucleotide was studied using semiclassical dynamics simulation. Pulsed laser excitation of the guanine molecule is found to cause electron transfer from the guanine molecule to the dimer, which then dissociates via sequential cleavage of the C5C5' and C6C6' bonds. Subsequently, electrons transfer back to the guanine molecule as the dimer splits into two monomers. The splitting of the cyclobutane dimer was found to be in the femtosecond time scale. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Investigation of structure and vibrational properties of cyclobutane pirimidine dimer

    Directory of Open Access Journals (Sweden)

    Petković Milena M.

    2013-01-01

    Full Text Available We performed a theoretical analysis of the structure and vibrational properties of cyclobutane pyrimidine dimer, which is the main product in a photochemical reaction involving two molecules of 1-methylthymine. Thymine is a pyrimidine base that has the highest yield of the dimerization photoproducts. Methylation in position one was chosen because in this position thymine is linked to sugar in DNA. The calculations were performed at the B3LYP/cc-pVTZ level with a Gaussian program package. All molecular geometries were optimized without symmetry constraints in vacuum and D2O. Vibrational frequencies were calculated in the harmonic approximation. It was shown that there are two stable isomers, CPD(cis-syn and CPD(trans-syn. CPD(trans-syn is more stable both in vacuum and in D2O. By dissolving these molecules in D2O, both structures become more stable, although the stabilization of the less stable isomer is more pronounced due to its larger dipole moment. Thus, the difference in stability of the two isomers in D2O is almost two times lower than in vacuum. Because of the similarity of the two isomers’ structures, the difference in their vibrational spectra is not pronounced. Within the harmonic approximation, there is only a slight difference in the C=O and C-H stretching region. The difference in the N-H stretching region is more pronounced; in the CPD(cis-syn molecule the two bonds vibrate separately, whereas in the CPD(trans-syn the two modes couple, and this coupling results in symmetric and asymmetric N-H stretching. The observation shows that a slight difference in geometry can be reflected in the shape of the infrared spectra. A more detailed analysis of the vibrational properties would involve computation of anharmonic coupling terms, which would enable a more precise determination of the peak positions.

  7. Stereoselective formation of a cyclobutane pyrimidine dimer by using N4-acetyl protection of the cytosine base.

    Science.gov (United States)

    Nishiguchi, Kosuke; Yamamoto, Junpei; Iwai, Shigenori

    2008-01-01

    The cytosine base in DNA undergoes hydrolytic deamination at a considerable rate when UV radiation induces formation of a cyclobutane pyrimidine dimer (CPD) with an adjacent pyrimidine base. As a part of our study on the synthesis of CPD-containing oligonucleotides, we have prepared properly-protected thymidylyl-(3' 5')-N(4)-acetyl-2'-deoxycytidine, and the solution of this compound was UV-irradiated using acetophenone as a sensitizer. In this reaction, hydrolysis of the acetylamino group occurred, and a trans-syn cyclobutane thymine-uracil dimer with the syn-anti conformation around the glycosidic bonds was formed stereoselectively.

  8. Direct Observation of Thymine Dimer Repair in DNA by Photolyase

    Science.gov (United States)

    Zhong, Dongping

    2006-03-01

    Departments of Physics, Chemistry, and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, 191 West Woodruff Avenue, OH 43210. Photolyase uses light energy to split ultraviolet-induced cyclobutane pyrimidine dimers in damaged DNA, but its molecular mechanism has never been directly revealed. We report here the direct mapping of catalytic processes through femtosecond synchronization of the enzymatic dynamics with the repair function. We observed direct electron transfer from the excited flavin cofactor to the dimer in 170 ps and back electron transfer from the repaired thymines in 560 ps. Both reactions are strongly modulated by active-site solvation to achieve maximum repair efficiency. These results show that the photocycle of DNA repair by photolyase is through a radical mechanism and completed on subnanosecond time scale at the dynamic active site with no net electron change in redox states of the flavin cofactor.

  9. Chemical synthesis and translesion replication of a cis–syn cyclobutane thymine–uracil dimer

    Science.gov (United States)

    Takasawa, Kohei; Masutani, Chikahide; Hanaoka, Fumio; Iwai, Shigenori

    2004-01-01

    The cytosine base in DNA undergoes hydrolytic deamination at a considerable rate when UV radiation induces formation of a cyclobutane pyrimidine dimer (CPD) with an adjacent pyrimidine base. We have synthesized a phosphoramidite building block of a cis–syn cyclobutane thymine–uracil dimer (T[]U), which is the deaminated form of the CPD at a TC site, and incorporated it into oligodeoxyribonucleotides. The previously reported method for synthesis of the thymine dimer (T[]T) was applied, using partially protected thymidylyl-(3′–5′)-2′-deoxyuridine as the starting material, and after triplet- sensitized irradiation, the configuration of the base moiety in the major product was determined by NMR spectroscopy. Presence of the cis–syn cyclobutane dimer in the obtained oligonucleotides was confirmed by UV photoreversal and reaction with T4 endonuclease V. Using a 30mer containing T[]U, translesion synthesis by human DNA polymerase η was analyzed. There was no difference in the results between the templates containing T[]T and T[]U and pol η bypassed both lesions with the same efficiency, incorporating two adenylates. This enzyme showed fidelity to base pair formation, but this replication causes a C→T transition because the original sequence is TC. PMID:15020710

  10. A QM/MM investigation of thymine dimer radical anion splitting catalyzed by DNA photolyase.

    Science.gov (United States)

    Masson, Fanny; Laino, Teodoro; Rothlisberger, Ursula; Hutter, Jürg

    2009-02-02

    On the mend: The repair reaction of the thymine dimer by DNA photolyase (see picture) is studied by hybrid quantum mechanical/molecular mechanical dynamics simulations based on the X-ray structure of the enzyme-DNA complex. The dynamics of splitting of the thymine dimer radical anion within the DNA photolyase active site is characterized. The model includes the protein environment. DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane pyrimidine dimer in damaged DNA. Herein, we investigate the repair reaction of the thymine dimer by means of hybrid quantum mechanical/molecular mechanical (QM/MM) dynamics simulations based on the X-ray structure of an enzyme-DNA complex. In analogy to the self-repair reaction, we find that the splitting mechanism of the cyclobutane ring is asynchronously concerted and is complete within a few picoseconds upon electron uptake. A few distinct processes characterize the dynamics of splitting of the thymine dimer radical anion within the DNA photolyase active site: continuous solvation reordering of the catalytic region, proton transfer from Glu283 to the dimer, as well as tight interactions of the cationic side chains of Arg232 and Arg350 with the thymine dimer. This points to the important role of the active-site hydrogen bond and salt-bridge patterns in stabilizing the thymine dimer anion and slowing down the electron back-transfer process. Comparison of the repair efficiency with respect to the self-repair reaction is also discussed.

  11. Preferential cis-syn thymine dimer bypass by DNA polymerase eta occurs with biased fidelity.

    Science.gov (United States)

    McCulloch, Scott D; Kokoska, Robert J; Masutani, Chikahide; Iwai, Shigenori; Hanaoka, Fumio; Kunkel, Thomas A

    2004-03-04

    Human DNA polymerase eta (Pol eta) modulates susceptibility to skin cancer by promoting DNA synthesis past sunlight-induced cyclobutane pyrimidine dimers that escape nucleotide excision repair (NER). Here we have determined the efficiency and fidelity of dimer bypass. We show that Pol eta copies thymine dimers and the flanking bases with higher processivity than it copies undamaged DNA, and then switches to less processive synthesis. This ability of Pol eta to sense the dimer location as synthesis proceeds may facilitate polymerase switching before and after lesion bypass. Pol eta bypasses a dimer with low fidelity and with higher error rates at the 3' thymine than at the 5' thymine. A similar bias is seen with Sulfolobus solfataricus DNA polymerase 4, which forms a Watson-Crick base pair at the 3' thymine of a dimer but a Hoogsteen base pair at the 5' thymine (ref. 3). Ultraviolet-induced mutagenesis is also higher at the 3' base of dipyrimidine sequences. Thus, in normal people and particularly in individuals with NER-defective xeroderma pigmentosum who accumulate dimers, errors made by Pol eta during dimer bypass could contribute to mutagenesis and skin cancer.

  12. Quantum Yield of Cyclobutane Pyrimidine Dimer Formation Via the Triplet Channel Determined by Photosensitization.

    Science.gov (United States)

    Liu, Lizhe; Pilles, Bert M; Gontcharov, Julia; Bucher, Dominik B; Zinth, Wolfgang

    2016-01-21

    UV-induced formation of the cyclobutane pyrimidine dimer (CPD) lesion is investigated by stationary and time-resolved photosensitization experiments. The photosensitizer 2'-methoxyacetophenone with high intersystem crossing efficiency and large absorption cross-section in the UV-A range was used. A diffusion controlled reaction model is presented. Time-resolved experiments confirmed the validity of the reaction model and provided information on the dynamics of the triplet sensitization process. With a series of concentration dependent stationary illumination experiments, we determined the quantum efficiency for CPD formation from the triplet state of the thymine dinucleotide TpT to be 4 ± 0.2%.

  13. Mapping Thymine Dimer Splitting in Damaged DNA by Photolyase

    Science.gov (United States)

    Liu, Zheyun; Tan, Chuang; Li, Jiang; Guo, Xunmin; Wang, Lijuan; Zhong, Dongping

    2010-06-01

    Photolyases uses light energy to convert UV-damaged cyclobutane pyrimidine dimer (CPD) to normal bases. We observed the formation and decay of semiquinone flavin and CPD anion intermediate, the recovery of hydroquinone flavin in ground state, and the formation of normal thymine bases in real time with femtosecond time resolution. By monitoring the decay and formation of all reactants, intermediates and products, the functional dynamics of the elementary steps during CPD repair have been mapped out. All elementary reaction steps, namely forward electron transfer, back electron transfer, bond breakage and electron return occur in sub-nanosecond scale. These dynamics are synergistically correlated for maximum of repair efficiency through a redox photocycle with no net change of electrons.

  14. γ-Irradiation of Thymine Dimers in Aqueous Solution

    Science.gov (United States)

    Deering, R. A.; Snipes, Wallace

    1968-01-01

    Thymine dimers were irradiated in aqueous solution with 60Co γ-rays in N2 or O2. Thymine and unidentified non-UV-absorbing products appeared. The thymine was identified by spectrophotometry, chromatography, and ability to support the growth of Escherichia coli 15 T-. Residual dimer was determined by a UV-reversibility assay. The G-values for dimer breakage were approximately equal in N2 and O2. At low γ-doses, about two thymines were produced per dimer broken in N2, whereas only about one thymine appeared per dimer broken in O2. For dimer irradiated in frozen solution, the yield of thymine was at least 100 times less than in liquid. PMID:4934290

  15. The photochemistry of thymine in frozen aqueous solution: trimeric and minor dimeric products.

    Science.gov (United States)

    Shetlar, Martin D; Basus, Vladimir J

    2013-01-01

    Early work identified three compounds, namely the c,s cyclobutane dimer, the so-called (6-4) photoproduct (5-hydroxy-6-4'-(5-methylpyrimidin-2'-one)-5,6-dihydrothymine) and a trimer hydrate, as products formed upon UV irradiation of thymine in frozen aqueous solution. More recent work has shown that an (α-4) product, namely α-4'-(5'-methylpyrimidine-2'-one)-thymine, is a likely product formed under these reaction conditions. During a thorough reinvestigation of the photochemistry of Thy in ice at -78.5°C, we found that a variety of other products could be detected. In addition to the c,s dimer, the other three known cyclobutane dimers, namely the c,a, t,s and t,a forms, are produced, although in considerably smaller amounts. The so-called "spore product" of thymine (5,6-dihydro-5-(α-thyminyl)thymine) is likewise formed. Two other dimers have been identified as minor products; one of these has been determined to be 5-(thymin-3-yl)-5,6-dihydrothymine and the other has been tentatively assigned to be a (5-4) adduct (6-hydroxy-5-4'-(5-methylpyrimidin-2'-one)-5,6-dihydrothymine). Compounds with the behavior expected of true trimeric compounds have been isolated via HPLC and characterized by mass spectrometry and photochemical behavior. One of these materials, putatively containing an oxetane ring, decomposes thermally to a secondary trimeric product that is then converted into the known trimer hydrate. © 2013 Wiley Periodicals, Inc. Photochemistry and Photobiology © 2013 The American Society of Photobiology.

  16. Thymine dimer-induced structural changes to the DNA duplex examined with reactive probes (†).

    Science.gov (United States)

    Rumora, Amy E; Kolodziejczak, Katarzyna M; Malhowski Wagner, Anne; Núñez, Megan E

    2008-12-09

    Despite significant progress in the past decade, questions still remain about the complete structural, dynamic, and thermodynamic effect of the cis-syn cyclobutane pyrimidine dimer lesion (hereafter called the thymine dimer) on double-stranded genomic DNA. We examined a 19-mer oligodeoxynucleotide duplex containing a thymine dimer lesion using several small, base-selective reactive chemical probes. These molecules probe whether the presence of the dimer causes the base pairs to be more accessible to the solution, either globally or adjacent to the dimer. Though all of the probes confirm that the overall structure of the dimer-containing duplex is conserved compared to that of the undamaged parent duplex, reactions with both diethyl pyrocarbonate and Rh(bpy)(2)(chrysi)(3+) indicate that the duplex is locally destabilized near the lesion. Reactions with potassium permanganate and DEPC hint that the dimer-containing duplex may also be globally more accessible to the solution through a subtle shift in the double-stranded DNA ↔ single-stranded DNA equilibrium. To begin to distinguish between kinetic and thermodynamic effects, we determined the helix melting thermodynamic parameters for the dimer-containing and undamaged parent duplexes by microcalorimetry and UV melting. The presence of the thymine dimer causes this DNA duplex to be slightly less stable enthalpically but slightly less unstable entropically at 298 K, causing the overall free energy of duplex melting to remain unchanged by the dimer lesion within the error of the experiment. Here we consider these results in the context of what has been learned about the thymine dimer lesion from NMR, X-ray crystallographic, and molecular biological methods.

  17. Sequence-dependent thymine dimer formation and photoreversal rates in double-stranded DNA.

    Science.gov (United States)

    Law, Yu Kay; Forties, Robert A; Liu, Xin; Poirier, Michael G; Kohler, Bern

    2013-08-01

    The kinetics of thymine-thymine cyclobutane pyrimidine dimer (TT-CPD) formation was studied at 23 thymine-thymine base steps in two 247-base pair DNA sequences irradiated at 254 nm. Damage was assayed site-specifically and simultaneously on both the forward and reverse strands by detecting emission from distinguishable fluorescent labels at the 5'-termini of fragments cleaved at CPD sites by T4 pyrimidine dimer glycosylase and separated by gel electrophoresis. The total DNA strand length of nearly 1000 bases made it possible to monitor damage at all 9 tetrads of the type XTTY, where X and Y are non-thymine bases. TT-CPD yields for different tetrads were found to vary by as much as an order of magnitude, but similar yields were observed at all instances of a given tetrad. Kinetic analysis of CPD formation at 23 distinct sites reveals that both the formation and reversal photoreactions depend sensitively on the identity of the nearest-neighbour bases on the 5' and the 3' side of a photoreactive TT base step. The lowest formation and reversal rates occur when two purine bases flank a TT step, while the highest formation and reversal rates are observed for tetrads with at least one flanking C. Overall, the results show that the probabilities of CPD formation and photoreversal depend principally on interactions with nearest-neighbour bases.

  18. Base flipping of the thymine dimer in duplex DNA.

    Science.gov (United States)

    O'Neil, Lauren L; Grossfield, Alan; Wiest, Olaf

    2007-10-11

    Exposure of two adjacent thymines in DNA to UV light of 260-320 nm can result in the formation of the cis,syn-cyclobutane pyrimidine dimer (CPD). The structure of DNA containing an intrahelical CPD lesion has been previously studied experimentally and computationally. However, the structure of the extrahelical, flipped-out, CPD lesion, which has been shown to be the structure that binds to the CPD repair enzyme, DNA photolyase, has yet to be reported. In this work the structure of both the flipped-in and the flipped-out CPD lesions in duplex DNA is reported. These structures were calculated using 8 ns molecular dynamics (MD) simulations. These structures are then used to define the starting and ending points for the base-flipping process for the CPD lesion. Using a complex, two-dimensional pseudodihedral coordinate, the potential of mean force (PMF) for the base-flipping process was calculcated using novel methodology. The free energy of the flipped-out CPD is roughly 6.5 kcal/mol higher than that of the flipped-in state, indicating that the barrier to flipping out is much lower for CPD than for undamaged DNA. This may indicate that the flipped-out CPD lesion may be recognized by its repair enzyme, DNA photolyase, whereas previous studies of other damaged, as well as nondamaged, bases indicate that they are recognized by enzymes in the intrahelical, flipped-in state.

  19. Deoxyribozymes that catalyze photochemistry: cofactor-dependent and -independent photorepair of thymine dimers.

    Science.gov (United States)

    Sen, Dipankar; Chinnapen, Daniel J F

    2003-01-01

    Experimental strategies involving in vitro selection, designed to test the validity of the "RNA World Hypothesis", have demonstrated a significantly broader catalytic range for RNA (and, nucleic acids in general) than found in naturally occurring ribozymes. We wished to explore whether photochemical reactions could be catalyzed by nucleic acid enzymes. In vitro selection experiments were carried out to obtain "photolyase" deoxyribozymes, capable of photoreversing thymine cyclobutane dimers in the presence of a cofactor, serotonin. During in vitro selection from a thymine-dimer containing random DNA library, irradiated with light >300 nm, two pools of catalytic nucleic molecules emerged--one that required serotonin for activity, and another pool that, surprisingly, did not. Characterization of the serotonin-independent clones indicated the optimal wavelength for its repair activity (approximately 1,400-fold) to be approximately 300 nm, notably red-shifted from the absorption maximum of the DNA itself. The folded enzyme may contain a G-quadruplex (whose spectra have red-shifted tails relative to duplex absorbance), and our hypothesis has the folded enzyme as an antenna for the efficient channelling of light or electrons to the thymine dimer, much in the manner of protein photolyases.

  20. [Mechanisms of targeted frameshift mutations--insertion formation under error-prone or SOS synthesis of DNA containing CIS-SYN cyncyclobutane thymine dimers].

    Science.gov (United States)

    Grebneva, E A

    2014-01-01

    Up to now the mechanism of formation of frameshift mutations caused by cyclobutane pyrimidine dimers has not been yet explained satisfactorily. Mechanisms of different mutations are usually considered in polymerase model. Here, the alternative polymerase-tautomer model of ultraviolet mutagenesis is developed. The mechanism of targeted insertion formation caused by cis-syn cyclobutane thymine dimers is proposed. Insertions are mutations when one or several DNA bases are inserted.Targeted insertions are mutations of a frameshift type--when one or severalnucleotides are inserted opposite damageswhich may stop synthesis of DNA. Targeted insertions are induced bycyclobutane pyrimidine dimmers. Ultraviolet irradiation may result in a change of tautomer state of DNA bases. A thymine base may form 5 rare tautomer forms that are stable if the base is a part of cyclobutane dimer. As it was shown by structural analysis, one rare tautomeric form of thymine forms hydrogen bonds with no one canonical DNA base. Therefore, under SOS or error-prone synthesis of DNA containing cis-syn cyclobutane thymine dimers with such rare tautomeric_form a specialize or modified DNA polymerase leaves a single nucleotide gap opposite the cis-syn cyclobutane thymine dimer. According to Streisinger model, if the DNA composition within this region is homogeneous, the end of the growing DNA strand can slip and form complementary pairs with a template nucleotide neighboring to the dimer of such type a loop is formed. Further elongation of the daughter strand leads to the appearance of targeted insertion in the daughter strand. Here, it is first shown that cis-syn cyclobutane thymine dimers with one or both bases in the specific tautomer conformation--opposite which it is impossible to insert a canonical base with a hydrogen bond formation--results in targeted insertions. Moreover, the model of forming targeted single--and several-base insertions is developed. The polymerase-tautomer model of

  1. Accuracy of thymine-thymine dimer bypass by Saccharomyces cerevisiae DNA polymerase eta.

    Science.gov (United States)

    Washington, M T; Johnson, R E; Prakash, S; Prakash, L

    2000-03-28

    The Saccharomyces cerevisiae RAD30 gene functions in error-free replication of UV-damaged DNA. RAD30 encodes a DNA polymerase, Pol eta, which inserts two adenines opposite the two thymines of a cis-syn thymine-thymine (T-T) dimer. Here we use steady-state kinetics to determine the accuracy of DNA synthesis opposite the T-T dimer. Surprisingly, the accuracy of DNA synthesis opposite the damaged DNA is nearly indistinguishable from that opposite nondamaged DNA, with frequencies of misincorporation of about 10(-2) to 10(-3). These studies support the hypothesis that unlike most DNA polymerases, Pol eta is able to tolerate distortions in DNA resulting from damage, which then enables the polymerase to utilize the intrinsic base pairing ability of the T-T dimer.

  2. Electronic excited states responsible for dimer formation upon UV absorption directly by thymine strands: joint experimental and theoretical study.

    Science.gov (United States)

    Banyasz, Akos; Douki, Thierry; Improta, Roberto; Gustavsson, Thomas; Onidas, Delphine; Vayá, Ignacio; Perron, Marion; Markovitsi, Dimitra

    2012-09-12

    The study addresses interconnected issues related to two major types of cycloadditions between adjacent thymines in DNA leading to cyclobutane dimers (TTs) and (6-4) adducts. Experimental results are obtained for the single strand (dT)(20) by steady-state and time-resolved optical spectroscopy, as well as by HPLC coupled to mass spectrometry. Calculations are carried out for the dinucleoside monophosphate in water using the TD-M052X method and including the polarizable continuum model; the reliability of TD-M052X is checked against CASPT2 calculations regarding the behavior of two stacked thymines in the gas phase. It is shown that irradiation at the main absorption band leads to cyclobutane dimers (TTs) and (6-4) adducts via different electronic excited states. TTs are formed via (1)ππ* excitons; [2 + 2] dimerization proceeds along a barrierless path, in line with the constant quantum yield (0.05) with the irradiation wavelength, the contribution of the (3)ππ* state to this reaction being less than 10%. The formation of oxetane, the reaction intermediate leading to (6-4) adducts, occurs via charge transfer excited states involving two stacked thymines, whose fingerprint is detected in the fluorescence spectra; it involves an energy barrier explaining the important decrease in the quantum yield of (6-4) adducts with the irradiation wavelength.

  3. Flavonols Protect Against UV Radiation-Induced Thymine Dimer Formation in an Artificial Skin Mimic.

    Science.gov (United States)

    Maini, Sabia; Fahlman, Brian M; Krol, Ed S

    2015-01-01

    Exposure of skin to ultraviolet light has been shown to have a number of deleterious effects including photoaging, photoimmunosuppression and photoinduced DNA damage which can lead to the development of skin cancer. In this paper we present a study on the ability of three flavonols to protect EpiDerm™, an artificial skin mimic, against UV-induced damage. EpiDerm™ samples were treated with flavonol in acetone and exposed to UVA (100 kJ/m(2) at 365 nm) and UVB (9000 J/m(2) at 310 nm) radiation. Secretion of matrix metalloproteinase-1 (MMP-1) and tumor necrosis factor-α (TNF-a) were determined by ELISA, cyclobutane pyrimidine dimers were quantified using LC-APCI-MS. EpiDerm™ treated topically with quercetin significantly decreased MMP-1 secretion induced by UVA (100 µM) or UVB (200 µM) and TNF-a secretion was significantly reduced at 100 µM quercetin for both UVA and UVB radiation. In addition, topically applied quercetin was found to be photostable over the duration of the experiment. EpiDerm™ samples were treated topically with quercetin, kaempferol or galangin (52 µM) immediately prior to UVA or UVB exposure, and the cyclobutane thymine dimers (T-T (CPD)) were quantified using an HPLC-APCI MS/MS method. All three flavonols significantly decreased T-T (CPD) formation in UVB irradiated EpiDerm™, however no effect could be observed for the UVA irradiation experiments as thymine dimer formation was below the limit of quantitation. Our results suggest that flavonols can provide protection against UV radiation-induced skin damage through both antioxidant activity and direct photo-absorption. This article is open to POST-PUBLICATION REVIEW. Registered readers (see "For Readers") may comment by clicking on ABSTRACT on the issue's contents page.

  4. Photosensitized [2 + 2] cycloaddition of N-acetylated cytosine affords stereoselective formation of cyclobutane pyrimidine dimer.

    Science.gov (United States)

    Yamamoto, Junpei; Nishiguchi, Kosuke; Manabe, Koichiro; Masutani, Chikahide; Hanaoka, Fumio; Iwai, Shigenori

    2011-02-01

    Photocycloaddition between two adjacent bases in DNA produces a cyclobutane pyrimidine dimer (CPD), which is one of the major UV-induced DNA lesions, with either the cis-syn or trans-syn structure. In this study, we investigated the photosensitized intramolecular cycloaddition of partially-protected thymidylyl-(3'→5')-N(4)-acetyl-2'-deoxy-5-methylcytidine, to clarify the effect of the base modification on the cycloaddition reaction. The reaction resulted in the stereoselective formation of the trans-syn CPD, followed by hydrolysis of the acetylamino group. The same result was obtained for the photocycloaddition of thymidylyl-(3'→5')-N(4)-acetyl-2'-deoxycytidine, whereas both the cis-syn and trans-syn CPDs were formed from thymidylyl-(3'→5')-thymidine. Kinetic analyses revealed that the activation energy of the acid-catalyzed hydrolysis is comparable to that reported for the thymine-cytosine CPD. These findings provided a new strategy for the synthesis of oligonucleotides containing the trans-syn CPD. Using the synthesized oligonucleotide, translesion synthesis by human DNA polymerase η was analyzed.

  5. Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer.

    Science.gov (United States)

    Horikoshi, Naoki; Tachiwana, Hiroaki; Kagawa, Wataru; Osakabe, Akihisa; Matsumoto, Syota; Iwai, Shigenori; Sugasawa, Kaoru; Kurumizaka, Hitoshi

    2016-02-26

    The cyclobutane pyrimidine dimer (CPD) is induced in genomic DNA by ultraviolet (UV) light. In mammals, this photolesion is primarily induced within nucleosomal DNA, and repaired exclusively by the nucleotide excision repair (NER) pathway. However, the mechanism by which the CPD is accommodated within the nucleosome has remained unknown. We now report the crystal structure of a nucleosome containing CPDs. In the nucleosome, the CPD induces only limited local backbone distortion, and the affected bases are accommodated within the duplex. Interestingly, one of the affected thymine bases is located within 3.0 Å from the undamaged complementary adenine base, suggesting the formation of complementary hydrogen bonds in the nucleosome. We also found that UV-DDB, which binds the CPD at the initial stage of the NER pathway, also efficiently binds to the nucleosomal CPD. These results provide important structural and biochemical information for understanding how the CPD is accommodated and recognized in chromatin. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Photosensitized Cleavage of the Thymine Dimer in DNA via Carbazole Nucleoside

    OpenAIRE

    Yoshimura, Yoshinaga; Taya, Yuta; Matsumura, Hiroshi; Fujimoto, Kenzo

    2008-01-01

    We report the catalytic repair of a thymine dimer incorporated in a DNA duplex via oligodeoxynucleotide (ODN) containing carbazole nucleoside. The occurrence of an electron transfer between carbazole nucleoside and thymine dimer is evidenced by fluorescence quenching measurements. Carbazole nucleoside acts as a good electron donor for the catalytic repair of a thymine dimer.

  7. Photoinduced repair of a thymine dimer in DNA via carbazole nucleoside.

    Science.gov (United States)

    Yoshimura, Yoshinaga; Fujimoto, Kenzo

    2006-01-01

    We report the photoinduced repair of a thymine dimer incorporated in a DNA duplex via oligodeoxynucleotide (ODN) containing carbazole nucleoside (K). The occurrence of an electron transfer between K and thymine dimer is evidenced by fluorescence quenching measurements. K acts as a good electron donor for the photoinduced repair of a thymine dimer.

  8. Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.

    Science.gov (United States)

    Li, Ying; Dutta, Shuchismita; Doublié, Sylvie; Bdour, Hussam Moh'd; Taylor, John-Stephen; Ellenberger, Tom

    2004-08-01

    Ultraviolet-induced DNA damage poses a lethal block to replication. To understand the structural basis for this, we determined crystal structures of a replicative DNA polymerase from bacteriophage T7 in complex with nucleotide substrates and a DNA template containing a cis-syn cyclobutane pyrimidine dimer (CPD). When the 3' thymine is the templating base, the CPD is rotated out of the polymerase active site and the fingers subdomain adopts an open orientation. When the 5' thymine is the templating base, the CPD lies within the polymerase active site where it base-pairs with the incoming nucleotide and the 3' base of the primer, while the fingers are in a closed conformation. These structures reveal the basis for the strong block of DNA replication that is caused by this photolesion.

  9. Examining the base stacking interaction in a dinucleotide context via reversible cyclobutane dimer analogue formation under UV irradiation.

    Science.gov (United States)

    Liu, Degang; Li, Lei

    2013-11-14

    Substituted tolyl groups are considered as close isosteres of the thymine (T) residue. They can be recognized by DNA polymerases as if they were thymine. Although these toluene derivatives are relatively inert toward radical additions, our recent finding suggests that the dinucleotide analogue TpTo (To = 2'-deoxy-1-(3-tolyl)-β-D-ribofuranose) supports an ortho photocycloaddition reaction upon UV irradiation, producing two cyclobutane pyrimidine dimer (CPD) analogues 2 and 3. Our report here further shows that formation of these CPD species is reversible under UVC irradiation, resembling the photochemical property of the CPD species formed between two Ts. Analyzing the stability of these CPD analogues suggests that one (2) is more stable than the other (3). The TpTo conformer responsible for 2 formation is also more stable than that responsible for 3 formation, as indicated by the Gibbs free energy change calculated from the constructed Bordwell thermodynamic cycle. These different stabilities are not due to the varying photochemical properties, as proved by quantum yields determined from the corresponding photoreactions. Instead, they are ascribed to the different stacking interaction between the T and the To rings both in the TpTo dinucleotide as well as in the formed CPD analogues. Factors contributing to the ring stacking interactions are also discussed. Our proof-of-concept approach suggests that a carefully designed Bordwell cycle coupled with reversible CPD formations under UV irradiation can be very useful in studying DNA base interactions.

  10. Anions of the hydrogen-bonded thymine dimer: ab initio study

    Science.gov (United States)

    Jalbout, Abraham F.; Smets, Johan; Adamowicz, Ludwik

    2001-11-01

    Theoretical calculations have been performed to determine the ability of the hydrogen-bonded thymine dimer to form stable anions. The major conclusions of this work are: (i) three of the hydrogen-bonded conformers of the thymine dimer can form stable dipole-bound anions with excess electrons; (ii) thymine dimer can form a covalent anion that has a structure dissimilar from the structures of the neutral dimer; (iii) in the covalent thymine-dimer anion the excess electron is localized in a π-orbital on one of the thymine molecules and this molecule shows an out-of-plane distortion; (iv) the covalent thymine-dimer anion is stable with respect to an adiabatic electron detachment.

  11. Distinct mechanisms of cis-syn thymine dimer bypass by Dpo4 and DNA polymerase eta.

    Science.gov (United States)

    Johnson, Robert E; Prakash, Louise; Prakash, Satya

    2005-08-30

    UV-light-induced cyclobutane pyrimidine dimers (CPDs) present a severe block to synthesis by replicative DNA polymerases (Pols), whereas Poleta promotes proficient and error-free replication through CPDs. Although the archael Dpo4, which, like Poleta, belongs to the Y family of DNA Pols, can also replicate through a CPD, it is much less efficient than Poleta. The x-ray crystal structure of Dpo4 complexed with either the 3'-thymine (T) or the 5' T of a cis-syn TT dimer has indicated that, whereas the 3' T of the dimer forms a Watson-Crick base pair with the incoming dideoxy ATP, the 5' T forms a Hoogsteen base pair with the dideoxy ATP in syn conformation. Based upon these observations, a similar mechanism involving Hoogsteen base pairing of the 5' T of the dimer with the incoming A has been proposed for Poleta. Here we examine the mechanisms of CPD bypass by Dpo4 and Poleta using nucleotide analogs that specifically disrupt the Hoogsteen or Watson-Crick base pairing. Our results show that both Dpo4 and Poleta incorporate dATP opposite the 5' T of the CPD via Watson-Crick base pairing and not by Hoogsteen base pairing. Furthermore, opposite the 3' T of the dimer, the two Pols differ strikingly in the mechanisms of dATP incorporation, with Dpo4 incorporating opposite an abasic-like intermediate and Poleta using the normal Watson-Crick base pairing. These observations have important implications for the mechanisms used for the inefficient vs. efficient bypass of CPDs by DNA Pols.

  12. Role of adenine in thymine-dimer repair by reduced flavin-adenine dinucleotide.

    Science.gov (United States)

    Li, Guifeng; Sichula, Vincent; Glusac, Ksenija D

    2008-08-28

    We present a study of excited-state behavior of reduced flavin cofactors using femtosecond optical transient absorption spectroscopy. The reduced flavin cofactors studied were in two protonation states: flavin-adenine dinucleotide (FADH2 and FADH-) and flavin-mononucleotide (FMNH2 and FMNH-). We find that FMNH- exhibits multiexponential decay dynamics due to the presence of two bent conformers of the isoalloxazine ring. FMNH2 exhibits an additional fast deactivation component that is assigned to an iminol tautomer. Reduced flavin cofactors also exhibit a long-lived component that is attributed to the semiquinone and the hydrated electron that are produced in photoinduced electron transfer to the solvent. The presence of adenine in FADH2 and FADH- further changes the excited-state dynamics due to intramolecular electron transfer from the isoalloxazine to the adenine moiety of cofactors. This electron transfer is more pronounced in FADH2 due to pi-stacking interactions between two moieties. We further studied cyclobutane thymine dimer (TT-dimer) repair via FADH- and FMNH- and found that the repair is much more efficient in the case of FADH-. These results suggest that the adenine moiety plays a significant role in the TT-dimer repair dynamics. Two possible explanations for the adenine mediation are presented: (i) a two-step electron transfer process, with the initial electron transfer occurring from flavin to adenine moiety of FADH-, followed by a second electron transfer from adenine to TT-dimer; (ii) the preconcentration of TT-dimer molecules around the flavin cofactor due to the hydrophobic nature of the adenine moiety.

  13. Formation of the main UV-induced thymine dimeric lesions within isolated and cellular DNA as measured by high performance liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Douki, T; Court, M; Sauvaigo, S; Odin, F; Cadet, J

    2000-04-21

    UVB radiation-induced formation of dimeric photoproducts at bipyrimidine sites within DNA has been unambiguously associated with the lethal and mutagenic properties of sunlight. The main lesions include the cyclobutane pyrimidine dimers and the pyrimidine (6-4) pyrimidone adducts. The latter compounds have been shown in model systems to be converted into their Dewar valence isomers upon exposure to UVB light. A new direct assay, based on the use of liquid chromatography coupled to tandem mass spectrometry, is now available to simultaneously detect each of the thymine photoproducts. It was applied to the determination of the yields of formation of the thymine lesions within both isolated and cellular DNA exposed to either UVC or UVB radiation. The cis-syn cyclobutane thymine dimer was found to be the major photoproduct within cellular DNA, whereas the related (6-4) adduct was produced in an approximately 8-fold lower yield. Interestingly, the corresponding Dewar valence isomer could not be detected upon exposure of human cells to biologically relevant doses of UVB radiation.

  14. Thymine dimer photoreversal in purine-containing trinucleotides.

    Science.gov (United States)

    Pan, Zhengzheng; Chen, Jinquan; Schreier, Wolfgang J; Kohler, Bern; Lewis, Frederick D

    2012-01-12

    Cyclobutane-pyrimidine dimer yields in UV-irradiated DNA are controlled by the equilibrium between forward and reverse photoreactions. Past studies have shown that dimer yields are suppressed at sites adjacent to a purine base, but the underlying causes are unclear. In order to investigate whether this suppression is the result of repair by electron transfer from a neighboring nucleobase, the yields and dynamics of the reverse reaction were studied using trinucleotides containing a cis-syn dimer (TT) flanked on the 5' or the 3' side by adenine or guanine. The probability of forming an excited state on TT or on the purine base was varied by tuning the irradiation wavelength between 240 and 280 nm. Cleavage quantum yields decrease by an order of magnitude over this wavelength range and are less than 1% at 280 nm, a wavelength that excites the purine base with more than 95% probability. Conditional quantum yields of cleavage for the trinucleotides given excitation of TT are similar in magnitude to the quantum yield of cleavage of unmodified TT. These results indicate that within experimental uncertainty all photoreversal in these single-stranded substrates is the result of direct electronic excitation of TT. Photolyase-like repair of TT due to electron transfer from an adjacent purine is negligible in these substrates. Instead, the observed variation in photoreversal quantum yields for adenine- versus guanine-flanked cis-syn dimer could be due to uncertainties in absorption cross sections or to a modest quenching effect by the purine on the excited state of TT. Pump-probe measurements reveal that the excited-state lifetimes of A or G in the dimer-containing trinucleotides are unperturbed by the neighboring dimer, indicating that electron transfer from purine base to TT is not competitive with rapid excited-state deactivation. Pump-probe measurements on unmodified TT in aqueous solution indicate that cleavage is most likely complete on a picosecond or subpicosecond

  15. 2'-Methoxyacetophenone: An Efficient Photosensitizer for Cyclobutane Pyrimidine Dimer Formation.

    Science.gov (United States)

    Liu, Lizhe; Pilles, Bert M; Reiner, Anne M; Gontcharov, Julia; Zinth, Wolfgang

    2015-11-16

    Stationary and time-resolved experiments show that 2'-methoxyacetophenone (2-M) is an interesting compound for the investigation of triplet states in thymine samples. Time-resolved emission experiments show that the fluorescence lifetime of 2-M is 660 ps. A similar time constant of 680 ps is found in transient IR experiments. The data indicate efficient intersystem crossing (≈97%) from the fluorescent singlet state to the triplet state. The lifetime of the triplet state of 2-M dissolved in D2O at room temperature and ambient oxygen concentration is 400 ns. 2-M has a strong absorption in the UV-A range and can photosensitize the triplet state of a thymidine dinucleotide with light at a wavelength of 320 nm. The experiments show that 2-M is well-suited for time-resolved experiments on the triplet-sensitizing process. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. A direct ab initio molecular dynamics (MD) study on the repair reactions of stacked thymine dimer

    Science.gov (United States)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2008-09-01

    DNA repair reactions of the thymine dimer (T) 2 following the hole capture have been investigated by means of direct ab initio molecular dynamics (MD) method in order to elucidate the mechanism of repair processes of thymine dimer interacting with a photo-enzyme. The thymine dimer has two C-C single bonds between thymine rings at neutral state expressed by (T dbnd T). After the hole capture of (T dbnd T), one of the C-C bonds was preferentially broken, while the structure of (T dbnd T) + was spontaneously changed to an intermediate having a C-C single bond expressed by (T-T) +. Time scale of the C-C bond breaking and formation of the intermediate was estimated to be 60-180 fs. The mechanism of repair reactions of the thymine dimer was discussed on the basis of theoretical results.

  17. Replication of cyclobutane pyrimidine dimer analogue by Ex Taq DNA polymerase

    Directory of Open Access Journals (Sweden)

    Masayuki Ogino et al

    2007-01-01

    Full Text Available We previously reported an efficient and reversible template-directed photoligation using 5-carboxyvinyl-2'-deoxyuridine (CVU-containing ODN at the 5'-terminal. This method forms d(T-CVU as a cyclobutane pyrimidine dimer (CPD analogue between the 3'-terminal thymidine and the 5'-terminal CVU of two oligodeoxynucleotides (ODNs. In this study, we performed PCR using a DNA template containing d(T-CVU. Then, we found that two adenines were incorporated opposite the d(T-CVU.

  18. Thymine dimer formation as a probe of the path of DNA in and between nucleosomes in intact chromatin.

    OpenAIRE

    Pehrson, J R

    1989-01-01

    Photo-induced thymine dimer formation was used to probe nucleosome structure in nuclei. The distribution of thymine dimers in the nucleosome and recent studies of the structure of thymine dimer-containing DNA suggest that the rate of thymine dimer formation is affected by the direction and degree of DNA bending. This premise was used to construct a model of the path of DNA in the nucleosome, which has the following features. (i) There are four regions of sharp bending, two which have been see...

  19. Defective thymine dimer excision by cell-free extracts of xeroderma pigmentosum cells.

    Science.gov (United States)

    Mortelmans, K; Friedberg, E C; Slor, H; Thomas, G; Cleaver, J E

    1976-01-01

    Crude extracts of normal human diploid fibroblasts and of human peripheral blood lymphocytes excise thymine dimers from purified ultraviolet-irradiated DNA, or from the DNA presumably present as chromatin in unfractionated cell-free preparations of cells that had been labeled with [3H]thymidine. Extracts of xeroderma pigmentosum cells from complementation groups A, C, and D also excise thymine dimers from purified DNA, but extracts of group A cells do not excise dimers from the DNA of radioactively labeled unfractionated cell-free preparations. PMID:1066689

  20. Dynamics and mechanism of DNA repair in a biomimetic system: flavin-thymine dimer adduct.

    Science.gov (United States)

    Kao, Ya-Ting; Song, Qin-Hua; Saxena, Chaitanya; Wang, Lijuan; Zhong, Dongping

    2012-01-25

    To mimic photolyase for efficient repair of UV-damaged DNA, numerous biomimetic systems have been synthesized, but all show low repair efficiency. The molecular mechanism of this low-efficiency process is still poorly understood. Here we report our direct mapping of the repair processes of a flavin-thymine dimer adduct with femtosecond resolution. We followed the entire dynamic evolution and observed direct electron transfer (ET) from the excited flavin to the thymine dimer in 79 ps. We further observed two competitive pathways, productive dimer ring splitting within 435 ps and futile back-ET in 95 ps. Our observations reveal that the underlying mechanism for the low repair quantum yield of flavin-thymine dimer adducts is the short-lived excited flavin moiety and the fast dynamics of futile back-ET without repair. © 2012 American Chemical Society

  1. Mechanism for repair of thymine dimers by photoexcitation of proximal 8-oxo-7,8-dihydroguanine.

    Science.gov (United States)

    Anusiewicz, Iwona; Świerszcz, Iwona; Skurski, Piotr; Simons, Jack

    2013-02-14

    A wide range of experimental data from earlier studies by other workers are combined with recent data from the Burrows group to interpret that group's thymine dimer (T = T) repair rate data for 8-oxo-7,8-dihydroguanine (OG)-containing DNA duplexes. The focus of this effort is to explain (i) how and why the repair rates vary as the sequence location and distance of the OG relative to the T═T is changed and (ii) why the spatial extent over which repair is observed is limited to OG-T═T distances of ~6 Å. It is proposed that, if the OG and T═T are within ~5-6 Å, a Coulomb potential moves the energy of the OG(+)···T═T(-) ion-pair state below the photoexcited OG*···T═T state, even in the absence of full solvent relaxation, thus enhancing forward electron transfer from OG* to T═T by allowing it to occur as a radiationless internal conversion process rather than by overcoming a solvation-related barrier. The rate of this forward electron transfer is estimated to be ~10% of the decay rate of the photoexcited OG*. For OG-to-T═T distances beyond 5-6 Å, electron transfer is still exothermic, but it must occur through solvent reorganization, overcoming an energy barrier, which presumably renders this rate too slow to be detected in the experiments under study here. Once an electron has been injected into the T═T, as many other workers have shown, the reaction proceeds through two low-energy barriers first connecting T═T(-) to an intermediate in which the C(5)-C(5') bond of the cyclobutane unit is cleaved, and onward to where the cyclobutane unit is fully broken and two intact thymine sites are established. Our ab initio data show that the energy landscape for these bond cleavages is altered very little by the presence of the proximal OG(+) cation, which therefore allows us to use data from the earlier studies to conclude that it takes ~100 ps for complete bond cleavage to occur. The experimentally determined overall T═T repair quantum yield of 1

  2. Thymine dimer repair by electron transfer from photo-excited 2',3',5'-tri-O-acetyl-8-oxo-7,8-dihydroguanosine or 2',3',5'-tri-O-acetyl-ribosyluric acid - a theoretical study

    Science.gov (United States)

    Marchaj, Marzena; Sieradzan, Iwona; Anusiewicz, Iwona; Skurski, Piotr; Simons, Jack

    2013-07-01

    Electronic structure calculations are combined with published experimental data from another laboratory to interpret trends in the rates of thymine dimer repair induced by photo-exciting the title molecules or their deprotonated derivatives. Opening of the thymine dimer's cyclobutane ring is believed to be initiated by electron transfer from the photo-excited molecule and to then pass over thermally accessible energy barriers. Therefore, the repair rates are determined by rates of accessing activation barriers connecting the photo-excited state to the electron-transferred state. These barriers are shown to depend on the electronic excitation energy and electron-binding energy of the donor and the electron affinity of the thymine dimer acceptor. For neutral donors, the barriers also depend on the distance between the donor and the thymine dimer through a screened Coulomb interaction between the donor cation and acceptor anion. For the deprotonated (anionic) donors, this Coulomb-derived distance dependence is absent. For both neutral and anionic donors, the range for electron transfer is spatially limited by the strength of the electronic couplings. The model put forth here rationalizes why anionic donors can be expected to perform better than neutrals and offers a framework for designing electron transfer agents optimal for a given electron acceptor.

  3. Fate of Thymine-containing Dimers in the Deoxyribonucleic Acid of Ultraviolet-irradiated Bacillus subtilis

    Science.gov (United States)

    Shuster, Robert C.

    1967-01-01

    The fate of ultraviolet-induced, thymine-containing dimers in the deoxyribonucleic acid (DNA) of Bacillus subtilis was investigated in both the wild type (UVR) and an ultraviolet light-sensitive (UVS) mutant. During incubation in the dark, dimers were excised from the DNA of the UVRB. subtilis, but remained in the DNA of the UVS mutant. About 40% of the excised dimers recovered in the wild type were in the acid-soluble fraction; the remainder were in the incubation medium. A UVS mutant of Escherichia coli K-12, shown previously to be defective in dimer excision, was irradiated with ultraviolet light and incubated under visible light for 3 hr. About 65% of thymine-containing photoproducts were removed from the DNA. These photoproducts were not recovered in the acid-soluble fraction. In comparison, the UVS mutant of B. subtilis lost only 13% of such photoproducts from DNA when exposed to light under the same conditions. PMID:4960923

  4. The radical cationic repair pathway of cyclobutane pyrimidine dimer: the effect of sugar-phosphate backbone.

    Science.gov (United States)

    Ebrahimi, Ali; Habibi-Khorassani, Mostafa; Shahraki, Asiyeh

    2013-01-01

    Radical cationic repair process of cis-syn thymine dimer has been investigated when (1) sugar-phosphate backbones were substituted by hydrogen atoms, (2) phosphate group was substituted by two hydrogen atoms each on a sugar ring and (3) sugar-phosphate backbone was taken into account. The effect of the interactions between N1 and N1' lone pairs and the C6-C6' antibonding orbital are the most important evidences for the cleavage of the C6-C6' bond in the first step of radical cationic repair mechanism in the absence of the sugar-phosphate backbone. The impact of the N1 and N1' lone pairs on the C6-C6' bond cleavage decreases and the energy barrier of the cleavage of that bond significantly increases in the presence of the deoxynucleoside sugars and the sugar-phosphate backbone. © 2012 Wiley Periodicals, Inc. Photochemistry and Photobiology © 2012 The American Society of Photobiology.

  5. Role of human DNA polymerase κ in extension opposite from a cis-syn thymine dimer.

    Science.gov (United States)

    Vasquez-Del Carpio, Rodrigo; Silverstein, Timothy D; Lone, Samer; Johnson, Robert E; Prakash, Louise; Prakash, Satya; Aggarwal, Aneel K

    2011-04-29

    Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase κ (Polκ), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Polκ in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure reveals a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Polκ in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Role of Human DNA Polymerase kappa in Extension Opposite from a cis-syn Thymine Dimer

    Energy Technology Data Exchange (ETDEWEB)

    R Vasquez-Del Carpio; T Silverstein; S Lone; R Johnson; L Prakash; S Prakash; A Aggarwal

    2011-12-31

    Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase {Kappa} (Pol{Kappa}), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Pol{Kappa} in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure reveals a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Pol{Kappa} in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.

  7. Influence of cytosine methylation on ultraviolet-induced cyclobutane pyrimidine dimer formation in genomic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Rochette, Patrick J. [Division of Pathology, Department of Medical Biology, Universite Laval, Quebec, QC (Canada); Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, QC (Canada); Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT (United States); Lacoste, Sandrine [Division of Pathology, Department of Medical Biology, Universite Laval, Quebec, QC (Canada); Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, QC (Canada); Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB (Canada); Therrien, Jean-Philippe [Division of Pathology, Department of Medical Biology, Universite Laval, Quebec, QC (Canada); Bastien, Nathalie [Division of Pathology, Department of Medical Biology, Universite Laval, Quebec, QC (Canada); Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, QC (Canada); Brash, Douglas E. [Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT (United States); Drouin, Regen, E-mail: Regen.Drouin@USherbrooke.ca [Division of Pathology, Department of Medical Biology, Universite Laval, Quebec, QC (Canada); Division of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Sherbrooke, QC (Canada)

    2009-06-01

    The ultraviolet (UV) component of sunlight is the main cause of skin cancer. More than 50% of all non-melanoma skin cancers and >90% of squamous cell carcinomas in the US carry a sunlight-induced mutation in the p53 tumor suppressor gene. These mutations have a strong tendency to occur at methylated cytosines. Ligation-mediated PCR (LMPCR) was used to compare at nucleotide resolution DNA photoproduct formation at dipyrimidine sites either containing or lacking a methylated cytosine. For this purpose, we exploited the fact that the X chromosome is methylated in females only on the inactive X chromosome, and that the FMR1 (fragile-X mental retardation 1) gene is methylated only in fragile-X syndrome male patients. Purified genomic DNA was irradiated with UVC (254 nm), UVB (290-320 nm) or monochromatic UVB (302 and 313 nm) to determine the effect of different wavelengths on cyclobutane pyrimidine dimer (CPD) formation along the X-linked PGK1 (phosphoglycerate kinase 1) and FMR1 genes. We show that constitutive methylation of cytosine increases the frequency of UVB-induced CPD formation by 1.7-fold, confirming that methylation per se is influencing the probability of damage formation. This was true for both UVB sources used, either broadband or monochromatic, but not for UVC. Our data prove unequivocally that following UVB exposure methylated cytosines are significantly more susceptible to CPD formation compared with unmethylated cytosines.

  8. Accuracy of thymine–thymine dimer bypass by Saccharomyces cerevisiae DNA polymerase η

    Science.gov (United States)

    Washington, M. Todd; Johnson, Robert E.; Prakash, Satya; Prakash, Louise

    2000-01-01

    The Saccharomyces cerevisiae RAD30 gene functions in error-free replication of UV-damaged DNA. RAD30 encodes a DNA polymerase, Pol η, which inserts two adenines opposite the two thymines of a cis-syn thymine–thymine (T–T) dimer. Here we use steady-state kinetics to determine the accuracy of DNA synthesis opposite the T–T dimer. Surprisingly, the accuracy of DNA synthesis opposite the damaged DNA is nearly indistinguishable from that opposite nondamaged DNA, with frequencies of misincorporation of about 10−2 to 10−3. These studies support the hypothesis that unlike most DNA polymerases, Pol η is able to tolerate distortions in DNA resulting from damage, which then enables the polymerase to utilize the intrinsic base pairing ability of the T–T dimer. PMID:10725365

  9. Effects of microinjected photoreactivating enzyme on thymine dimer removal and DNA repair synthesis in normal human and xeroderma pigmentosum fibroblasts.

    NARCIS (Netherlands)

    L. Roza (Len); W. Vermeulen (Wim); J.B.A. Bergen Henegouwen (Jacqueline); A.P.M. Eker (André); N.G.J. Jaspers (Nicolaas); P.H.M. Lohman (Paul); J.H.J. Hoeijmakers (Jan)

    1990-01-01

    textabstractUV-induced thymine dimers (10 J/m2 of UV-C) were assayed in normal human and xeroderma pigmentosum (XP) fibroblasts with a monoclonal antibody against these dimers and quantitative fluorescence microscopy. In repair-proficient cells dimer-specific immunofluorescence gradually decreased

  10. Spore Photoproduct (SP) Lyase from Bacillus subtilis Specifically Binds to and Cleaves SP (5-Thyminyl-5,6-Dihydrothymine) but Not Cyclobutane Pyrimidine Dimers in UV-Irradiated DNA

    Science.gov (United States)

    Slieman, Tony A.; Rebeil, Roberto; Nicholson, Wayne L.

    2000-01-01

    The predominant photolesion in the DNA of UV-irradiated dormant bacterial spores is the thymine dimer 5-thyminyl-5,6-dihydrothymine, commonly referred to as spore photoproduct (SP). A major determinant of SP repair during spore germination is its direct reversal by the enzyme SP lyase, encoded by the splB gene in Bacillus subtilis. SplB protein containing an N-terminal tag of six histidine residues [(6His)SplB] was purified from dormant B. subtilis spores and shown to efficiently cleave SP but not cyclobutane cis,syn thymine-thymine dimers in vitro. In contrast, SplB protein containing an N-terminal 10-histidine tag [(10His)SplB] purified from an Escherichia coli overexpression system was incompetent to cleave SP unless the 10-His tag was first removed by proteolysis at an engineered factor Xa site. To assay the parameters of binding of SplB protein to UV-damaged DNA, a 35-bp double-stranded oligonucleotide was constructed which carried a single pair of adjacent thymines on one strand. Irradiation of the oligonucleotide in aqueous solution or at 10% relative humidity resulted in formation of cyclobutane pyrimidine dimers (Py◊Py) or SP, respectively. (10His)SplB was assayed for oligonucleotide binding using a DNase I protection assay. In the presence of (10His)SplB, the SP-containing oligonucleotide was selectively protected from DNase I digestion (half-life, >60 min), while the Py◊Py-containing oligonucleotide and the unirradiated oligonucleotide were rapidly digested by DNase I (half-lives, 6 and 9 min, respectively). DNase I footprinting of (10His)SplB bound to the artificial substrate was carried out utilizing the 32P end-labeled 35-bp oligonucleotide containing SP. DNase I footprinting showed that SplB protected at least a 9-bp region surrounding SP from digestion with DNase I with the exception of two DNase I-hypersensitive sites within the protected region. (10His)SplB also caused significant enhancement of DNase I digestion of the SP

  11. Synthesis and characterization of a [3-15N]-labeled cis-syn thymine dimer-containing DNA duplex.

    Science.gov (United States)

    Bdour, Hussam M; Kao, Jeff Lung-Fa; Taylor, John-Stephen

    2006-02-17

    Cis-syn thymine dimers are the major photoproducts of DNA and are the principal cause of mutations induced by sunlight. To better understand the nature of base pairing with cis-syn thymine dimers, we have synthesized a decamer oligodeoxynucleotide (ODN) containing a cis-syn thymine dimer labeled at the N3 of both T's with 15N by two efficient routes from [3-15N]-thymidine phosphoramidite. In the postsynthetic irradiation route, an ODN containing an adjacent pair of [3-15N]-labeled T's was irradiated and the cis-syn dimer-containing ODN isolated by HPLC. In the mixed building block route, a mixture of cis-syn and trans-syn dimer-containing ODNs was synthesized from a mixture of [3-15N]-labeled thymine dimer phosphoramidites after which the cis-syn dimer-containing ODN was isolated by HPLC. The N3-nitrogen and imino proton signals of an (15)N-labeled thymine dimer-containing decamer duplex were assigned by 2D 1H-15N heterocorrelated HSQC NMR spectroscopy, and the 15N-1H coupling constant was found to be 1.8 Hz greater for the 5'-T than for the 3'-T. The larger coupling constant is indicative of weaker H-bonding that is consistent with the more distorted nature of the 5'-base pair found in solution state NMR and crystallographic structures.

  12. Optimization of DNA extraction from a scleractinian coral for the detection of thymine dimers by immunoassay.

    Science.gov (United States)

    Banaszak, Anastazia T

    2007-01-01

    Ultraviolet (UV)-B is known to cause DNA damage, principally by the formation of thymine dimers, but little research has been conducted in coral reef environments where UV doses are high. The majority of tropical reef-dwelling corals form a mutualistic symbiosis with the dinoflagellate Symbiodinium but few studies have been conducted on in situ DNA damage in corals and none have investigated the symbiotic components separately. The aim of this research was to quantify DNA damage in both the coral host and the dinoflagellate symbiont. The first step in this investigation was to optimize the extraction of DNA from the host, Porites astreoides, as well as the symbiont. The optimization was divided into a series of steps: the preservation of the samples, separation of the coral tissue from the skeleton, separation of the host tissue from the algal cells to prevent cross contamination as well as the extraction and purification of genomic DNA from the algae that are located intracellularly within the invertebrate animal tissue. The best preservation method was freezing at low temperatures without ethanol. After scraping with a razor blade, the coral tissue can be divided into host and algal components and the DNA extracted using modifications of published techniques yielding DNA suitable for the quantification of thymine dimer formation using antibodies. Preliminary data suggest that in P. astreoides collected from 1 m depth, thymine dimers form approximately 2.8 times more frequently in the host DNA than in the DNA of its symbionts.

  13. Site-specific effect of thymine dimer formation on dAn.dTn tract bending and its biological implications.

    OpenAIRE

    Wang, C I; Taylor, J.S.

    1991-01-01

    dAn.dTn sequences, otherwise known as A tracts, are hotspots for cis-syn thymine dimer formation and deletion mutations induced by UV light. Such A tracts are also known to bend DNA, suggesting that some biological effects of UV light might be related to the distinctive structure and properties of cis-syn dimer-containing A tracts. To investigate the effect of thymine dimer formation on A-tract bending multimers of all possible dimer monoadducts of a dA6.dT6-containing decamer known to bend D...

  14. MONITORING ULTRAVIOLET-B-INDUCED DNA-DAMAGE IN INDIVIDUAL DIATOM CELLS BY IMMUNOFLUORESCENT THYMINE DIMER DETECTION

    NARCIS (Netherlands)

    BUMA, AGJ; VANHANNEN, EJ; ROZA, L; VELDHUIS, MJW; GIESKES, WWC

    We developed a method to investigate the effect of ultraviolet-B radiation (UVBR) on the formation of thymine dimers in microalgal DIVA that can be used for both laboratory and in situ research. Antibody labeling of dimers was followed by a secondary antibody (fluorescein isothiocyanate) staining to

  15. Monitoring Ultraviolet-B-Induced DNA-Damage in Individual Diatom Cells by Immunofluorescent Thymine Dimer Detection

    NARCIS (Netherlands)

    Buma, A.G.J.; Van Hannen, E.J.; Roza, L.; Veldhuis, M.; Gieskes, W.W.C.

    1995-01-01

    We developed a method to investigate the effect of ultraviolet- B radiation (UVBR) on the formation of thymine dimers in microalgal DIVA that can be used for both laboratory and in situ research. Antibody labeling of dimers was followed by a secondary antibody (fluorescein isothiocyanate) staining

  16. Synthesis of a trans-syn thymine dimer building block. Solid phase synthesis of CGTAT[t,s]TATGC.

    OpenAIRE

    Taylor, J.S.; Brockie, I R

    1988-01-01

    The synthesis of a building block for the sequence specific introduction of the trans-syn thymine dimer into oligonucleotides via solid phase DNA synthesis technology is described. CGTAT[t,s]TATGC was synthesized in 48% overall yield by a partially automated procedure. The stepwise coupling yield for addition of the trans-syn thymine dimer building block was 58%. The dimer containing oligonucleotide was characterized by 500 MHz 1H COSY and NOESY spectroscopy and 202.5 MHz 31P NMR. The 1H chem...

  17. Site-specific analysis of UV-induced cyclobutane pyrimidine dimers in nucleotide excision repair-proficient and -deficient hamster cells: Lack of correlation with mutational spectra

    Energy Technology Data Exchange (ETDEWEB)

    Vreeswijk, Maaike P.G., E-mail: vreeswijk@lumc.nl [Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, P.O. Box 9600, Postzone S4-P, 2300 RC Leiden (Netherlands); Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Building 2, Postzone S-04, P.O. Box 9600, 2300 RC Leiden (Netherlands); Meijers, Caro M.; Giphart-Gassler, Micheline; Vrieling, Harry; Zeeland, Albert A. van; Mullenders, Leon H.F.; Loenen, Wil A.M. [Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, P.O. Box 9600, Postzone S4-P, 2300 RC Leiden (Netherlands)

    2009-04-26

    Irradiation of cells with UVC light induces two types of mutagenic DNA photoproducts, i.e. cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4) pyrimidone photoproducts (6-4PP). To investigate the relationship between the frequency of UV-induced photolesions at specific sites and their ability to induce mutations, we quantified CPD formation at the nucleotide level along exons 3 and 8 of the hprt gene using ligation-mediated PCR, and determined the mutational spectrum of 132 UV-induced hprt mutants in the AA8 hamster cell line and of 165 mutants in its nucleotide excision repair-defective derivative UV5. In AA8 cells, transversions predominated with a strong strand bias towards thymine-containing photolesions in the non-transcribed strand. As hamster AA8 cells are proficient in global genome repair of 6-4PP but selectively repair CPD from the transcribed strand of active genes, most mutations probably resulted from erroneous bypass of CPD in the non-transcribed strand. However, the relative incidence of CPD and the positions where mutations most frequently arose do not correlate. In fact some major damage sites hardly gave rise to the formation of mutations. In the repair-defective UV5 cells, mutations were almost exclusively C > T transitions caused by photoproducts at PyC sites in the transcribed strand. Even though CPD were formed at high frequencies at some TT sites in UV5, these photoproducts did not contribute to mutation induction at all. We conclude that, even in the absence of repair, large variations in the level of induction of CPD at different sites throughout the two exons do not correspond to frequencies of mutation induction.

  18. Ultraviolet-induced mutations in Cockayne syndrome cells are primarily caused by cyclobutane dimer photoproducts while repair of other photoproducts is normal

    Energy Technology Data Exchange (ETDEWEB)

    Parris, C.N.; Kraemer, K.H. (National Cancer Institute, Bethesda, MD (United States))

    1993-08-01

    The authors compared the contribution to mutagenesis on Cockayne syndrome (CS) cells of the major class of UV photoproducts, the cyclobutane pyrimidine dimer, to that of other DNA photoproducts by using the mutagenesis shuttle vector pZ189. Lymphoblastoid cell lines from the DNA repair-deficient disorders CS and xeroderma pigmentosum (XP) and a normal line were transfected with UV-treated pZ189. Cyclobutane dimers were selectively removed before transfection by photoreactivation (PR), leaving nondimer photoproducts intact. After UV exposure and replication in CS and XP cells, plasmid survival was abnormally elevated. After PR, plasmid survival increased and mutation frequency in CS cells decreased to normal levels but remained abnormal in XP cells. Sequence analysis of >200 mutant plasmids showed that with CS cells a major mutational hot spot was caused by unrepaired cyclobutane dimers. These data indicate that with both CS and XP cyclobutane dimers are major photoproducts generating reduced plasmid survival and increased mutation frequency. However, unlike XP, CS cells are proficient in repair of nondimer photoproducts. Since XP but not CS patients have a high frequency of UV-induced skin cancers, the data suggest that prevention of UV-induced skin cancers is associated with proficient repair of nondimer photoproducts. 38 refs., 3 figs., 2 tabs.

  19. Interaction between thymine dimer and flavin-adenine dinucleotide: a DFT and direct ab initio molecular dynamics study.

    Science.gov (United States)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2008-06-19

    The interaction between the fully reduced flavin-adenine dinucleotide (FADH (-)) and thymine dimer (T) 2 has been investigated by means of density functional theory (DFT) calculations. The charges of FADH (-) and (T) 2 were calculated to be -0.9 and -0.1, respectively, at the ground state. By photoirradiation, an electron transfer occurred from FADH (-) to (T) 2 at the first excited state. Next, the reaction dynamics of electron capture of (T) 2 have been investigated by means of the direct ab initio molecular dynamics (MD) method (HF/3-21G(d) and B3LYP/6-31G(d) levels) in order to elucidate the mechanism of the repair process of thymine dimer caused by the photoenzyme. The thymine dimer has two C-C single bonds between thymine rings (C 5-C 5' and C 6-C 6' bonds) at the neutral state, which is expressed by (T) 2. After the electron capture of (T) 2, the C 5-C 5' bond was gradually elongated and then it was preferentially broken. The time scale of the C-C bond breaking and formation of the intermediate with a single bond (T) 2 (-) was estimated to be 100-150 fs. The present calculations confirmed that the repair reaction of thymine dimer takes place efficiently via an electron-transfer process from the FADH (-) enzyme.

  20. Is a thymine dimer replicated via a transient abasic site intermediate? A comparative study using non-natural nucleotides.

    Science.gov (United States)

    Devadoss, Babho; Lee, Irene; Berdis, Anthony J

    2007-04-17

    UV light causes the formation of thymine dimers that can be misreplicated to induce mutagenesis and carcinogenesis. This report describes the use of a series of non-natural indolyl nucleotides in probing the ability of the high-fidelity bacteriophage T4 DNA polymerase to replicate this class of DNA lesion. Kinetic data reveal that indolyl analogues containing large pi-electron surface areas are incorporated opposite the thymine dimer almost as effectively as an abasic site, a noninstructional lesion. However, there are notable differences in the kinetic parameters for each DNA lesion that indicate distinct mechanisms for their replication. For example, the rate constants for incorporation opposite a thymine dimer are considerably slower than those measured opposite an abasic site. In addition, the magnitude of these rate constants depends equally upon contributions from pi-electron density and the overall size of the analogue. In contrast, binding of a nucleotide opposite a thymine dimer is directly correlated with the overall pi-electron surface area of the incoming dXTP. In addition to defining the kinetics of polymerization, we also provide the first reported characterization of the enzymatic removal of natural and non-natural nucleotides paired opposite a thymine dimer through exonuclease degradation or pyrophosphorolysis activity. Surprisingly, the exonuclease activity of the bacteriophage enzyme is activated by a thymine dimer but not by an abasic site. This dichotomy suggests that the polymerase can "sense" bulky lesions to partition the damaged DNA into the exonuclease domain. The data for both nucleotide incorporation and excision are used to propose models accounting for polymerase "switching" during translesion DNA synthesis.

  1. Elucidation of the Dexter-Type Energy Transfer in DNA by Thymine-Thymine Dimer Formation Using Photosensitizers as Artificial Nucleosides.

    Science.gov (United States)

    Antusch, Linda; Gaß, Nadine; Wagenknecht, Hans-Achim

    2017-01-24

    C-nucleosides of 4-methylbenzophenone, 4-methoxybenzophenone, and 2'-methoxyacetophenone were synthetically incorporated as internal photosensitizers into DNA double strands. This structurally new approach makes it possible to study the distance dependence of thymidine dimer formation because the site of photoinduced triplet energy transfer injection is clearly defined. The counterstrands to these modified strands lacked the phosphodiester bond between the two adjacent thymidines that are supposed to react with each other. Their dimerization could be evidenced by gel electrophoresis because the covalent connection by cyclobutane formation between the two thymidines changes the mobility. A shallow exponential distance dependence for the formation of thymidine dimers over up to 10 A-T base pairs was observed that agrees with a Dexter-type triplet-triplet energy transfer mechanism. Concomitantly, a significant amount of photoinduced DNA crosslinking was observed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Prediction of thymine dimer repair by electron transfer from photoexcited 8-aminoguanine or its deprotonated anion.

    Science.gov (United States)

    Sieradzan, Iwona; Marchaj, Marzena; Anusiewicz, Iwona; Skurski, Piotr; Simons, Jack

    2014-09-04

    Electronic structure methods are used to estimate differences in reaction barriers for transfer of an electron from singlet ππ* excited 8-aminoguanine (A) or deprotonated 8-aminoguanine anion (A(-)) to a proximal thymine dimer site compared to barriers when ππ* excited 8-oxoguanine (O) or deprotonated 8-oxoguanine (O(-)) serve as the electron donor. It is predicted that the barrier for photoexcited A should be lower than for photoexcited O, and the barrier for photoexcited A(-) should be lower than for photoexcited O(-). Moreover, A, O(-), and A(-) are predicted to have ππ* excited states at energies near where O does, which allows them to be excited by photons low enough in energy to avoid exciting or ionizing any of DNA's bases. The origin of the differences in barriers is suggested to be the lower ionization potential of A compared to O and the lower electron detachment energy of A(-) compared to O(-). Because O and O(-) have been experimentally shown to produce thymine dimer repair, it is proposed that A and A(-) are promising repair agents deserving experimental study.

  3. Nuclear dynamics investigation of the initial electron transfer in the cyclobutane pyrimidine dimer lesion repair process by photolyases

    CERN Document Server

    Joubert-Doriol, Loic; Olivucci, Massimo; Izmaylov, Artur F

    2016-01-01

    Photolyases are proteins capable of harvesting the sunlight to repair DNA damages caused by UV light. In this work we focus on the first step in the repair process of the cyclobutane pyrimidine dimer photoproduct (CPD) lesion, which is an electron transfer (ET) from a flavine cofactor to CPD, and study the role of various nuclear degrees of freedom (DOF) in this step. The ET step has been experimentally studied using transient spectroscopy and the corresponding data provide excellent basis for testing the quality of quantum dynamical models. Based on previous theoretical studies of electronic structure and conformations of the protein active site, we present a procedure to build a diabatic Hamiltonian for simulating the ET reaction in a molecular complex mimicking the enzyme's active site. We generate a reduced nuclear dimensional model that provides a first non-empirical quantum dynamical description of the structural features influencing the ET rate. By varying the nuclear DOF parametrization in the model t...

  4. UV-induced bond modifications in thymine and thymine dideoxynucleotide: structural elucidation of isomers by differential mobility mass spectrometry.

    Science.gov (United States)

    St-Jacques, Antony; Anichina, Janna; Schneider, Bradley B; Covey, Thomas R; Bohme, Diethard K

    2010-07-15

    Differential mobility spectrometry has been applied to reveal the occurrence of isomerization of thymine nucleobase and of thymine dideoxynucleotide d(5'-TT-3') due to bond redisposition induced by UV irradiation at 254 nm of frozen aqueous solutions of these molecules. Collision-induced dissociation (CID) spectra of electrosprayed photoproducts of the thymine solution suggest the presence of two isomers (the so-called cyclobutane and 6,4-photoproducts) in addition to the proton-bound thymine dimer, and these were separated using differential mobility spectrometry/mass spectrometry (DMS/MS) techniques with water as the modifier. Similar experiments with d(5'-TT-3') revealed the formation of a new isomer of deprotonated thymine dideoxynucleotide upon UV irradiation that was easily distinguished using DMS/MS with isopropanol as the modifier. The results reinforce the usefulness of DMS/MS in isomer separation.

  5. Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage

    Science.gov (United States)

    Knips, Alexander; Zacharias, Martin

    2017-01-01

    The photo-induced cis-syn-cyclobutane pyrimidine (CPD) dimer is a frequent DNA lesion. In bacteria photolyases efficiently repair dimers employing a light-driven reaction after flipping out the CPD damage to the active site. How the repair enzyme identifies a damaged site and how the damage is flipped out without external energy is still unclear. Employing molecular dynamics free energy calculations, the CPD flipping process was systematically compared to flipping undamaged nucleotides in various DNA global states and bound to photolyase enzyme. The global DNA deformation alone (without protein) significantly reduces the flipping penalty and induces a partially looped out state of the damage but not undamaged nucleotides. Bound enzyme further lowers the penalty for CPD damage flipping with a lower free energy of the flipped nucleotides in the active site compared to intra-helical state (not for undamaged DNA). Both the reduced penalty and partial looping by global DNA deformation contribute to a significantly shorter mean first passage time for CPD flipping compared to regular nucleotides which increases the repair likelihood upon short time encounter between repair enzyme and DNA.

  6. Detection of UV-induced mutagenic thymine dimer using graphene oxide.

    Science.gov (United States)

    Chung, Chan Ho; Kim, Joong Hyun; Chung, Bong Hyun

    2014-12-02

    In this paper, we report for the first time that graphene oxide (GO) can interact with mutagenic DNA but not intact DNA. After UV-irradiated fluorophore-linked DNA containing thymine repeats was mixed with GO, a decrease in fluorescence was observed in a time-dependent manner. In contrast, no fluorescence change was observed with intact DNA, indicating that UV irradiation of DNA resulted in the formation of mutagenic bases. Because GO is known to act as a fluorescence quencher, the decreased fluorescence implies adsorption of the UV-irradiated DNA onto GO. It appears that the decreased fluorescence might result from the greater accessibility of hydrophobic methyl groups and phenyl rings of thymine dimers to GO and from deformed DNA structures with less effective charge shielding under salt-containing conditions. Using this affinity of GO for mutagenic DNA, we could detect UV-irradiated DNA at concentrations as low as 100 pM. We were also able to analyze the ability of phototoxic drugs to catalyze the formation of mutagens under UV irradiation with GO. Because our method is highly sensitive and feasible and does not require the pretreatment of DNA, we propose that it could accelerate the screening of potential phototoxic drug candidates that would be able to sensitize mutagenic dsDNA.

  7. On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA.

    Science.gov (United States)

    Baggesen, Lisbeth Munksgaard; Hoffmann, Søren Vrønning; Nielsen, Steen Brøndsted

    2014-01-01

    Solar light leads to thymine dimers that are mutagenic and primary cause of skin cancer. Here, we report absorption and synchrotron radiation circular dichroism (CD) spectra of Tn single strands with different number n of bases (n = 2-7, 10, 11) recorded after various 254 nm irradiation times. From a principal component analysis of the CD spectra, we extract fingerprint spectra of both the cyclobutane pyrimidine dimer (CPD) and the pyrimidine (6-4) pyrimidone photoadduct (64PP). Extending the CD measurements to the vacuum ultraviolet region in combination with systematic examinations of size effects is a new approach to gain insight on the dimeric photoproducts. We find a simple linear correlation between n and average number of dimers formed after 1 h of irradiation. The probability for a thymine to engage in a dimer increases from 32% for n = 2 to 41% for n = 11, which implies limited effects of terminal thymines, i.e., the reaction does not occur preferentially at the extremities of the single strands as previously stated. It is even possible to form two dimers with only two bridging thymines. Finally, experiments conducted on calf thymus DNA provided a similar signature of the photodimer, but differences are also evident. © 2013 The American Society of Photobiology.

  8. Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: Similarities and differences

    Science.gov (United States)

    Ai, Yue-Jie; Zhang, Feng; Cui, Gang-Long; Luo, Yi; Fang, Wei-Hai

    2010-08-01

    2-aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized π1π∗ excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed.

  9. On the Formation of Thymine Photodimers in Thymine Single Strands and Calf Thymus DNA

    DEFF Research Database (Denmark)

    Baggesen, Lisbeth Munksgård; Hoffmann, S.V.; Nielsen, Steen Brøndsted

    2014-01-01

    Solar light leads to thymine dimers that are mutagenic and primary cause of skin cancer. Here, we report absorption and synchrotron radiation circular dichroism (CD) spectra of Tn single strands with different number n of bases (n = 2–7, 10, 11) recorded after various 254 nm irradiation times. From...... a principal component analysis of the CD spectra, we extract fingerprint spectra of both the cyclobutane pyrimidine dimer (CPD) and the pyrimidine (6-4) pyrimidone photoadduct (64PP). Extending the CD measurements to the vacuum ultraviolet region in combination with systematic examinations of size effects...

  10. Structures and energetics of base flipping of the thymine dimer depend on DNA sequence.

    Science.gov (United States)

    O'Neil, Lauren L; Wiest, Olaf

    2008-04-03

    The cis,syn-cyclobutane pyrimidine dimer (CPD) is a photoinduced DNA lesion leading to a significant distortion of the DNA structure. Its repair by DNA photolyase requires a flip of the damaged base into an extrahelical position. This base flip is expected to be sequence-dependent, but the structures and energetics as a function of the bases 3' and 5' to the CPD lesion are unknown. Eight-nanosecond MD simulations of four different hexadecamer duplexes with the CPD were performed for the flipped-in and flipped-out structures. Analysis of these results indicates clear sequence-dependent differences. Significant disruptions of the base pairs to the 3' side of the CPD are observed for the flipped-out structures with adjacent A-T pairs, whereas those with G-C pairs adjacent show no such distortions. The conformational spaces occupied by these two duplexes are significantly different. The structural differences correlate well with the free energy differences for base flipping calculated using the previously established 2D potential of mean force (PMF) method. The energy differences for base flipping in duplexes containing A, T, G, and C pairs adjacent to the CPD were found to be 6.25-6.5, 5.25-5.5, 7.25-7.5, and 6.5-6.75 kcal/mol, respectively. These energy differences of up to 2 kcal/mol should be large enough to be detected experimentally using sensitive probes.

  11. Cyclobutane pyrimidine dimers form preferentially at the major p53 mutational hotspot in UVB-induced mouse skin tumors.

    Science.gov (United States)

    You, Y H; Szabó, P E; Pfeifer, G P

    2000-11-01

    The most prevalent DNA lesion induced by UV irradiation is the cyclobutane pyrimidine dimer (CPD) which forms at positions of neighboring pyrimidines. In mouse skin tumors induced by irradiation with UVB (280-320 nm) lamps or solar UV simulators, a major mutational hotspot occurs at codon 270 (Arg-->Cys) involving a sequence change from 5'-TCGT to 5'-TTGT. We have shown previously that CPD formation by UVB or sunlight is enhanced up to 10-fold at 5'-CCG and 5'-TCG sequences due to the presence of 5-methylcytosine bases. Sequence analysis showed that the CpG at codon 270 is methylated in mouse epidermis at a level of approximately 85%. Irradiation of mouse skin or mouse cells in culture produced the strongest CPD signal within exon 8 at the 5'-TCG sequence which is part of codon 270. Time course experiments showed that CPDs at this particular sequence persist longer than at several neighboring positions. The data suggest that formation of CPDs is responsible for induction of the major p53 mutational hotspot in UV-induced mouse skin tumors.

  12. QM/MM & Monte Carlo simulation of single wall nano tube carbon SWNT (15, 15) binding with thymine dimer

    OpenAIRE

    Soudeh Safari; Mohammad Mahmoodi Hashemi

    2016-01-01

    In this research, we have studied of thymine dimer binding on the relative energies and dipole moment values and the structural properties of solvent effect (water, methanol and ethanol) surrounding single-walled and multi walled carbon nanotube, by using QM/MM simulation, those calculations have carried out with the Gaussian and Hyper Chem package. In this study we investigated the polar solvents effects on SWCNT within the Onsager self - consistent reaction field (SCRF) model using a Hartre...

  13. The effect of pi-stacking, h-bonding, and electrostatic interactions on the ionization energies of nucleic acid bases: adenine-adenine, thymine-thymine and adenine-thymine dimers

    Energy Technology Data Exchange (ETDEWEB)

    Bravaya, Ksenia B.; Kostko, Oleg; Ahmed, Musahid; Krylov, Anna I.

    2009-09-02

    A combined theoretical and experimental study of the ionized dimers of thymine and adenine, TT, AA, and AT, is presented. Adiabatic and vertical ionization energies(IEs) for monomers and dimers as well as thresholds for the appearance of the protonated species are reported and analyzed. Non-covalent interactions stronglyaffect the observed IEs. The magnitude and the nature of the effect is different for different isomers of the dimers. The computations reveal that for TT, the largestchanges in vertical IEs (0.4 eV) occur in asymmetric h-bonded and symmetric pi- stacked isomers, whereas in the lowest-energy symmetric h-bonded dimer the shiftin IEs is much smaller (0.1 eV). The origin of the shift and the character of the ionized states is different in asymmetric h-bonded and symmetric stacked isomers. Inthe former, the initial hole is localized on one of the fragments, and the shift is due to the electrostatic stabilization of the positive charge of the ionized fragment by thedipole moment of the neutral fragment. In the latter, the hole is delocalized, and the change in IE is proportional to the overlap of the fragments' MOs. The shifts in AAare much smaller due to a less effcient overlap and a smaller dipole moment. The ionization of the h-bonded dimers results in barrierless (or nearly barrierless) protontransfer, whereas the pi-stacked dimers relax to structures with the hole stabilized by the delocalization or electrostatic interactions.

  14. Cyclobutane pyrimidine dimers photolyase from extremophilic microalga: Remarkable UVB resistance and efficient DNA damage repair

    Energy Technology Data Exchange (ETDEWEB)

    Li, Chongjie [Key Laboratory of Marine Bioactive Substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao 266061 (China); Ma, Li [Key Laboratory of Biofuels, and Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 (China); Mou, Shanli [Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao (China); Wang, Yibin, E-mail: wangyibin@fio.org.cn [Key Laboratory of Marine Bioactive Substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao 266061 (China); Zheng, Zhou; Liu, Fangming; Qi, Xiaoqing; An, Meiling; Chen, Hao [Key Laboratory of Marine Bioactive Substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao 266061 (China); Miao, Jinlai, E-mail: miaojinlai@163.com [Key Laboratory of Marine Bioactive Substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao 266061 (China); State Key Laboratory of Biological Fermentation Engineering of Beer (In Preparation), Qingdao (China)

    2015-03-15

    Highlights: • Chlamydomonas sp. ICE-L photolyase gene PHR2 is first cloned and expressed in E. coli. • PHR2 complemented E. coli could efficiently survival from UV radiation. • Expressed PHR2 photolyase has distinct photo-reactivation activity in vitro. - Abstract: Bacteria living in the Antarctic region have developed several adaptive features for growth and survival under extreme conditions. Chlamydomonas sp. ICE-Lis well adapted to high levels of solar UV radiation. A putative photolyase was identified in the Chlamydomonas sp. ICE-L transcriptome. The complete cDNA sequence was obtained by RACE-PCR. This PHR encoding includes a polypeptide of 579 amino acids with clear photolyase signatures belonging to class II CPD-photolyases, sharing a high degree of homology with Chlamydomonas reinhardtii (68%). Real-time PCR was performed to investigate the potential DNA damage and responses following UVB exposure. CPD photolyase mRNA expression level increased over 50-fold in response to UVB radiation for 6 h. Using photolyase complementation assay, we demonstrated that DNA photolyase increased photo-repair more than 116-fold in Escherichia coli strain SY2 under 100 μw/cm{sup 2} UVB radiation. To determine whether photolyase is active in vitro, CPD photolyase was over-expressed. It was shown that pyrimidine dimers were split by the action of PHR2. This study reports the unique structure and high activity of the enzyme. These findings are relevant for further understanding of molecular mechanisms of photo-reactivation, and will accelerate the utilization of photolyase in the medical field.

  15. The Roles of Several Residues of Escherichia coli DNA Photolyase in the Highly Efficient Photo-Repair of Cyclobutane Pyrimidine Dimers

    Directory of Open Access Journals (Sweden)

    Lei Xu

    2010-01-01

    Full Text Available Escherichia coli DNA photolyase is an enzyme that repairs the major kind of UV-induced lesions, cyclobutane pyrimidine dimer (CPD in DNA utilizing 350–450 nm light as energy source. The enzyme has very high photo-repair efficiency (the quantum yield of the reaction is ~0.85, which is significantly greater than many model compounds that mimic photolyase. This suggests that some residues of the protein play important roles in the photo-repair of CPD. In this paper, we have focused on several residues discussed their roles in catalysis by reviewing the existing literature and some hypotheses.

  16. The effect of pi-stacking, H-bonding, and electrostatic interactions on the ionization energies of nucleic acid bases: adenine-adenine, thymine-thymine and adenine-thymine dimers.

    Science.gov (United States)

    Bravaya, Ksenia B; Kostko, Oleg; Ahmed, Musahid; Krylov, Anna I

    2010-03-14

    A combined theoretical and experimental study of the ionized dimers of thymine and adenine, TT, AA, and AT, is presented. Experimentally observed and computed adiabatic and vertical ionization energies (IEs) for monomers and dimers as well as thresholds for the appearance of the protonated species are reported and analyzed. Non-covalent interactions strongly affect the observed IEs. The magnitude and the nature of the effect is different for different isomers of the dimers. The computations reveal that for TT, the largest changes in vertical IEs (0.4 eV) relative to the monomer occur in asymmetric H-bonded and symmetric pi-stacked isomers, whereas in the lowest-energy symmetric H-bonded dimer the shift in IEs is much smaller (0.2 eV). The origin of the shift and the character of the ionized states is different in asymmetric H-bonded and symmetric stacked isomers. In the former, the initial hole is localized on one of the fragments, and the shift is due to the electrostatic stabilization of the positive charge of the ionized fragment by the dipole moment of the neutral fragment. In the latter, the hole is delocalized, and the change in IE is proportional to the overlap of the fragments' MOs. Relative to TT, the shifts in AA and AT are much smaller due to a less efficient overlap, smaller dipole of A and the large energy gap between ionized states of A and T monomers in the case of AT dimer. The ionization of the H-bonded dimers results in barrierless (or nearly barrierless) proton transfer, whereas the pi-stacked dimers relax to structures with the hole stabilized by the delocalization or electrostatic interactions.

  17. Computational study of thymine dimer radical anion splitting in the self-repair process of duplex DNA.

    Science.gov (United States)

    Masson, Fanny; Laino, Teodoro; Tavernelli, Ivano; Rothlisberger, Ursula; Hutter, Jürg

    2008-03-19

    Formation of the thymine dimer is one of the most important types of photochemical damage in DNA, responsible for several biological pathologies. Though specifically designed proteins (photolyases) can efficiently repair this type of damage in living cells, an autocatalytic activity of the DNA itself was recently discovered, allowing for a self-repair mechanism. In this paper, we provide the first molecular dynamics study of the splitting of thymine dimer radical anions, using a quantum mechanical/molecular mechanics (QM/MM) approach based on density functional theory (DFT) to describe the quantum region. A set of seven statistically representative molecular dynamics trajectories is analyzed. Our calculations predict an asynchronously concerted process in which C5-C5' bond breaking is barrierless while C6-C6' bond breaking is characterized by a small free energy barrier. An upper bound of 2.5 kcal/mol for this barrier is estimated. Moreover, the molecular dynamics study and the low free energy barrier involved in C6-C6' bond breaking characterize the full process as being an ultrafast reaction.

  18. Efficient photosensitized splitting of the thymine dimer/oxetane unit on its modifying beta-cyclodextrin by a binding electron donor.

    Science.gov (United States)

    Tang, Wen-Jian; Song, Qin-Hua; Wang, Hong-Bo; Yu, Jing-Yu; Guo, Qing-Xiang

    2006-07-07

    Two modified beta-cyclodextrins (beta-CDs) with a thymine dimer and a thymine oxetane adduct respectively, TD-CD and Ox-CD, have been prepared, and utilized to bind an electron-rich chromophore, indole or N,N-dimethylaniline (DMA), to form a supramolecular complex. We have examined the photosensitized splitting of the dimer/oxetane unit in TD-CD/Ox-CD by indole or DMA via an electron-transfer pathway, and observed high splitting efficiencies of the dimer/oxetane unit. On the basis of measurements of fluorescence spectra and splitting quantum yields, it is suggested that the splitting reaction occurs in a supramolecular complex by an inclusion interaction between the modified beta-CDs and DMA or indole. The back electron transfer, which leads low splitting efficiencies for the covalently-linked chromophore-dimer/oxetane compounds, is suppressed in the non-covalently-bound complex, and the mechanism has been discussed.

  19. Enzymatic Reaction with Unnatural Substrates: DNA Photolyase (Escherichia coli) Recognizes and Reverses Thymine [2+2] Dimers in the DNA Strand of a DNA/PNA Hybrid Duplex

    Science.gov (United States)

    Ramaiah, Danaboyina; Kan, Yongzhi; Koch, Troels; Orum, Henrik; Schuster, Gary B.

    1998-10-01

    Peptide nucleic acids (PNA) are mimics with normal bases connected to a pseudopeptide chain that obey Watson--Crick rules to form stable duplexes with itself and natural nucleic acids. This has focused attention on PNA as therapeutic or diagnostic reagents. Duplexes formed with PNA mirror some but not all properties of DNA. One fascinating aspect of PNA biochemistry is their reaction with enzymes. Here we show an enzyme reaction that operates effectively on a PNA/DNA hybrid duplex. A DNA oligonucleotide containing a cis, syn-thymine [2+2] dimer forms a stable duplex with PNA. The hybrid duplex is recognized by photolyase, and irradiation of the complex leads to the repair of the thymine dimer. This finding provides insight into the enzyme mechanism and provides a means for the selective repair of thymine photodimers.

  20. Wavelength-dependent induction of thymine dimers and growth rate reduction in the marine diatom Cyclotella sp. exposed to ultraviolet radiation

    NARCIS (Netherlands)

    Buma, A.G.J.; Engelen, A.H; Gieskes, W.W C

    1997-01-01

    Cultures of the marine diatom Cyclotella sp. were subjected to various polychromatic exposures of UVB radiation (280-320 nm), UVA radiation (320-400 nm) and photosynthetically active radiation, PAR (400-700 nm). Changes in growth rate and residual thymine dimer content (a measure for DNA damage)

  1. A light-responsive reversible molecule-gated system using thymine-modified mesoporous silica nanoparticles.

    Science.gov (United States)

    He, Dinggeng; He, Xiaoxiao; Wang, Kemin; Cao, Jie; Zhao, Yingxiang

    2012-02-28

    In this paper, a reversible light-responsive molecule-gated system based on mesoporous silica nanoparticles (MSN) functionalized with thymine derivatives is designed and demonstrated. The closing/opening protocol and release of the entrapped guest molecules is related by a photodimerization-cleavage cycle of thymine upon different irradiation. In the system, thymine derivatives with hydrophilicity and biocompatibility were grafted on the pore outlets of MSN. The irradiation with 365 nm wavelength UV light to thymine-functionalized MSN led to the formation of cyclobutane dimer in the pore outlet, subsequently resulting in blockage of pores and strongly inhibiting the diffusion of guest molecules from pores. With 240 nm wavelength UV light irradiation, the photocleavage of cyclobutane dimer opened the pore and allowed the release of the entrapped guest molecules. As a proof-of-the-concept, Ru(bipy)(3)(2+) was selected as the guest molecule. Then the light-responsive loading and release of Ru(bipy)(3)(2+) were investigated. The results indicated that the system had an excellent loading amount (53 μmol g(-1) MSN) and controlled release behavior (82% release after irradiation for 24 h), and the light-responsive loading and release procedure exhibited a good reversibility. Besides, the light-responsive system loaded with Ru(bipy)(3)(2+) molecule could also be used as a light-switchable oxygen sensor. © 2012 American Chemical Society

  2. Theoretical investigation of the coupling between hydrogen-atom transfer and stacking interaction in adenine-thymine dimers.

    Science.gov (United States)

    Villani, Giovanni

    2013-04-15

    Three different dimers of the adenine-thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N-N and N-O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N-N bridge than for the N-O one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Crystal structure of a DNA decamer containing a cis-syn thymine dimer.

    Science.gov (United States)

    Park, HaJeung; Zhang, Kaijiang; Ren, Yingjie; Nadji, Sourena; Sinha, Nanda; Taylor, John-Stephen; Kang, ChulHee

    2002-12-10

    It is well known that exposure to UV induces DNA damage, which is the first step in mutagenesis and a major cause of skin cancer. Among a variety of photoproducts, cyclobutane-type pyrimidine photodimers (CPD) are the most abundant primary lesion. Despite its biological importance, the precise relationship between the structure and properties of DNA containing CPD has remained to be elucidated. Here, we report the free (unbound) crystal structure of duplex DNA containing a CPD lesion at a resolution of 2.0 A. Our crystal structure shows that the overall helical axis bends approximately 30 degrees toward the major groove and unwinds approximately 9 degrees, in remarkable agreement with some previous theoretical and experimental studies. There are also significant differences in local structure compared with standard B-DNA, including pinching of the minor groove at the 3' side of the CPD lesion, a severe change of the base pair parameter in the 5' side, and serious widening of both minor and major groves both 3' and 5' of the CPD. Overall, the structure of the damaged DNA differs from undamaged DNA to an extent that DNA repair proteins may recognize this conformation, and the various components of the replicational and transcriptional machinery may be interfered with due to the perturbed local and global structure.

  4. Wavelength dependence of ultraviolet radiation-induced DNA damage as determined by laser irradiation suggests that cyclobutane pyrimidine dimers are the principal DNA lesions produced by terrestrial sunlight

    Science.gov (United States)

    Besaratinia, Ahmad; Yoon, Jae-in; Schroeder, Christi; Bradforth, Stephen E.; Cockburn, Myles; Pfeifer, Gerd P.

    2011-01-01

    To elucidate the involvement of specific ultraviolet (UV) wavelengths in solar mutagenesis, we used a laser system to investigate the induction of DNA damage, both in the overall genome and at the nucleotide resolution level, in the genomic DNA of transgenic Big Blue mouse fibroblasts irradiated with a series of UV wavelengths, inclusive of UVC (λ320 nm). Subsequently, we sought correlation between the locations of UV-induced DNA lesions in the cII transgene of irradiated DNA samples and the frequency distribution and codon position of the induced cII mutations in counterpart mouse cells irradiated with simulated sunlight. Using a combination of enzymatic digestion assays coupled with gel electrophoresis, immunodot blot assays, and DNA footprinting assays, we demonstrated a unique wavelength-dependent formation of photodimeric lesions, i.e., cyclobutane pyrimidine dimers (CPDs) and (6–4) photoproducts [(6–4)PPs], based on direct UV absorption of DNA, in irradiated mouse genomic DNA, which could partially explain the induction of mutations in mouse cells irradiated with simulated sunlight. Most notably, there was a divergence of CPD and (6–4)PP formation at an irradiation wavelength of 296 nm in mouse genomic DNA. Whereas substantial formation of (6–4)PPs was detectable in samples irradiated at this wavelength, which intensified as the irradiation wavelength decreased, only small quantities of these lesions were found in samples irradiated at wavelengths of 300–305 nm, with no detectable level of (6–4)PPs in samples irradiated with longer wavelengths. Although CPD formation followed the same pattern of increase with decreasing wavelengths of irradiation, there were substantial levels of CPDs in samples irradiated with UVB wavelengths borderlined with UVA, and small but detectable levels of these lesions in samples irradiated with longer wavelengths. Because the terrestrial sunlight spectrum rolls off sharply at wavelengths ∼300 nm, our findings

  5. Yeast pol eta holds a cis-syn thymine dimer loosely in the active site during elongation opposite the 3'-T of the dimer, but tightly opposite the 5'-T.

    Science.gov (United States)

    Sun, Liping; Zhang, Kaijiang; Zhou, Lilly; Hohler, Paul; Kool, Eric T; Yuan, Fenghua; Wang, Zhigang; Taylor, John Stephen

    2003-08-12

    Polymerase eta is a member of the Y family of DNA polymerases which is able to bypass thymine dimers efficiently and in a relatively error-free manner. To elucidate the mechanism of dimer bypass, the efficiency of dAMP and pyrene nucleotide insertion opposite the thymine dimer and its N3-methyl derivatives was determined. Pol eta inserts pyrene nucleotide with greater efficiency than dAMP opposite the 3'-T of an undimerized or dimerized T and is an effective inhibitor of DNA synthesis by pol eta. Substitution of the N3H of the 3'-T of an undimerized T or a dimerized T with a methyl group has little effect on the insertion efficiency of pyrene nucleotide but greatly inhibits the insertion of dAMP. Together, these results suggest that the error-free insertion of dAMP opposite the 3'-T of the cis-syn thymine dimer happens by way of a loosely held dimer in the active site which can be displaced from the active site by pyrene nucleotide. In contrast, pol eta cannot insert pyrene nucleotide opposite the 5'-T of the dimer, whereas it can insert dAMP with efficiency comparable to that opposite the 3'-T. The inability to insert pyrene nucleotide opposite the 5'-T of the dimer is consistent with the idea that while the polymerase binds loosely to a templating nucleotide, it binds tightly to the nucleotide to its 3'-side. Overall, the results show a marked difference from similar studies on pol I family polymerases, and suggest mechanisms by which this Y family polymerase can process damaged DNA efficiently.

  6. Photosensitized splitting of thymine dimer or oxetane unit by a covalently N-linked carbazole via electron transfer in different marcus regions.

    Science.gov (United States)

    Wu, Qing-Qing; Song, Qin-Hua

    2010-08-05

    Although many similarities exist between the two classes of enzymes, cyclobutane photolyases and (6-4) photolyases have certain important differences. The most significant difference is in their repair quantum yields, cyclobutane photolyases with a uniformly high efficiency (0.7-0.98) and very low repair efficiency for (6-4) photolyases (0.05-0.1). To understand the significant difference, we prepared two classes of model compounds, covalently N-linked dimer- (1) or oxetane-carbazole (2) compounds with a dimethylene or trimethylene group as a linker. Under light irradiation, the dimer or oxetane unit of model compounds can be sensitized to split by the excited carbazole via an intramolecular electron transfer. The splitting reaction of dimer or oxetane unit in model compounds is strongly solvent dependent. In nonpolar solvents, such as cyclohexane or THF, no fluorescence quenching of the carbazole moiety of model compounds relative to a free carbazole, N-methylcarbazole, was observed and thus no splitting occurred. In polar solvents, two classes of model compounds reveal two reverse solvent effects on the splitting quantum yield. One is an inverse relation between the quantum yield and the polarity of the solvent for dimer-model systems, and another is a normal relation for oxetane-model systems. This phenomenon was also observed with another two classes of model compounds, covalently linked dimer- or oxetane-indole. Based on Marcus theory and thermodynamic data, it has been rationalized that the two reverse solvent effects derive from back electron transfer in the splitting process lying in the different Marcus regions. Back electron transfer lies in the Marcus inverted region for dimer-model systems and the normal region for oxetane-model systems. From repair solvent behavior of the two classes of model compounds, we gained some insights into the major difference in the repair efficiency for the two classes of photolyases.

  7. Residues at a Single Site Differentiate Animal Cryptochromes from Cyclobutane Pyrimidine Dimer Photolyases by Affecting the Proteins' Preferences for Reduced FAD.

    Science.gov (United States)

    Xu, Lei; Wen, Bin; Wang, Yuan; Tian, Changqing; Wu, Mingcai; Zhu, Guoping

    2017-06-19

    Cryptochromes (CRYs) and photolyases belong to the cryptochrome/photolyase family (CPF). Reduced FAD is essential for photolyases to photorepair UV-induced cyclobutane pyrimidine dimers (CPDs) or 6-4 photoproducts in DNA. In Drosophila CRY (dCRY, a type I animal CRY), FAD is converted to the anionic radical but not to the reduced state upon illumination, which might induce a conformational change in the protein to relay the light signal downstream. To explore the foundation of these differences, multiple sequence alignment of 650 CPF protein sequences was performed. We identified a site facing FAD (Ala377 in Escherichia coli CPD photolyase and Val415 in dCRY), hereafter referred to as "site 377", that was distinctly conserved across these sequences: CPD photolyases often had Ala, Ser, or Asn at this site, whereas animal CRYs had Ile, Leu, or Val. The binding affinity for reduced FAD, but not the photorepair activity of E. coli photolyase, was dramatically impaired when replacing Ala377 with any of the three CRY residues. Conversely, in V415S and V415N mutants of dCRY, FAD was photoreduced to its fully reduced state after prolonged illumination, and light-dependent conformational changes of these mutants were severely inhibited. We speculate that the residues at site 377 play a key role in the different preferences of CPF proteins for reduced FAD, which differentiate animal CRYs from CPD photolyases. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. In Vivo Spectrum of UVC-induced Mutation in Mouse Skin Epidermis May Reflect the Cytosine Deamination Propensity of Cyclobutane Pyrimidine Dimers.

    Science.gov (United States)

    Ikehata, Hironobu; Mori, Toshio; Yamamoto, Masayuki

    2015-11-01

    Although ultraviolet radiation (UVR) has a genotoxicity for inducing skin cancers, the skin may tolerate UVC component because the epidermal layer prevents this short wavelength range from passing through. Here, UVC genotoxicity for mouse skin was evaluated in terms of DNA damage formation and mutagenicity. UVC induced UVR photolesions and mutations remarkably in the epidermis but poorly in the dermis, confirming the barrier ability of the epidermis against shorter UVR wavelengths. Moreover, the epidermis itself responded to UVC mutagenicity with mutation induction suppression, which suppressed the mutant frequencies to a remarkably low, constant level regardless of UVC dose. The mutation spectrum observed in UVC-exposed epidermis showed a predominance of UV-signature mutation, which occurred frequently in 5'-TCG-3', 5'-TCA-3' and 5'-CCA-3' contexts. Especially, for the former two contexts, the mutations recurred at several sites with more remarkable recurrences at the 5'-TCG-3' sites. Comparison of the UVC mutation spectrum with those observed in longer UVR wavelength ranges led us to a mechanism that explains why the sequence context preference of UV-signature mutation changes according to the wavelength, which is based on the difference in the mCpG preference of cyclobutane pyrimidine dimer (CPD) formation among UVR ranges and the sequence context-dependent cytosine deamination propensity of CPD. © 2015 The American Society of Photobiology.

  9. Octyl Methoxycinnamate Modulates Gene Expression and Prevents Cyclobutane Pyrimidine Dimer Formation but not Oxidative DNA Damage in UV-Exposed Human Cell Lines

    Science.gov (United States)

    Duale, Nur; Olsen, Ann-Karin; Christensen, Terje; Butt, Shamas T.; Brunborg, Gunnar

    2010-01-01

    Octyl methoxycinnamate (OMC) is one of the most widely used sunscreen ingredients. To analyze biological effects of OMC, an in vitro approach was used implying ultraviolet (UV) exposure of two human cell lines, a primary skin fibroblast (GM00498) and a breast cancer (MCF-7) cell lines. End points include cell viability assessment, assay of cyclobutane pyrimidine dimers (CPDs) and oxidated DNA lesions using alkaline elution and lesion-specific enzymes, and gene expression analysis of a panel of 17 DNA damage–responsive genes. We observed that OMC provided protection against CPDs, and the degree of protection correlated with the OMC-mediated reduction in UV dose. No such protection was found with respect to oxidative DNA lesions. Upon UV exposure in the presence of OMC, the gene expression studies showed significant differential changes in some of the genes studied and the expression of p53 protein was also changed. For some genes, the change in expression seemed to be delayed in time by OMC. The experimental approach applied in this study, using a panel of 17 genes in an in vitro cellular system together with genotoxicity assays, may be useful in the initial screening of active ingredients in sunscreens. PMID:20071424

  10. Increased cyclooxygenase expression and thymine dimer formation after repeated exposures of humans to low doses of solar simulated radiation.

    Science.gov (United States)

    Narbutt, Joanna; Lesiak, Aleksandra; Jochymski, Cezary; Kozlowski, Wojciech; Sysa-Jedrzejowska, Anna; Norval, Mary

    2007-10-01

    The impact of repeated doses of solar simulated radiation (SSR) has not been evaluated, particularly to determine if photoadaptation and photoprotection develop over time. In this study, erythema, pigmentation, cyclooxygenase (COX)-1 and 2 expression and thymine dimer (dTT) formation were evaluated in the skin of irradiated subjects of phototype II or III. Groups of 7-10 volunteers were whole-body irradiated with a low dose of SSR on each of 10 consecutive days followed by a single erythemal ultraviolet B (UVB) dose on a small body area, or irradiated only with the single erythemal UVB dose on a small body area, or irradiated with the low dose of SSR on each of 30 consecutive days, or were unirradiated. Erythema and pigmentation were measured 24 h after the final SSR or UVB, and skin biopsies collected for the assessment of COX(+) cells and dTT(+) nuclei. The repeated SSR exposures induced a small increase in pigmentation without erythema, and were slightly protective against the erythemal effects of the subsequent high UVB dose. The number of COX-1(+) and 2(+) cells increased as a result of 10-days SSR and rose still further after 30-days SSR, indicating that photoadaptation had not developed. The SSR exposures did not result in any protection against the further increase in COX-1 and 2 expression caused by the erythemal UVB dose. In contrast, for dTT formation, the repeated SSR exposures led to a limited degree of both photoadaptation and photoprotection.

  11. Single-molecule analysis of thymine dimer-containing G-quadruplexes formed from the human telomere sequence.

    Science.gov (United States)

    Wolna, Anna H; Fleming, Aaron M; Burrows, Cynthia J

    2014-12-09

    The human telomere plays crucial roles in maintaining genome stability. In the presence of suitable cations, the repetitive 5'-TTAGGG-3' human telomere sequence can fold into G-quadruplexes that adopt the hybrid, basket, or propeller fold. The telomere sequence is hypersensitive to UV-induced thymine dimer (T=T) formation, yet it does not cause telomere shortening. In this work, the potential structural disruption and thermodynamic stability of the T=T-containing natural telomere sequences were studied to understand why this damage is tolerated in telomeres. First, established methods, such as thermal melting measurements, electrophoretic mobility shift assays, and circular dichroism spectroscopy, were utilized to determine the effects of the damage on these structures. Second, a single-molecule ion channel recording technique using α-hemolysin (α-HL) was employed to examine further the structural differences between the damaged sequences. It was observed that the damage caused slightly lower thermal stabilities and subtle changes in the circular dichroism spectra for hybrid and basket folds. The α-HL experiments determined that T=Ts disrupt double-chain reversal loop formation but are tolerated in edgewise and diagonal loops. The largest change was observed for the T=T-containing natural telomere sequence when the propeller fold (all double-chain reversal loops) was studied. On the basis of the α-HL experiments, it was determined that a triplexlike structure exists under conditions that favor a propeller structure. The biological significance of these observations is discussed.

  12. Photoaddition of p-aminobenzoil acid to thymine and thymidine

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, A.A.; Wainschel, L.A.; Shetlar, M.D. (California Univ., San Francisco, CA (United States). School of Pharmacy)

    1992-05-01

    Several studies in the literature have shown that DNA is damaged after UV irradiation in the presence of the sunscreen agent p-aminobenzoic acid (PABA), both in vivo and in vitro. One type of damage has been shown to be the result of increased yields of pyrimidime cyclobutane dimer formation. However, it has been suggested that other types of lesions are produced as well. We have studied the photochemistry of the thymine-PABA and thymidine-PABA systems and report here the isolation and characterization of thymine-PABA and thymidine-PABA photoadducts. These products have been identified, respectively as 5-(2-amino-5-carboxyphenyl)-5,6-dihydrothymine and isomeric forms of 5-(2-amino-5-carboxyphenyl)-5,6-dihydrothymidine. The quantum yields for the formation of these ducts in deaerated aqueous solutions at pH 7.0 have been determined to be 9.5 x 10{sup -4} and 4.3 x 10{sup -3} for the thymine and thymidine based adducts respectively. A pH profile for the thymine-PABA system indicated a maximum quantum yield for adduct formation at pH 6.5, although it could be detected over the whole pH range studied (pH 3.5-11.0). (Author).

  13. Immunological detection of UV induced cyclobutane pyrimidine dimers and (6-4) photoproducts in DNA from reference bacteria and natural aquatic populations.

    Science.gov (United States)

    Kraft, Stephanie; Stephanie, Kraft; Obst, Ursula; Ursula, Obst; Schwartz, Thomas; Thomas, Schwartz

    2011-03-01

    UV light-caused DNA damage is a widespread field of study. As UV light has the biological effect of inactivating or killing bacteria, it is used for water disinfection. Due to this application, it is important to study the DNA damage efficiencies and regeneration capacities in bacteria after UV irradiation. Two monoclonal antibodies, anti-CPD and anti-(6-4) PP, were applied for an immunoassay of UV-induced DNA modifications. Cyclobutane pyrimidine dimer (CPD) and 6-4 photoproduct (6-4 PP) were detected in the reference bacteria Pseudomonas aeruginosa and Enterococcus faecium, and in natural water communities. The antibody-mediated detection signals increased with the UV doses from 100-400J/m(2). Here, the CPD-specific signals were stronger than the (6-4) PP-specific signals. These immunological results were in accordance with parallel cultivation experiments. All UV-irradiated bacteria showed a reduction of their growth rate depending on UV application by several orders of magnitudes. The immunoassay was also applied to three types of natural aquatic habitats with different cell densities. Besides artificial UV irradiation, it was possible to visualize natural sunlight effects on these natural bacterial communities. Light-dependent and dark repair processes were distinguished using the established immunological assays. The antibody-mediated analyses presented are fast methods to detect UV-induced DNA lesions and repair capacities in selected bacterial species as well as in entire natural mixed populations. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. The 0.8% ultraviolet B content of an ultraviolet A sunlamp induces 75% of cyclobutane pyrimidine dimers in human keratinocytes in vitro.

    Science.gov (United States)

    Woollons, A; Kipp, C; Young, A R; Petit-Frère, C; Arlett, C F; Green, M H; Clingen, P H

    1999-06-01

    Tanning lamps, emitting predominantly ultraviolet (UV) A, are used widely throughout the U.K. and other countries, but little is known about the long-term risks associated with their use, especially with respect to skin cancer. We have exposed normal human epidermal keratinocytes to a commercial tanning lamp and used the comet assay in association with DNA repair enzymes T4 endonuclease V and endonuclease III to investigate the relative yields of directly formed cyclobutane pyrimidine dimers (CPDs) and indirectly formed types of oxidative DNA damage. To put the risk of using tanning lamps into perspective, the sunbed used in this study (five Philips Performance 80W-R UVA tubes at a distance of 35 cm) was found to be approximately 0.7 times as potent at inducing CPDs as U.K. natural sunlight around noon on a fine summer day. This compares with a relative risk for CPD induction and erythema of 0.8 and 0.7 times, respectively, calculated from the relevant action spectra of tanning lamps and British noontime sunlight. To determine the relative contribution of UVB and UVA to the induction of CPDs and oxidative DNA damage, we modified the spectral output of the tanning lamps with a series of Schott WG UVB filters. The induction of CPDs was more dependent on the UVB component of the sunbed than oxidative types of damage. Schott WG UVB filters with 50% transmission at 305 nm reduced the yield of T4 endonuclease V sites by 42% while there was only a 17% decrease in the yield of endonuclease III sites. CPD induction was not completely abolished after irradiation through WG335 and WG345 nm filters despite there being no detectable UVB. From these data, it was estimated that, although the tanning lamps emitted only 0.8% of their total output in the UVB range, these wavelengths were responsible for the induction of over 75% of CPDs and 50% of the oxidative damage to DNA.

  15. Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer Lesion.

    Science.gov (United States)

    Mu, Hong; Geacintov, Nicholas E; Zhang, Yingkai; Broyde, Suse

    2015-09-01

    Mammalian global genomic nucleotide excision repair requires lesion recognition by XPC, whose detailed binding mechanism remains to be elucidated. Here we have delineated the dynamic molecular pathway and energetics of lesion-specific and productive binding by the Rad4/yeast XPC lesion recognition factor, as it forms the open complex [Min, J. H., and Pavletich, N. P. (2007) Nature 449, 570-575; Chen, X., et al. (2015) Nat. Commun. 6, 5849] that is required for excision. We investigated extensively a cis-syn cyclobutane pyrimidine dimer in mismatched duplex DNA, using high-level computational approaches. Our results delineate a preferred correlated motion mechanism, which provides for the first time an atomistic description of the sequence of events as Rad4 productively binds to the damaged DNA.

  16. Effects of accessory proteins on the bypass of a cis-syn thymine-thymine dimer by Saccharomyces cerevisiae DNA polymerase eta.

    Science.gov (United States)

    McCulloch, Scott D; Wood, Adam; Garg, Parie; Burgers, Peter M J; Kunkel, Thomas A

    2007-07-31

    Among several hypotheses to explain how translesion synthesis (TLS) by DNA polymerase eta (pol eta) suppresses ultraviolet light-induced mutagenesis in vivo despite the fact that pol eta copies DNA with low fidelity, here we test whether replication accessory proteins enhance the fidelity of TLS by pol eta. We first show that the single-stranded DNA binding protein RPA, the sliding clamp PCNA, and the clamp loader RFC slightly increase the processivity of yeast pol eta and its ability to recycle to new template primers. However, these increases are small, and they are similar when copying an undamaged template and a template containing a cis-syn TT dimer. Consequently, the accessory proteins do not strongly stimulate the already robust TT dimer bypass efficiency of pol eta. We then perform a comprehensive analysis of yeast pol eta fidelity. We show that it is much less accurate than other yeast DNA polymerases and that the accessory proteins have little effect on fidelity when copying undamaged templates or when bypassing a TT dimer. Thus, although accessory proteins clearly participate in pol eta functions in vivo, they do not appear to help suppress UV mutagenesis by improving pol eta bypass fidelity per se.

  17. TNF-alpha impairs the S-G2/M cell cycle checkpoint and cyclobutane pyrimidine dimer repair in premalignant skin cells: Role of the PI3K-Akt pathway

    DEFF Research Database (Denmark)

    Faurschou, A.; Gniadecki, R.; Calay, D.

    2008-01-01

    proportion of UVB-treated HaCaT cells containing unrepaired cyclobutane pyrimidine dimers (CPDs) escaped the G2/M cell cycle checkpoint in the presence of TNF-alpha (9.5 +/- 3.3 vs 4.8 +/- 2.2%). After treatment with the PI3K inhibitor LY294002, only 1.2 +/- 0.7% of CPD-containing HaCaT cells were actively......Tumor necrosis factor-alpha (TNF-alpha) is induced by UVB radiation and has been implicated in the early stages of skin carcinogenesis. Here, we show that in normal keratinocytes and the transformed keratinocyte cell lines, HaCaT and A431, TNF-alpha stimulates protein kinase B/Akt, which results...

  18. Photoexcitation Dynamics of Thymine in Acetonitrile and an Ionic Liquid Probed by Time-resolved Infrared Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Manna, Arpan; Park, Seongchul; Lee, Taegon; Lim, Manho [Pusan National University, Busan(Korea, Republic of)

    2016-07-15

    Femtosecond transient IR absorption spectroscopy was used to probe the decay mechanism of electronically excited thymine (a naturally occurring pyrimidine base in DNA) dissolved in an ionic liquid ([Bmim][BF{sub 4}]) or CD{sub 3}CN after the absorption of UV light (267 nm). In both solvents, an absorption band grew on a picosecond timescale, along with decaying bleach and evolving red-shifted absorption signals. A population analysis of the observed kinetic data suggested that most of the photoexcited thymine underwent a sub-picosecond non-radiative relaxation to the vibrationally hot ground electronic state. About 4% (16%) of the excited thymine in the ionic liquid (CD{sub 3}CN) relaxed to an intermediate electronic state, which relaxed into a low-lying triplet state by intersystem crossing (ISC) (ISC did not relax to the ground electronic state within the experimental period (1 ns)). The low ISC yield for thymine in an ionic liquid was correlated with molecular properties of the solvent. This observation is significant because the ISC to triplet state transition for excited thymine has been considered as a precursor to cyclobutane-pyrimidine dimer formation, which led to functional damage of the base after UV absorption. This finding may shed light on the photostability of DNA in ionic liquids.

  19. A doorway state leads to photostability or triplet photodamage in thymine DNA.

    Science.gov (United States)

    Kwok, Wai-Ming; Ma, Chensheng; Phillips, David Lee

    2008-04-16

    Ultraviolet irradiation of DNA produces electronic excited states that predominantly eliminate the excitation energy by returning to the ground state (photostability) or following minor pathways into mutagenic photoproducts (photodamage). The cyclobutane pyrimidine dimer (CPD) formed from photodimerization of thymines in DNA is the most common form of photodamage. The underlying molecular processes governing photostability and photodamage of thymine-constituted DNA remain unclear. Here, a combined femtosecond broadband time-resolved fluorescence and transient absorption spectroscopies were employed to study a monomer thymidine and a single-stranded thymine oligonucleotide. We show that the protecting deactivation of a thymine multimer is due to an ultrafast single-base localized stepwise mechanism where the initial excited state decays via a doorway state to the ground state or proceeds via the doorway state to a triplet state identified as a major precursor for CPD photodamage. These results provide new mechanistic characterization of and a dynamic link between the photoexcitation of DNA and DNA photostability and photodamage.

  20. On the intermolecular vibrational modes of the guanine⋯cytosine, adenine⋯thymine and formamide⋯formamide H-bonded dimers

    Science.gov (United States)

    Florián, Jan; Leszczynski, Jerzy; Johnson, Benny G.

    1995-04-01

    Harmonic force fields, frequencies, and IR and Raman intensities of the intermolecular vibrational modes in the cyclic formamide dimer and the guanine-cytosine and adenine-thymine DNA base pairs were calculated using several ab initio methods, including Hartree-Fock, MP2 and gradient-corrected density functional theory (DFT), with various basis sets. A polar environment was modeled using the polarizable continuum model (SCRF). The effect of electron correlation upon calculated Raman intensities was investigated using DFT. The normal coordinate analysis was carried out in internal coordinates observing C 2h symmetry of the formamide dimer. These coordinates were also generalized for the DNA base pairs, allowing force constants, frequencies and intensities of the characteristic intermolecular vibrational modes to be compared among the H-bonded complexes studied. In addition, coordinates defined in this way are directly related to standard DNA interbase structural parameters as pseudodyad, tilt and propeller twist angles. Extensive coupling of the intramolecular wagging vibrations of the amino groups participating in H-bonding with the tilt and propeller twist vibrations was obtained for the lowest frequency normal modes.

  1. Facially-selective thymine-thymine photodimerization in TTT triads.

    Science.gov (United States)

    Neelakandan, Prakash P; Pan, Zhengzheng; Hariharan, Mahesh; Lewis, Frederick D

    2012-06-01

    Irradiation of alkane-linked DNA hairpins possessing TTT steps with flanking purine bases yields products identified as the cis-syn (2 + 2) dimers formed between the central thymine and its 3'- and 5'-neighbors. Selective formation of the 3'-dimer is attributed to ground state conformational effects and electron transfer quenching by purine bases.

  2. DNA polymerases eta and kappa are responsible for error-free translesion DNA synthesis activity over a cis-syn thymine dimer in Xenopus laevis oocyte extracts.

    Science.gov (United States)

    Yagi, Yoshihiko; Ogawara, Daichi; Iwai, Shigenori; Hanaoka, Fumio; Akiyama, Masahiro; Maki, Hisaji

    2005-11-21

    In translesion synthesis (TLS), specialized DNA polymerases (pols) facilitate progression of replication forks stalled by DNA damage. Although multiple TLS pols have been identified in eukaryotes, little is known about endogenous TLS pols and their relative contributions to TLS in vivo because of their low cellular abundance. Taking advantage of Xenopus laevis oocyte cells, with their extraordinary size and abundant enzymes involved in DNA metabolism, we have identified and characterized endogenous TLS pols for DNA damage induced by ultraviolet (UV) irradiation. We designed a TLS assay which monitors primer elongation on a synthetic oligomer template over a single UV-induced lesion, either a cys-syn cyclobutane pyrimidine dimer (CPD) or a pyrimidine (6-4) pyrimidone photoproduct. Four distinct TLS activities (TLS1-TLS4) were identified in X. laevis oocyte extracts, using three template/primer (T/P) DNA substrates having various sites at which primer extension is initiated relative to the lesion. TLS1 and TLS2 activities appear to be sequence-dependent. TLS3 and TLS4 extended the primers over the CPD in an error-free manner irrespective of sequence context. Base insertion opposite the CPD of the T/P substrate in which the 3'-end of the primer is placed one base upstream of the lesion was observed only with TLS3. TLS3 and TLS4 showed primer extension with similar efficiencies on the T/P substrate whose 3'-primer terminal dinucleotide (AA) was complementary to the CPD lesion. Investigations with antibodies and recombinant pols revealed that TLS3 and TLS4 were most likely attributable to pol eta and pol kappa, respectively. These results indicate that error-free insertion in CPD bypass is due mainly to pol eta (TLS3) in the extracts, and suggest that pol kappa (TLS4) may assist pol eta (TLS3) in error-free extension during CPD bypass.

  3. Dynamics and mechanism of UV-damaged DNA repair in indole-thymine dimer adduct: molecular origin of low repair quantum efficiency.

    Science.gov (United States)

    Guo, Xunmin; Liu, Zheyun; Song, Qinhua; Wang, Lijuan; Zhong, Dongping

    2015-02-26

    Many biomimetic chemical systems for repair of UV-damaged DNA showed very low repair efficiency, and the molecular origin is still unknown. Here, we report our systematic characterization of the repair dynamics of a model compound of indole-thymine dimer adduct in three solvents with different polarity. By resolving all elementary steps including three electron-transfer processes and two bond-breaking and bond-formation dynamics with femtosecond resolution, we observed the slow electron injection in 580 ps in water, 4 ns in acetonitrile, and 1.38 ns in dioxane, the fast back electron transfer without repair in 120, 150, and 180 ps, and the slow bond splitting in 550 ps, 1.9 ns, and 4.5 ns, respectively. The dimer bond cleavage is clearly accelerated by the solvent polarity. By comparing with the biological repair machine photolyase with a slow back electron transfer (2.4 ns) and a fast bond cleavage (90 ps), the low repair efficiency in the biomimetic system is mainly determined by the fast back electron transfer and slow bond breakage. We also found that the model system exists in a dynamic heterogeneous C-clamped conformation, leading to a stretched dynamic behavior. In water, we even identified another stacked form with ultrafast cyclic electron transfer, significantly reducing the repair efficiency. Thus, the comparison of the repair efficiency in different solvents is complicated and should be cautious, and only the dynamics by resolving all elementary steps can finally determine the total repair efficiency. Finally, we use the Marcus electron-transfer theory to analyze all electron-transfer reactions and rationalize all observed electron-transfer dynamics.

  4. Urinary levels of thymine dimer as a biomarker of exposure to ultraviolet radiation in humans during outdoor activities in the summer.

    Science.gov (United States)

    Liljendahl, Tove Sandberg; Blomqvist, Anna; Andersson, Eva M; Barregard, Lars; Segerbäck, Dan

    2013-05-01

    The incidence of skin cancer is rising rapidly in many countries, presumably due to increased leisure time exposure to solar ultraviolet radiation (UVR). UVR causes DNA lesions, such as the thymine dimer (T=T), which have been causatively linked to the development of skin cancer. T=T is clearly detectable in urine and may, thereby, be a potentially valuable biomarker of UVR exposure. The objective of this study was to evaluate the relationship between UVR exposure and urinary levels of T=T in a field study involving outdoor workers. Daily ambient and personal exposure of 52 beach lifeguards and agricultural workers to UVR were determined (employing 656 personal polysulphone dosimeters). In 22 of these subjects, daily urinary T=T levels (120 samples) were measured, the area of skin exposed calculated and associations assessed utilizing mixed statistical models. The average daily UVR dose was approximately 600 J/m(2) (7.7 standard erythemal doses), i.e. about 20% of ambient UVR. T=T levels were correlated to UVR dose, increasing by about 6 fmol/µmol creatinine for each 100 J/m(2) increase in dose (average of the three preceding days). This is the first demonstration of a relationship between occupational UVR exposure and urinary levels of a biomarker of DNA damage. On a population level, urinary levels of T=T can be used as a biomarker for UVR exposure in the field.

  5. Photoinduced formation mechanism of the thymine-thymine (6-4) adduct.

    Science.gov (United States)

    Giussani, Angelo; Serrano-Andrés, Luis; Merchán, Manuela; Roca-Sanjuán, Daniel; Garavelli, Marco

    2013-02-21

    The photoinduced mechanism leading to the formation of the thymine-thymine (6-4) photolesion has been studied by using the CASPT2//CASSCF approach over a dinucleotide model in vacuo. Following light absorption, localization of the excitation on a single thymine leads to fast singlet-triplet crossing that populates the triplet (3)(nπ*) state of thymine. This state, displaying an elongated C(4)═O bond, triggers (6-4) dimer formation by reaction with the C(5)═C(6) double bond of the adjacent thymine, followed by a second intersystem crossing, which acts as a gate between the excited state of the reactant and the ground state of the photoproduct. The requirement of localized excitation on just one thymine, whose main decay channel (by radiationless repopulation of its ground state) is nonphotochemical, can rationalize the experimentally observed low quantum yield of formation for the thymine-thymine (6-4) adduct.

  6. Kinetics of Thymine Photodimerization in DNA

    Science.gov (United States)

    Wulff, Daniel L.

    1963-01-01

    The kinetics of thymine photodimerization in E. coli DNA have been measured at various wavelengths of ultraviolet light. The initial quantum yield is not strongly dependent on wavelength. The ratio of thymine dimer to thymine in the photostationary state is much more dependent on wavelength. At the 235 mμ photosteady state 1.7 per cent of the thymine is present as dimer. This shifts to 6.5 per cent at 254 mμ and to 20 per cent of 275 mμ. While the change in position of the photosteady state with wavelength fails to fit a simple model, the data do indicate that not all thymines are capable of participation in dimer formation. PMID:14062455

  7. Resistance of the genome of Escherichia coli and Listeria monocytogenes to irradiation evaluated by the induction of cyclobutane pyrimidine dimers and 6-4 photoproducts using gamma and UV-C radiations

    Science.gov (United States)

    Beauchamp, S.; Lacroix, M.

    2012-08-01

    The effect of gamma and UV-C irradiation on the production of cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4 PPs) in DNA was investigated to compare the natural resistance of the genome of a Gram-positive bacterium and a Gram-negative bacterium against irradiation. Solution of pure DNA and bacterial strains Listeria monocytogenes and Escherichia coli were irradiated using gamma and UV-C rays. Extracted DNA from bacteria and pure DNA samples were then analysed by ELISA using anti-CPDs and anti-6-4 PPs monoclonal antibodies. The results show that gamma rays, as well as UV-C rays, induce the formation of CPDs and 6-4 PPs in DNA. During UV-C irradiation, the three samples showed a difference in their sensitivity against formation of CPDs (P≤0.05). Pure DNA was the most sensitive while the genome of L. monocytogenes was the most resistant. Also during UV-C irradiation, the genome of L. monocytogenes was the only one to show a significant resistance against formation of 6-4 PPs (P≤0.05). During gamma irradiation, for both types of lesion, pure DNA and the genome of E. coli did not show significant difference in their sensitivity (P>0.05) while the genome of L. monocytogenes showed a resistance against formation of CPDs and 6-4 PPs.

  8. Combined QM/MM Investigation on the Light-Driven Electron-Induced Repair of the (6-4) Thymine Dimer Catalyzed by DNA Photolyase

    NARCIS (Netherlands)

    Faraji, Shirin; Groenhof, Gerrit; Dreuw, Andreas

    2013-01-01

    The (6-4) photolyases are blue-light-activated enzymes that selectively bind to DNA and initiate splitting of mutagenic thymine (6-4) thymine photoproducts (T(6-4)T-PP) via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH(-)) to the lesion triggering repair. In the present

  9. Mechanism of the Decay of Thymine Triplets in DNA Single Strands.

    Science.gov (United States)

    Pilles, Bert M; Bucher, Dominik B; Liu, Lizhe; Clivio, Pascale; Gilch, Peter; Zinth, Wolfgang; Schreier, Wolfgang J

    2014-05-01

    The decay of triplet states and the formation of cyclobutane pyrimidine dimers (CPDs) after UV excitation of the all-thymine oligomer (dT)18 and the locked dinucleotide TLpTL were studied by nanosecond IR spectroscopy. IR marker bands characteristic for the CPD lesion and the triplet state were observed from ∼1 ns (time resolution of the setup) onward. The amplitudes of the CPD marker bands remain constant throughout the time range covered (up to 10 μs). The triplet decays with a time constant of ∼10 ns presumably via a biradical intermediate (lifetime ∼60 ns). This biradical has often been invoked as an intermediate for CPD formation via the triplet channel. The present results lend strong support to the existence of this intermediate, yet there is no indication that its decay contributes significantly to CPD formation.

  10. Silibinin prevents ultraviolet radiation-caused skin damages in SKH-1 hairless mice via a decrease in thymine dimer positive cells and an up-regulation of p53-p21/Cip1 in epidermis.

    Science.gov (United States)

    Dhanalakshmi, Sivanandhan; Mallikarjuna, G U; Singh, Rana P; Agarwal, Rajesh

    2004-08-01

    Non-melanoma skin cancer (NMSC) accounts for >1 million new cases each year in the US alone suggesting that more approaches are needed for its prevention and control. Earlier studies by us have shown that silymarin (a crude form of biologically active silibinin with some other isomers), isolated from milk thistle, affords strong protection against ultraviolet (UV) radiation-induced NMSC in SKH-1 hairless mice; however, the molecular mechanisms of its efficacy are not known. Here, we assessed the effect of silibinin on UV-induced DNA damage and p53-p21/Cip1 accumulation, and their roles in UV-induced cell proliferation and apoptosis in SKH-1 hairless mouse epidermis. Topical application of silibinin prior to, or immediately after, UV irradiation resulted in a very strong protective effect against UV-induced thymine dimer positive cells in epidermis accounting for 76-85% (P formation (P thymine dimer positive cells and an up-regulation of p53-p21/Cip1 possibly leading to an inhibition in both cell proliferation and apoptosis. Comparable effects of silibinin following its pre- or post-UV application suggest that mechanisms other than sunscreen effect are operational in silibinin efficacy against UV-caused skin damages.

  11. On the wavelength dependence of UV induced thymine photolesions: a synchrotron radiation circular dichroism study.

    Science.gov (United States)

    Madsen, Marlene Møller; Jones, Nykola C; Nielsen, Steen Brøndsted; Hoffmann, Søren Vrønning

    2016-11-09

    Solar mutagenesis via the formation of thymine dimer photoproducts is a primary cause of skin cancer. The aim of this study is to provide a direct method for following the development of photolesions in thymine single strands and to determine how the formation of these photoproducts depends on the excitation wavelength in the ultraviolet (UV) between 210 nm and 325 nm. Experiments were performed both with a 20 Hz pulsed, intense, tunable laser as well as UV lamps (at 254 nm and 302 nm), but we find that only the dose matters at these wavelengths for the yield of photoproducts. Hence in both cases the lesion process is due to one-photon absorption. The formation and yields of the photoproducts as the irradiation dose is increased is followed through measurement of synchrotron radiation circular dichroism (SRCD) spectra. A principal component analysis (PCA) of the SRCD data yields CD signatures for each of the resulting photoproducts and reveals a strong irradiation wavelength dependence upon which products are formed; cyclobutane pyrimidine dimers (CPDs) are formed primarily at higher irradiation wavelengths (from 250 to 300 nm); the 6,4 pyrimidine-pyrimidone photoadduct (64PP) is formed in the range 210 to 285 nm, with a higher rate of formation in the lower part of that range, while in the very lowest irradiation wavelength range (210 to 240 nm) we find thymidine monophosphate (dTMP), which indicates cleavage of the DNA backbone. Our work demonstrates the strength of SRCD spectroscopy compared to ordinary absorption spectroscopy, as the latter is not sufficient to obtain fingerprints of the thymine photoproducts.

  12. Combined QM/MM investigation on the light-driven electron-induced repair of the (6-4) thymine dimer catalyzed by DNA photolyase.

    Science.gov (United States)

    Faraji, Shirin; Groenhof, Gerrit; Dreuw, Andreas

    2013-09-05

    The (6-4) photolyases are blue-light-activated enzymes that selectively bind to DNA and initiate splitting of mutagenic thymine (6-4) thymine photoproducts (T(6-4)T-PP) via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH(-)) to the lesion triggering repair. In the present work, the repair mechanism after the initial electron transfer and the effect of the protein/DNA environment are investigated theoretically by means of hybrid quantum mechanical/molecular mechanical (QM/MM) simulations using X-ray structure of the enzyme-DNA complex. By comparison of three previously proposed repair mechanisms, we found that the lowest activation free energy is required for the pathway in which the key step governing the repair photocycle is electron transfer coupled with the proton transfer from the protonated histidine, His365, to the N3' nitrogen of the pyrimidone thymine. The transfer simultaneously occurs with concerted intramolecular OH transfer without formation of an oxetane or isolated water molecule intermediate. In contrast to previously suggested mechanisms, this newly identified pathway requires neither a subsequent two-photon process nor electronic excitation of the photolesion.

  13. Detection of thymine [2+2] photodimer repair in DNA: selective reaction of KMnO4.

    OpenAIRE

    Ramaiah, D; Koch, T; Orum, H; Schuster, G B

    1998-01-01

    The specific reaction of potassium permanganate with thymine in single-stranded DNA was employed to analyze thymine [2+2] dimer repair in DNA and in DNA/peptide nucleic acid hybrid duplexes. This simple and highly sensitive chemical assay is convenient for monitoring repair of thymine dimers in oligonucleotides.

  14. Bypass of a site-specific cis-Syn thymine dimer in an SV40 vector during in vitro replication by HeLa and XPV cell-free extracts.

    Science.gov (United States)

    Ensch-Simon, I; Burgers, P M; Taylor, J S

    1998-06-02

    The key step in skin cancer induction by UV light is thought to be the mutagenic DNA synthesis past a DNA photoproduct in a proto-oncogene or tumor suppressor gene. To investigate this critical step, we have constructed an SV40 vector containing a cis-syn thymine dimer, the major DNA photoproduct induced by UVB light, within an AseI site at a location that would initially be replicated by leading strand synthesis. When the dimer-containing SV40 vector was incubated with cell-free HeLa extracts in the presence of TAg, and then digested with AseI, a 2325 bp fragment corresponding to inhibition of cleavage at the dimer site was observed, suggesting that the dimer had terminated synthesis and/or had been bypassed. When the reaction was limited to one round of replication and the products of restriction enzyme digestion were examined by denaturing gel electrophoresis, bands corresponding to both termination and bypass were observed in roughly a one-to-one ratio. Whereas increasing the dNTP concentration from 10 microM to 1 mM increased the ratio of bypass to termination from 0.6 to 2.6, it had no effect on the site of termination, which occurred exclusively one nucleotide before the dimer. Experiments in which dGTP was held constant at 25 microM and various combinations of the remaining nucleotides were raised from 25 microM to 1 mM showed substantial increases in the bypass-to-termination ratio, with the greatest effect seen for raising all three nucleotides to 1 mM. Replication by primary fibroblast XPV extracts was also investigated and found to be greatly stimulated by rhRPA, whereas the stimulatory effect for HeLa cell extracts was variable. In the presence of rhRPA, the XPV extracts were also found to bypass the cis-syn dimer, which contrasts with a recent report that could not detect dimer bypass in SV40 transformed XPV extracts in the absence of added replication factors [Cordeiro-Stone, M., et al. (1997) J. Biol. Chem. 272, 13945-13954].

  15. Evidence for Watson-Crick and not Hoogsteen or wobble base pairing in the selection of nucleotides for insertion opposite pyrimidines and a thymine dimer by yeast DNA pol eta.

    Science.gov (United States)

    Hwang, Hanshin; Taylor, John-Stephen

    2005-03-29

    We have recently reported that pyrene nucleotide is preferentially inserted opposite an abasic site, the 3'-T of a thymine dimer, and most undamaged bases by yeast DNA polymerase eta (pol eta). Because pyrene is a nonpolar molecule with no H-bonding ability, the unusually high efficiencies of dPMP insertion are ascribed to its superior base stacking ability, and underscore the importance of base stacking in the selection of nucleotides by pol eta. To investigate the role of H-bonding and base pair geometry in the selection of nucleotides by pol eta, we determined the insertion efficiencies of the base-modified nucleotides 2,6-diaminopurine, 2-aminopurine, 6-chloropurine, and inosine which would make a different number of H-bonds with the template base depending on base pair geometry. Watson-Crick base pairing appears to play an important role in the selection of nucleotide analogues for insertion opposite C and T as evidenced by the decrease in the relative insertion efficiencies with a decrease in the number of Watson-Crick H-bonds and an increase in the number of donor-donor and acceptor-acceptor interactions. The selectivity of nucleotide insertion is greater opposite the 5'-T than the 3'-T of the thymine dimer, in accord with previous work suggesting that the 5'-T is held more rigidly than the 3'-T. Furthermore, insertion of A opposite both Ts of the dimer appears to be mediated by Watson-Crick base pairing and not by Hoogsteen base pairing based on the almost identical insertion efficiencies of A and 7-deaza-A, the latter of which lacks H-bonding capability at N7. The relative efficiencies for insertion of nucleotides that can form Watson-Crick base pairs parallel those for the Klenow fragment, whereas the Klenow fragment more strongly discriminates against mismatches, in accord with its greater shape selectivity. These results underscore the importance of H-bonding and Watson-Crick base pair geometry in the selection of nucleotides by both pol eta and the

  16. Tautomerization of Thymine Using Ultraviolet Light.

    Science.gov (United States)

    Vinje, Jakob; Falck, Merete; Mazzola, Federico; Cooil, Simon Phillip; Koch, Henrik; Høyvik, Ida-Marie; Wells, Justin

    2017-09-26

    Ultraviolet-light-induced changes to the nucleobase thymine deposited onto a MoS2 surface were studied using photoelectron spectroscopy and first-principles calculations. These measurements suggest changes in the molecular structure indicated by changes in core electron binding energies. The experimental work has been interpreted by means of ab initio calculations using coupled cluster singles and doubles (CCSD) linear response theory. Contrary to the expected behavior, i.e., the dimerization of two thymine molecules into a pyrimidine dimer, a shift between two tautomeric forms was observed upon UV-exposure. Exposure to ionizing radiation is known to induce damage in many biological molecules, and the present work gives additional insight into its effects on thymine, the interactions of the molecules, and finally how certain UV photoproducts may be avoided.

  17. Nature and possible mechanisms of formation of potential mutations arising at emerging of thymine dimers after irradiation of double-stranded DNA by ultraviolet light

    Science.gov (United States)

    Grebneva, H. A.

    2003-01-01

    The mutagenesis under ultraviolet (UV)-irradiation is discussed. It is assumed, that the basic damages resulting in transitions, transversions, mutations of the frameshift and complex mutations are changes of the tautomeric state of the bases. The bases may be a part of dimers or may be not the dimer components. We consider such rare tautomeric states, which may influence the character of base pairing. A model of the formation of the above rare tautomeric forms of nucleotide bases under the UV-irradiation of the DNA is proposed. In the case of a radiation deexcitation of the DNA, which has absorbed the UV-quantum of the triplet energy level, there occur strong forced oscillations. They may result in changes of the lengths of hydrogen bonds between DNA bases. As a result, at H-bond shortening, the hydrogen atom may be almost in the center of H-bond. In the case of H-bond elongation, it may remain near the partner atom. Because of the H-bond breaking, during the formation of dimers, rare tautomeric forms of bases influencing the character of pairing can be realized. If a pair of the bases is not a part of dimer, then the only new stable configuration of the hydrogen atoms is the one that occurred at double-proton phototautomerism. It is shown that only those dimers are mutational, in which the change of a tautomeric state of the DNA bases have taken place. This is one of the differences between the proposed model and the standard one. The latter assumes, that from the point of view of ability of forming the mutations all the dimers are identical, and the DNA-polymerase is sometimes mistaken, incidentally building uncomplementary bases in. The consideration is only of qualitative character, it needs experimental verification, subsequent study by methods of quantum chemistry and theoretical physics. A list of problems to be studied in this respect is given.

  18. SHORT COMMUNICATION SYNTHESIS OF CYCLOBUTANE ...

    African Journals Online (AJOL)

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    ______. *Corresponding author. E-mail: songzq@hotmail.com. SHORT COMMUNICATION. SYNTHESIS OF CYCLOBUTANE ANALOGUES. Yan Bai Yin1, Zhan Qian Song1*, Zong De Wang2, Shi Bin Shang1 and Zhao Sheng Cai1. 1Institute of Chemical Industry of Forest Products Chinese Academy of Forestry, Nanjing,.

  19. Formation of extended straight molecular chains by pairing of thymine molecules on the Ag-Si(111) surface

    Science.gov (United States)

    Krull, C.; Valencia, S.; Pascual, J. I.; Theis, W.

    2009-04-01

    Here, we report on the assembly of thymine molecules into extended straight chains of single and multiple dimer rows on a Si(111)/Ag sqrt{3}× sqrt{3} R30° surface. Using variable temperature scanning tunneling microscopy, we follow the nucleation process and formation of self-assembled structures. Submonolayer coverages at 120 K are disordered and exhibit a high density of thymine dimers. Upon annealing the dimers assemble into extended dimer chains along three equivalent high-symmetry surface directions. At low coverages single dimer rows are favored. At increased coverage chains with multiple dimer rows are observed, with a preference to an even multiplicity. We show that a complex cross-talk between H-bond thymine-thymine interactions and commensurization of dimer chains to the Ag/Si surface leads to this specific layout.

  20. Formation of extended straight molecular chains by pairing of thymine molecules on the Ag-Si(111) surface

    Energy Technology Data Exchange (ETDEWEB)

    Krull, C.; Valencia, S.; Pascual, J.I.; Theis, W. [Freie Universitaet Berlin, Institut fuer Experimentalphysik, Berlin (Germany)

    2009-04-15

    Here, we report on the assembly of thymine molecules into extended straight chains of single and multiple dimer rows on a Si(111)/Ag {radical}(3) x {radical}(3) R30 surface. Using variable temperature scanning tunneling microscopy, we follow the nucleation process and formation of self-assembled structures. Submonolayer coverages at 120 K are disordered and exhibit a high density of thymine dimers. Upon annealing the dimers assemble into extended dimer chains along three equivalent high-symmetry surface directions. At low coverages single dimer rows are favored. At increased coverage chains with multiple dimer rows are observed, with a preference to an even multiplicity. We show that a complex cross-talk between H-bond thymine-thymine interactions and commensurization of dimer chains to the Ag/Si surface leads to this specific layout. (orig.)

  1. Photophysics and photochemistry of thymine deoxy-dinucleotide in water: a PCM/TD-DFT quantum mechanical study.

    Science.gov (United States)

    Improta, Roberto

    2012-12-13

    We here report a fully quantum mechanical study of the main photochemical and photophysical decay routes in aqueous solution of thymine deoxy-dinucleotide (TpT(-) and TpTNa) and of its analogue locked in C3-endo puckering, characterizing five different representative backbone conformers and discussing the chemical physical effects modulating the yield of the different photoproducts. Our approach is based on time-dependent DFT calculations, using the last generation M052X functional, whereas solvent effects are included by means of the polarizable continuum model. Especially when at least one of the sugars adopts C3-endo puckering, a barrierless path on the bright ππ* excitons leads to the S(1)/S(0) crossing region corresponding to the formation of cyclobutane pyrimidine dimer. Charge transfer excited states involving the transfer of an electron from the 5' Thy toward the 3' Thy are involved in the formation of the oxetane intermediate in the path leading to 6-4 pyrimidine pyrimidinone adducts. A non-negligible energy barrier is associated with this latter pathway, which is possible only when one of the two nucleotides adopts C2-endo puckering. Monomer-like decay pathways, involving ππ* or nπ* excited states localized on a single base, are shown to be operative also for loosely stacked bases.

  2. DNA base stacking: the stacked uracil/uracil and thymine/thymine minima.

    Science.gov (United States)

    Hunter, Ruairidh S; van Mourik, Tanja

    2012-10-15

    The potential energy surfaces of stacked uracil dimer (U/U) and stacked thymine dimer (T/T) have been explored at the counterpoise (CP)-corrected M06-2X/6-31+G(d) level of theory, in the gas phase and in solution (with water and, for U/U, 1,4-dioxane as the solvents) modeled by a continuum solvent using the polarizable continuum model. Potential energy scans were created by rotation of one monomer around its center-of-mass, whereas the other monomer remained still. Both face-to-back (one molecule exactly on top of the other) and face-to-face (one base molecule flipped by 180°) structures were considered. Five or six (dependent on whether CP correction is included or not) stacked uracil dimer minima and six stacked thymine dimer minima were located. A number of transition states on the U/U and T/T potential energy surfaces were likewise identified. The general effect of the continuum solvent is a flattening of the potential energy surface. Comparison of the gas-phase M06-2X/6-31+G(d) U/U interaction energies with estimated CCSD(T)/complete basis set values (where available) show the excellent performance of this functional for stacking energies. Copyright © 2012 Wiley Periodicals, Inc.

  3. 1H NMR study of the exchangeable protons of the duplex d(GCGTTGCG).d(CGCAACGC) containing a thymine photodimer.

    OpenAIRE

    Kemmink, J.; Boelens, R.; de Koning, T; van der Marel, G A; van Boom, J H; Kaptein, R.

    1987-01-01

    A comparison is presented of the imino proton NMR spectra of the double stranded octamer d(GCGTTGCG).d(CGCAACGC) and the same octamer in which the two central thymine residues occur as a cis-syn thymine dimer. Except for the terminal base pairs all imino protons were detected and assigned in the NMR spectrum. The spectra show that in the thymine dimer duplex, contrary to common belief, all base pairs occur in a hydrogen bonded form, although the hydrogen bonds of the two central AT base pairs...

  4. The interaction of melanin with ionizing and UVC radiations: Characterization of thymine damage

    Energy Technology Data Exchange (ETDEWEB)

    Huselton, C.A.

    1988-01-01

    These studies were undertaken to determine whether melanin could protect DNA against the harmful effects of ionizing or UVC radiations. A simple, in vitro, model system was developed to evaluate eumelanin (Sigma melanin) as a radioprotector of solutions of 0.1 mM thymine or thymidine exposed to 570Gy of ionizing radiation. Sigma melanin was compared to several amino acids, other biomolecules or to other forms of melanin. To investigate the role of melanin as a passive screen of UVC radiation, melanotic (I{sub 3}), amelanotic (AMEL) cells (both derived from a Cloudman S91 melanoma) and non-melanotic (EMT6) cells were labelled with radioactive dTHd and exposed to 0, 1, 5 or 10KJ/m{sup 2} of UVC. The DNA was extracted; the bases hydrolyzed with concentrated HCl. Thymine bases were separated by reverse phase HPLC. No difference in dimer content was observed between I{sub 3} and AMEL cells, but EMT6 cells had nearly twice the amount of dimer. Overall thymine degradation was more pronounced in I{sub 3} cells than in the other two cell lines, due to the production of non-dimer thymine damage. This damage was identified as thymine glycol by HPLC and mass spectrometry. Melanin, upon exposure to UVC, appears to enhance thymine damage by producing oxidative damage.

  5. Analysis of ultrafast relaxation in photoexcited DNA base pairs of adenine and thymine

    Science.gov (United States)

    Samoylova, E.; Schultz, T.; Hertel, I. V.; Radloff, W.

    2008-05-01

    The photoinduced dynamics in base pairs of adenine and thymine were analyzed by femtosecond pump-probe spectroscopy. On the short-time scale up to a few picoseconds, the characteristic time constants for the dimers are quite similar to the corresponding values of the monomers. This leads to the conclusion that ultrafast intramolecular relaxation proceeds via ππ ∗ and nπ ∗ states of one component within the dimer. On the long-time scale, we obtained a novel time constant of roughly 40 ps for the thymine dimer and the adenine-thymine base pair. This time constant was never observed in the monomers and is tentatively assigned to an intermolecular relaxation process, possibly via a hydrogen transfer state.

  6. P-aminobenzoic acid can sensitize the formation of pyrimidine dimers in DNA: direct chemical evidence

    Energy Technology Data Exchange (ETDEWEB)

    Sutherland, J.C.; Griffin, K.P. (Brookhaven National Lab., Upton, NY (USA))

    1984-09-01

    Thymine-containing photoproducts with chromatographic properties similar to those of cyclobutyl pyrimidine dimers can be formed in (/sup 3/H)-thymine-labeled DNA in solution by 313 nm ultraviolet radiation in the presence of para-aminobenzoic acid (PABA), a compound used in sunscreen preparations. In the absence of PABA, similar fluences of 313 nm radiation do not produce significant numbers of these photoproducts. The thymine-containing photoproducts can be reversed by 254 nm radiation so that the tritium label migrates with the mobility of thymine monomer, a behavior characteristic of thymine-containing cyclobutyl pyrimidine dimers. This result supports previous, but less direct, data from other laboratories indicating that PABA can sensitize dimer formation in the DNA of bacterial and mammalian cells.

  7. Translesion synthesis past guanine(C8)-thymine(N3) intrastrand cross-links catalyzed by selected A- and Y-family polymerases.

    Science.gov (United States)

    Lee, Young-Ae; Lee, Yuan-Cho; Geacintov, Nicholas E; Shafirovich, Vladimir

    2016-05-24

    Oxidatively generated guanine radicals in DNA can undergo various nucleophilic reactions including the formation of C8-guanine cross-links with adjacent or nearby N3-thymines in DNA in the presence of O2. These G[8-3]T lesions have been identified in the DNA of human cells exposed to oxidative stress, and are most likely genotoxic if not removed by cellular defence mechanisms. The abilities of several representative polymerases to bypass the G[8-3]T lesions in two different sequence contexts, G*T* and G*CT*, were assessed in vitro. The polymerase BF (bacillus fragment) from Bacillus stearothermophilus, the Y-family archaeal polymerases Dpo4 from Sulfolobus sulfataricus P2, and human DNA pol κ and pol η were selected for the study. The A-family polymerase BF was strongly blocked, while relatively weak translesion synthesis was observed in the case of Y-family polymerases Dpo4 and pol κ. Primer extension catalyzed by pol η was also partially stalled at various positions at or near the G[8-3]T cross-linked bases, but a significant and distributive primer extension was observed beyond the sites of the lesions with the efficiency being consistently greater in the case of G*CT* than in the case of G*T* lesions. The results obtained with pol η are compared with translesion synthesis past other intrastrand cross-linked lesions with previously published results of others that include the isomeric G[8-5m]T lesions generated by ionizing radiation, the cis-syn cyclobutane pyrimidine dimer and the 6-4 photoproduct generated by UV irradiation, and the Pt-G*G* lesions derived from the reactions of the chemotherapeutic agent cisplatin with DNA.

  8. Dynamics of UV-excited uracil, thymine, and cytosine

    Science.gov (United States)

    Hudock, Hanneli

    The excited state dynamics of nucleic acids has been a subject of much experimental and theoretical interest. Nucleic acid bases readily absorb UV radiation, which can lead to mutagenic dimer formation. The dynamics of UV-excited nucleic acids is an important step in understanding how these dimers form. The pyrimidine bases (uracil, thymine, and cytosine) have been studied with ab initio multiple spawning molecular dynamics and high level electronic structure methods. This work has involved both gas-phase and aqueous dynamics as well as simulation of the time-resolved photoelectron spectrum, transient absorption, fluorescence, and reaction rates. With these findings, complete relaxation mechanisms are proposed for the pyrimidines and comparisons are made directly to experimental results.

  9. Comment on ‘To stack or not to stack: Performance of a new density functional for the uracil and thymine dimers’ [Chem. Phys. Lett. 459 (2008) 164

    Science.gov (United States)

    van Mourik, Tanja

    2009-04-01

    A Letter by Gu et al. [J. Gu, J. Wang, J. Leszczynski, Y. Xie, H.F. Schaefer III, Chem. Phys. Lett. 459 (2008) 164] presented MP2/6-31+G(d) and MP2/TZVPP stacking energies for the uracil and thymine dimers, with the aim to assess the performance of the new M06-2X density functional. However, the stacking energies were not corrected for the basis set superposition error (BSSE). Here we show that correction for this error dramatically changes the results. BSSE correction severely reduces the stacking energy of the thymine dimer, whereas the stacked uracil dimer structure considered by Gu et al. is not even a minimum on the MP2/6-31+G(d) potential energy surface.

  10. 1D self-assembly of chemisorbed thymine on Cu(110) driven by dispersion forces

    Science.gov (United States)

    Temprano, I.; Thomas, G.; Haq, S.; Dyer, M. S.; Latter, E. G.; Darling, G. R.; Uvdal, P.; Raval, R.

    2015-03-01

    Adsorption of thymine on a defined Cu(110) surface was studied using reflection-absorption infrared spectroscopy (RAIRS), temperature programmed desorption (TPD), and scanning tunnelling microscopy (STM). In addition, density functional theory (DFT) calculations were undertaken in order to further understand the energetics of adsorption and self-assembly. The combination of RAIRS, TPD, and DFT results indicates that an upright, three-point-bonded adsorption configuration is adopted by the deprotonated thymine at room temperature. DFT calculations show that the upright configuration adopted by individual molecules arises as a direct result of strong O-Cu and N-Cu bonds between the molecule and the surface. STM data reveal that this upright thymine motif self-assembles into 1D chains, which are surprisingly oriented along the open-packed [001] direction of the metal surface and orthogonal to the alignment of the functional groups that are normally implicated in H-bonding interactions. DFT modelling of this system reveals that the molecular organisation is actually driven by dispersion interactions, which cause a slight tilt of the molecule and provide the major driving force for assembly into dimers and 1D chains. The relative orientations and distances of neighbouring molecules are amenable for π-π stacking, suggesting that this is an important contributor in the self-assembly process.

  11. Ultraviolet-B-induced cyclobutane-pyrimidine dimer formation and repair in arctic marine macrophytes

    NARCIS (Netherlands)

    van de Poll, W.H.; Hanelt, D; Hoyer, K.; Buma, A.G.J.; Breeman, Arno

    2002-01-01

    The significance of ultraviolet-B radiation (UVBR: 280-315 nm)-induced DNA damage as a stress factor for Arctic marine macrophytes was examined in the Kongsfjord (Spitsbergen, 78degrees55.5'N, 11degrees56.0'E) in summer. UVBR penetration in the water column was monitored as accumulation of

  12. Synthon preference in a hydrated β-resorcylic acid structure and its cocrystal with thymine.

    Science.gov (United States)

    Sridhar, Balasubramanian

    2015-12-01

    Multicomponent crystals or cocrystals play a significant role in crystal engineering, the main objective of which is to understand the role of intermolecular interactions and to utilize such understanding in the design of novel crystal structures. Molecules possessing carboxylic acid and amide functional groups are good candidates for forming cocrystals. β-Resorcylic acid monohydrate, C7H6O4·H2O, (I), crystallizes in the triclinic space group P-1 with one β-resorcylic acid molecule and one water molecule in the asymmetric unit. The cocrystal thymine-β-resorcylic acid-water (1/1/1), C5H6N2O2·C7H6O4·H2O, (II), crystallizes in the orthorhombic space group Pca21, with one molecule each of thymine, β-resorcylic acid and water in the asymmetric unit. All available donor and acceptor atoms in (I) and (II) are utilized for hydrogen bonding. The acid and amide functional groups are well known for the formation of self-complementary acid-acid and amide-amide homosynthons. In (I), an acid-acid homosynthon is observed, while in (II), an amide-acid heterosynthon is present. In (I), the β-resorcylic acid molecule exhibits the expected intramolecular S(6) motif between the hydroxy and carbonyl O atoms, and an intermolecular R2(2)(8) dimer motif between the carboxylic acid groups; only the former motif is observed in (II). The water solvent molecule in (I) propagates the discrete dimers into two-dimensional hydrogen-bonded sheets. In (II), thymine and β-resorcylic acid molecules do not form self-complementary amide-amide and acid-acid homosynthons; instead, a thymine-β-resorcylic acid heterosynthon is observed. With the help of the water molecule, this heterosynthon is aggregated into a three-dimensional hydrogen-bonded network. The absence of thymine base pairing in (II) might be linked to the availability of additional functional groups and the preference of the donor and acceptor hydrogen-bond combinations.

  13. Structure-activity relationship studies of illudins: analogues possessing a spiro-cyclobutane ring.

    Science.gov (United States)

    McMorris, Trevor C; Cong, Qiang; Kelner, Michael J

    2003-12-12

    Bicyclic and tricyclic analogues of anticancer sesquiterpene illudin S have been synthesized. These contain a spiro-cyclobutane instead of spiro-cyclopropane structure. The cytotoxicity of the former is less than that of the corresponding cyclopropane-containing compounds.

  14. The effect of microhydration on ionization energies of thymine

    Energy Technology Data Exchange (ETDEWEB)

    Khistyev, Kirill; Bravaya, Ksenia B.; Kamarchik, Eugene; Kostko, Oleg; Ahmed, Musahid; Krylov, Anna I.

    2011-01-03

    A combined theoretical and experimental study of the effect of microhydration on ionization energies (IEs) of thymine is presented. The experimental IEs are derived from photoionization efficiency curves recorded using tunable synchrotron VUV radiation. The onsets of the PIE curves are 8.85+-0.05, 8.60+-0.05, 8.55+-0.05, and 8.40+-0.05 eV for thymine, thymine mono-, di-, and tri-hydrates, respectively. The computed (EOM-IP-CCSD/cc-pVTZ) AIEs are 8.90, 8.51, 8.52, and 8.35 eV for thymine and the lowest isomers of thymine mono-, di-, and tri-hydrates. Due to large structural relaxation, the Franck-Condon factors for the 0<-- 0 transitions are very small shifting the apparent PIE onsets to higher energies. Microsolvation strongly affects IEs of thymine -- addition of each water molecule reduces the first vertical IE by 0.10-0.15 eV. The adiabatic IE decreases even more (up to 0.4 eV). The magnitude of the effect varies for different ionized states and for different isomers. For the ionized states that are localized on thymine the dominant contribution to the IE reduction is the electrostatic interaction between the delocalized positive charge on thymine and the dipole moment of the water molecule.

  15. Polyanthumin, a novel cyclobutane chalcone trimmer from Memecylon polyanthum.

    Science.gov (United States)

    Chen, Guan; Cui, Cheng-Bin; Qi, Ai-Di; Li, Chang-Wei; Tao, Zun-Wei; Ren, Rong

    2015-01-01

    A novel unusual trimmer chalcone, polyanthumin (1), together with five known compounds myricetin 3-O-(3″-O-galloyl)-α-l-rhamnopyranoside (2), sulfuretin (3), fustin (4), gallic acid (5), and ethyl gallate (6), was isolated from the dry stems of Memecylon polyanthum H.L. Li. Among them, compound 1 is a new chalcone trimmer with a novel cyclobutane skeleton in nature. Compounds 3 and 4 are flavonoids carrying a single 7-OH in A ring, which provided the first example of these class flavonoids from the family Melastomataceae. In addition, the antitumor activities for 2-4 were reported for the first time in this study. The antitumor effects of the isolated compounds 1-6 in vitro were assayed by the SRB method using human cancer K562 cells, with the inhibition rates ranging from 39.4% to 54.5% at 100 μg/ml. The IC50 values of compounds 1 and 3 for the inhibition of K562 cell proliferation were determined to be 45.4 and 30.5 μg/ml, respectively. To the best of our knowledge, compound 1 was the second sample as chalcone trimer. In addition, the antitumor activities for 2-4 were reported for the first time in this study.

  16. Structure, Vibrational Spectra and Ring Puckering Barrier of Cyclobutane

    Energy Technology Data Exchange (ETDEWEB)

    Xantheas, Sotiris S.; Blake, Thomas A.

    2006-09-02

    We present the results of high level ab initio calculations on the structure and puckering barrier of cyclobutane in an effort to establish the minimum theoretical requirements needed for their accurate description. Our best computed value for the puckering angle is 29.68o. Furthermore we found that accurate estimates for the barrier between the minimum (D2d) and transition state (D4h) configurations require both higher levels of electron correlation [MP4, CCSD(T)] and basis sets of quadruple-z quality or larger. By performing CCSD(T) calculations with basis sets as large as cc-pV5Z we obtained a complete basis set (CBS) estimate of 498 cm-1 for the puckering barrier. Our estimate for the barrier is within 10 cm-1 to the value proposed originally, but it lies ~50 cm-1 higher than the one obtained more recently, therefore revisiting the analysis of the experimental data might be warranted. The results of the current study can serve as a guide for calculations on the substituted four member ring compounds. To this end we present a method for estimating the barrier height at higher levels of electron correlation [MP4, CCSD(T)] from the MP2 results.

  17. The self assembly of thymine at Au(110)/liquid interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Molina Contreras, J.R. [Departamento de Ingenieria Electrica y Electronica, Instituto Tecnologico de Aguascalientes, Mexico (Mexico); Smith, C.I.; Bowfield, A.; Weightman, P. [Physics Department, University of Liverpool (United Kingdom); Tillner, F. [Fachbereich Physik, Universitaet Konstanz (Germany)

    2012-06-15

    We show that thymine self-assembles into an ordered structure when adsorbed at a Au(110)/liquid interface. Reflection anisotropy spectroscopy (RAS) shows that as found for cytosine and adenine the adsorbed thymine molecules are oriented essentially vertically on the Au(110) surface with the molecule aligned along one of the principal axes of the Au(110) surface. Simulations of the RA spectra to an empirical model indicates that as found for adsorbed cytosine and adenine, thymine is aligned along the [1 anti 10] direction on the Au(110) surface. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. Selective product amplification of thymine photodimer by recognition-directed supramolecular assistance.

    Science.gov (United States)

    Skene, W G; Berl, Volker; Risler, Hélène; Khoury, Richard; Lehn, Jean-Marie

    2006-10-07

    Two symmetric ditopic supramolecular templates (1 and 2) each presenting two hydrogen bonding recognition subunits were synthesized. Each such subunit comprises the same donor and acceptor pattern, capable of binding a substrate molecule with complementary hydrogen bonding groups to form a supramolecular complex. Substrate molecules, such as thymine or uracil derivatives, yield 2 : 1 complexes with the acceptors involving two hydrogen bonds to each subunit with ideal orientation for subsequent [2 + 2] dimerization upon photoirradiation. Selective syn photoproduct formation and concomitant suppression of the trans isomer are favored by orientation of the two guest nucleobases within the template cleft. Complementary donor and acceptor hydrogen bonding induced positioning of the two substrates and steric hindrance within the template clefts are responsible for the selective product formation.

  19. Modeling of the Hydration Shell of Uracil and Thymine

    Directory of Open Access Journals (Sweden)

    Jerzy Leszczynski

    2000-03-01

    Full Text Available The molecular geometry of complexes of uracil and thymine with 11 water molecules was calculated using the density functional theory with the B3LYP functional. The standard 6-31G(d basis set has been employed. It was found that the arrangement of water molecules forming a locked chain around the nucleobases significantly differs for uracil and thymine. The presence of a methyl group in thymine results in strong non-planarity of the hydrated shell. The existence of C-H...O hydrogen bonds between the water molecules and the hydrophobic part of the nucleobases is established. Interactions with water molecules cause some changes in the geometry of uracil and thymine which can be explained by the contribution of a zwitter-ionic dihydroxy resonance form into the total structure of the molecules.

  20. Thrilling strain! Donor-acceptor-substituted cyclobutanes for the synthesis of (hetero)cyclic compounds.

    Science.gov (United States)

    Reissig, Hans-Ulrich; Zimmer, Reinhold

    2015-04-20

    The analogy goes further: Following the often-studied donor-acceptor-substituted cyclopropanes, the corresponding cyclobutane derivatives were employed for the ring-strain-driven stereoselective syntheses of carbo- and heterocycles. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Structures of hydrated Li+-thymine and Li+-uracil complexes by IRMPD spectroscopy in the N-H/O-H stretching region.

    Science.gov (United States)

    Gillis, Elizabeth A L; Rajabi, Khadijeh; Fridgen, Travis D

    2009-02-05

    The interaction of lithium ions with two pyrimidine nucleobases, thymine and uracil, as well as the solvation of various complexes by one and two water molecules, has been studied in the gas phase. IRMPD spectra are reported for each of B-Li(+)-(H(2)O)(n) (n = 1-2) and B(2)-Li-(H(2)O)(m) (m = 0-1) for B = thymine, uracil over the 2500-4000 cm(-1) region. Calculations were performed using the B3LYP density functional in conjunction with the 6-31+G(d,p) basis set to model the vibrational spectra as well as MP2/6-311++G(2d,p) theory to model the thermochemistry of potential structures. Experimental and theoretical results were used in combination to determine structures of each complex, which are reported here. The lithium cation in all complexes was found to bond to the O4 oxygen in both thymine and uracil, and the first two water molecules of solvation were found to bond to Li(+). The experimental spectra obtained for BLi(+)(H(2)O)(n) (n = 1-2) and B(2)Li(+) for thymine and uracil clearly resemble one another, suggesting similar structural features in terms of bonding between the base and Li(+), as well as for solvation. This was confirmed through theoretical work. The addition of water to the lithium ion-bound DNA base dimers has been shown to induce a significant change in structure of the dimer to a hydrogen-bonded system similar to base pairing in the Watson-Crick model of DNA.

  2. The role of dimer formation in the self-assemblies of DNA base molecules on Cu(111) surfaces: A scanning tunneling microscope study

    Science.gov (United States)

    Furukawa, Masashi; Tanaka, Hiroyuki; Kawai, Tomoji

    2001-08-01

    For the purpose of understanding the self-assembly formation mechanism of DNA base molecules, guanine, adenine, cytosine, and thymine molecules were deposited on Cu(111) surfaces, and were observed using a low-temperature (≈80 K) scanning tunneling microscope (STM). Single-molecular-scale STM images revealed that guanine, adenine, and cytosine molecules can form ordered one- and/or two-dimensional unique structures, but thymine molecules, however, randomly aggregate into small clusters. Semiempirical molecular orbital (MO) calculation indicates that there exists predominantly stable dimer structures for the former three molecules, while such phenomena cannot be observed among the possible thymine dimer and even trimer structures. Based on experimental and theoretical results, we have concluded that specific hydrogen-bonded nucleus formation is a decisive process in the two-dimensional self-assembly formation of DNA base molecules on Cu(111) surfaces.

  3. DETECTION OF UV-B-INDUCED THYMINE DIMER IN A CYANOBACTERIUM, SCYTONEMA SP.

    Directory of Open Access Journals (Sweden)

    Pavan Kumar

    2014-02-01

    Full Text Available DNA molecule is one of the major targets for UVR that can alter its molecular structure by forming different types of lesions leading to chronic mutagenic and even death of the cell. In comparison to UV-B, the wavelength of UV-A has poor efficiency in inducing the DNA damage; because they are not absorbed by native DNA. Before assessing the impact of UV-B radiation on DNA, we observed its effects on growth and survival of the test organism Scytonema sp. It was observed that growth and survival were severely affected by UV-B radiation for different durations. UV-B treatment causes loss in the cooperative binding property of DNA which is evident from the failure of complementary strands of DNA.

  4. Kinetics and mechanism of protection of thymine from sulphate ...

    Indian Academy of Sciences (India)

    Unknown

    The rates and the quantum yields (φ) of oxidation of thymine by sulphate radical anion ... quantum yields (φexptl) and the quantum yields calculated (φcl) assuming caffeic acid acting only as a scavenger of ... Even though sugar radicals are actually responsible for strand break formation in DNA, experimental results clearly ...

  5. Melanin offers protection against induction of cyclobutane pyrimidine dimers and 6-4 photoproducts by UVB in cultured human melanocytes

    NARCIS (Netherlands)

    Smit, N.P.M.; Vink, A.A.; Kolb, R.M.; Steenwinkel, M.J.S.T.; Berg, P.T.M. van den; Nieuwpoort, F. van; Roza, L.; Pavel, S.

    2001-01-01

    The goal of this investigation was to correlate the melanin content in human pigmentary cells with the generation of UVB-induced photoproducts and to examine the relationship between the melanin content and the removal of the photoproducts. Cultured melanocytes from light-skinned individuals

  6. Neutron scattering in dimers

    DEFF Research Database (Denmark)

    Gudel, H. U.; Furrer, A.; Kjems, Jørgen

    1986-01-01

    Insulating compounds containing dimers of transition metal and rare earth ions have been studied by inelastic neutron scattering (INS). Energy splittings can be directly determined, and the corresponding parameters are easily extracted from the experimental data. The intensities of dimer excitati......Insulating compounds containing dimers of transition metal and rare earth ions have been studied by inelastic neutron scattering (INS). Energy splittings can be directly determined, and the corresponding parameters are easily extracted from the experimental data. The intensities of dimer...

  7. Cockayne syndrome group B protein enhances elongation by RNA polymerase II.

    Science.gov (United States)

    Selby, C P; Sancar, A

    1997-10-14

    Cockayne syndrome (CS) is characterized by impaired physical and mental development. Two complementation groups, CSA and CSB, have been identified. Here we report that the CSB gene product enhances elongation by RNA polymerase II. CSB stimulated the rate of elongation on an undamaged template by a factor of about 3. A thymine-thymine cyclobutane dimer located in the template strand is known to be a strong block to transcription. Addition of CSB to the blocked polymerase resulted in addition of one nucleotide to the nascent transcript. Finally, addition of transcription factor IIS is known to cause polymerase blocked at a thymine-thymine cyclobutane dimer to digest its nascent transcript, and CSB counteracted this transcript shortening action of transcription factor IIS. Thus a deficiency in transcription elongation may contribute to the CS phenotype.

  8. A Bis-benzopyrroloisoquinoline Alkaloid Incorporating a Cyclobutane Core and a Chlorophenanthroindolizidine Alkaloid with Cytotoxic Activity from Ficus fistulosa var. tengerensis.

    Science.gov (United States)

    Al-Khdhairawi, Amjad Ayad Qatran; Krishnan, Premanand; Mai, Chun-Wai; Chung, Felicia Fei-Lei; Leong, Chee-Onn; Yong, Kien-Thai; Chong, Kam-Weng; Low, Yun-Yee; Kam, Toh-Seok; Lim, Kuan-Hon

    2017-10-27

    Tengerensine (1), isolated as a racemate and constituted from a pair of bis-benzopyrroloisoquinoline enantiomers, and tengechlorenine (2), purified as a scalemic mixture and constituted from a pair of chlorinated phenanthroindolizidine enantiomers, were isolated from the leaves of Ficus fistulosa var. tengerensis, along with three other known alkaloids. The structures of 1 and 2 were determined by spectroscopic data interpretation and X-ray diffraction analysis. The enantiomers of 1 were separated by chiral-phase HPLC, and the absolute configurations of (+)-1 and (-)-1 were established via experimental and calculated ECD data. Compound 1 is notable in being a rare unsymmetrical cyclobutane adduct and is the first example of a dimeric benzopyrroloisoquinoline alkaloid, while compound 2 represents the first naturally occurring halogenated phenanthroindolizidine alkaloid. Compound (+)-1 displayed a selective in vitro cytotoxic effect against MDA-MB-468 cells (IC50 7.4 μM), while compound 2 showed pronounced in vitro cytotoxic activity against all three breast cancer cell lines tested (MDA-MB-468, MDA-MB-231, and MCF7; IC50 values of 0.038-0.91 μM).

  9. Bioinspired Adhesive Hydrogel Driven by Adenine and Thymine.

    Science.gov (United States)

    Liu, Xin; Zhang, Qin; Gao, Zijian; Hou, Ruibin; Gao, Guanghui

    2017-05-24

    Bioinspired strategies have drawn much attention for designing intelligent hydrogels with promising performance. Herein, we present a bioinspired adhesive hydrogel driven by adenine and thymine, which are the basic units of DNA. The adhesive hydrogel exhibited promising adhesive property for the surface of various solid materials, including muscle tissues, plastics, rubbers, glasses, metals, ceramics, carnelians, and woods. The maximum peeling strength of hydrogels was 330 N m-1 on aluminum, superior to that of PAAm hydrogels with 70 N m-1. The strong adhesive behavior remained more than 30 times repeated peeling tests. Moreover, the swelling behavior, morphological structure, mechanical strength, and peeling adhesive strength were also investigated and confirmed the formation and various characteristics of adhesive hydrogels driven by adenine and thymine. Thus, the biomimetic strategy to design promising adhesive hydrogels can provide various opportunities in tissue engineering, such as wound dressing, bioglues, and tissue adhesives.

  10. Synthesis and Characterization of Thymine-15N2

    Directory of Open Access Journals (Sweden)

    XU Jian-fei

    2016-02-01

    Full Text Available A novel and mild synthesis method of thymine-15N2 was designed. Ethyl formate and ethyl propionate as raw materials, the intermediate ethyl 2-formylpropionate was condensed under sodium metal, the target compound thymine-15N2 was obtained by condensation with isotope urea-15N2 under acid catalysis. Synthesis route had the advantages of simple operation, short process flow and less side product. The yield was more than 80% and isotope 15N abundance did not diluted. The product was characterized by HPLC, IR, MS, 1H NMR and 13C NMR. The chemical purity was more than 99% and 15N enrichment was more than 98 atom%.

  11. Liquid crystal dimers

    CERN Document Server

    Kumar Pal, Santanu

    2017-01-01

    This book covers in-depth discussion of design principles, synthesis and thermal behavior of all types of liquid crystal (LC) dimers. The text presents recent advances in the field of LC dimers consisting of different mesogenic units such as calamitic, discotic and bent-core molecules. It starts with a chapter on the introduction of liquid crystal dimers, including their odd-even behavior, basic classification of dimers and common mesophases in dimers. The text shows how the molecular architectures are being used to develop new materials to study a range of interesting phenomena such as the biaxial nematic phase containing rod-like and disc-like mesogenic units. Finally, the text presents perspectives related to technological relevance of these dimers such as dopants in LC display mixtures exhibiting faster relaxation time, strong flexoelectric coupling and others to effect control over the properties of these materials.

  12. Cloning and characterization of Rhodotorula glutinis thymine hydroxylase.

    Science.gov (United States)

    Neidigh, Jonathan W; Darwanto, Agus; Williams, Adides A; Wall, Nathan R; Sowers, Lawrence C

    2009-05-01

    Thymine hydroxylase (TH) is a member of the alpha-ketoglutarate-dependent nonheme iron dioxygenase family that includes a series of DNA repair proteins including alkB. Substantial interest in this family of enzymes derives from their capacity to modify DNA bases and precursors by oxidation. Previously, a sequence has been published for cloned Rhodotorula glutinis TH. However, the minimal reported activity of this enzyme, coupled with inconsistencies with previously published mass spectrometry data, compelled us to reexamine TH. The sequence reported here differs from the previously reported sequence at two amino acid positions and is consistent with previously reported mass spectrometry data. The cloned enzyme characterized in this report displayed substantial activity, indicating that the sequence differences are critical for activity. The substrate selectivity of TH against a series of pyrimidine analogues is consistent with that reported for the wild-type enzyme and, in part, explains the mode of selection of uracil analogues. A preliminary model of the active site has been constructed for the purposes of comparing TH with other members of this family. TH and alkB share in common the capacity to oxidize N-methyl groups. However, TH has the added capacity to oxidize the 5-methyl group of thymine, a property that is potentially important for enzymes that could act on DNA and modify DNA-protein interactions.

  13. D-dimer Test

    Science.gov (United States)

    ... Acidosis and Alkalosis Adrenal Insufficiency and Addison Disease Alcoholism Allergies Alzheimer Disease Anemia Angina Ankylosing Spondylitis Anthrax ... know? D-dimer concentrations may rise in the elderly, and false positives may be seen with high ...

  14. Expression and characterization of thymine-DNA glycosylase from Aeropyrum pernix.

    Science.gov (United States)

    Liu, Xi-Peng; Li, Chun-Peng; Hou, Jing-Li; Liu, Yu-Fen; Liang, Ru-Bing; Liu, Jian-Hua

    2010-03-01

    The recombinant thymine-DNA glycosylase (TDG) from Aeropyrum pernix (A. pernix) was expressed in Escherichia coli. The enzymatic activity of recombinant A. pernix TDG (ApeTDG) was characterized using oligonucleotides containing a thymine/uracil base as substrate. ApeTDG had distinct glycosylase activity on T/G mismatch. The optimal temperature and pH for thymine removal were 65-70 degrees C and pH 7.0-8.5, respectively. High concentration of NaCl inhibited the thymine removal. Divalent ions had different influence on the thymine removal by ApeTDG. Ca(2+) and Mg(2+) had no inhibition on the enzymic activity, but Ni(2+), Co(2+), Cu(2+), Mn(2+), and Zn(2+) completely inhibited the excision reaction. As derived from a hyperthermophilic archaea, ApeTDG protein was heat-resistant at 75 degrees C. ApeTDG also had a relatively weak DNA glycosylase activity on uracil base, with the following order: U/C>U/G approximately U/T>U/U approximately U/I approximately U/AP approximately U/->U/A. Additional mismatch located at 3' of T/G had less inhibition on the thymine removal than that located at 5' of T/G, and two additional mismatches located at each side of T/G completely inhibited the excision of thymine. Together, these data suggest that ApeTDG is a TDG protein with weak UDG activity. (c) 2009 Elsevier Inc. All rights reserved.

  15. Photoproducts in DNA irradiated In vitro and In vivo under extreme environmental conditions

    Science.gov (United States)

    Riklis, Emanuel

    UV-irradiated DNA forms different photoproducts in accordance with its state of hydration, and the environment in which the irradiation takes place. Photoproducts in addition to the well-known thymine dimer are produced, some of which probably not recognized due to being heat or acid labile, and milder methods for DNA hydrolysis are needed. The isolation, structure and properties of photoproducts which are formed in UV-irradiated frozen thymine solutions are described. Urea, n-propylurea and dihydrothymine are obtained as photolytic products by high radiation doses in low concentrations of thymine. The cyclobutane cis-anti thymine dimer is obtained at high concentrations of thymine, following several cycles of freezing, thawing and irradiations. A trimer is obtained with 290 nm UV light filtered through Pyrex. It reverts back to thymine dimer and thymine when reirradiated in solution. The cis-syn dimer is obtained at all concentrations of frozen thymine and in a dose dependent form. The adduct 5-hydroxy-6-4' (5'- methylpyrimid 2'-1) dihydrothymine is also obtained. In vacuum-dried thymine or DNA, other photoproducts are formed, including the spore-product, TDHT. Several solvent systems were used to develop chromatograms that allow seperation of photoproducts.

  16. Cyclic mismatch binding ligand CMBL4 binds to the 5'-T-3'/5'-GG-3' site by inducing the flipping out of thymine base.

    Science.gov (United States)

    Mukherjee, Sanjukta; Dohno, Chikara; Asano, Kaori; Nakatani, Kazuhiko

    2016-09-06

    A newly designed cyclic bis-naphthyridine carbamate dimer CMBL4: with a limited conformational flexibility was synthesized and characterized. Absorption spectra revealed that two naphthyridines in CMBL4: were stacked on each other in aqueous solutions. The most efficient binding of CMBL4: to DNA was observed for the sequence 5'-T-3'/5'-GG-3' (T/GG) with the formation of a 1:1 complex, which is one of possible structural elements involved in the higher order structures of (TGG)n repeat DNA triggering the genome microdeletion. Surface plasmon resonance assay also showed the binding of CMBL4: with TGG repeat DNA. Potassium permanganate oxidation studies of CMBL4: -bound duplex containing the T/GG site showed that the CMBL4: -binding accelerated the oxidation of thymine at that site, which suggests the flipping out of the thymine base from a π-stack. Preferential binding was observed for CMBL4: compared with its acyclic variants, which suggests the marked significance of the macrocyclic structure for the recognition of the T/GG site. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Purification and Characterization of the Danaus Plexippus Cryptochromes

    Science.gov (United States)

    2006-01-01

    16. Kao, Y., Saxena, C., Wang, L., Sancar, A., and Zhong, D. (2005) Direct observation of thymine dimer repair in DNA by photolyase. Proc. Natl. Acad...analogous blue-light photoreceptors. Photolyase utilizes blue-light to repair DNA damage such as cyclobutane pyrimidine dimer (Pyr<>Pyr) through a well...including soil detoxification, light production in bioluminescent bacteria, and both formation and reduction of oxidative stress (13). Flavins exist in

  18. Multiple-charge transfer and trapping in DNA dimers

    Science.gov (United States)

    Tornow, Sabine; Bulla, Ralf; Anders, Frithjof B.; Zwicknagl, Gertrud

    2010-11-01

    We investigate the charge transfer characteristics of one and two excess charges in a DNA base-pair dimer using a model Hamiltonian approach. The electron part comprises diagonal and off-diagonal Coulomb matrix elements such a correlated hopping and the bond-bond interaction, which were recently calculated by Starikov [E. B. Starikov, Philos. Mag. Lett. 83, 699 (2003)10.1080/0950083031000151374] for different DNA dimers. The electronic degrees of freedom are coupled to an ohmic or a superohmic bath serving as dissipative environment. We employ the numerical renormalization group method in the nuclear tunneling regime and compare the results to Marcus theory for the thermal activation regime. For realistic parameters, the rate that at least one charge is transferred from the donor to the acceptor in the subspace of two excess electrons significantly exceeds the rate in the single charge sector. Moreover, the dynamics is strongly influenced by the Coulomb matrix elements. We find sequential and pair transfer as well as a regime where both charges remain self-trapped. The transfer rate reaches its maximum when the difference of the on-site and intersite Coulomb matrix element is equal to the reorganization energy which is the case in a guanine/cytosine (GC)-dimer. Charge transfer is completely suppressed for two excess electrons in adenine/thymine (AT)-dimer in an ohmic bath and replaced by damped coherent electron-pair oscillations in a superohmic bath. A finite bond-bond interaction W alters the transfer rate: it increases as function of W when the effective Coulomb repulsion exceeds the reorganization energy (inverted regime) and decreases for smaller Coulomb repulsion.

  19. Transient dimers of allergens.

    Directory of Open Access Journals (Sweden)

    Juha Rouvinen

    Full Text Available BACKGROUND: Allergen-mediated cross-linking of IgE antibodies bound to the FcepsilonRI receptors on the mast cell surface is the key feature of the type I allergy. If an allergen is a homodimer, its allergenicity is enhanced because it would only need one type of antibody, instead of two, for cross-linking. METHODOLOGY/PRINCIPAL FINDINGS: An analysis of 55 crystal structures of allergens showed that 80% of them exist in symmetric dimers or oligomers in crystals. The majority are transient dimers that are formed at high protein concentrations that are reached in cells by colocalization. Native mass spectrometric analysis showed that native allergens do indeed form transient dimers in solution, while hypoallergenic variants of them exist almost solely in the monomeric form. We created a monomeric Bos d 5 allergen and show that it has a reduced capability to induce histamine release. CONCLUSIONS/SIGNIFICANCE: The results suggest that dimerization would be a very common and essential feature for allergens. Thus, the preparation of purely monomeric variants of allergens could open up novel possibilities for specific immunotherapy.

  20. Gemini (dimeric) Surfactants

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 3. Gemini (dimeric) Surfactants - The Two-Faced Molecules. B S Sekhon. General Article Volume 9 Issue 3 March 2004 pp 42-49. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/009/03/0042-0049 ...

  1. Anethole Isomerization and Dimerization Induced by Acid Sites or UV Irradiation

    Directory of Open Access Journals (Sweden)

    Elena Stashenko

    2010-07-01

    Full Text Available The formation of cis-anethole and various dimers as a result of the exposure of trans-anethole to microporous solid acids (dealuminated HY zeolites, or UV-Vis irradiation was established by means of high resolution gas chromatography coupled to mass spectrometry. 3,4-bis-(4-Methoxyphenyl-(E-hex-2-ene was the most abundant compound among eight different methoxyphenyl-disubstituted hexenes produced by electrophilic addition and elimination reactions induced by HY zeolites. (1a,2a,3b,4b-1,2-bis(4-Methoxyphenyl-3,4-dimethylcyclobutane was the principal component in the mixture of 5 methoxyphenyl-disubstituted cyclobutanes found, together with cis-anethole, after UV-Vis irradiation of a trans-anethole solution in toluene.

  2. Thymine utilization in Escherichia coli K12. On the role of deoxyribose 1-phosphate and thymidine phosphorylase

    DEFF Research Database (Denmark)

    Jensen, Kaj Frank; Leer, Johan Christian; Nygaard, Per

    1973-01-01

    to be presented in this paper indicate that the ability of different thymine auxotrophs to grow on progressively lower thymine concentrations is a function of their capacity to increase the internal pool of deoxyribose 1-phosphate and/or the level of thymidine phosphorylase. Thymine incorporation in wild...... to the external thymine concentration. The experiments in vivo led us to conclude that the incorporation of exogenous thymine occurs via thymidine, which is synthesized from thymine and deoxyribose 1-phosphate, catalyzed by thymidine phosphorylase. In accordance with this studies in vitro with purified thymidine...

  3. Novel fluorescent CdTe quantum dot-thymine conjugate—synthesis, properties and possible application

    Science.gov (United States)

    Rodzik, Łucja; Lewandowska-Łańcucka, Joanna; Szuwarzyński, Michał; Szczubiałka, Krzysztof; Nowakowska, Maria

    2017-01-01

    Novel, highly fluorescent cadmium telluride quantum dots conjugated with thymine and stabilized with thioglycolic acid were obtained and characterized. Successful formation of the conjugate was confirmed by elemental analysis, and UV-vis, fluorescence and Fourier transform infrared spectroscopies. Crystal structure and composition of the conjugates were characterized with xray diffraction and x-ray photoelectron spectroscopy. The size of the conjugates was 4-6 nm as demonstrated using atomic force microscopy and high resolution transmission electron microscopy imaging. The plasmon resonance fluorescence band at 540 nm on excitation at 351 nm was observed for these nanoparticles. The intensity of this band increased with the increase in the amount of conjugated thymine with no shift in its position. Based on the fluorescence measurements it was found that the CdTe-thymine conjugate interacted efficiently and selectively not only with adenine, a nucleobase complementary to thymine, but also with adenine-containing modified nucleosides, i.e., 5‧-deoxy-5‧-(methylthio)adenosine and 2‧-O-methyladenosine, the urinary tumor markers which allow monitoring of the disease progression. To the best of our knowledge, as yet, there have been no studies presented in literature on that type of the interaction with CdTe-thymine conjugates. Therefore, the system presented can be considered as a working component of a selective adenine/adenosine biosensor with potential application in cancer diagnosis.

  4. Catabolism of exogenously supplied thymidine to thymine and dihydrothymine by platelets in human peripheral blood

    Energy Technology Data Exchange (ETDEWEB)

    Pero, R.W.; Johnson, D.; Olsson, A.

    1984-11-01

    The interference of platelets with the estimation of unscheduled DNA synthesis in human peripheral mononuclear leukocytes following genotoxic exposure was studied. A 96% reduction in the unscheduled DNA synthesis value was achieved by incubating (/sup 3/H)thymidine with platelet-rich plasma for 5 hr at 37 degrees. Using radioactive thymine-containing compounds, together with quantitative analyses based on thin-layer and ion-exchange chromatographies, we have shown that thymidine was converted to thymine which, in turn, was converted to dihydrothymine in platelet-rich plasma. The enzymes responsible were separated from platelet lysates by gel filtration and were identified as thymidine phosphorylase and dihydrothymine dehydrogenase. The phosphorylase reversibly catalyzed the formation of thymine from thymidine and converted bromodeoxyuridine to bromouracil. The dehydrogenase reversibly catalyzed the interconversion of thymine and dihydrothymine in a reaction dependent on NADP(H), and it was inhibited by diazouracil and by thymine. Nearly all the thymidine-catabolizing activity found in whole blood samples supplied exogenously with thymidine was accounted for by the platelets. Since most genetic toxicological tests that use blood samples do not involve removing platelets from the blood cell cultures, then it is concluded that precautions should be taken in the future to determine the influence of platelets on these test systems. This is particularly true for methods dependent on thymidine pulses such as unscheduled DNA synthesis, or those dependent on bromodeoxyuridine, such as sister chromatid exchanges, since this nucleoside is also a substrate for thymidine phosphorylase.

  5. Internal Energies of Ion-Sputtered Neutral Tryptophan and Thymine Molecules Determined by Vacuum Ultraviolet Photoionization

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jia; Takahashi, Lynelle; Wilson, Kevin R.; Leone, Stephen R.; Ahmed, Musahid

    2010-03-11

    Vacuum ultraviolet photoionization coupled to secondary neutral mass spectrometry (VUV-SNMS) of deposited tryptophan and thymine films are performed at the Chemical Dynamics Beamline. The resulting mass spectra show that while the intensity of the VUV-SNMS signal is lower than the corresponding secondary ion mass spectroscopy (SIMS) signal, the mass spectra are significantly simplified in VUV-SNMS. A detailed examination of tryptophan and thymine neutral molecules sputtered by 25 keV Bi3 + indicates that the ion-sputtered parent molecules have ~;;2.5 eV of internal energy. While this internal energy shifts the appearance energy of the photofragment ions for both tryptophan and thymine, it does not change the characteristic photoionizaton efficiency (PIE) curves of thymine versus photon energy. Further analysis of the mass spectral signals indicate that approximately 80 neutral thymine molecules and 400 tryptophan molecules are sputtered per incident Bi3 + ion. The simplified mass spectra and significant characteristic ion contributions to the VUV-SNMS spectra indicate the potential power of the technique for organic molecule surface analysis.

  6. The formation of DNA photodamage: the role of exciton localization.

    Science.gov (United States)

    Rössle, Shaila; Friedrichs, Jana; Frank, Irmgard

    2010-06-21

    The electronic structure during the formation of a cyclobutane pyrimidine dimer (CPD) between two thymine bases is investigated using semi-empirical and first-principles approaches. The dimerization of two isolated thymine bases is found to have no barrier or a very small barrier in agreement with previous studies suggesting low photostability of DNA. The well-known high photostability of DNA can only be explained taking other factors into account. We investigate the role of the exciton location in the particular environment. Different model systems, from isolated thymine bases to an oligonucleotide in aqueous solution, are discussed. Analysis of the frontier orbitals allows one to understand the connection between the location of the exciton, the relative orientation of the thymine bases, and the observed reactivity.

  7. Effect of Thymine Starvation on Messenger Ribonucleic Acid Synthesis in Escherichia coli

    Science.gov (United States)

    Luzzati, Denise

    1966-01-01

    Luzzati, Denise (Institut de Biologie Physico-Chimique, Paris, France). Effect of thymine starvation on messenger ribonucleic acid synthesis in Escherichia coli. J. Bacteriol. 92:1435–1446. 1966.—During the course of thymine starvation, the rate of synthesis of messenger ribonucleic acid (mRNA, the rapidly labeled fraction of the RNA which decays in the presence of dinitrophenol or which hybridizes with deoxyribonucleic acid) decreases exponentially, in parallel with the viability of the thymine-starved bacteria. The ability of cell-free extracts of starved bacteria to incorporate ribonucleoside triphosphates into RNA was determined; it was found to be inferior to that of extracts from control cells. The analysis of the properties of cell-free extracts of starved cells shows that their decreased RNA polymerase activity is the consequence of a modification of their deoxyribonucleic acid, the ability of which to serve as a template for RNA polymerase decreases during starvation. PMID:5332402

  8. Selective amine catalysed steroidal dimerization

    Indian Academy of Sciences (India)

    Synthesis of steroidal dimers: Selective amine catalysed steroidal dimerization. SHAMSUZZAMANa,∗, MOHD GULFAM ALAMa,b and TABASSUM SIDDIQUIa. aDepartment of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh 202 002, India. bSchool of Distance Education (Chemical Science Programme), ...

  9. The structure of metallo-DNA with consecutive thymine-HgII-thymine base pairs explains positive entropy for the metallo base pair formation.

    Science.gov (United States)

    Yamaguchi, Hiroshi; Sebera, Jakub; Kondo, Jiro; Oda, Shuji; Komuro, Tomoyuki; Kawamura, Takuya; Dairaku, Takenori; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Burda, Jaroslav V; Kojima, Chojiro; Sychrovský, Vladimír; Tanaka, Yoshiyuki

    2014-04-01

    We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem Hg(II)-mediated T-T base pairs (thymine-Hg(II)-thymine, T-Hg(II)-T) with NMR spectroscopy in solution. This is the first 3D structure of metallo-DNA (covalently metallated DNA) composed exclusively of 'NATURAL' bases. The T-Hg(II)-T base pairs whose chemical structure was determined with the (15)N NMR spectroscopy were well accommodated in a B-form double helix, mimicking normal Watson-Crick base pairs. The Hg atoms aligned along DNA helical axis were shielded from the bulk water. The complete dehydration of Hg atoms inside DNA explained the positive reaction entropy (ΔS) for the T-Hg(II)-T base pair formation. The positive ΔS value arises owing to the Hg(II) dehydration, which was approved with the 3D structure. The 3D structure explained extraordinary affinity of thymine towards Hg(II) and revealed arrangement of T-Hg(II)-T base pairs in metallo-DNA.

  10. STABILITY OF THE NEW ANTICANCER PLATINUM ANALOG 1,2-DIAMINOMETHYL-CYCLOBUTANE-PLATINUM(II)-LACTATE (LOBAPLATIN-D19466) IN INTRAVENOUS SOLUTIONS

    NARCIS (Netherlands)

    GUCHELAAR, HJ; UGES, DRA; AULENBACHER, P; DEVRIES, EGE; MULDER, NH

    The chemical stability of the new anticancer platinum analogue 1,2-diaminomethyl-cyclobutane-platinum(II)-lactate (D19466) in infusion media was studied in an accelerated stability testing experiment with a selective HPLC-UV method. Variables were time, temperature, light, concentration, and

  11. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide

    DEFF Research Database (Denmark)

    Nielsen, P.E.; Egholm, M.; Berg, R.H.

    1991-01-01

    A polyamide nucleic acid (PNA) was designed by detaching the deoxyribose phosphate backbone of DNA in a computer model and replacing it with an achiral polyamide backbone. On the basis of this model, oligomers consisting of thymine-linked aminoethylglycyl units were prepared. These oligomers reco...

  12. Ionization-induced proton transfer in thymine-ammonia van der Waals clusters

    Science.gov (United States)

    Kim, Nam Joon; Kim, Hyung Min; Kim, Seong Keun

    2007-03-01

    Ion intensity distribution of thymine-ammonia clusters produced in a supersonic jet was investigated using the resonant 2-photon ionization technique. The mass spectrum of Thym(NH3)n (m = 1-7) exhibited an anomalously strong ion intensity for n = 1 in contrast to the nearly negligible ion signals for n > 1. We suggest that proton transfer from the thymine radical cation to an ammonia molecule following the ionization of the clusters is responsible for the observed anomaly. It is also proposed that charge migration occurring with the proton transfer leads to an ion core switch from the thymine radical cation to the newly formed ammonium ion. The subsequent evaporation of other ammonia molecules in the cluster ion as a consequence of the energy released from the reaction results in extensive loss of ion signals for n > 1, and at their expense, an anomalously large ion intensity for n = 1. This mechanism is supported by density functional theory calculations on the thymine-ammonia 1:1 complex ion performed along the reaction coordinate of the proton transfer. The formation of the ammonium ion in the cluster is also confirmed by the fragmentation feature of metastable Thym(NH3)1+ (m = 1-4) obtained using reflectron time-of-flight mass spectrometry.

  13. Mechanisms for the formation of thymine under astrophysical conditions and implications for the origin of life.

    Science.gov (United States)

    Bera, Partha P; Nuevo, Michel; Materese, Christopher K; Sandford, Scott A; Lee, Timothy J

    2016-04-14

    Nucleobases are the carriers of the genetic information in ribonucleic acid and deoxyribonucleic acid (DNA) for all life on Earth. Their presence in meteorites clearly indicates that compounds of biological importance can form via non-biological processes in extraterrestrial environments. Recent experimental studies have shown that the pyrimidine-based nucleobases uracil and cytosine can be easily formed from the ultraviolet irradiation of pyrimidine in H2O-rich ice mixtures that simulate astrophysical processes. In contrast, thymine, which is found only in DNA, is more difficult to form under the same experimental conditions, as its formation usually requires a higher photon dose. Earlier quantum chemical studies confirmed that the reaction pathways were favorable provided that several H2O molecules surrounded the reactants. However, the present quantum chemical study shows that the formation of thymine is limited because of the inefficiency of the methylation of pyrimidine and its oxidized derivatives in an H2O ice, as supported by the laboratory studies. Our results constrain the formation of thymine in astrophysical environments and thus the inventory of organic molecules delivered to the early Earth and have implications for the role of thymine and DNA in the origin of life.

  14. Mechanisms for the formation of thymine under astrophysical conditions and implications for the origin of life

    Energy Technology Data Exchange (ETDEWEB)

    Bera, Partha P., E-mail: Partha.P.Bera@nasa.gov, E-mail: Timothy.J.Lee@nasa.gov; Nuevo, Michel; Materese, Christopher K. [Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, California 94035 (United States); Bay Area Environmental Research Institute, Petaluma, California 94952 (United States); Sandford, Scott A.; Lee, Timothy J., E-mail: Partha.P.Bera@nasa.gov, E-mail: Timothy.J.Lee@nasa.gov [Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, California 94035 (United States)

    2016-04-14

    Nucleobases are the carriers of the genetic information in ribonucleic acid and deoxyribonucleic acid (DNA) for all life on Earth. Their presence in meteorites clearly indicates that compounds of biological importance can form via non-biological processes in extraterrestrial environments. Recent experimental studies have shown that the pyrimidine-based nucleobases uracil and cytosine can be easily formed from the ultraviolet irradiation of pyrimidine in H{sub 2}O-rich ice mixtures that simulate astrophysical processes. In contrast, thymine, which is found only in DNA, is more difficult to form under the same experimental conditions, as its formation usually requires a higher photon dose. Earlier quantum chemical studies confirmed that the reaction pathways were favorable provided that several H{sub 2}O molecules surrounded the reactants. However, the present quantum chemical study shows that the formation of thymine is limited because of the inefficiency of the methylation of pyrimidine and its oxidized derivatives in an H{sub 2}O ice, as supported by the laboratory studies. Our results constrain the formation of thymine in astrophysical environments and thus the inventory of organic molecules delivered to the early Earth and have implications for the role of thymine and DNA in the origin of life.

  15. Labeling of thymine with {sup 99m} technetium: a suggestion of a chemical model

    Energy Technology Data Exchange (ETDEWEB)

    Gutfilen, Bianca; Silva, Claudia Ribeiro da; Bernardo Filho, Mario [Universidade do Estado, Rio de Janeiro, RJ (Brazil). Inst. de Biologia. Dept. de Biofisica e Biometria; Ribeiro, Barbara Luzia Almeida [Instituto Nacional do Cancer, Rio de Janeiro, RJ (Brazil). Centro de Pesquisa Basica; Mattos, Maura Ferreira [Universidade do Estado, Rio de Janeiro, RJ (Brazil). Inst. de Quimica

    1996-03-01

    Successful targeting of diagnose but also to stage cancer. It has been shown that certain tumor cells are permeable to low level of exogenous adenosine-diphosphate and adenosine-triphosphate nucleotides, that are incorporated into intracellular pools. We present the labeling of a nucleotide precursor, a base, thymine technetium-99m ({sup 99m} Tc). (author)

  16. High-resolution electron spectroscopy and structures of lithium-nucleobase (adenine, uracil, and thymine) complexes.

    Science.gov (United States)

    Krasnokutski, Serge A; Lee, Jung Sup; Yang, Dong-Sheng

    2010-01-28

    Li complexes of adenine, uracil, and thymine were produced by laser vaporization of rods made of Li and nucleobase powders in a metal-cluster beam source and studied by pulsed-field-ionization zero-electron-kinetic-energy (ZEKE) spectroscopy and density functional theory calculations. The ZEKE measurements determined the adiabatic ionization energies of the three neutral complexes and frequencies of several vibrational modes for the metal-adenine and -uracil ions. The measured spectra were compared with spectral simulations to determine the preferred metal binding sites. For adenine, the most stable structure is formed by Li/Li(+) bidentately binding to both the N7 atom of the imidazole ring and the NH(2) group of the pyrimidine ring. For uracil and thymine, the ideal site for Li/Li(+) coordination is the O4 atom. Although it has only a small effect on the geometries of uracil and thymine, lithium coordination forces the rotation of the NH(2) group out of the adenine plane. The adiabatic ionization energies of the three complexes follow the trend of uracil (33910+/-5 cm(-1))>thymine (33386+/-5 cm(-1))>adenine (32240+/-5 cm(-1)), whereas their metal-ligand bond dissociation energies are about the same, (92-97) +/-6 kJ mol(-1). For all three complexes, the neutral bond energies are smaller than those of the corresponding ions due to a weaker electrostatic interaction and stronger electron repulsion.

  17. A computational study of base-catalyzed reactions of cyclic 1,2-diones: cyclobutane-1,2-dione

    Directory of Open Access Journals (Sweden)

    Nargis Sultana

    2013-03-01

    Full Text Available The reaction of cyclobutane-1,2-dione with hydroxide was studied by a variety of ab initio (MP2, SCS-MP2, CCSD(T, CEPA/1 and density functional (M06-2X methods. Three possible reaction paths of the initially formed tetrahedral adduct leading to either 1-hydroxycyclopropane-1-carboxylate (benzilic acid type rearrangement, path A, α-oxobutanoate (path B or γ-oxobutanoate (path C were considered. Although the latter two products show similar or even more negative Gibbs free energies of reaction than calculated for the benzilic acid type rearrangement, the Gibbs free energies of activation are substantially higher. According to the calculations, the only feasible reaction appears to be the formation of 1-hydroxycyclopropane-1-carboxylate, which is corroborated by previous experimental observations.

  18. Thermodynamic Potential for the Abiotic Synthesis of Adenine, Cytosine, Guanine, Thymine, Uracil, Ribose, and Deoxyribose in Hydrothermal Systems

    NARCIS (Netherlands)

    LaRowe, D.E.; Regnier, P.

    2008-01-01

    The thermodynamic potential for the abiotic synthesis of the five common nucleobases (adenine, cytosine, guanine, thymine, and uracil) and two monosaccharides (ribose and deoxyribose) from formaldehyde and hydrogen cyanide has been quantified under temperature, pressure, and bulk composition

  19. The Ammonia Dimer Revisited

    Science.gov (United States)

    Dawes, Richard; Van Der Avoird, Ad

    2012-06-01

    The conclusion from microwave spectra by Nelson, Fraser, and Klemperer that the ammonia dimer has a nearly cyclic structure led to much debate about the issue of whether (NH_3)_2 is hydrogen bonded. This structure was surprising because most {ab initio} calculations led to a classical, nearly linear, hydrogen-bonded structure. An obvious explanation of the discrepancy between the outcome of these calculations and the microwave data which led Nelson {et al.} to their ``surprising structure'' might be the effect of vibrational averaging: the electronic structure calculations focus on finding the minimum of the intermolecular potential, the experiment gives a vibrationally averaged structure. Isotope substitution studies seemed to indicate, however, that the complex is nearly rigid. Additional data became available from high-resolution molecular beam far-infrared spectroscopy in the Saykally group. These spectra, displaying large tunneling splittings, indicate that the complex is very floppy. The seemingly contradictory experimental data were explained when it became possible to calculate the vibration-rotation-tunneling (VRT) states of the complex on a six-dimensional intermolecular potential surface. The potential used was a simple model potential, with parameters fitted to the far-infrared data. Now, for the first time, a six-dimensional potential was computed by high level {ab initio} methods and this potential will be used in calculations of the VRT states of (NH_3)_2 and (ND_3)_2. So, we will finally be able to answer the question whether the conclusions from the model calculations are indeed a valid explanation of the experimental data. D. Nelson, G. T. Fraser, and W. Klemperer J. Chem. Phys. 83 6201 (1985) J. G. Loeser, C. A. Schmuttenmaer, R. C. Cohen, M. J. Elrod, D. W. Steyert, R. J. Saykally, R. E. Bumgarner, and G. A. Blake J. Chem. Phys. 97 4727 (1992) E. H. T. Olthof, A. van der Avoird, and P. E. S. Wormer J. Chem. Phys. 101 8430 (1994) E. H. T. Olthof

  20. Temperature dependence of the cross section for the fragmentation of thymine via dissociative electron attachment

    Energy Technology Data Exchange (ETDEWEB)

    Kopyra, Janina [Faculty of Science, Siedlce University, 3 Maja 54, 08-110 Siedlce (Poland); Abdoul-Carime, Hassan, E-mail: hcarime@ipnl.in2p3.fr [Université de Lyon, Université Claude Bernard Lyon1, Institut de Physique Nucléaire de Lyon, CNRS/IN2P3 UMR 5822, 43 Bd du 11 novembre 1918, 69622 Villeurbanne Cedex (France)

    2015-05-07

    Providing experimental values for absolute Dissociative Electron Attachment (DEA) cross sections for nucleobases at realistic biological conditions is a considerable challenge. In this work, we provide the temperature dependence of the cross section, σ, of the dehydrogenated thymine anion (T − H){sup −} produced via DEA. Within the 393-443 K temperature range, it is observed that σ varies by one order of magnitude. By extrapolating to a temperature of 313 K, the relative DEA cross section for the production of the dehydrogenated thymine anion at an incident energy of 1 eV decreases by 2 orders of magnitude and the absolute value reaches approximately 6 × 10{sup −19} cm{sup 2}. These quantitative measurements provide a benchmark for theoretical prediction and also a contribution to a more accurate description of the effects of ionizing radiation on molecular medium.

  1. Photo-sensible (thymine containing) azo-polysiloxanes: synthesis and light induced effects

    Energy Technology Data Exchange (ETDEWEB)

    Enea, R; Hurduc, N; Iordache, I [Technical University of Iasi, Department of Natural and Synthetic Polymers, Bd.Mangeron 71, 700050-Iasi (Romania); Apostol, I; Damian, V [National Institute for Laser, plasma and Radiation Physics, Atomistilor str. 409, 077125, Bucharest-Magurele (Romania)], E-mail: nhurduc@ch.tuiasi.ro, E-mail: ileana.apostol@inflpr.ro

    2008-03-15

    Abstract. The paper presents the possibility to obtain azo-polysiloxanes modified with thymine and their light induced processing with potential interest in opto-electronics or biomolecules nanomanipulation. The presence of the thymine group in the polymeric structure can confer to material biological properties, in the same time the capacity of tymine to generate H-bonds being useful to the relief geometry stabilization in time. The investigated polymers were obtained in a two step reaction, starting from a polysiloxane containing chlorobenzyl groups in the side chain. The azopolysiloxanes' photochromic behaviour was investigated in solid state, using thin films etalated on the surface of a quartz slide. The effect of surface relief structuration process under the action of UV (355 nm) laser radiation was studied. Laser induced effects on the material surface depends on the incident laser fluence and number of pulses.

  2. Thymine photoproduct formation and inactivation of intact spores of Bacillus subtilis irradiated with short wavelength UV (200-300nm) at atmospheric pressure and in vacuo

    Science.gov (United States)

    Lindberg, C.; Horneck, G.

    Vacuum exposure renders the survival of spores of Bacillus subtilis approximately five times more sensitive to ultraviolet light irradiation than exposure under atmospheric conditions. The photoproduct formation in spores irradiated under ultrahigh vacuum (UHV) conditions is compared to the photoproduct formation in spores irradiated at atmospheric pressure. Compared to irradiation at atmospheric pressure, where only the ``spore photoproduct'' 5-thyminyl-5,6-dihydrothymine (TDHT) can be detected, two additional photoproducts, known as the c,s and t,s isomers of thymine dimer (T???T) are produced in vacuo. The spectral efficiencies for photoproduct formation in spores under atmospheric and vacuum conditions are compared. Since there is no increased formation of TDHT after irradiation in vacuum, TDHT cannot be made responsible for the observed vacuum effect. ``Vacuum specific'' photoproducts may cause a synergistic response of spores to the simultaneous action of ultraviolet light (UV) and UHV. Three different mechanisms are discussed for the enhanced sensitivity of B. subtilis spores to UV radiation in vacuum. The experiments described contribute valuable research information on the chance for survival of microorganisms in outer space.

  3. Experimental and Theoretical Study of Strong Low-Terahertz Absorption of Thymine

    Science.gov (United States)

    Zhang, W.-D.; Bykhovski, A.; Deibel, J. A.; Brown, E. R.

    2017-07-01

    The absorption coefficient of a nucleobase-thymine-in powder form was measured with terahertz spectroscopy in both frequency- and time-domain experiments. For frequencies below 3 THz, a strong signature was observed at 1.27 THz. Furthermore, molecular-dynamic simulations were conducted to reveal that the 1.27 THz absorption signature is related to a transverse optical phonon mode. The simulations also indicated that bound water molecules are vital to the vibrational mode.

  4. DNA Bases Thymine and Adenine in Bio-Organic Light Emitting Diodes

    OpenAIRE

    Eliot F. Gomez; Venkatraman, Vishak; Grote, James G.; Steckl, Andrew J.

    2014-01-01

    We report on the use of nucleic acid bases (NBs) in organic light emitting diodes (OLEDs). NBs are small molecules that are the basic building blocks of the larger DNA polymer. NBs readily thermally evaporate and integrate well into the vacuum deposited OLED fabrication. Adenine (A) and thymine (T) were deposited as electron-blocking/hole-transport layers (EBL/HTL) that resulted in increases in performance over the reference OLED containing the standard EBL material NPB. A-based OLEDs reached...

  5. Association of thymine glycol lesioned DNA with repair enzyme endonuclease III-molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Pinak, Miroslav [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    2001-07-01

    The 2 nanoseconds molecular dynamics (MD) simulation has been performed for the system consisting of repair enzyme and DNA 30-mer with native thymine at position 16 replaced by thymine glycol (TG) solvated in water environment. After 950 picoseconds of MD the enzyme and DNA associated together to form complex that lasted stable up to 2 ns when simulation was terminated. At the contact area of enzyme and DNA there is glutamic acid located as close as 1.6 A to the C3' atom of phosphodiester bond of TG. Initial B-DNA molecule was bent and kinked at the TG during MD. This distortion caused that phosphodiester bond was easier accessible by amino acids of enzyme. The negative value of electrostatic energy (-26 kcal/mol) discriminates TG from nearly neutral native thymine and contributes to the specific recognition of this lesion. Higher number of close water molecules at TG site before formation of complex (compared with other nucleotides) indicates that glycosyl bond of the lesion is easily approached by repair enzyme during scanning of DNA surface and suggests the importance of specific hydration at the lesion during recognition process. (author)

  6. Adventures in Holographic Dimer Models

    Energy Technology Data Exchange (ETDEWEB)

    Kachru, Shamit; /Stanford U., Phys. Dept. /SLAC; Karch, Andreas; /Washington U., Seattle; Yaida, Sho; /Stanford U., Phys. Dept.

    2011-08-12

    We abstract the essential features of holographic dimer models, and develop several new applications of these models. Firstly, semi-holographically coupling free band fermions to holographic dimers, we uncover novel phase transitions between conventional Fermi liquids and non-Fermi liquids, accompanied by a change in the structure of the Fermi surface. Secondly, we make dimer vibrations propagate through the whole crystal by way of double trace deformations, obtaining nontrivial band structure. In a simple toy model, the topology of the band structure experiences an interesting reorganization as we vary the strength of the double trace deformations. Finally, we develop tools that would allow one to build, in a bottom-up fashion, a holographic avatar of the Hubbard model.

  7. Photochemistry of alkyl halide dimers

    Science.gov (United States)

    Fan, Y. B.; Randall, K. L.; Donaldson, D. J.

    1993-03-01

    Dimers and other small clusters of CH3I, C2H5I, i- and n-C3H7I, HI, CF3I, CH3Br, and C2H5Br formed in a supersonic expansion are irradiated at 248 and 193 nm and the halogen molecule product probed via laser induced fluorescence spectroscopy. Both dimers and larger clusters of RI (R=H, alkyl) excited at each wavelength yield I2 in its ground electronic state with very little internal energy. Clusters of CF3I and those containing alkyl bromides do not give halogen molecule products after excitation at either wavelength. A model for the dynamics in the dimer excited state which explains these results is presented.

  8. Adventures in holographic dimer models

    Science.gov (United States)

    Kachru, Shamit; Karch, Andreas; Yaida, Sho

    2011-03-01

    We abstract the essential features of holographic dimer models, and develop several new applications of these models. Firstly, semi-holographically coupling free band fermions to holographic dimers, we uncover novel phase transitions between conventional Fermi liquids and non-Fermi liquids, accompanied by a change in the structure of the Fermi surface. Secondly, we make dimer vibrations propagate through the whole crystal by way of double trace deformations, obtaining nontrivial band structure. In a simple toy model, the topology of the band structure experiences an interesting reorganization as we vary the strength of the double trace deformations. Finally, we develop tools that would allow one to build, in a bottom-up fashion, a holographic avatar of the Hubbard model.

  9. Dynamics and energetics of Ge(001) dimers

    NARCIS (Netherlands)

    van Houselt, Arie; van Gastel, Raoul; Poelsema, Bene; Zandvliet, Henricus J.W.

    2006-01-01

    The dynamic behavior of surface dimers on Ge(001) has been studied by positioning the tip of a scanning tunneling microscope over single flip-flopping dimers and measuring the tunneling current as a function of time. We observe that not just symmetric, but also asymmetric appearing dimers exhibit

  10. Invertase-labeling gold-dendrimer for in situ amplified detection mercury(II) with glucometer readout and thymine-Hg(2+)-thymine coordination chemistry.

    Science.gov (United States)

    Qiu, Zhenli; Shu, Jian; Jin, Guixiao; Xu, Mingdi; Wei, Qiaohua; Chen, Guonan; Tang, Dianping

    2016-03-15

    A simple, low-cost transducer with glucometer readout was designed for sensitive detection of mercury(II) (Hg(2+)), coupling with thymine-Hg(2+)-thymine (T-Hg(2+)-T) coordination chemistry and invertase-functionalized gold-dendrimer nanospheres for the signal amplification. Initially, nanogold-encapsulated poly(amidoamine) dendrimers (Au DENs) were synthesized by in-situ reduction of gold(III). Thereafter, the as-prepared Au DENs were utilized for the labeling of invertase and T-rich signal DNA probe. In the presence of target Hg(2+), the functionalized Au DENs were conjugated to capture DNA probe-modified electrode via T-Hg(2+)-T coordination chemistry. Accompanying the Au DENs, the labeled invertase could hydrolyze sucrose into glucose, which could be quantitatively monitored by an external personal glucometer (PGM). The PGM signal increased with the increasing target Hg(2+) in the sample. Under the optimal conditions, our designed sensing platform exhibited good PGM responses toward target Hg(2+), and allowed the detection of Hg(2+) at a concentration as low as 4.2 pM. This sensing system also displayed remarkable specificity relative to target Hg(2+) against other competing ions, and could be applied for reliable monitoring of spiked Hg(2+) into the environmental water samples with satisfactory results. With the advantages of cost-effectiveness, simplicity, portability, and convenience, our strategy provides a tremendous potential to be a promising candidate for point-of-use monitoring of non-glucose targets by the public. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Water-soluble mercury ion sensing based on the thymine-Hg2+-thymine base pair using retroreflective Janus particle as an optical signaling probe.

    Science.gov (United States)

    Chun, Hyeong Jin; Kim, Saemi; Han, Yong Duk; Kim, Dong Woo; Kim, Ka Ram; Kim, Hyo-Sop; Kim, Jae-Ho; Yoon, Hyun C

    2018-01-06

    Herein, we report an optical sensing platform for mercury ions (Hg2+) in water based on the integration of Hg2+-mediated thymine-thymine (T-T) stabilization, a biotinylated stem-loop DNA probe, and a streptavidin-modified retroreflective Janus particle (SA-RJP). Two oligonucleotide probes, including a stem-loop DNA probe and an assistant DNA probe, were utilized. In the absence of Hg2+, the assistant DNA probe does not hybridize with the stem-loop probe due to their T-T mismatch, so the surface-immobilized stem-loop DNA probe remains a closed hairpin structure. In the presence of Hg2+, the DNA forms a double-stranded structure with the loop region via Hg2+-mediated T-T stabilization. This DNA hybridization induces stretching of the stem-loop DNA probe, exposing biotin. To translate these Hg2+-mediated structural changes in DNA probe into measurable signal, SA-RJP, an optical signaling label, is applied to recognize the exposed biotin. The number of biospecifically bound SA-RJPs is proportional to the concentration of Hg2+, so that the concentration of Hg2+ can be quantitatively analyzed by counting the number of RJPs. Using the system, a highly selective and sensitive measurement of Hg2+ was accomplished with a limit of detection of 0.027nM. Considering the simplified optical instrumentation required for retroreflection-based RJP counting, RJP-assisted Hg2+ measurement can be accomplished in a much easier and inexpensive manner. Moreover, the detection of Hg2+ in real drinking water samples including tap and commercial bottled water was successfully carried out. Copyright © 2018 Elsevier B.V. All rights reserved.

  12. Evidence of formation of adenine dimer cation radical in DNA: the importance of adenine base stacking.

    Science.gov (United States)

    Kobayashi, Kazuo

    2010-04-29

    Deprotonation of the adenine (A) base in both mononucleotide and oligonucleotide (ODN) was measured by nanosecond pulse radiolysis. The cation radical (A(+*)) of deoxyadenosine (dA), produced by oxidation with SO(4)(-*), rapidly deprotonated to form the neutral A radical (A(- H)(*)) with a rate constant of 2.0 x 10(7) s(-1) and a pK(a) value of 4.2, as determined by transient spectroscopy. A similar process was observed in experiments performed on a variety of double-stranded ODNs containing adenine x thymine (A x T) base pairs. The transient spectrum of A(+)(*) in an ODN composed of alternating A x T pairs was essentially identical to that of free dA and differed from the spectra of ODNs containing AA and AAA. In contrast, the spectra of A(- H)(*) were not affected by the sequence. These results suggest that the positive charge on A(+)(*) in ODNs is delocalized as the dimer is stabilized by pi-orbital stacking between adjacent A's. The rate constants for deprotonation of A(+)(*) in ODNs containing AA and AAA (0.9-1.1 x 10(7) s(-1)) were a factor of 2 smaller than the rate constants for deprotonation of A(+)(*) in ODNs containing alternating A x T and dA (2.0 x 10(7) s(-1)). This suggests that the formation of a charge resonance stabilized dimer AA(+)(*) in DNA produced a significant barrier to deprotonation.

  13. Structure and dynamics of poly(T) single-strand DNA: implications toward CPD formation.

    Science.gov (United States)

    Johnson, Andrew T; Wiest, Olaf

    2007-12-27

    The formation of cyclobutane pyrimidine dimers between adjacent thymines by UV radiation is thought to be the first event in a cascade leading to skin cancer. Recent studies showed that thymine dimers are fully formed within 1 ps of UV irradiation, suggesting that the conformation at the moment of excitation is the determining factor in whether a given base pair dimerizes. MD simulations on the 50 ns time scale are used to study the populations of reactive conformers that exist at any given time in T18 single-strand DNA. Trajectory analysis shows that only a small percentage of the conformations fulfill distance and dihedral requirements for thymine dimerization, in line with the experimentally observed quantum yield of 3%. Plots of the pairwise interactions in the structures predict hot spots of DNA damage where dimerization in the ssT18 is predicted to be most favored. The importance of hairpin formation by intra-strand base pairing for distinguishing reactive and unreactive base pairs is discussed in detail. The data presented thus explain the structural origin of the results from the ultrafast studies of thymine dimer formation.

  14. Dimeric guaianolides from Artemisia absinthium.

    Science.gov (United States)

    Turak, Ablajan; Shi, She-Po; Jiang, Yong; Tu, Peng-Fei

    2014-09-01

    Five dimeric guaianolides, absinthins A-E, and seven known dimeric guaianolides were isolated from Artemisia absinthium. Their structures were elucidated based on 1D- and 2D-NMR experiments, including (1)H NMR, (13)C NMR, DEPT, (1)H-(1)H COSY, HSQC, HMBC, and NOESY, and through HRESIMS data analysis. The absolute configuration of the known compound, anabsinthin, was determined by X-ray crystallographic analysis. The isolated compounds were tested to assess their inhibitory activities on lipopolysaccharide (LPS)-induced nitric oxide (NO) production in BV-2 cells; absinthin C and isoanabsinthin exhibited significant inhibitory effects with IC50 values of 1.52 and 1.98μM, respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Antiparallel dimer and actin assembly†

    OpenAIRE

    Grintsevich, Elena E.; Phillips, Martin; Pavlov, Dmitry; Phan, Mai; Reisler, Emil; Muhlrad, Andras

    2010-01-01

    Antiparallel dimer (APD) is a unique actin species, which can be detected in the early stages of actin polymerization. In this work, we introduce novel tools to examine the effects of the APD on actin polymerization. We document that bifunctional methanothiosulfonate (MTS) reagents are an attractive alternative to the routinely used p-phenylenemaleimide (pPDM) for APD detection, allowing for a fast and efficient cross-linking under conditions of actin polymerization at neutral pH. We report a...

  16. Thymine- and Adenine-Functionalized Polystyrene Form Self-Assembled Structures through Multiple Complementary Hydrogen Bonds

    Directory of Open Access Journals (Sweden)

    Yu-Shian Wu

    2014-06-01

    Full Text Available In this study, we investigated the self-assembly of two homopolymers of the same molecular weight, but containing complementary nucleobases. After employing nitroxide-mediated radical polymerization to synthesize poly(vinylbenzyl chloride, we converted the polymer into poly(vinylbenzyl azide through a reaction with NaN3 and then performed click chemistry with propargyl thymine and propargyl adenine to yield the homopolymers, poly(vinylbenzyl triazolylmethyl methylthymine (PVBT and poly(vinylbenzyl triazolylmethyl methyladenine (PVBA, respectively. This PVBT/PVBA blend system exhibited a single glass transition temperature over the entire range of compositions, indicative of a miscible phase arising from the formation of multiple strong complementary hydrogen bonds between the thymine and adenine groups of PVBT and PVBA, respectively; Fourier transform infrared and 1H nuclear magnetic resonance spectroscopy confirmed the presence of these noncovalent interactions. In addition, dynamic rheology, dynamic light scattering and transmission electron microscopy provided evidence for the formation of supramolecular network structures in these binary PVBT/PVBA blend systems.

  17. Solitary waves in dimer binary collision model

    Science.gov (United States)

    Ahsan, Zaid; Jayaprakash, K. R.

    2017-01-01

    Solitary wave propagation in nonlinear diatomic (dimer) chains is a very interesting topic of research in the study of nonlinear lattices. Such waves were recently found to be supported by the essentially nonlinear granular lattice and Toda lattice. An interesting aspect of this discovery is attributed to the realization of a spectrum of the mass ratio (the only system parameter governing the dynamics) that supports the propagation of such waves corresponding to the considered interaction potential. The objective of this exposition is to explore solitary wave propagation in the dimer binary collision (BC) model. Interestingly, the dimer BC model supports solitary wave propagation at a discrete spectrum of mass ratios similar to those observed in granular and Toda dimers. Further, we report a qualitative and one-to-one correspondence between the spectrum of the mass ratio corresponding to the dimer BC model and those corresponding to granular and Toda dimer chains.

  18. Dimer geometry, amoebae and a vortex dimer model

    Science.gov (United States)

    Nash, Charles; O'Connor, Denjoe

    2017-09-01

    We present a geometrical approach and introduce a connection for dimer problems on bipartite and non-bipartite graphs. In the bipartite case the connection is flat but has non-trivial {Z}2 holonomy round certain curves. This holonomy has the universality property that it does not change as the number of vertices in the fundamental domain of the graph is increased. It is argued that the K-theory of the torus, with or without punctures, is the appropriate underlying invariant. In the non-bipartite case the connection has non-zero curvature as well as non-zero Chern number. The curvature does not require the introduction of a magnetic field. The phase diagram of these models is captured by what is known as an amoeba. We introduce a dimer model with negative edge weights which correspond to vortices. The amoebae for various models are studied with particular emphasis on the case of negative edge weights. Vortices give rise to new kinds of amoebae with certain singular structures which we investigate. On the amoeba of the vortex full hexagonal lattice we find the partition function corresponds to that of a massless Dirac doublet.

  19. Mechanisms for the Formations of the Thymine Under Astrophysical Conditions and Implications for the Origin of Life

    Science.gov (United States)

    Bera, Partha P.; Nuevo, Michel; Materese, Christopher K.; Sandford, Scott A.; Lee, Timothy J.

    2016-01-01

    Nucleobases are the carriers of the genetic information in ribonucleic acid and deoxyribonucleic acid (DNA) for all life on Earth. Their presence in meteorites clearly indicates that compounds of biological importance can form via non-biological processes in extraterrestrial environments. Recent experimental studies have shown that the pyrimidine-based nucleobases uracil and cytosine can be easily formed from the ultraviolet irradiation of pyrimidine in H2O-rich ice mixtures that simulate astrophysical processes. In contrast, thymine, which is found only in DNA, is more difficult to form under the same experimental conditions, as its formation usually requires a higher photon dose. Earlier quantum chemical studies confirmed that the reaction pathways were favorable provided that several H2O molecules surrounded the reactants. However, the present quantum chemical study shows that the formation of thymine is limited because of the inefficiency of the methylation of pyrimidine and its oxidized derivatives in an H2O ice, as supported by the laboratory studies. Our results constrain the formation of thymine in astrophysical environments and thus the inventory of organic molecules delivered to the early Earth and have implications for the role of thymine and DNA in the origin of life.

  20. Enzymatic synthesis of DNA strands containing α-L-LNA (α-L-configured locked nucleic acid) thymine nucleotides

    DEFF Research Database (Denmark)

    Højland, Torben; Veedu, Rakesh N; Vester, Birte

    2012-01-01

    We describe the first enzymatic incorporation of an α-L-LNA nucleotide into an oligonucleotide. It was found that the 5'-triphosphate of α-L-LNA is a substrate for the DNA polymerases KOD, 9°N(m), Phusion and HIV RT. Three dispersed α-L-LNA thymine nucleotides can be incorporated into DNA strands...

  1. Reduced Graphene Oxide/α-Cyclodextrin-Based Electrochemical Sensor: Characterization and Simultaneous Detection of Adenine, Guanine and Thymine

    Directory of Open Access Journals (Sweden)

    Erhan ZOR

    2016-12-01

    Full Text Available Graphene, the rising star of carbon nanomaterials, is a single layer of sp2-bonded carbon atoms patterned in a 2D honeycomb network. Thanks to its unique features, graphene has attracted enormous attention and it has arisen various applications in the fields of optical and electrochemical sensors. In the present work, reduced graphene oxide/alpha cyclodextrin (rGO/α-CD is proposed as a nanocomposite for individual and simultaneous detection of adenine, guanine and thymine. rGO/α-CD has been characterized by FT-IR, Raman spectroscopy, AFM, HR-TEM and SEM techniques. Cyclic voltammetry, differential pulse voltammetry and chronoamperometry techniques were utilized for detection of adenine, guanine and thymine. The limit of detection (LOD values for adenine, guanine and thymine were calculated to be 145.5, 38.9 and 52.9 nmol L-1, respectively. The results show that the developed sensor can be utilized for the determination of adenine, guanine and thymine in human serum, indicating its promising application in the analysis of real samples.

  2. Enhanced Chiral Recognition by Cyclodextrin Dimers

    Directory of Open Access Journals (Sweden)

    Bart Jan Ravoo

    2011-07-01

    Full Text Available In this article we investigate the effect of multivalency in chiral recognition. To this end, we measured the host-guest interaction of a β-cyclodextrin dimer with divalent chiral guests. We report the synthesis of carbohydrate-based water soluble chiral guests functionalized with two borneol, menthol, or isopinocampheol units in either (+ or (– configuration. We determined the interaction of these divalent guests with a β-cyclodextrin dimer using isothermal titration calorimetry. It was found that—in spite of a highly unfavorable conformation—the cyclodextrin dimer binds to guest dimers with an increased enantioselectivity, which clearly reflects the effect of multivalency.

  3. Synthesis of the C8’-epimeric thymine pyranosyl amino acid core of amipurimycin

    Directory of Open Access Journals (Sweden)

    Pramod R. Markad

    2016-08-01

    Full Text Available The C8’-epimeric pyranosyl amino acid core 2 of amipurimycin was synthesized from D-glucose derived alcohol 3 in 13 steps and 14% overall yield. Thus, the Sharpless asymmetric epoxidation of allyl alcohol 7 followed by trimethyl borate mediated regio-selective oxirane ring opening with azide, afforded azido diol 10. The acid-catalyzed 1,2-acetonide ring opening in 10 concomitantly led to the formation of the pyranose ring skeleton to give 2,7-dioxabicyclo[3.2.1]octane 12. Functional group manipulation in 12 gave 21 that on stereoselective β-glycosylation afforded the pyranosyl thymine nucleoside 2 – a core of amipurimycin.

  4. The hepatitis B virus x protein inhibits thymine DNA glycosylase initiated base excision repair.

    Directory of Open Access Journals (Sweden)

    Maarten A A van de Klundert

    Full Text Available The hepatitis B virus (HBV genome encodes the X protein (HBx, a ubiquitous transactivator that is required for HBV replication. Expression of the HBx protein has been associated with the development of HBV infection-related hepatocellular carcinoma (HCC. Previously, we generated a 3D structure of HBx by combined homology and ab initio in silico modelling. This structure showed a striking similarity to the human thymine DNA glycosylase (TDG, a key enzyme in the base excision repair (BER pathway. To further explore this finding, we investigated whether both proteins interfere with or complement each other's functions. Here we show that TDG does not affect HBV replication, but that HBx strongly inhibits TDG-initiated base excision repair (BER, a major DNA repair pathway. Inhibition of the BER pathway may contribute substantially to the oncogenic effect of HBV infection.

  5. Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA.

    Science.gov (United States)

    Malik, Shuja S; Coey, Christopher T; Varney, Kristen M; Pozharski, Edwin; Drohat, Alexander C

    2015-10-30

    Thymine DNA Glycosylase (TDG) performs essential functions in maintaining genetic integrity and epigenetic regulation. Initiating base excision repair, TDG removes thymine from mutagenic G ·: T mispairs caused by 5-methylcytosine (mC) deamination and other lesions including uracil (U) and 5-hydroxymethyluracil (hmU). In DNA demethylation, TDG excises 5-formylcytosine (fC) and 5-carboxylcytosine (caC), which are generated from mC by Tet (ten-eleven translocation) enzymes. Using improved crystallization conditions, we solved high-resolution (up to 1.45 Å) structures of TDG enzyme-product complexes generated from substrates including G·U, G·T, G·hmU, G·fC and G·caC. The structures reveal many new features, including key water-mediated enzyme-substrate interactions. Together with nuclear magnetic resonance experiments, the structures demonstrate that TDG releases the excised base from its tight product complex with abasic DNA, contrary to previous reports. Moreover, DNA-free TDG exhibits no significant binding to free nucleobases (U, T, hmU), indicating a Kd > 10 mM. The structures reveal a solvent-filled channel to the active site, which might facilitate dissociation of the excised base and enable caC excision, which involves solvent-mediated acid catalysis. Dissociation of the excised base allows TDG to bind the beta rather than the alpha anomer of the abasic sugar, which might stabilize the enzyme-product complex. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. A dimeric sesquiterpene, gochnatiolide A

    Directory of Open Access Journals (Sweden)

    Hui-Ping Xiong

    2009-11-01

    Full Text Available The title compound [systematic name: 5′a-hydroxy-1′,3,6,8′-tetrakis(methylene-3a,4,5,5′,5′a,6,6′,6a,7,7′,7′a,8′,9a,9b,10′a,10′b-hexadecahydrospiro[azuleno[4,5-b]furan-9(2H,3′-[3H]benz[1,8]azuleno[4,5-b]furan]-2,2′,8,9′(1′H,3H,4′H-tetrone acetone 0.92-solvate], C30H30O7·0.92C3H6O, is a dimeric sequiterpene formed by a cyclohexane system connecting two monomeric sesquiterpene lactone units of dehydrozaluzanin C. It was isolated from Ainsliaea henryi.

  7. Quantum dimer model for the pseudogap metal.

    Science.gov (United States)

    Punk, Matthias; Allais, Andrea; Sachdev, Subir

    2015-08-04

    We propose a quantum dimer model for the metallic state of the hole-doped cuprates at low hole density, p. The Hilbert space is spanned by spinless, neutral, bosonic dimers and spin S = 1/2, charge +e fermionic dimers. The model realizes a "fractionalized Fermi liquid" with no symmetry breaking and small hole pocket Fermi surfaces enclosing a total area determined by p. Exact diagonalization, on lattices of sizes up to 8 × 8, shows anisotropic quasiparticle residue around the pocket Fermi surfaces. We discuss the relationship to experiments.

  8. Antineoplastic Agents 582. Isolation and Structure of a Cyclobutane-type Sesquiterpene Cancer Cell Growth Inhibitor from Coprinus cinereus (Coprinaceae)‡

    Science.gov (United States)

    Pettit, George R.; Meng, Yanhui; Pettit, Robin K.; Herald, Delbert L.; Hogan, Fiona; Cichacz, Zbigniew A.

    2010-01-01

    Bioassay-guided (murine P388 lymphocytic leukemia and human cancer cell lines) separation of an ethyl acetate extract prepared from the inky cap fungus Coprinus cinereus led to the isolation of three new sesquiterpenes, 7,7a-diepicoprinastatin 1 (1), 14-hydroxy-5-desoxy-2S,3S,9R-illudosin (2), and 4,5-dehydro-5-deoxyarmillol (3), together with the known armillol (4). The structure and relative configuration of 1 was determined by single-crystal X-ray diffraction experiments. The structures of compounds 2, 3, and 4 were each deduced by a combination of HRMS and 1D and 2D NMR techniques. Cyclobutane 2 led to modest inhibition of the murine P388 leukemia cell line. PMID:20598551

  9. Antineoplastic agents 582. Part 1: Isolation and structure of a cyclobutane-type sesquiterpene cancer cell growth inhibitor from Coprinus cinereus (Coprinaceae).

    Science.gov (United States)

    Pettit, George R; Meng, Yanhui; Pettit, Robin K; Herald, Delbert L; Hogan, Fiona; Cichacz, Zbigniew A

    2010-07-15

    Bioassay-guided (murine P388 lymphocytic leukemia and human cancer cell lines) separation of an ethyl acetate extract prepared from the inky cap fungus Coprinus cinereus led to the isolation of three new sesquiterpenes, 7,7a-diepicoprinastatin 1 (1), 14-hydroxy-5-desoxy-2S,3S,9R-illudosin (2), and 4,5-dehydro-5-deoxyarmillol (3), together with the known armillol (4). The structure and relative configuration of 1 was determined by single-crystal X-ray diffraction experiments. The structures of compounds 2, 3, and 4 were each deduced by a combination of HRMS and 1D and 2D NMR techniques. Cyclobutane 2 led to modest inhibition of the murine P388 leukemia cell line.

  10. Chiral Cyclobutane β-Amino Acid-Based Amphiphiles: Influence of Cis/Trans Stereochemistry on Solution Self-Aggregation and Recognition.

    Science.gov (United States)

    Sorrenti, Alessandro; Illa, Ona; Pons, Ramon; Ortuño, Rosa M

    2015-09-08

    Novel diastereomeric anionic amphiphiles based on the rigid cyclobutane β-amino acid scaffold have been synthesized and deeply investigated with the aim of generating new functional supramolecular architectures on the basis of the rational design of original amphiphilic molecules and the control of their self-assembly. The main interest has been focused on the effect that cis/trans stereochemistry exerts on their molecular organization and recognition. In diluted solutions, the relative stereochemistry mainly influences the headgroup solvation and anionic-charge stabilization, i.e., better stabilized in the cis diastereoisomer due to intramolecular hydrogen-bonding and/or charge-dipole interactions. This provokes differences in their physicochemical behavior (pKa, cmc, conductivity) as well as in the structural parameters of the spherical micelles formed. Although both diastereoisomers form fibers that evolve with time from the spherical micelles, they display markedly different morphology and kinetics of formation. In the lyotropic liquid crystal domain, the greatest differences are observed at the highest concentrations and can be ascribed to different hydrogen-bonding and molecular packing imposed by the stereochemical constraints. Remarkably, the spherical micelles of the two anionic surfactants show dramatically diverse enantioselection ability for bilirubin enantiomers. In addition, both the surfactants form heteroaggregates with bilirubin at submicellar concentrations but with a different expression of supramolecular chirality. This points out that the unlike relative configuration of the two surfactants influences their chiral recognition ability as well as the fashion in which chirality is expressed at the supramolecular level by controlling the molecular organization in both micellar aggregates and surfactant/bilirubin heteroaggregates. All these differential features can be appropriate and useful for the design and development of new soft materials with

  11. The Ultraviolet Photochemistry and Photobiology of Vegetative Cells and Spores of Bacillus megaterium

    Science.gov (United States)

    Donnellan, J. E.; Stafford, R. S.

    1968-01-01

    The ultraviolet (UV) photochemistry and photobiology of spores and vegetative cells of Bacillus megaterium have been studied. The response of vegetative cells of B. megaterium appears qualitatively similar to those of Escherichia coli, Micrococcus radiodurans, and Bacillus subtilis with respect to photoproduct formation and repair mechanisms. UV irradiation, however, does not produce cyclobutane-type thymine dimers in the DNA of spores, although other thymine photo-products are produced. The photoproducts do not disappear after photoreactivation, but they are eliminated from the DNA by a dark-repair mechanism different from that found for dimers in vegetative cells. Irradiations performed at three wavelengths produce the same amounts of spore photoproduct and give the same survival curves. Variation of the sporulation medium before irradiation results in comparable alterations in the rate of spore photoproduct production and in survival. PMID:4966691

  12. Synthesis of new dimeric carvacrol compounds

    Directory of Open Access Journals (Sweden)

    Uttam B. More

    2008-12-01

    Full Text Available The polymer supported carvacrol anion was reacted with 1,2-dibromoethane, 1,4-dibromoethane, oxalyl dichloride, malonyl dichloride, succinyl dichloride, glutaroyl dichloride, and adipoyl dichloride to afford the corresponding dimeric carvacryl ethers or esters

  13. Formation of cystine slipknots in dimeric proteins.

    Directory of Open Access Journals (Sweden)

    Mateusz Sikora

    Full Text Available We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher.

  14. Bioactive dimeric carbazole alkaloids from Murraya koenigii.

    Science.gov (United States)

    Uvarani, Chokkalingam; Sankaran, Mathan; Jaivel, Nanjundan; Chandraprakash, Kumarasamy; Ata, Athar; Mohan, Palathurai S

    2013-06-28

    Phytochemical studies on the CHCl3 extract of the fruit pulp of Murraya koenigii afforded three new dimeric carbazole alkaloids, bisgerayafolines A-C (1-3). Bisgerayafolines A-C (1-3) are structurally unique dimeric carbazole alkaloids comprising geranyl moieties incorporated in their structures. Compounds 1-3 exhibited various levels of antioxidant, anti-α-glucosidase, DNA binding, and cytotoxic activities and protein interactions.

  15. Methyl groups of thymine bases are important for nucleic acid recognition by DtxR.

    Science.gov (United States)

    Chen, C S; White, A; Love, J; Murphy, J R; Ringe, D

    2000-08-29

    The expression of diphtheria toxin is controlled by the diphtheria toxin repressor (DtxR). Under conditions of high iron concentration, DtxR binds the tox operator to inhibit transcription. To study how DNA binding specificity is achieved by this repressor, we solved the crystal structure of the nickel(II) activated DtxR(C102D) mutant complexed with a 43mer DNA duplex containing the DtxR consensus binding sequence. Structural analysis of this complex and comparison with a previously determined DtxR(C102D)-Ni(II)-tox operator ternary complex revealed unusual van der Waals interactions between Ser37/Pro39 of the repressor helix-turn-helix (HTH) motif and the methyl groups of specific thymine bases in the consensus binding sequence. Gel mobility shift assays utilizing deoxyuridine modified duplex DNA probes proved the importance of these interactions: the four methyl groups shown to interact with Ser37/Pro39 in the crystal structure contribute a total of 3.4 kcal/mol to binding energy. Thus, in addition to making base-specific hydrogen-bonding interactions to the DNA through its Gln43 residue, DtxR also recognizes methyl groups at certain positions in the DNA sequence with its Ser37 and Pro39 side chains, to achieve binding specificity toward its cognate operator sequences.

  16. Thymine DNA Glycosylase Gene Knockdown Can Affect the Differentiation of Pig Preadipocytes

    Directory of Open Access Journals (Sweden)

    Lian-Jiang Zhang

    2016-08-01

    Full Text Available Aims: To study the effect of thymine DNA glycosylase (TDG gene knockdown on the differentiation of pig preadipocytes. Methods: Preadipocytes were obtained from subcutaneous adipose tissue from the neck of 1- to 7-day-old pigs. The TDG gene was knocked down using siRNA, and cell differentiation was induced. The mRNA expression level was measured using fluorescence quantitative PCR, and the protein expression level was determined using Western blot analysis. The DNA methylation levels in promoter regions of differentiation-related genes were also evaluated. Results: TDG gene knockdown decreased the mRNA expression levels of the peroxisome proliferator-activated receptorγ (PPARγ and Fatty acid binding proteins 4(FABP4 Also known as aP2 genes (PP>0.05. In addition, after induced differentiation, the lipid droplet production significantly decreased, and the percentages of methylation in the promoter regions of C/EBPα, PPARγ, and aP2 genes were 0.9%, 80%, and 76%, respectively. In contrast, the percentages of methylation in the negative control groups were 0.5%, 67.5%, and 58%, respectively. Conclusion: TDG gene knockdown could inhibit the differentiation of pig preadipocytes and affect the DNA methylation levels of some transcription factors.

  17. DNA Bases Thymine and Adenine in Bio-Organic Light Emitting Diodes

    Science.gov (United States)

    Gomez, Eliot F.; Venkatraman, Vishak; Grote, James G.; Steckl, Andrew J.

    2014-11-01

    We report on the use of nucleic acid bases (NBs) in organic light emitting diodes (OLEDs). NBs are small molecules that are the basic building blocks of the larger DNA polymer. NBs readily thermally evaporate and integrate well into the vacuum deposited OLED fabrication. Adenine (A) and thymine (T) were deposited as electron-blocking/hole-transport layers (EBL/HTL) that resulted in increases in performance over the reference OLED containing the standard EBL material NPB. A-based OLEDs reached a peak current efficiency and luminance performance of 48 cd/A and 93,000 cd/m2, respectively, while T-based OLEDs had a maximum of 76 cd/A and 132,000 cd/m2. By comparison, the reference OLED yielded 37 cd/A and 113,000 cd/m2. The enhanced performance of T-based devices is attributed to a combination of energy levels and structured surface morphology that causes more efficient and controlled hole current transport to the emitting layer.

  18. Role of loop residues and cations on the formation and stability of dimeric DNA G-quadruplexes.

    Science.gov (United States)

    Cevec, Mirko; Plavec, Janez

    2005-11-22

    Formation of guanine-quadruplexes by four DNA oligonucleotides with common sequence dG4-loop-dG4 has been studied by a combination of NMR and UV spectroscopy. The loops consisted of 1',2'-dideoxyribose, propanediol, hexaethylene glycol, and thymine residues. The comparison of data on modified and parent oligonucleotides gave insight into the role of loop residues on formation and stability of dimeric G-quadruplexes. All modified oligonucleotides fold into dimeric fold-back G-quadruplexes in the presence of sodium ions. Multiple structures form in the presence of potassium and ammonium ions, which is in contrast to the parent oligonucleotide with dT4 loop. 15N-filtered 1H NMR spectra demonstrate that all studied G-quadruplexes exhibit three 15NH4(+) ion binding sites. Topology of intermolecular G-quadruplexes was evaluated by NMR measurements and diffusion experiments. The spherical, prolate-ellipsoid and symmetric cylinder models were used to interpret experimental translational diffusion constants in terms of diameters and lengths of unfolded oligonucleotides and their respective G-quadruplexes. UV melting and annealing curves show that oligonucleotides with non-nucleosidic loop residues fold faster, exhibit no hysteresis, and are less stable than dimeric d(G4T4G4)2 which can be attributed to the absence of H-bonds, stacking between loop residues and the outer G-quartets as well as cation-pi interactions. Oligonucleotide consisting of hexaethylene glycol linkage with only two phosphate groups in the loop exhibits higher melting temperature and more negative deltaH(o) and deltaG(o) values than oligonucleotides with four 1',2'-dideoxyribose or propanediol residues.

  19. D-dimers (DD) in CVST.

    Science.gov (United States)

    Wang, Hui Fang; Pu, Chuan Qiang; Yin, Xi; Tian, Cheng Lin; Chen, Ting; Guo, Jun Hong; Shi, Qiang

    2017-06-01

    We were interested in further confirming whether D-dimers (DD) are indeed elevated in cerebral venous sinus thrombosis (CVST) as reported in those studies. CVST patients who had a plasma D-dimer test (139 cases) were included and divided into two groups: elevated D-dimer group (EDG) (>0.5 μg/mL; 65 cases) and normal D-dimer group (NDG) (≤0.5 μg/mL; 74 cases). The two groups were compared in terms of demographic data, clinical manifestation, laboratory and imaging data, using inferential statistical methods. The chi-squared and Fisher exact test showed that, compared to the NDG (74 cases), patients with elevated D-dimer levels were more likely to have a shorter symptom duration (SD) (30 ± 83.9 versus 90 ± 58.9 d, p = 0.003), more risk factors (75.4% versus 52.7%, p = 0.006), higher multiple venous sinus involvement (75.4% versus 59.5%, p = 0.037), increased fibrinogen (43.1% versus 18.9%, p = 0.037) and higher levels of blood glucose (18.3% versus 11%, p = 0.037). According to correlation analyses, D-dimer levels were positively correlated with number of venous sinuses involvement (NVS) (r = 0.321, p = 0.009) in the EDG. Multivariate logistic regression analysis showed that SD (OR, 0.025; 95% CI, 1.324-6.043; p = 0.000), NVS (OR, 1.573; 95% CI, 1.15-2.151; p = 0.005) and risk factors (OR, 3.321; 95% CI, 1.451-7.564; p = 0.004) were significantly different between the two groups. D-dimer is elevated in patients with acute/subacute CVST.

  20. Calix[4]arene supported clusters: a dimer of [Mn(III)Mn(II)] dimers

    DEFF Research Database (Denmark)

    Taylor, Stephanie M; McIntosh, Ruaraidh D; Beavers, Christine M

    2011-01-01

    Phosphinate ligands allow for the transformation of a calix[4]arene supported [Mn(III)(2)Mn(II)(2)] tetramer cluster motif into an unusual [Mn(III)Mn(II)](2) dimer of dimers; the clusters self-assemble in the crystal to form bi-layer arrays reminiscent of the typical packing of calixarene solvates....

  1. Early Events of DNA Photodamage

    Science.gov (United States)

    Schreier, Wolfgang J.; Gilch, Peter; Zinth, Wolfgang

    2015-04-01

    Ultraviolet (UV) radiation is a leading external hazard to the integrity of DNA. Exposure to UV radiation triggers a cascade of chemical reactions, and many molecular products (photolesions) have been isolated that are potentially dangerous for the cellular system. The early steps that take place after UV absorption by DNA have been studied by ultrafast spectroscopy. The review focuses on the evolution of excited electronic states, the formation of photolesions, and processes suppressing their formation. Emphasis is placed on lesions involving two thymine bases, such as the cyclobutane pyrimidine dimer, the (6-4) lesion, and its Dewar valence isomer.

  2. Adsorption of adenine and thymine on zeolites: FT-IR and EPR spectroscopy and X-ray diffractometry and SEM studies.

    Science.gov (United States)

    Baú, João Paulo T; Carneiro, Cristine E A; de Souza Junior, Ivan G; de Souza, Cláudio M D; da Costa, Antonio C S; di Mauro, Eduardo; Zaia, Cássia T B V; Coronas, Joaquin; Casado, Clara; de Santana, Henrique; Zaia, Dimas A M

    2012-02-01

    The interactions of adenine and thymine with and adsorption on zeolites were studied using different techniques. There were two main findings. First, as shown by X-ray diffractometry, thymine increased the decomposition of the zeolites (Y, ZSM-5) while adenine prevented it. Second, zeolite Y adsorbed almost the same amount of adenine and thymine, thus both nucleic acid bases could be protected from hydrolysis and UV radiation and could be available for molecular evolution. The X-ray diffractometry and SEM showed that artificial seawater almost dissolved zeolite A. The adsorption of adenine on ZSM-5 zeolite was higher than that of thymine (Student-Newman-Keuls test-SNK pzeolite, when compared to other zeolites (SNK pzeolites was not statistically different (SNK p>0.05). The adsorption of adenine and thymine on zeolites did not depend on pore size or Si/Al ratio and it was not explained only by electrostatic forces; rather van der Waals interactions should also be considered.

  3. Dynamic interplay between adhesive and lateral E-cadherin dimers

    DEFF Research Database (Denmark)

    Klingelhöfer, Jörg; Laur, Oscar Y; Troyanovsky, Regina B

    2002-01-01

    E-cadherin, an adhesive transmembrane protein of epithelial adherens junctions, forms two types of detergent-resistant dimers: adhesive dimers consisting of cadherin molecules derived from two neighboring cells and lateral dimers incorporating cadherins of the same cell. Both dimers depend...... on the integrity of the same residue, Trp156. While the relative amounts of these complexes are not certain, we show here that in epithelial A-431 cells, adhesive dimers may be a prevalent form. Inactivation of the calcium-binding sites, located between successive cadherin ectodomains, drastically reduced...... the amount of adhesive dimers and concomitantly increased the amount of lateral dimers. A similar interdependence of adhesive and lateral dimers was observed in digitonin-permeabilized cells. In these cells, adhesive dimers immediately disassembled after lowering the Ca2+ concentration below 0.1 m...

  4. Structure of active dimeric human telomerase.

    Science.gov (United States)

    Sauerwald, Anselm; Sandin, Sara; Cristofari, Gaël; Scheres, Sjors H W; Lingner, Joachim; Rhodes, Daniela

    2013-04-01

    Telomerase contains a large RNA subunit, TER, and a protein catalytic subunit, TERT. Whether telomerase functions as a monomer or dimer has been a matter of debate. Here we report biochemical and labeling data that show that in vivo-assembled human telomerase contains two TERT subunits and binds two telomeric DNA substrates. Notably, catalytic activity requires both TERT active sites to be functional, which demonstrates that human telomerase functions as a dimer. We also present the three-dimensional structure of the active full-length human telomerase dimer, determined by single-particle EM in negative stain. Telomerase has a bilobal architecture with the two monomers linked by a flexible interface. The monomer reconstruction at 23-Å resolution and fitting of the atomic structure of the TERT subunit from beetle Tribolium castaneum into the EM density reveals the spatial relationship between RNA and protein subunits, providing insights into telomerase architecture.

  5. Photoionization of helium dimers; Photoionisation von Heliumdimeren

    Energy Technology Data Exchange (ETDEWEB)

    Havermeier, Tilo

    2010-06-09

    The helium dimer is one of the most weakly bound systems in the universe. This makes it an interesting quantum mechanical object for investigation. These Van der Waals Clusters can be produced in an expansion of a cryogenic gas jet through a small nozzle into vacuum. In the present experiment we examine the interaction of He dimers with synchrotron radiation at an energy range from 64 to 78 eV. We observed different pathways leading to single ionization of both He atoms of the dimer compound. This two close standing ions begin now to dissociate in cause of their coulomb potential. All charged fragments were detected in coincidence with a COLTRIMS system. Especially Interatomic Coulombic Decay (ICD) and the two step process (TS1) were clearly identified. Furthermore a distribution of the internuclear distance was obtained from the measured Kinetic Energy Release (KER). (orig.)

  6. End binding proteins are obligatory dimers.

    Directory of Open Access Journals (Sweden)

    Indrani Sen

    Full Text Available End binding (EB proteins are responsible for the recruitment of an array of microtubule plus-end tracking proteins (+TIPs to growing microtubules ends. EBs encompass an N-terminal calponin homology domain that confers microtubule tip tracking activity to the protein. The C-terminal domain of EBs contains a coiled coil that mediates the parallel dimerization of EB monomers. This part of the protein is also responsible for partner binding. While dimerization is not essential for microtubule tip tracking by EBs it is a prerequisite for +TIP partner binding. The concentration of EBs in cells has been estimated to be in the range of hundreds of nanomoles. In contrast, in in vitro single molecule experiments EB concentrations of subnanomoles are employed. From a mechanistic point of view it is important to assess the oligomerization state of EBs at physiologically and experimentally relevant protein concentrations, in particular if the goal of a study is to model the behavior of EB-dependent dynamic +TIP networks. Here we have determined the stability of the EB1 and EB3 dimers using multi-angle light scattering and fluorescence analytical ultracentrifugation. We show that these EBs form stable dimers and do not dissociate even at very low nanomolar concentrations. The dimers remained stable at both room temperature as well as at the physiologically relevant temperature of 37°C. Together, our results reveal that EBs are obligatory dimers, a conclusion that has implications for the mechanistic understanding of these key proteins involved in the orchestration of dynamic protein networks at growing microtubule ends.

  7. Synthesis of Methoxyethyl Nucleoside Dimer Phosphoramidates

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Gi Weon; Kang, Yong Han [Hanyang University, Ansan (Korea, Republic of)

    2016-05-15

    Four types of methoxyethyl (MOE) nucleoside phosphoramidites, which are categorized as second-generation building blocks of antisense oligonucleotide drugs, were synthesized. Also, three types of MOE nucleoside dimer phosphoramidites were synthesized to increase the efficiency and oligomer purity in solid phase synthesis. The block-like dimer phosphoramidites can prevent or minimize the formation of the (N-1) mer impurity, thereby affording the fabrication of pure oligonucleotides and reducing the synthesis time by performing coupling reactions in the order of 2 + 2 + 2.

  8. A Novel Dimer of α-Tocopherol

    Directory of Open Access Journals (Sweden)

    Anjan Patel

    2008-01-01

    Full Text Available Decomposition of the complex 4, formed between the α-tocopherol ortho-quinone methide (2 and NMMO, by fast heating from −78∘C to 70∘C in inert solvents produces a novel α-tocopherol dimer with 6H,12H-dibenzo[b,f][1,5]dioxocine structure (5 which—in contrast to the well-known spiro-dimer of α-tocopherol (3—is symmetrical. This is the first example of a direct reaction of the highly transient zwitterionic, aromatic precursor 2a in the formation of the ortho-quinone methide 2.

  9. Theoretical investigation on hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

    Science.gov (United States)

    Anithaa, V S; Vijayakumar, S; Sudha, M; Shankar, R

    2017-11-06

    The interaction of diketo and keto-enol form of thymine and uracil tautomers with acridine (Acr), phenazine (Phen), benzo[c]cinnoline (Ben), 1,10-phenanthroline (1,10-Phe), and 4,7-phenenthroline (4,7-Phe) intercalating drug molecules was studied using density functional theory at B3LYP/6-311++G** and M05-2×/6-311++G** levels of theory. From the interaction energy, it is found that keto-enol form tautomers have stronger interaction with intercalators than diketone form tautomers. On complex formation of thymine and uracil tautomers with benzo[c]cinnoline the drug molecules have high interaction energy values of -20.14 (BenT3) and -20.55 (BenU3) kcal mol-1, while phenazine has the least interaction energy values of -6.52 (PhenT2) and -6.67 (PhenU2) kcal mol-1. The closed shell intermolecular type interaction between the molecules with minimum elliptical value of 0.018 and 0.019 a.u at both levels of theory has been found from topological analysis. The benzo[c]cinnoline drug molecule with thymine and uracil tautomers has short range intermolecular N-H…N, C-H…O, and O-H...N hydrogen bonds (H-bonds) resulting in higher stability than other drug molecules. The proper hydrogen bonds N-H..N and O-H..N have the frequency shifted toward the lower side (red shifted) with the elongation in their bond length while the improper hydrogen bond C-H...O has the frequency shifted toward the higher side (blue shifted) of the spectral region with the contraction in their bond length. Further, the charge transfer between proton acceptor and donor along with stability of the bond is studied using natural bond orbital (NBO) analysis. Graphical abstract Hydrogen bond interaction of diketo/keto-enol form uracil and thymine tautomers with intercalators.

  10. {5'-O-[Bis(4-methoxyphenyl)(phenyl)methyl]-2'-deoxy-β-D-threopentofuranosyl}thymine ethyl acetate 0.25-solvate.

    Science.gov (United States)

    Zou, Pei; Wu, Hao; Liu, Yaling; Xie, Minhao; Wang, Hongyong

    2012-11-01

    The title compound, C(31)H(32)N(2)O(7)·0.25C(4)H(8)O(2), is a key intermediate in the synthesis of [(18)F]fluorine-labelled thymidine ((18)F-FLT), which is the most widely used molecular imaging probe for positron emission tomography (PET). The crystallographic asymmetric unit contains two independent thymine molecules plus one partially occupied site for an ethyl acetate molecule. The two independent thymine molecules show similar geometrical features, except that the dimethoxytrityl groups adopt different orientations with respect to the remainder of the molecule. Each thymine base adopts an anti conformation with respect to the attached deoxyribose ring, and the deoxyribose rings show C3-endo puckering. The conformation of the side chain at the C1 position of the deoxyribose ring is gauche+. Intermolecular N-H···O and O-H···O hydrogen bonds link the molecules into one-dimensional chains.

  11. (Cyclobutane-1,1-dicarboxylato-κ2O,O′(1,10-phenanthroline-κ2N,N′platinum(II dihydrate

    Directory of Open Access Journals (Sweden)

    Pavel Štarha

    2013-06-01

    Full Text Available The title compound, [Pt(C6H6O4(C12H8N2]·2H2O, which crystallizes as two independent formula units, has the metal atom in a square-planar geometry defined by two O atoms of the chelating cyclobutane-1,1-dicarboxylate dianion and two N atoms of the chelating 1,10-phenanthroline molecule (r.m.s. deviations of the PtO2N2 units = 0.026 and 0.026 Å. Adjacent complex and water molecules are connected through intermolecular O—H...O hydrogen bonds and C—H...O, C...O [shortest C...O distance = 3.140 (5 Å], π–π [shortest C...C distances = 3.234 (6 and 3.347 (6 Å] and Pt...π [shortest Pt...C distance = 3.358 (4 Å] interactions into a three-dimensional network.

  12. cGAS dimerization entangles DNA recognition.

    Science.gov (United States)

    Kranzusch, Philip J; Vance, Russell E

    2013-12-12

    Detection of foreign DNA in the cell cytosol triggers potent antiviral responses. In this issue of Immunity, Li et al. (2013) provide new structural and biochemical data indicating that a cytosolic DNA sensor, cyclic GMP-AMP synthase (cGAS), is activated by DNA-induced dimerization. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Ligand regulation of a constitutively dimeric EGF receptor

    Science.gov (United States)

    Freed, Daniel M.; Alvarado, Diego; Lemmon, Mark A.

    2015-06-01

    Ligand-induced receptor dimerization has traditionally been viewed as the key event in transmembrane signalling by epidermal growth factor receptors (EGFRs). Here we show that the Caenorhabditis elegans EGFR orthologue LET-23 is constitutively dimeric, yet responds to its ligand LIN-3 without changing oligomerization state. SAXS and mutational analyses further reveal that the preformed dimer of the LET-23 extracellular region is mediated by its domain II dimerization arm and resembles other EGFR extracellular dimers seen in structural studies. Binding of LIN-3 induces only minor structural rearrangements in the LET-23 dimer to promote signalling. Our results therefore argue that EGFR can be regulated by allosteric changes within an existing receptor dimer--resembling signalling by insulin receptor family members, which share similar extracellular domain compositions but form covalent dimers.

  14. Universal bosonic tetramers of dimer-atom-atom structure

    OpenAIRE

    Deltuva, A.

    2012-01-01

    Unstable four-boson states having an approximate dimer-atom-atom structure are studied using momentum-space integral equations for the four-particle transition operators. For a given Efimov trimer the universal properties of the lowest associated tetramer are determined. The impact of this tetramer on the atom-trimer and dimer-dimer collisions is analyzed. The reliability of the three-body dimer-atom-atom model is studied.

  15. Optimization of Environmentally Benign Polymers Based on Thymine and Polyvinyl Sulfonate Using Plackett-Burman Design and Surface Response

    Directory of Open Access Journals (Sweden)

    Julieta Ledesma

    2013-01-01

    Full Text Available Traditional approaches to the development of integrated circuits involve the use and/or manufacture of toxic materials that have a potential environmental impact. An extensive research has been done to design environmentally benign synthetic polymers containing nucleic acid bases, which can be used to enhance the photoresistor technologies. Water soluble, environmentally benign photopolymers of 1-(4-vinylbenzyl thymine (VBT and vinylphenyl sufonate (VPS undergo a photodimerization reaction when exposed to low levels of ultraviolet irradiation leading to an immobilization of the copolymer on a variety of substrates. Plackett-Burman design (PBD and central composite design (CCD were applied to identify the significant factors influencing the polymer crosslinking and dye adsorption processes, which are relevant in the fabrication of copolymer films for potential photoresist use. The PBD results assigned a maximum absorption signal of 0.67, while optimal conditions obtained in this experiment following the CCD method predictions provided a response of 0.83 ± 0.03, being a solid foundation for further use of this methodology in the production of potential photoresistors. The pH effect was relevant for low concentrations but not significant for higher concentrations. To the best of our knowledge, this was the first report applying statistical experimental designs to optimize the crosslinking of thymine-based polymers.

  16. Ultraviolet Spectrum And Chemical Reactivity Of CIO Dimer

    Science.gov (United States)

    Demore, William B.; Tschuikow-Roux, E.

    1992-01-01

    Report describes experimental study of ultraviolet spectrum and chemical reactivity of dimer of chlorine monoxide (CIO). Objectives are to measure absorption cross sections of dimer at near-ultraviolet wavelengths; determine whether asymmetrical isomer (CIOCIO) exists at temperatures relevant to Antarctic stratosphere; and test for certain chemical reactions of dimer. Important in photochemistry of Antarctic stratosphere.

  17. Determination of the Tetramer-Dimer Equilibrium Constant of Rabbit ...

    African Journals Online (AJOL)

    Hemoglobin is a tetrameric protein which is able to dissociate into dimers. The dimers can in turn dissociate into tetramers. It has been found that dimers are more reactive than tetramers. The difference in the reactivity of these two species has been used to determine the tetramerdimer dissociation constant of various ...

  18. 21 CFR 176.120 - Alkyl ketene dimers.

    Science.gov (United States)

    2010-04-01

    ... Use Only as Components of Paper and Paperboard § 176.120 Alkyl ketene dimers. Alkyl ketene dimers may... section. (a) The alkyl ketene dimers are manufactured by the dehydrohalogenation of the acyl halides... an adjuvant in the manufacture of paper and paperboard under such conditions that the alkyl ketene...

  19. Measurement of pyrimidine dimers in spheroplasts of Bacillus subtilis

    Energy Technology Data Exchange (ETDEWEB)

    Hadden, C.T.

    1979-01-01

    A method is described for making spheroplasts of Bacillus subtilis which are permeable to exogenous enzymes. Conditions are described for measuring small numbers of pyrimidine dimers in the DNA of uv-irradiated cells by use of a partially purified Micrococcus luteus extract containing an enzyme specific for pyrimidine dimers. The system will detect as few as 10 to 12 pyrimidine dimers per genome.

  20. Plasmonic rod dimers as elementary planar chiral meta-atoms

    CERN Document Server

    Zhukovsky, Sergei V; Chigrin, Dmitry N

    2011-01-01

    Electromagnetic response of metallic rod dimers is theoretically calculated for arbitrary planar arrangement of rods in the dimer. It is shown that dimers without an in-plane symmetry axis exhibit elliptical dichroism and act as "atoms" in planar chiral metamaterials. Due to a very simple geometry of the rod dimer, such planar metamaterials are much easier in fabrication than conventional split-ring or gammadion-type structures, and lend themselves to a simple analytical treatment based on coupled dipole model. Dependencies of metamaterial's directional asymmetry on the dimer's geometry are established analytically and confirmed in numerical simulations.

  1. A comparative study of the DG-OMEGA (DG Omega), DGII, and GAT method for the structure elucidation of a methylene-acetal linked thymine dinucleotide

    NARCIS (Netherlands)

    van Kampen, A. H. C.; Beckers, M. L. M.; Buydens, L. M. C.

    1997-01-01

    This research continues the investigation of the properties of the recently developed structure elucidation method DG-OMEGA (DG Omega). Towards this end it was applied for the structure determination of a methylene-acetal linked thymine dinucleotide. The performance of DG Omega was compared to the

  2. The direct observation of a psoralen-thymine UVA induced solid-state cycloaddition reaction product by single-crystal x-ray diffractometry.

    Science.gov (United States)

    Pfluger, C E; Ostrander, R L

    1989-04-01

    Single-crystal x-ray diffraction methods have been used to directly observe and simultaneously determine the molecular structure of the UVA induced cis-syn photocycloaddition product in a partially photolyzed single crystal of a psoralen(pyrone ring side)-DNA(thymine) interaction model compound, 1'-(8-oxypsoralen)-8'(thym-1"yl)3',6'-dioxaoctane.

  3. Revisiting the optical $PT$-symmetric dimer

    CERN Document Server

    Morales, J D Huerta; López-Aguayo, S; Rodríguez-Lara, B M

    2016-01-01

    Optics has proved a fertile ground for the experimental simulation of quantum mechanics. Most recently, optical realizations of $\\mathcal{PT}$-symmetric quantum mechanics have been shown, both theoretically and experimentally, opening the door to international efforts aiming at the design of practical optical devices exploiting this symmetry. Here, we focus on the optical $\\mathcal{PT}$-symmetric dimer, a two-waveguide coupler were the materials show symmetric effective gain and loss, and provide a review of the linear and nonlinear optical realizations from a symmetry based point of view. We go beyond a simple review of the literature and show that the dimer is just the smallest of a class of planar $N$-waveguide couplers that are the optical realization of Lorentz group in 2+1 dimensions. Furthermore, we provide a formulation to describe light propagation through waveguide couplers described by non-Hermitian mode coupling matrices based on a non-Hermitian generalization of Ehrenfest theorem.

  4. Revisiting the Optical PT-Symmetric Dimer

    Directory of Open Access Journals (Sweden)

    José Delfino Huerta Morales

    2016-08-01

    Full Text Available Optics has proved a fertile ground for the experimental simulation of quantum mechanics. Most recently, optical realizations of PT -symmetric quantum mechanics have been shown, both theoretically and experimentally, opening the door to international efforts aiming at the design of practical optical devices exploiting this symmetry. Here, we focus on the optical PT -symmetric dimer, a two-waveguide coupler where the materials show symmetric effective gain and loss, and provide a review of the linear and nonlinear optical realizations from a symmetry-based point of view. We go beyond a simple review of the literature and show that the dimer is just the smallest of a class of planar N-waveguide couplers that are the optical realization of the Lorentz group in 2 + 1 dimensions. Furthermore, we provide a formulation to describe light propagation through waveguide couplers described by non-Hermitian mode coupling matrices based on a non-Hermitian generalization of the Ehrenfest theorem.

  5. Fibrillar dimer formation of islet amyloid polypeptides

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, Chi-cheng [Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States); de Pablo, Juan J. [Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-05-08

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

  6. Noncovalent Interactions in the Catechol Dimer

    Directory of Open Access Journals (Sweden)

    Vincenzo Barone

    2017-09-01

    Full Text Available Noncovalent interactions play a significant role in a wide variety of biological processes and bio-inspired species. It is, therefore, important to have at hand suitable computational methods for their investigation. In this paper, we report on the contribution of dispersion and hydrogen bonds in both stacked and T-shaped catechol dimers, with the aim of delineating the respective role of these classes of interactions in determining the most stable structure. By using second-order Møller–Plesset (MP2 calculations with a small basis set, specifically optimized for these species, we have explored a number of significant sections of the interaction potential energy surface and found the most stable structures for the dimer, in good agreement with the highly accurate, but computationally more expensive coupled cluster single and double excitation and the perturbative triples (CCSD(T/CBS method.

  7. Palmitoylated APP Forms Dimers, Cleaved by BACE1.

    Directory of Open Access Journals (Sweden)

    Raja Bhattacharyya

    Full Text Available A major rate-limiting step for Aβ generation and deposition in Alzheimer's disease brains is BACE1-mediated cleavage (β-cleavage of the amyloid precursor protein (APP. We previously reported that APP undergoes palmitoylation at two cysteine residues (Cys186 and Cys187 in the E1-ectodomain. 8-10% of total APP is palmitoylated in vitro and in vivo. Palmitoylated APP (palAPP shows greater preference for β-cleavage than total APP in detergent resistant lipid rafts. Protein palmitoylation is known to promote protein dimerization. Since dimerization of APP at its E1-ectodomain results in elevated BACE1-mediated cleavage of APP, we have now investigated whether palmitoylation of APP affects its dimerization and whether this leads to elevated β-cleavage of the protein. Here we report that over 90% of palAPP is dimerized while only ~20% of total APP forms dimers. PalAPP-dimers are predominantly cis-oriented while total APP dimerizes in both cis- and trans-orientation. PalAPP forms dimers 4.5-times more efficiently than total APP. Overexpression of the palmitoylating enzymes DHHC7 and DHHC21 that increase palAPP levels and Aβ release, also increased APP dimerization in cells. Conversely, inhibition of APP palmitoylation by pharmacological inhibitors reduced APP-dimerization in coimmunoprecipitation and FLIM/FRET assays. Finally, in vitro BACE1-activity assays demonstrate that palmitoylation-dependent dimerization of APP promotes β-cleavage of APP in lipid-rich detergent resistant cell membranes (DRMs, when compared to total APP. Most importantly, generation of sAPPβ-sAPPβ dimers is dependent on APP-palmitoylation while total sAPPβ generation is not. Since BACE1 shows preference for palAPP dimers over total APP, palAPP dimers may serve as novel targets for effective β-cleavage inhibitors of APP as opposed to BACE1 inhibitors.

  8. 99mTc-thymine scintigraphy may be a promising method in the diagnosis of breast cancer

    Directory of Open Access Journals (Sweden)

    Monica Pires Ribeiro

    2013-01-01

    Full Text Available OBJECTIVE: Mammography has been established as the gold standard for the detection of breast cancer, and imaging techniques such as ultrasonography, magnetic resonance imaging, scintigraphy and positron emission tomography may be useful to improve its sensitivity and specificity. The objective of this study with breast scintigraphy was to evaluate the uptake of 99mTc-thymine in mammary lesions. METHODS: A total of 45 patients were included in this study. Thirty-three patients (73% were subjected to surgery or percutaneous biopsy, providing histopathological data. The other 12 patients who remained under surveillance received clinical examinations and biannual mammography with a normal follow-up of at least three years, the data from which were used for comparison with the scintimammography results. RESULTS: The majority of patients (64.4% had clinically impalpable lesions with a mammogram diagnosis of microcalcifications, impalpable nodules, or focal asymmetry. Of the studied lesions, 87% were smaller or equal to 20 mm in diameter, and 22% had malignant histopathological findings. Scintigraphy with 99mTc-thymine had a sensitivity of 70%, a specificity of 85.7%, positive and negative predictive values of 58.3% and 90.9%, respectively, and an accuracy of 82.2%. CONCLUSIONS: The results of this study are consistent with those previously reported by other authors. The good specificity and high negative predictive value of this technique and the absence of uptake in the heart indicate that it may be a promising complementary method in clinical practice and that it may contribute to reducing unnecessary benign biopsies.

  9. 99mTc-thymine scintigraphy may be a promising method in the diagnosis of breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Ribeiro, Monica Pires; Souza, Sergio Augusto Lopes de; Lopes, Flavia Paiva Proenca Lobo; Rosado-de-Castro, Paulo Henrique; Fonseca, Lea Mirian Barbosa da; Gutfilen, Bianca [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Faculdade de Medicina. Hospital Universitario Clementino Fraga Filho, Departamento de Radiologia

    2013-05-01

    Objective: Mammography has been established as the gold standard for the detection of breast cancer, and imaging techniques such as ultrasonography, magnetic resonance imaging, scintigraphy and positron emission tomography may be useful to improve its sensitivity and specificity. The objective of this study with breast scintigraphy was to evaluate the uptake of {sup 99m}Tc-thymine in mammary lesions. Methods: A total of 45 patients were included in this study. Thirty-three patients (73%) were subjected to surgery or percutaneous biopsy, providing histopathological data. The other 12 patients who remained under surveillance received clinical examinations and biannual mammography with a normal follow-up of at least three years, the data from which were used for comparison with the scintimammography results. Results: The majority of patients (64.4%) had clinically impalpable lesions with a mammogram diagnosis of microcalcifications, impalpable nodules, or focal asymmetry. Of the studied lesions, 87% were smaller or equal to 20 mm in diameter, and 22% had malignant histopathological findings. Scintigraphy with {sup 99m}Tc-thymine had a sensitivity of 70%, a specificity of 85.7%, positive and negative predictive values of 58.3% and 90.9%, respectively, and an accuracy of 82.2%. Conclusions: The results of this study are consistent with those previously reported by other authors. The good specificity and high negative predictive value of this technique and the absence of uptake in the heart indicate that it may be a promising complementary method in clinical practice and that it may contribute to reducing unnecessary benign biopsies. (author)

  10. A peroxide-bridged imidazole dimer formed from a photochromic naphthalene-bridged imidazole dimer.

    Science.gov (United States)

    Hatano, Sayaka; Abe, Jiro

    2012-04-28

    2,4,5-Triphenylimidazole (lophine) is known as the first chemiluminescence substrate, and its oxidized derivative, the 2,4,5-triphenylimidazolyl radical, corresponds to the coloured species in the photochromic reaction of hexaarylbiimidazole (HABI). We report the first direct observation of the O(2) adduct of the imidazolyl radical that forms the end-on peroxide-bridged imidazole dimer. The ring-opening reaction of the peroxide-bridged imidazole dimer leading to the formation of an N-benzoylbenzamidine derivative supports the presence of the 4,5-epidioxide of lophine as a reaction intermediate of its chemiluminescence. This journal is © the Owner Societies 2012

  11. Mutation of the little finger domain in human DNA polymerase η alters fidelity when copying undamaged DNA.

    Science.gov (United States)

    Beardslee, Renee A; Suarez, Samuel C; Toffton, Shannon M; McCulloch, Scott D

    2013-10-01

    DNA polymerase η (pol η) synthesizes past cyclobutane pyrimidine dimer and possibly 7,8-dihydro-8-oxoguanine (8-oxoG) lesions during DNA replication. Loss of pol η is associated with an increase in mutation rate, demonstrating its indispensable role in mutation suppression. It has been recently reported that β-strand 12 (amino acids 316-324) of the little finger region correctly positions the template strand with the catalytic core of the enzyme. The authors hypothesized that modification of β-strand 12 residues would disrupt correct enzyme-DNA alignment and alter pol η's activity and fidelity. To investigate this, the authors purified proteins containing the catalytic core of the polymerase, incorporated single amino acid changes to select β-strand 12 residues, and evaluated DNA synthesis activity for each pol η. Lesion bypass efficiencies and replication fidelities when copying DNA-containing cis-syn cyclobutane thymine-thymine dimer and 8-oxoG lesions were determined and compared with the corresponding values for the wild-type polymerase. The results confirm the importance of the β-strand in polymerase function and show that fidelity is most often altered when undamaged DNA is copied. Additionally, it is shown that DNA-protein contacts distal to the active site can significantly affect the fidelity of synthesis. Copyright © 2013 Wiley Periodicals, Inc.

  12. Dimeric assembly of enterocyte brush border enzymes

    DEFF Research Database (Denmark)

    Danielsen, E M

    1994-01-01

    The noncovalent, dimeric assembly of small intestinal brush border enzymes was studied by sedimentation analysis in density gradients of extracts of pulse-labeled pig jejunal mucosal explants. Like aminopeptidase N (EC 3.4.11.2), sucrase-isomaltase (EC 3.2.1.48-10), aminopeptidase A (EC 3...... appearance of the liposome-reconstituted enzyme [Norén et al. (1986) J. Biol. Chem. 261, 12306-12309], showing only the inner, membrane-anchored domains of the monomers to be in close contact with one another while the outer domains are far apart. In contrast to the other brush border enzymes studied...

  13. Novel covalently linked insulin dimer engineered to investigate the function of insulin dimerization

    DEFF Research Database (Denmark)

    Vinther, Tine N.; Norrman, Mathias; Strauss, Holger M.

    2012-01-01

    in the circulation, and it is stabilized by hexamer formation in the presence of zinc ions during storage in the pancreatic ß-cell. Due to the transient nature of insulin dimer, direct investigation of this important form is inherently difficult. To address the relationship between insulin oligomerization...

  14. Synthesis of dimeric lactose and dimeric (sialyl) Lewis(X) glycolipids.

    Science.gov (United States)

    Gege, Christian; Schmidt, Richard R

    2002-06-12

    To investigate structural requirements for the homophilic interaction between carbohydrates on planar model membranes, divalent derivatives with enforced proximity between the two carbohydrate epitopes (lactose, Lewis(X), and sialyl Lewis(X)) were synthesized by use of a dimeric membrane anchor as scaffold.

  15. Cytotoxic sesquiterpene lactone dimers isolated from Inula japonica.

    Science.gov (United States)

    Xu, Xing-Yu; Sun, Peng; Guo, De-An; Liu, Xuan; Liu, Jun-Hua; Hu, Li-Hong

    2015-03-01

    Two new sesquiterpene lactone dimers, neojaponicone B (1) and inulanolide E (2) along with five known sesquiterpene lactone dimers (3-7, resp.) were isolated from the aerial parts of Inula japonica Thunb. The chemical structures of 1 and 2 were elucidated by detailed spectroscopic analysis. The relative configuration of 2 was confirmed by biomimetic transformation from the known sesquiterpene lactone dimer inulanolide A (3). The cytotoxicities of the isolated sesquiterpene lactone dimers were evaluated against 6T-CEM and Jurkat cell lines. All compounds showed potent cytotoxicities with IC50 value of 2.2-5.9μm. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. The role of dimerization in prion replication.

    Science.gov (United States)

    Tompa, Peter; Tusnády, Gábor E; Friedrich, Peter; Simon, István

    2002-04-01

    The central theme in prion diseases is the conformational transition of a cellular protein from a physiologic to a pathologic (so-called scrapie) state. Currently, two alternative models exist for the mechanism of this autocatalytic process; in the template assistance model the prion is assumed to be a monomer of the scrapie conformer, whereas in the nucleated polymerization model it is thought to be an amyloid rod. A recent variation on the latter assumes disulfide reshuffling as the mechanism of polymerization. The existence of stable dimers, let alone their mechanistic role, is not taken into account in either of these models. In this paper we review evidence supporting that the dimerization of either the normal or the scrapie state, or both, has a decisive role in prion replication. The contribution of redox changes, i.e., the temporary opening and possible rearrangement of the intramolecular disulfide bridge is also considered. We present a model including these features largely ignored so far and show that it adheres satisfactorily to the observed phenomenology of prion replication.

  17. Modelling study of dimerization in mammalian defensins

    Directory of Open Access Journals (Sweden)

    Verma Chandra

    2006-12-01

    Full Text Available Abstract Background Defensins are antimicrobial peptides of innate immunity functioning by non-specific binding to anionic phospholipids in bacterial membranes. Their cationicity, amphipathicity and ability to oligomerize are considered key factors for their action. Based on structural information on human β-defensin 2, we examine homologous defensins from various mammalian species for conserved functional physico-chemical characteristics. Results Based on homology greater than 40%, structural models of 8 homologs of HBD-2 were constructed. A conserved pattern of electrostatics and dynamics was observed across 6 of the examined defensins; models backed by energetics suggest that the defensins in these 6 organisms are characterized by dimerization-linked enhanced functional potentials. In contrast, dimerization is not energetically favoured in the sheep, goat and mouse defensins, suggesting that they function efficiently as monomers. Conclusion β-defensin 2 from some mammals may work as monomers while those in others, including humans, work as oligomers. This could potentially be used to design human defensins that may be effective at lower concentrations and hence have therapeutic benefits.

  18. A retrospective evaluation of the age-adjusted D-dimer versus the conventional D-dimer for pulmonary embolism.

    Science.gov (United States)

    Sheele, Johnathan M; Tang, Annie; Farhan, Obada; Morris, Nathan

    2018-01-23

    : The conventional D-dimer cut-off value of at least 500 μg FEU/l has good sensitivity but poor specificity for identifying pulmonary embolism. An elevated age-adjusted D-dimer value (age in years × 10 μg FEU/l) for patients at least 50 years old has been recommended as a better cut-off with adequate sensitivity and improved specificity for identifying pulmonary embolism compared with the conventional value. We retrospectively reviewed 3117 patient encounters in which a D-dimer was ordered. The D-dimer value, age of the patient, and the computed tomography radiology report was evaluated. The sensitivity and specificity of the age-adjusted D-dimer was calculated using bootstrapping. With an assumed 99% sensitivity for the conventional D-dimer cut-off the specificity was 39.2% [95% confidence interval (CI): 37.5-41.0%]. The sensitivity of the age-adjusted D-dimer was 91.8% (95% CI: 83.8-97.2%) with a specificity of 51.0% (95% CI: 49.1-53.1%). The sensitivity of the age-adjusted D-dimer was unacceptably low compared with the conventional D-dimer cut-off.

  19. Rapid and ultrasensitive detection of microRNA by target-assisted isothermal exponential amplification coupled with poly (thymine)-templated fluorescent copper nanoparticles

    Science.gov (United States)

    Park, Kwan Woo; Batule, Bhagwan S.; Kang, Kyoung Suk; Park, Ki Soo; Park, Hyun Gyu

    2016-10-01

    We devised a novel method for rapid and ultrasensitive detection of target microRNA (miRNA) by employing target-assisted isothermal exponential amplification (TAIEA) combined with poly (thymine)-templated fluorescent copper nanoparticles (CuNPs) as signaling probes. The target miRNA hybridizes to the unimolecular template DNA and works as a primer for the extension reaction to form double-stranded product, which consequently generates two nicking endonuclease recognition sites. By simultaneous nicking and displacement reactions, exponential amplification generates many poly (thymine) strands as final products, which are employed for the synthesis of fluorescent CuNPs. Based on the fluorescent signal from CuNPs, target miRNA is detected as low as 0.27 fM around 1 h of total analysis time. The diagnostic capability of this system has been successfully demonstrated by reliably detecting target miRNA from different cell lysates, showing its great potential towards real clinical applications.

  20. Genes of the thymidine salvage pathway: thymine-7-hydroxylase from a Rhodotorula glutinis cDNA library and iso-orotate decarboxylase from Neurospora crassa.

    Science.gov (United States)

    Smiley, Jeffrey A; Kundracik, Melisa; Landfried, Daniel A; Barnes, Vincient R; Axhemi, Armend A

    2005-05-25

    Genes for two enzymes in the thymidine salvage pathway, thymine-7-hydroxylase (THase; official name thymine dioxygenase) and iso-orotate decarboxylase (IDCase) have been isolated from fungal sources. THase was isolated from a Rhodotorula glutinis cDNA library using a degenerate oligonucleotide based on the published amino acid sequence. The coding sequence was transferred to an Escherichia coli expression system, from which recombinant THase activity was measured using 14C-labeled thymine. The THase sequence shows an almost complete avoidance of codons ending in A or T: 95.8% GC content is present in the third position of codons. A connection between this codon bias and the role of the thymidine salvage pathway in pyrimidine metabolism is proposed. The THase sequence is similar to Group I Fe+2-dependent, alphaKG-dependent dioxygenases. The R. glutinis THase gene was used to locate the probable THase genes in the sequenced genomes of Neurospora crassa and Aspergillus nidulans. The genes neighboring THase in these two genomes are similar to each other, and are similar to the mammalian 2-amino-3-carboxymuconate-6-semialdhyde decarboxylase (ACMSD), leading to their identification as IDCase genes. The N. crassa version was isolated by PCR of genomic DNA, and IDCase activity was measured in recombinant E. coli carrying this gene. A new family of decarboxylases, using similar substrates, is identified by virtue of the protein sequence similarity.

  1. Disrupting Dimerization Translocates Soluble Epoxide Hydrolase to Peroxisomes.

    Directory of Open Access Journals (Sweden)

    Jonathan W Nelson

    Full Text Available The epoxyeicosatrienoic acid (EET neutralizing enzyme soluble epoxide hydrolase (sEH is a neuronal enzyme, which has been localized in both the cytosol and peroxisomes. The molecular basis for its dual localization remains unclear as sEH contains a functional peroxisomal targeting sequence (PTS. Recently, a missense polymorphism was identified in human sEH (R287Q that enhances its peroxisomal localization. This same polymorphism has also been shown to generate weaker sEH homo-dimers. Taken together, these observations suggest that dimerization may mask the sEH PTS and prevent peroxisome translocation. In the current study, we test the hypothesis that dimerization is a key regulator of sEH subcellular localization. Specifically, we altered the dimerization state of sEH by introducing substitutions in amino acids responsible for the dimer-stabilizing salt-bridge. Green Fluorescent Protein (GFP fusions of each of mutants were co-transfected into mouse primary cultured cortical neurons together with a PTS-linked red fluorescent protein to constitutively label peroxisomes. Labeled neurons were analyzed using confocal microscopy and co-localization of sEH with peroxisomes was quantified using Pearson's correlation coefficient. We find that dimer-competent sEH constructs preferentially localize to the cytosol, whereas constructs with weakened or disrupted dimerization were preferentially targeted to peroxisomes. We conclude that the sEH dimerization status is a key regulator of its peroxisomal localization.

  2. Disrupting Dimerization Translocates Soluble Epoxide Hydrolase to Peroxisomes.

    Science.gov (United States)

    Nelson, Jonathan W; Das, Anjali J; Barnes, Anthony P; Alkayed, Nabil J

    2016-01-01

    The epoxyeicosatrienoic acid (EET) neutralizing enzyme soluble epoxide hydrolase (sEH) is a neuronal enzyme, which has been localized in both the cytosol and peroxisomes. The molecular basis for its dual localization remains unclear as sEH contains a functional peroxisomal targeting sequence (PTS). Recently, a missense polymorphism was identified in human sEH (R287Q) that enhances its peroxisomal localization. This same polymorphism has also been shown to generate weaker sEH homo-dimers. Taken together, these observations suggest that dimerization may mask the sEH PTS and prevent peroxisome translocation. In the current study, we test the hypothesis that dimerization is a key regulator of sEH subcellular localization. Specifically, we altered the dimerization state of sEH by introducing substitutions in amino acids responsible for the dimer-stabilizing salt-bridge. Green Fluorescent Protein (GFP) fusions of each of mutants were co-transfected into mouse primary cultured cortical neurons together with a PTS-linked red fluorescent protein to constitutively label peroxisomes. Labeled neurons were analyzed using confocal microscopy and co-localization of sEH with peroxisomes was quantified using Pearson's correlation coefficient. We find that dimer-competent sEH constructs preferentially localize to the cytosol, whereas constructs with weakened or disrupted dimerization were preferentially targeted to peroxisomes. We conclude that the sEH dimerization status is a key regulator of its peroxisomal localization.

  3. Exact Solution of a Generalized Nonlinear Schrodinger Equation Dimer

    DEFF Research Database (Denmark)

    Christiansen, Peter Leth; Maniadis, P.; Tsironis, G.P.

    1998-01-01

    We present exact solutions for a nonlinear dimer system defined throught a discrete nonlinear Schrodinger equation that contains also an integrable Ablowitz-Ladik term. The solutions are obtained throught a transformation that maps the dimer into a double Sine-Gordon like ordinary nonlinear...

  4. Stochastic optimization-based study of dimerization kinetics

    Indian Academy of Sciences (India)

    We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end, we study dimerization kinetics of protein as a model system. We follow the dimerization kinetics using a stochastic simulation algorithm and combine it with three different optimization ...

  5. D-Dimer and thrombus burden in acute pulmonary embolism.

    Science.gov (United States)

    Keller, Karsten; Beule, Johannes; Balzer, Jörn Oliver; Dippold, Wolfgang

    2018-01-17

    Thrombus burden in pulmonary embolism (PE) is associated with higher D-Dimer-levels and poorer prognosis. We aimed to investigate i) the influence of right ventricular dysfunction (RVD), deep venous thrombosis (DVT), and high-risk PE-status on D-Dimer-levels and ii) effectiveness of D-Dimer to predict RVD in normotensive PE patients. Overall, 161 PE patients were analyzed retrospectively, classified in 5 subgroups of thrombus burden according to clinical indications and compared regarding D-Dimer-levels. Linear regression models were computed to investigate the association between D-Dimer and the groups. In hemodynamically stable PE patients, a ROC curve was calculated to assess the effectiveness of D-Dimer for predicting RVD. Overall, 161 patients (60.9% females, 54.0% aged >70 years) were included in this analysis. The D-Dimer-level was associated with group-category in a univariate linear regression model (β 0.050 (95%CI 0.002-0.099), P = .043). After adjustment for age, sex, cancer, and pneumonia in a multivariate model we observed an association between D-Dimer and group-category with borderline significance (β 0.047 (95%CI 0.002-0.096), P = .058). The Kruskal-Wallis test demonstrated that D-Dimer increased significantly with higher group-category. In 129 normotensive patients, patients with RVD had significantly higher D-Dimer values compared to those without (1.73 (1.11/3.48) vs 1.17 (0.65/2.90) mg/l, P = .049). A ROC curve showed an AUC of 0.61, gender non-specific, with calculated optimal cut-off of 1.18 mg/l. Multi-variate logistic regression model confirmed an association between D-Dimer >1.18 mg/l and RVD (OR2.721 (95%CI 1.196-6.190), P = .017). Thrombus burden in PE is related to elevated D-Dimer levels, and D-Dimer values >1.18 mg/l were predictive for RVD in normotensive patients. D-Dimer levels were influenced by DVT, but not by cancer, pneumonia, age, or renal impairment. Copyright © 2018 Elsevier Inc. All rights reserved.

  6. Large D-Dimer Fluctuation in Normal Pregnancy

    DEFF Research Database (Denmark)

    Hedengran, Katrine K; Andersen, Malene R; Stender, Steen

    2016-01-01

    pregnancies were recruited. D-dimer was repeatedly measured during pregnancy, at active labor, and on the first and second postpartum days. Percentiles for each gestational week were calculated. Each individual D-dimer was normalized by transformation into percentiles for the relevant gestational age...... or delivery group. The range in percentage points during the pregnancy and the delivery was calculated, and reference intervals were calculated for each pregnancy trimester, during vaginal delivery and scheduled and emergency cesarean section, and for the first and second day postpartum. Results. D......-dimer increased during pregnancy; the maximal fluctuation was approximately 20 percentile points in approximately half of the women. In one out of ten women, the D-dimer values fluctuated by more than 50 percentile points. Conclusions. Due to the biological variation in D-dimer within each individual woman during...

  7. Antiparallel coiled-coil–mediated dimerization of myosin X

    Science.gov (United States)

    Lu, Qing; Ye, Fei; Wei, Zhiyi; Wen, Zilong; Zhang, Mingjie

    2012-01-01

    Processive movements of unconventional myosins on actin filaments generally require motor dimerization. A commonly accepted myosin dimerization mechanism is via formation of a parallel coiled-coil dimer by a stretch of amino acid residues immediately carboxyl-terminal to the motor’s lever-arm domain. Here, we discover that the predicted coiled-coil region of myosin X forms a highly stable, antiparallel coiled-coil dimer (anti-CC). Disruption of the anti-CC either by single-point mutations or by replacement of the anti-CC with a parallel coiled coil with a similar length compromised the filopodial induction activity of myosin X. We further show that the anti-CC and the single α-helical domain of myosin X are connected by a semirigid helical linker. The anti-CC–mediated dimerization may enable myosin X to walk on both single and bundled actin filaments. PMID:23012428

  8. Pi-dimer of an aniline dimer: an ESR-UV-vis spectroelectrochemical study.

    Science.gov (United States)

    Petr, Andreas; Wei, Di; Kvarnström, Carita; Ivaska, Ari; Dunsch, Lothar

    2007-11-01

    It is shown for the first time that the most important intermediate formed during aniline polymerization, the p-aminodiphenylamine, forms a pi-dimer under oxidation at room temperature in acidified organic solvents that are used in electropolymerization. N-Phenylquinonediimine, which is generally assumed to be formed under oxidation, is only formed in basic solutions and in ionic liquids. Most of the mechanistic studies reported so far take the formation of N-phenylquinonediimine under consideration, although it is not consistent with the UV-vis spectra measured during oxidation of p-aminodiphenylamine. The formation of a pi-dimer is very well consistent with the electronic spectra of the oxidation product. In this way the pi-dimer is very important for the interpretation of the UV-vis spectra of higher oligomers and polyaniline as well. Furthermore, it offers a new interpretation of the redox behavior of p-aminodiphenylamine as found by cyclic voltammetry and has to be considered in the mechanism of the electrochemical polyaniline formation.

  9. Ab initio Study of the Structural, Tautomeric, Pairing and Electronic Properties of Seleno-Derivatives of Thymine

    Energy Technology Data Exchange (ETDEWEB)

    Vazquez-Mayagoitia, Alvaro [ORNL; Fuentes-Cabrera, Miguel A [ORNL; Sumpter, Bobby G [ORNL; Luque, Javier [Universitat de Barcelona; Huertas, Oscar [Universitat de Barcelona; Orozco, Modesto [Institut de Recerca Biomedica, Parc Cientific de Barcelona, Barcelona, Spain; Felice, Rosa [INFM-CNR National Research Center S3; Brancolini, Giorgia [ORNL; Migliore, Agostino [University of Pennsylvania

    2009-01-01

    The structural, tautomeric, hydrogen-bonding, stacking and electronic properties of a seleno-derivative of thymine (T), denoted here as 4SeT and created by replacing O4 in T with Se, are investigated by means of ab initio computational techniques. The structural properties of T and 4SeT are very similar and the geometrical differences are mainly limited to the adjacent environment of the C-Se bond. The canonical keto form is the most stable tautomer, in gas phase and in aqueous solution, for both T and 4SeT. It is argued that the competition between two opposite trends, i.e. a decrease in the base-pairing ability and an increase of the stacking interaction upon incorporation of 4SeT into a duplex, likely explains the similar experimental melting points of a seleno-derivative duplex (Se-DNA) and its native counterpart. Interestingly, the underlying electronic structure shows that replacement of O4 with Se promotes a reduction in the HOMO-LUMO gap and an increase in inter-plane coupling, which suggests that Se-DNA could be potentially useful for nanodevice applications. This finding is further supported by the fact that transfer integrals between 4SeT---A stacked base pairs are larger than those determined for similarly stacked natural T---A pairs.

  10. DNA methylation patterns of candidate genes regulated by thymine DNA glycosylase in patients with TP53 germline mutations

    Energy Technology Data Exchange (ETDEWEB)

    Fortes, F.P. [CIPE, Laboratrio de Oncogentica Molecular, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Kuasne, H. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Departamento de Urologia, Faculdade de Medicina, Universidade Estadual Paulista, Botucatu, SP (Brazil); Marchi, F.A. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Programa Inter-Institucional em Bioinformtica, Instituto de Matemtica e Estatstica, Universidade So Paulo, So Paulo, SP (Brazil); Miranda, P.M. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Rogatto, S.R. [CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Departamento de Urologia, Faculdade de Medicina, Universidade Estadual Paulista, Botucatu, SP (Brazil); Achatz, M.I. [CIPE, Laboratrio de Oncogentica Molecular, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Departamento de Oncogentica, A.C. Camargo Cancer Center, So Paulo, SP (Brazil)

    2015-04-28

    Li-Fraumeni syndrome (LFS) is a rare, autosomal dominant, hereditary cancer predisposition disorder. In Brazil, the p.R337H TP53 founder mutation causes the variant form of LFS, Li-Fraumeni-like syndrome. The occurrence of cancer and age of disease onset are known to vary, even in patients carrying the same mutation, and several mechanisms such as genetic and epigenetic alterations may be involved in this variability. However, the extent of involvement of such events has not been clarified. It is well established that p53 regulates several pathways, including the thymine DNA glycosylase (TDG) pathway, which regulates the DNA methylation of several genes. This study aimed to identify the DNA methylation pattern of genes potentially related to the TDG pathway (CDKN2A, FOXA1, HOXD8, OCT4, SOX2, and SOX17) in 30 patients with germline TP53mutations, 10 patients with wild-type TP53, and 10 healthy individuals. We also evaluated TDG expression in patients with adrenocortical tumors (ADR) with and without the p.R337H TP53 mutation. Gene methylation patterns of peripheral blood DNA samples assessed by pyrosequencing revealed no significant differences between the three groups. However, increased TDG expression was observed by quantitative reverse transcription PCR in p.R337H carriers with ADR. Considering the rarity of this phenotype and the relevance of these findings, further studies using a larger sample set are necessary to confirm our results.

  11. DNA methylation patterns of candidate genes regulated by thymine DNA glycosylase in patients with TP53 germline mutations

    Directory of Open Access Journals (Sweden)

    F.P. Fortes

    2015-07-01

    Full Text Available Li-Fraumeni syndrome (LFS is a rare, autosomal dominant, hereditary cancer predisposition disorder. In Brazil, the p.R337H TP53 founder mutation causes the variant form of LFS, Li-Fraumeni-like syndrome. The occurrence of cancer and age of disease onset are known to vary, even in patients carrying the same mutation, and several mechanisms such as genetic and epigenetic alterations may be involved in this variability. However, the extent of involvement of such events has not been clarified. It is well established that p53 regulates several pathways, including the thymine DNA glycosylase (TDG pathway, which regulates the DNA methylation of several genes. This study aimed to identify the DNA methylation pattern of genes potentially related to the TDG pathway (CDKN2A, FOXA1, HOXD8, OCT4, SOX2, and SOX17 in 30 patients with germline TP53 mutations, 10 patients with wild-type TP53, and 10 healthy individuals. We also evaluated TDG expression in patients with adrenocortical tumors (ADR with and without the p.R337H TP53 mutation. Gene methylation patterns of peripheral blood DNA samples assessed by pyrosequencing revealed no significant differences between the three groups. However, increased TDG expression was observed by quantitative reverse transcription PCR in p.R337H carriers with ADR. Considering the rarity of this phenotype and the relevance of these findings, further studies using a larger sample set are necessary to confirm our results.

  12. Asymmetric monometallic nanorod nanoparticle dimer and related compositions and methods

    KAUST Repository

    Han, Yu

    2016-03-31

    The fabrication of asymmetric monometallic nanocrystals with novel properties for plasmonics, nanophotonics and nanoelectronics. Asymmetric monometallic plasmonic nanocrystals are of both fundamental synthetic challenge and practical significance. In an example, a thiol-ligand mediated growth strategy that enables the synthesis of unprecedented Au Nanorod-Au Nanoparticle (AuNR-AuNP) dimers from pre-synthesized AuNR seeds. Using high-resolution electron microscopy and tomography, crystal structure and three-dimensional morphology of the dimer, as well as the growth pathway of the AuNP on the AuNR seed, was investigated for this example. The dimer exhibits an extraordinary broadband optical extinction spectrum spanning the UV, visible, and near infrared regions (300 - 1300 nm). This unexpected property makes the AuNR-AuNP dimer example useful for many nanophotonic applications. In two experiments, the dimer example was tested as a surface- enhanced Raman scattering (SERS) substrate and a solar light harvester for photothermal conversion, in comparison with the mixture of AuNR and AuNP. In the SERS experiment, the dimer example showed an enhancement factor about 10 times higher than that of the mixture, when the excitation wavelength (660 nm) was off the two surface plasmon resonance (SPR) bands of the mixture. In the photothermal conversion experiment under simulated sunlight illumination, the dimer example exhibited an energy conversion efficiency about 1.4 times as high as that of the mixture.

  13. Paclitaxel dimers assembling nanomedicines for treatment of cervix carcinoma.

    Science.gov (United States)

    Pei, Qing; Hu, Xiuli; Liu, Shi; Li, Yang; Xie, Zhigang; Jing, Xiabin

    2017-05-28

    Poor water solubility and adverse side effects pose a challenge for clinical application of paclitaxel (PTX). In this work, a series of PTX dimers are synthesized by coupling two PTX molecules with dicarboxylic acids. As-synthesized PTX dimers form stable nanoparticles in aqueous solution without using any surfactants or adjuvants, and the solubility of PTX in water increases by 2500-fold compared to that of free PTX. These nanoparticles with high content of PTX are internalized by cancer cells and exhibit comparable cytotoxicity with Taxol. Furthermore, when the PTX dimers are incorporated into methoxypoly(ethylene glycol)2K-block-poly(d, l-lactide)2K (PEG-PDLLA) micelles, the loading content of PTX dimers is as high as 85wt%. The formed nanoparticles possess the high stability in biological conditions. Both in vitro and in vivo experiments show that these (PTX dimer)/PEG-PDLLA formulations possess effective cellular uptake and potent cytotoxicity, and exhibit reduced systemic toxicity and enhanced antitumor efficacy towards human cervical tumor. We believe these PTX dimers-based nanoparticles would be an alternative formulation for PTX, and such drug dimer assembling behaviors could be extended to other therapeutic agents. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Advances in Chemistry and Pharmacology of Triterpenoid Synthetic Dimers.

    Science.gov (United States)

    Bednarczyk-Cwynar, Barbara; Günther, Andrzej

    2017-01-01

    This review focuses on advances in chemistry and pharmacology of synthetic triterpenoid dimers, obtained from natural compounds. Synthetic triterpenoid dimers are divided into specific subgroups based on the structure of main triterpenoid monomeric skeleton. Synthetic triterpenoid derivatives of dimeric structure can be obtained through the covalent linkage of the C-3 hydroxyl or another group, via the C-2 atom or the C-17 carboxyl group (mainly anhydrides, amides or esters). Some triterpenes can undergo chemical transformations leading to the formation of cyclic dimers or other types of dimers. Most of the obtained triterpenoid dimers have been subjected to pharmacological tests evaluating their biological activity, mainly antiviral (HIV-1 RT, HCVpp, VSVpp, HIV-RT-C8166-CCR5), cytotoxic (against e.g. 388, MCF-7, SF-268, NCIH460, KM20L2, DU-145, Hep-G2, A549, BGC-823, PC-3), anti-inflammatory (iNOS, RAW 264.7) and antidiabetic (RMGPa inhibition). The authors also reported the ability of some of the obtained cyclic triterpenoid dimers to recognize anions and to form self-assembled structures. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  15. Human white blood cells contain cyclobutyl pyrimidine dimer photolyase

    Energy Technology Data Exchange (ETDEWEB)

    Sutherland, B.M.; Bennett, P.V. [Brookhaven National Lab., Upton, NY (United States)

    1995-10-10

    Although enzymatic photoreactivation of cyclobutyl pyrimidine dimers in DNA is present in almost all organisms, its presence in placental mammals is controversial. We tested human white blood cells for photolyase by using three defined DNAs (suprecoiled pET-2, nonsupercoiled bacteriphage {lambda}, and a defined-sequence 287-bp oligonucleotide), two dimer-specific endonucleases (T4 endonuclease V and UV endonuclease from Micrococcus luteus), and three assay methods. We show that human white blood cells contain photolyase that can photorepair pyrimidine dimers in defined supercoiled and linear DNAs and in a 287-bp oligonucleotide and that human photolyase is active on genomic DNA in intact human cells. 44 refs., 3 figs.

  16. Subsurface dimerization in III-V semiconductor (001) surfaces

    DEFF Research Database (Denmark)

    Kumpf, C.; Marks, L.D.; Ellis, D.

    2001-01-01

    We present the atomic structure of the c(8 X 2) reconstructions of InSb-, InAs-, and GaAs-(001) surfaces as determined by surface x-ray diffraction using direct methods. Contrary to common belief, group III dimers are not prominent on the surface, instead subsurface dimerization of group m atoms ...... takes place in the second bilayer, accompanied by a major rearrangement of the surface atoms above the dimers to form linear arrays. By varying the occupancies of four surface sites the (001)-c(8 X 2) reconstructions of III-V semiconductors can be described in a unified model....

  17. Dimeric Surfactants: Promising Ingredients of Cosmetics and Toiletries

    Directory of Open Access Journals (Sweden)

    Naveen Kumar

    2013-11-01

    Full Text Available Surfactants are an essential ingredient for cosmetic, toiletries and personal care products for enhancing their performance. Dimeric surfactants demonstrate superiority compared to conventional surfactants in all areas of application. Dimeric surfactants are extremely promising for utilization in various cosmetic formulations viz. shampoo, lotions, creams, conditioners etc. These surfactants possess extremely unique surface properties viz. lower surface tension, unique micellization, low critical micelle concentration (CMC and antimicrobial activity, higher solubilization etc. Dimerics enhance the performances of cosmetics in an extraordinary manner and provide eco-friendly preparations for human epidermis.

  18. Vison excitations in near-critical quantum dimer models

    Science.gov (United States)

    Strübi, G.; Ivanov, D. A.

    2011-06-01

    We study vison excitations in a quantum dimer model interpolating between the Rokhsar-Kivelson models on the square and triangular lattices. In the square-lattice case, the model is known to be critical and characterized by U(1) topological quantum numbers. Introducing diagonal dimers brings the model to a Z2 resonating-valence-bond phase. We study variationally the emergence of vison excitations at low concentration of diagonal dimers, close to the critical point. We find that, in this regime, vison excitations are large in size and their structure resembles vortices in type-II superconductors.

  19. Nanomechanical properties of vimentin intermediate filament dimers

    Energy Technology Data Exchange (ETDEWEB)

    Qin Zhao; Buehler, Markus J [Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 1-235A and B, Cambridge, MA 02139 (United States); Kreplak, Laurent, E-mail: mbuehler@MIT.ED [Department of Physics and Atmospheric Science, Dalhousie University, Halifax, NS, B3H 3J5 (Canada)

    2009-10-21

    The cell's cytoskeleton, providing the cell with structure and shape, consists of a complex array of structural proteins, including microtubules, microfilaments and intermediate filaments. Intermediate filaments play a crucial role in mechanotransduction and in providing mechanical stability to cells, in particular under large deformation. By utilizing molecular simulation, here we report a nanomechanical analysis of vimentin intermediate filament dimers, the basic building blocks of intermediate filaments. We describe a detailed analysis of the mechanical properties and associated deformation mechanisms, and find that mechanical stretch induces a transition from alpha-helices to beta-sheets, a phenomenon known as alpha-beta transition. A comparison of the Young's modulus predicted from simulation with experimental measurements is provided, and good agreement is found. We present an analysis of structural changes during deformation, domain unfolding patterns, rate dependence of the rupture force and associated changes in the energy landscape, and conclude with a discussion of potential implications for mechanobiology and the development of de novo protein materials.

  20. Coherent Electronic Coupling versus Localization in Individual Molecular Dimers

    NARCIS (Netherlands)

    Lippitz, Markus; Hübner, Christian G.; Christ, Thomas; Eichner, Holger; Bordat, Patrice; Herrmann, Andreas; Müllen, Klaus; Basché, Thomas

    2004-01-01

    We have investigated electronic excitation transfer in individual molecular dimers by time and spectrally resolved confocal fluorescence microscopy. The single molecule measurements allow for directly probing the distribution of the electronic coupling strengths due to static disorder in the polymer

  1. Universal dimer–dimer scattering in lattice effective field theory

    Directory of Open Access Journals (Sweden)

    Serdar Elhatisari

    2017-05-01

    Full Text Available We consider two-component fermions with short-range interactions and large scattering length. This system has universal properties that are realized in several different fields of physics. In the limit of large fermion–fermion scattering length aff and zero-range interaction, all properties of the system scale proportionally with aff. For the case with shallow bound dimers, we calculate the dimer–dimer scattering phase shifts using lattice effective field theory. We extract the universal dimer–dimer scattering length add/aff=0.618(30 and effective range rdd/aff=−0.431(48. This result for the effective range is the first calculation with quantified and controlled systematic errors. We also benchmark our methods by computing the fermion–dimer scattering parameters and testing some predictions of conformal scaling of irrelevant operators near the unitarity limit.

  2. Antiplasmodial dimeric chalcone derivatives from the roots of Uvaria siamensis.

    Science.gov (United States)

    Salae, Abdul-Wahab; Chairerk, Orapan; Sukkoet, Piyanut; Chairat, Therdsak; Prawat, Uma; Tuntiwachwuttikul, Pittaya; Chalermglin, Piya; Ruchirawat, Somsak

    2017-03-01

    Four dimeric chalcone derivatives, 8″,9″-dihydrowelwitschin H, uvarins A-C, a naphthalene derivative, 2-hydroxy-3-methoxy-6-(4'- hydroxyphenyl)naphthalene, and the known dimeric chalcones, dependensin and welwitschin E, flavonoids, a cyclohexane oxide derivative, an aromatic aldehyde were isolated from the roots of Uvaria siamensis (Annonaceae). The structures of the compounds were elucidated by spectroscopic analysis, as well as by comparison with literature data. The isolated compounds with a sufficient amount for biological assays were evaluated for their antimalarial, antimycobacterial, and cytotoxic activities. The dimeric chalcones 8″,9″-dihydrowelwitschin H, uvarins B and C, dependensin and welwitschin E showed strong antiplasmodial activity with IC50 values of 3.10, 3.02, 3.09, 4.21 and 3.99 μg/mL, respectively. A possible biosynthesis pathway of the dimeric chalcones is discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Tautomeric equilibrium of uracil and thymine in model protein-nucleic acid contacts. Spectroscopic and quantum chemical approach.

    Science.gov (United States)

    Samijlenko, Svitlana P; Yurenko, Yevgen P; Stepanyugin, Andriy V; Hovorun, Dmytro M

    2010-01-28

    This work deals with tautomeric transformations of uracil (Ura) and thymine (Thy) in their model complexes with the deprotonated carboxylic group. Essential changes in the UV spectra of the bases upon their interaction with NaAc, vanishing signals of both imino protons in (1)H NMR spectra, and a perceptible decrease in intensity of both IR bands, related to the stretching vibrations nu(C=O) of the carbonyl groups, imply involvement of enolic tautomers. Results of quantum chemical calculations of the double complexes of the Ura(Thy) tautomers with CH(3)COO(-) at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory proved to be incompatible with the spectral features: despite the fact that the complexes of the enolic tautomers are much closer in energy to the diketo ones as compared to isolated tautomers, the energy gap between them is such that in tautomeric equilibrium dominate diketo forms. Calculations of triple complexes of the type CH(3)COO(-):Ura(Thy) tautomer:Na(+), taking into account the effect of the Na(+) coordination with tautomers, show that three triple complexes formed by enolic tautomers appeared more stable than those formed by diketo ones. This makes the UV and (1)H NMR data understandable, but the high residual intensity of the nu(C=O) bands in the IR spectra remains unclear. At that ion, Na(+) itself was not able to disturb the tautomeric equilibrium in the coordination complexes of the type Ura(Thy) tautomer:Na(+). To evaluate the DMSO effect, the CPCM solvation model was applied to triple complexes of the Ura tautomers. It appeared that in the solution there is coexistence between the diketo and enolic tautomers in a ratio of 53%:47%. This makes possible reconciliation of our experimental data. The biological significance of high-energy tautomers of nucleotide bases is discussed.

  4. Formation of copper nanoparticles on poly(thymine) through surface-initiated enzymatic polymerization and its application for DNA detection.

    Science.gov (United States)

    Hu, Weiwen; Ning, Yong; Kong, Jinming; Zhang, Xueji

    2015-08-21

    Poly(thymine) (polyT) and double-stranded DNA (dsDNA) can act as efficient templates for the formation of copper nanoparticles (CuNPs) at a low concentration of CuSO4, and the formed CuNPs emit excellent fluorescence. In this work, we demonstrated a new and facile strategy for the highly sensitive and selective detection of DNA on streptavidin-functionalized magnetic beads (SA-MB) using DNA-templated CuNPs as the fluorescent probe. Target DNA (tDNA) was hybridized with the capture DNA that was immobilized on the surface of SA-MB. Surface initiated enzymatic polymerization (SIEP) was employed as the signal amplification method to generate the polyT at the 3' end of tDNA for the formation of CuNPs. The incorporation of polyT by SIEP resulted in ∼35.7 fold signal amplification compared to the dsDNA after hybridization without SIEP. A dose-response curve for detection of DNA was obtained, with a linear dynamic range of 0.1 nM to 10 nM. We showed that this method has a low pM limit of detection (LOD 98.2 pM) and it is also very sensitive to the mismatch type in a specific DNA sequence. In addition, it avoids rigorously controlled temperature, complex synthesis of the fluorescent probe and prelabeling of DNA strands and eliminates the use of sophisticated experimental techniques and equipment. Armed with these intriguing properties, the proposed system could provide an efficient tool for early diagnosis and risk assessment of malignancy.

  5. Glycogen Synthase Kinase-3 regulates IGFBP-1 gene transcription through the Thymine-rich Insulin Response Element

    Directory of Open Access Journals (Sweden)

    Marquez Rodolfo

    2004-09-01

    Full Text Available Abstract Background Hepatic expression of several gene products involved in glucose metabolism, including phosphoenolpyruvate carboxykinase (PEPCK, glucose-6-phosphatase (G6Pase and insulin-like growth factor binding protein-1 (IGFBP-1, is rapidly and completely inhibited by insulin. This inhibition is mediated through the regulation of a DNA element present in each of these gene promoters, that we call the Thymine-rich Insulin Response Element (TIRE. The insulin signalling pathway that results in the inhibition of these gene promoters requires the activation of phosphatidylinositol 3-kinase (PI 3-kinase. However, the molecules that connect PI 3-kinase to these gene promoters are not yet fully defined. Glycogen Synthase Kinase 3 (GSK-3 is inhibited following activation of PI 3-kinase. We have shown previously that inhibitors of GSK-3 reduce the activity of two TIRE-containing gene promoters (PEPCK and G6Pase, whose products are required for gluconeogenesis. Results In this report we demonstrate that in H4IIE-C3 cells, four distinct classes of GSK-3 inhibitor mimic the effect of insulin on a third TIRE-containing gene, IGFBP-1. We identify the TIRE as the minimum requirement for inhibition by these agents, and demonstrate that the target of GSK-3 is unlikely to be the postulated TIRE-binding protein FOXO-1. Importantly, overexpression of GSK-3 in cells reduces the insulin regulation of TIRE activity as well as endogenous IGFBP-1 expression. Conclusions These results implicate GSK-3 as an intermediate in the pathway from the insulin receptor to the TIRE. Indeed, this is the first demonstration of an absolute requirement for GSK-3 inhibition in insulin regulation of gene transcription. These data support the potential use of GSK-3 inhibitors in the treatment of insulin resistant states such as Type 2 diabetes mellitus, but suggest that it will be important to identify all TIRE-containing genes to assess potential side effects of these agents.

  6. Dimer representations of the Temperley–Lieb algebra

    Energy Technology Data Exchange (ETDEWEB)

    Morin-Duchesne, Alexi, E-mail: alexi.morin-duchesne@uclouvain.be [Institut de Recherche en Mathématique et Physique, Université Catholique de Louvain, Louvain-la-Neuve, B-1348 (Belgium); Rasmussen, Jørgen, E-mail: j.rasmussen@uq.edu.au [School of Mathematics and Physics, University of Queensland St Lucia, Brisbane, Queensland 4072 (Australia); Ruelle, Philippe, E-mail: philippe.ruelle@uclouvain.be [Institut de Recherche en Mathématique et Physique, Université Catholique de Louvain, Louvain-la-Neuve, B-1348 (Belgium)

    2015-01-15

    A new spin-chain representation of the Temperley–Lieb algebra TL{sub n}(β=0) is introduced and related to the dimer model. Unlike the usual XXZ spin-chain representations of dimension 2{sup n}, this dimer representation is of dimension 2{sup n−1}. A detailed analysis of its structure is presented and found to yield indecomposable zigzag modules.

  7. Dimeric analogs of immunosuppressive decapeptide fragment of ubiquitin.

    Science.gov (United States)

    Kluczyk, Alicja; Cydzik, Marzena; Biernat, Monika; Bąchor, Remigiusz; Pasikowski, Paweł; Stefanowicz, Piotr; Artym, Jolanta; Zimecki, Michał; Szewczuk, Zbigniew

    2012-07-01

    Our previous studies revealed that ubiquitin and its decapeptide fragment with the LEDGRTLSDY sequence, located on the exposed molecule loop, strongly suppressed the immune response. This suggested that the loop may serve as a functional epitope of ubiquitin molecule and that a possible mechanism of biological action of the synthesized peptides is associated with interfering in interactions of ubiquitin with other molecules. Ubiquitin is known to exist in oligomeric forms, which can interact with various oligomeric receptors. We designed and synthesized new dimeric analogs of the ubiquitin fragment, to probe whether dimeric peptides may have higher affinity towards the ubiquitin receptors responsible for immunosuppression, which are believed to form oligomeric structures. Three dimerization strategies, N-terminus to N-terminus, C-terminus to C-terminus, and N-terminus to C-terminus (head-to-tail) via PEG derivatives were used to synthesize the dimeric peptides on solid support. In the course of our research, we developed a new and straightforward procedure of dimerization where α-amino groups of the C-terminal lysine residues of two peptide fragments were linked by PEG spacer directly on solid support. The effect of dimeric analogs on the immunological response was tested in the AFC in vitro experiment. The immunological tests showed that the head-to-tail dimerization caused a more profound increase in the biological activity than other tested dimerization methods. Our results suggest that such orientation of peptide components may correspond to orientation of the hypothetic ubiquitin receptors responsible for the immunomodulatory activity. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.

  8. Dimers on Surface Graphs and Spin Structures. I

    DEFF Research Database (Denmark)

    Cimasoni, David; Reshetikhin, Nicolai

    2007-01-01

    Partition functions for dimers on closed oriented surfaces are known to be alternating sums of Pfaffians of Kasteleyn matrices. In this paper, we obtain the formula for the coefficients in terms of discrete spin structures.......Partition functions for dimers on closed oriented surfaces are known to be alternating sums of Pfaffians of Kasteleyn matrices. In this paper, we obtain the formula for the coefficients in terms of discrete spin structures....

  9. The influence of strain on the diffusion of Si dimers on Si(001)

    NARCIS (Netherlands)

    Zoethout, E.; Zoethout, E.; Gurlu, O.; Gürlü, O.; Zandvliet, Henricus J.W.; Poelsema, Bene

    2000-01-01

    The influence of lattice mismatch-induced tensile strain on the diffusion of Si dimers on Si(001) has been studied. The rate of surface diffusion of a Si dimer along the substrate dimer rows is relatively insensitive to tensile strain, whereas the rate of diffusion for a Si dimer across the

  10. Tubulin dimers oligomerize before their incorporation into microtubules.

    Directory of Open Access Journals (Sweden)

    Julien Mozziconacci

    Full Text Available In the presence of GTP, purified dimers of alpha- and beta-tubulin will interact longitudinally and laterally to self-assemble into microtubules (MTs. This property provides a powerful in vitro experimental system to describe MT dynamic behavior at the micrometer scale and to study effects and functioning of a large variety of microtubule associated proteins (MAPs. Despite the plethora of such data produced, the molecular mechanisms of MT assembly remain disputed. Electron microscopy (EM studies suggested that tubulin dimers interact longitudinally to form short oligomers which form a tube by lateral interaction and which contribute to MT elongation. This idea is however challenged: Based on estimated association constants it was proposed that single dimers represent the major fraction of free tubulin. This view was recently supported by measurements suggesting that MTs elongate by addition of single tubulin dimers. To solve this discrepancy, we performed a direct measurement of the longitudinal interaction energy for tubulin dimers. We quantified the size distribution of tubulin oligomers using EM and fluorescence correlation spectroscopy (FCS. From the distribution we derived the longitudinal interaction energy in the presence of GDP and the non-hydrolysable GTP analog GMPCPP. Our data suggest that MT elongation and nucleation involves interactions of short tubulin oligomers rather than dimers. Our approach provides a solid experimental framework to better understand the role of MAPs in MT nucleation and growth.

  11. Mechanism of bacterial signal transduction revealed by molecular dynamics of Tsr dimers and trimers of dimers in lipid vesicles.

    Directory of Open Access Journals (Sweden)

    Benjamin A Hall

    Full Text Available Bacterial chemoreceptors provide an important model for understanding signalling processes. In the serine receptor Tsr from E. coli, a binding event in the periplasmic domain of the receptor dimer causes a shift in a single transmembrane helix of roughly 0.15 nm towards the cytoplasm. This small change is propagated through the ≈ 22 nm length of the receptor, causing downstream inhibition of the kinase CheA. This requires interactions within a trimer of receptor dimers. Additionally, the signal is amplified across a 53,000 nm(2 array of chemoreceptor proteins, including ≈ 5,200 receptor trimers-of-dimers, at the cell pole. Despite a wealth of experimental data on the system, including high resolution structures of individual domains and extensive mutagenesis data, it remains uncertain how information is communicated across the receptor from the binding event to the downstream effectors. We present a molecular model of the entire Tsr dimer, and examine its behaviour using coarse-grained molecular dynamics and elastic network modelling. We observe a large bending in dimer models between the linker domain HAMP and coiled-coil domains, which is supported by experimental data. Models of the trimer of dimers, built from the dimer models, are more constrained and likely represent the signalling state. Simulations of the models in a 70 nm diameter vesicle with a biologically realistic lipid mixture reveal specific lipid interactions and oligomerisation of the trimer of dimers. The results indicate a mechanism whereby small motions of a single helix can be amplified through HAMP domain packing, to initiate large changes in the whole receptor structure.

  12. Dimer-atom-atom recombination in the universal four-boson system

    OpenAIRE

    Deltuva, A.

    2012-01-01

    The dimer-atom-atom recombination process in the system of four identical bosons with resonant interactions is studied. The description uses the exact Alt, Grassberger and Sandhas equations for the four-particle transition operators that are solved in the momentum-space framework. The dimer-dimer and atom-trimer channel contributions to the ultracold dimer-atom-atom recombination rate are calculated. The dimer-atom-atom recombination rate greatly exceeds the three-atom recombination rate.

  13. Preference for bridging versus terminal ligands in magnesium dimers.

    Science.gov (United States)

    Lioe, Hadi; White, Jonathan M; O'Hair, Richard A J

    2011-06-01

    Magnesium dimers play important roles in inorganic and organometallic chemistry. This study evaluates the inherent bridging ability of a range of different ligands in magnesium dimers. In the first part, the Cambridge Structural Database is interrogated to establish the frequency of different types of ligands found in bridging versus terminal positions in two key structural motifs: one in which there are two bridging ligands (the D(2h) "Mg(2)(μ-X(2))" structure); the other in which there are three bridging ligands (the C(3v) "Mg(2)(μ-X(3))" structure). The most striking finding from the database search is the overwhelming preference for magnesium dimers possessing two bridging ligands. The most common bridging ligands are C-, N-, and O-based. In the second part, DFT calculations (at the B3LYP/6-311+G(d) level of theory) are carried out to examine a wider range of structural types for dimers consisting of the stoichiometries Mg(2)Cl(3)R and Mg(2)Cl(2)R(2), where R = CH(3), SiH(3), NH(2), PH(2), OH, SH, CH(2)CH(3), CH=CH(2), C≡CH, Ph, OAc, F and Br. Consistent with the database search, the most stable magnesium dimers are those that contain two bridging ligands. Furthermore, it was demonstrated that the electronic effect of the bridging ligands is important in influencing the stability of the magnesium dimers. The preference for a bridging ligand, which reflects its ability to stabilize a magnesium dimer, follows the order: OH > NH(2) > C≡CH > SH > Ph > Br > PH(2) = CH=CH(2) > CH(2)CH(3) > CH(3) > SiH(3). Finally, the role that the ether solvent Me(2)O has on the stability of isomeric Mg(2)Cl(2)Me(2) dimers was studied. It was found that the first solvent molecule stabilizes the dimers, while the second solvent molecule can either have a stabilizing or destabilizing effect, depending on the isomer structure.

  14. Copper dimer interactions on a thermomechanical superfluid (4)He fountain.

    Science.gov (United States)

    Popov, Evgeny; Eloranta, Jussi

    2015-05-28

    Laser induced fluorescence imaging and frequency domain excitation spectroscopy of the copper dimer (B(1)Σg (+) ←X(1)Σu (+)) in thermomechanical helium fountain at 1.7 K are demonstrated. The dimers penetrate into the fountain provided that their average propagation velocity is ca. 15 m/s. This energy threshold is interpreted in terms of an imperfect fountain liquid-gas interface, which acts as a trap for low velocity dimers. Orsay-Trento density functional theory calculations for superfluid (4)He are used to characterize the dynamics of the dimer solvation process into the fountain. The dimers first accelerate towards the fountain surface and once the surface layer is crossed, they penetrate into the liquid and further slow down to Landau critical velocity by creating a vortex ring. Theoretical lineshape calculations support the assignment of the experimentally observed bands to Cu2 solvated in the bulk liquid. The vibronic progressions are decomposed of a zero-phonon line and two types of phonon bands, which correlate with solvent cavity interface compression (t < 200 fs) and expansion (200 < t < 500 fs) driven by the electronic excitation. The presented experimental method allows to perform molecular spectroscopy in bulk superfluid helium where the temperature and pressure can be varied.

  15. D-dimer and BNP levels in acute aortic dissection.

    Science.gov (United States)

    Sbarouni, Eftihia; Georgiadou, Panagiota; Marathias, Aikaterini; Geroulanos, Stefanos; Kremastinos, Dimitrios Th

    2007-11-15

    Early diagnosis and treatment are pivotal for patients with acute aortic dissection (AAD). D-dimer is a rule-out diagnostic test for pulmonary embolism but there is evidence that it may also be applicable to AAD. We evaluated plasma D-dimer, white cell blood count (WBC), C-reactive protein (CRP) and N-terminal pro-B-type natriuretic peptide (BNP) in 18 consecutive patients with established AAD, 21 consecutive patients with dilated ascending aortas scheduled for elective surgery and 8 normal subjects. Patients with AAD had significantly higher elevated D-dimer, compared to chronic aneurysms and normal controls (pD-dimer level higher than 700 ng/ml had a sensitivity of 94% and specificity of 59% for diagnosis of AAD. The WBC count was also significantly increased compared to the other groups (pD-dimer can be used as a 'rule-out' test in patients with suspected AAD and seems useful in the discrimination between AAD and chronic uncomplicated aneurysms, unlike CRP and BNP plasma levels.

  16. Cytotoxicity of bovine seminal ribonuclease: monomer versus dimer.

    Science.gov (United States)

    Lee, J Eugene; Raines, Ronald T

    2005-12-06

    Bovine seminal ribonuclease (BS-RNase) is a homologue of bovine pancreatic ribonuclease (RNase A). Unlike RNase A, BS-RNase has notable toxicity for human tumor cells. Wild-type BS-RNase is a homodimer linked by two intermolecular disulfide bonds. This quaternary structure endows BS-RNase with resistance to inhibition by the cytosolic ribonuclease inhibitor protein (RI), which binds tightly to RNase A and monomeric BS-RNase. Here, we report on the creation and analysis of monomeric variants of BS-RNase that evade RI but retain full enzymatic activity. The cytotoxic activity of these monomeric variants exceeds that of the wild-type dimer by up to 30-fold, indicating that the dimeric structure of BS-RNase is not required for cytotoxicity. Dimers of these monomeric variants are more cytotoxic than wild-type BS-RNase, suggesting that the cytotoxicity of the wild-type enzyme is limited by RI inhibition following dissociation of the dimer in the reducing environment of the cytosol. Finally, the cytotoxic activity of these dimers is less than that of the constituent monomers, indicating that their quaternary structure is a liability. These data provide new insight into structure-function relationships of BS-RNase. Moreover, BS-RNase monomers described herein are more toxic to human tumor cells than is any known variant or homologue of RNase A including Onconase, an amphibian homologue in phase III clinical trials for the treatment of unresectable malignant mesothelioma.

  17. Separation of antibody monomer-dimer mixtures by frontal analysis.

    Science.gov (United States)

    Reck, Jason M; Pabst, Timothy M; Hunter, Alan K; Carta, Giorgio

    2017-06-02

    The removal of aggregates, particularly soluble dimers, from monoclonal antibodies (mAbs) remains a persistent challenge in downstream processing. In this work, we have examined the separation of an antibody monomer from its dimer on the cation exchange resin Nuvia HR-S (Bio-Rad Laboratories) using frontal analysis. In this process, a mixture of monomer and dimer is continuously fed to the column under conditions where the mixture is favorably bound, resulting in two breakthrough fronts whose monomer and dimer compositions are determined by the multi-component equilibrium and kinetics of the system. Experimentally, the selectivity for dimer was found to vary substantially with ionic strength, being lowest when conditions favor the strongest binding, and increasing to a maximum at intermediate ionic strengths where rapid exchange with the bound monomer can occur. A mechanistic model is developed to describe the competitive binding frontal analysis process, assuming pore diffusion and a significant kinetic resistance to binding as a function of ionic strength. The model was solved numerically and was able to describe both the frontal analysis processes and batch adsorption experimental data, accounting for process parameters such as feed composition and salt concentration. The resulting model can be used to optimize column operating conditions for yield and purity. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Synthesis of a distinct water dimer inside fullerene C70

    Science.gov (United States)

    Zhang, Rui; Murata, Michihisa; Aharen, Tomoko; Wakamiya, Atsushi; Shimoaka, Takafumi; Hasegawa, Takeshi; Murata, Yasujiro

    2016-05-01

    The water dimer is an ideal chemical species with which to study hydrogen bonds. Owing to the equilibrium between the monomer and oligomer structure, however, selective generation and separation of a genuine water dimer has not yet been achieved. Here, we report a synthetic strategy that leads to the successful encapsulation of one or two water molecules inside fullerene C70. These endohedral C70 compounds offer the opportunity to study the intrinsic properties of a single water molecule without any hydrogen bonding, as well as an isolated water dimer with a single hydrogen bond between the two molecules. The unambiguously determined off-centre position of water in (H2O)2@C70 by X-ray diffraction provides insights into the formation of (H2O)2@C70. Subsequently, the 1H NMR spectroscopic measurements for (H2O)2@C70 confirmed the formation of a single hydrogen bond rapidly interchanging between the encapsulated water dimer. Our theoretical calculations revealed a peculiar cis-linear conformation of the dimer resulting from confinement effects inside C70.

  19. Structural basis for the suppression of skin cancers by DNA polymerase [eta

    Energy Technology Data Exchange (ETDEWEB)

    Silverstein, Timothy D.; Johnson, Robert E.; Jain, Rinku; Prakash, Louise; Prakash, Satya; Aggarwal, Aneel K. (Texas-MED); (Mount Sinai Hospital)

    2010-09-13

    DNA polymerase {eta} (Pol{eta}) is unique among eukaryotic polymerases in its proficient ability for error-free replication through ultraviolet-induced cyclobutane pyrimidine dimers, and inactivation of Pol{eta} (also known as POLH) in humans causes the variant form of xeroderma pigmentosum (XPV). We present the crystal structures of Saccharomyces cerevisiae Pol{eta} (also known as RAD30) in ternary complex with a cis-syn thymine-thymine (T-T) dimer and with undamaged DNA. The structures reveal that the ability of Pol{eta} to replicate efficiently through the ultraviolet-induced lesion derives from a simple and yet elegant mechanism, wherein the two Ts of the T-T dimer are accommodated in an active site cleft that is much more open than in other polymerases. We also show by structural, biochemical and genetic analysis that the two Ts are maintained in a stable configuration in the active site via interactions with Gln55, Arg73 and Met74. Together, these features define the basis for Pol{eta}'s action on ultraviolet-damaged DNA that is crucial in suppressing the mutagenic and carcinogenic consequences of sun exposure, thereby reducing the incidence of skin cancers in humans.

  20. Structure and mechanism of human DNA polymerase [eta

    Energy Technology Data Exchange (ETDEWEB)

    Biertümpfel, Christian; Zhao, Ye; Kondo, Yuji; Ramón-Maiques, Santiago; Gregory, Mark; Lee, Jae Young; Masutani, Chikahide; Lehmann, Alan R.; Hanaoka, Fumio; Yang, Wei (Sussex); (NIH); (Gakushuin); (Osaka)

    2010-11-03

    The variant form of the human syndrome xeroderma pigmentosum (XPV) is caused by a deficiency in DNA polymerase {eta} (Pol{eta}), a DNA polymerase that enables replication through ultraviolet-induced pyrimidine dimers. Here we report high-resolution crystal structures of human Pol{eta} at four consecutive steps during DNA synthesis through cis-syn cyclobutane thymine dimers. Pol{eta} acts like a 'molecular splint' to stabilize damaged DNA in a normal B-form conformation. An enlarged active site accommodates the thymine dimer with excellent stereochemistry for two-metal ion catalysis. Two residues conserved among Pol{eta} orthologues form specific hydrogen bonds with the lesion and the incoming nucleotide to assist translesion synthesis. On the basis of the structures, eight Pol{eta} missense mutations causing XPV can be rationalized as undermining the molecular splint or perturbing the active-site alignment. The structures also provide an insight into the role of Pol{eta} in replicating through D loop and DNA fragile sites.

  1. Characterization of oxygen dimer-enriched silicon detectors

    CERN Document Server

    Boisvert, V; Moll, M; Murin, L I; Pintilie, I

    2005-01-01

    Various types of silicon material and silicon p+n diodes have been treated to increase the concentration of the oxygen dimer (O2i) defect. This was done by exposing the bulk material and the diodes to 6 MeV electrons at a temperature of about 350 °C. FTIR spectroscopy has been performed on the processed material confirming the formation of oxygen dimer defects in Czochralski silicon pieces. We also show results from TSC characterization on processed diodes. Finally, we investigated the influence of the dimer enrichment process on the depletion voltage of silicon diodes and performed 24 GeV/c proton irradiations to study the evolution of the macroscopic diode characteristics as a function of fluence.

  2. Sequence-Specific DNA Binding by a Short Peptide Dimer

    Science.gov (United States)

    Talanian, Robert V.; McKnight, C. James; Kim, Peter S.

    1990-08-01

    A recently described class of DNA binding proteins is characterized by the "bZIP" motif, which consists of a basic region that contacts DNA and an adjacent "leucine zipper" that mediates protein dimerization. A peptide model for the basic region of the yeast transcriptional activator GCN4 has been developed in which the leucine zipper has been replaced by a disulfide bond. The 34-residue peptide dimer, but not the reduced monomer, binds DNA with nanomolar affinity at 4^circC. DNA binding is sequence-specific as judged by deoxyribonuclease I footprinting. Circular dichroism spectroscopy suggests that the peptide adopts a helical structure when bound to DNA. These results demonstrate directly that the GCN4 basic region is sufficient for sequence-specific DNA binding and suggest that a major function of the GCN4 leucine zipper is simply to mediate protein dimerization. Our approach provides a strategy for the design of short sequence-specific DNA binding peptides.

  3. Optofluidic taming of a colloidal dimer with a silicon nanocavity

    Energy Technology Data Exchange (ETDEWEB)

    Pin, C.; Renaut, C. [Groupe d' Optique de Champ Proche - LRC CEA n°DSM-08-36, Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS n°6303- Université de Bourgogne, Dijon (France); University Grenoble Alpes, INAC-SP2M-SINAPS, F-38000 Grenoble, France and CEA, INAC-SP2M-SINAPS, F-38000 Grenoble (France); University Grenoble Alpes, CNRS, CEA-Leti Minatec, LTM, F-38054 Grenoble Cedex (France); Cluzel, B., E-mail: benoit.cluzel@u-bourgogne.fr; Fornel, F. de [Groupe d' Optique de Champ Proche - LRC CEA n°DSM-08-36, Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR CNRS n°6303- Université de Bourgogne, Dijon (France); Peyrade, D. [University Grenoble Alpes, CNRS, CEA-Leti Minatec, LTM, F-38054 Grenoble Cedex (France); Picard, E.; Hadji, E. [University Grenoble Alpes, INAC-SP2M-SINAPS, F-38000 Grenoble, France and CEA, INAC-SP2M-SINAPS, F-38000 Grenoble (France)

    2014-10-27

    We report here the optical trapping of a heterogeneous colloidal dimer above a photonic crystal nanocavity used as an on-chip optical tweezer. The trapped dimer consists of a cluster of two dielectric microbeads of different sizes linked by van der Waals forces. The smallest bead, 1 μm in diameter, is observed to be preferentially trapped by the nanotweezer, leaving the second bead untrapped. The rotational nature of the trapped dimer Brownian motion is first evidenced. Then, in the presence of a fluid flow, control of its orientation and rotation is achieved. The whole system is found to show high rotational degrees of freedom, thereby acting as an effective flow-sensitive microscopic optical ball joint.

  4. Metal membrane with dimer slots as a universal polarizer

    DEFF Research Database (Denmark)

    Zhukovsky, Sergei; Zalkovskij, Maksim; Malureanu, Radu

    2014-01-01

    In this work, we show theoretically and confirm experimentally that thin metal membranes patterned with an array of slot dimers (or their Babinet analogue with metal rods) can function as a versatile spectral and polarization filter. We present a detailed covariant multipole theory for the electr......In this work, we show theoretically and confirm experimentally that thin metal membranes patterned with an array of slot dimers (or their Babinet analogue with metal rods) can function as a versatile spectral and polarization filter. We present a detailed covariant multipole theory......-shaped, and T-shaped. These particular shapes of dimers are found to be sensitive to variations of the slots lengths and orientation of elements. Theoretical results are well supported by full-wave three-dimensional simulations. Our findings were verified experimentally on the metal membranes fabricated using...

  5. Structure of the indole-benzene dimer revisited.

    Science.gov (United States)

    Biswal, Himansu S; Gloaguen, Eric; Mons, Michel; Bhattacharyya, Surjendu; Shirhatti, Pranav R; Wategaonkar, Sanjay

    2011-09-01

    The structure of the indole-benzene dimer has been investigated using experimental techniques, namely, UV spectroscopy and infrared-ultraviolet (IR/UV) double resonance spectroscopy, combined with quantum chemical calculations such as MP2 and dispersion corrected DFT methods. The red shift of the indole N-H stretch frequency in the dimer provides direct evidence that the experimentally observed indole-benzene dimer is an N-H···π bound hydrogen bonded complex. Theoretical investigations suggest that the potential energy surface (PES) of the complex is rather flat along the coordinate describing the tilt angle between the molecular planes of indole and benzene, with several minima of similar energies, namely, parallel displaced (PD), right-angle T-shaped (T), and other intermediate structures which can be categorized as tilted T-shaped (T') and tilted parallel displaced (PD') structures. Three different computational methods, namely, RI-MP2, RI-B97-D, and PBE1-DCP, are used to arrive at a new structural assignment after assessing their performance in predicting the structure of the pyrrole dimer, for which accurate experimental data are available. By comparing the computed IR spectra of PD, T, and T'/PD' structures with the experimental IR spectrum, the tilted T-shaped (T') structure was assigned to the indole-benzene dimer. The empirically dispersion-corrected functionals (RI-B97-D and PBE1-DCP) correctly reproduce the experimental IR spectrum whereas the popular post-Hartree-Fock, MP2 method gives disappointing results. These results are also in agreement with the experimental dissociation energy (D(0)) reported in the literature. The N-H stretch frequency of the indole-benzene dimer has been found to be a more pertinent parameter for the structural assignment than the dissociation energy (D(0)). © 2011 American Chemical Society

  6. ORF Alignment: NC_002754 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available rnary Complex With A Dna Polymerase pdb|1RYS|B Chain ... B, Replication Of A Cis-Syn Thymine Dimer At Atomic...mic Resolution pdb|1RYR|A Chain A, ... Replication Of A Cis-Syn Thymine Dimer At Atomic... ... Resolution pdb|1RYS|A Chain A, Replication Of A Cis-Syn ... Thymine Dimer At Ato

  7. Solution structure of the dimeric cytoplasmic domain of syndecan-4

    DEFF Research Database (Denmark)

    Shin, J; Lee, W; Lee, D

    2001-01-01

    between peptides at physiological pH. Commensurately, the NMR structures demonstrate that syndecan-4L is a compact intertwined dimer with a symmetric clamp shape in the central variable V region with a root-mean-square deviation between backbone atom coordinates of 0.95 A for residues Leu(186)-Ala(195...... in the center of the dimeric twist similar to our previously reported 4V structure. The overall topology of the central variable region within the 4L structure is very similar to that of 4V complexed with the phosphatidylinositol 4,5-bisphosphate; however, the intersubunit interaction mode is affected...

  8. Lipopeptides as dimerization inhibitors of HIV-1 protease

    OpenAIRE

    Schramm, H. J.; de Rosny, E.; Reboud-Ravaux, M.; Büttner, J.; Dick, A.; Schramm, W.

    1999-01-01

    In AIDS therapy, attempts have been made to inhibit the virus-encoded enzymes, e.g, HIV-1 protease, using active site-directed inhibitors. This approach is questionable, however, due to virus mutations and the high toxicity of the drugs, An alternative method to inhibit the dimeric HIV protease is the targeting of the interface region of the protease subunits in order to prevent subunit dimerization and enzyme activity, This approach should be less prone to inactivation by mutation, A list of...

  9. Identification of Trimer and Dimer of 4-hydroxy-3-methoxy ...

    African Journals Online (AJOL)

    The effect of intermolecular hydrogen bonding on the molecular structure of vanillin has been studied using negative ion chemical ionization (NICl) mass spectrometry methods. The [Trimer-H2O] and [Dimer-H2O] were observed at m/z 438 and 286 respectively in NICl (CH4) mass spectrum of vanillin. The NICl (Cl) mass ...

  10. Cationic zinc (II) dimers and one dimensional coordination polymer ...

    Indian Academy of Sciences (India)

    A zinc coordination polymer was synthesised by treating in situ generation of 2 in the presence of 4,4′-bipyridine. These new molecules, dimers and polymer, were characterized by FT-IR, NMR, UV-vis, fluorescent and single crystal X-ray diffraction techniques. Zinc polymer is the first example of 1D coordination polymer ...

  11. Dimerization effect of sucrose octasulfate on rat FGF1

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Artur

    2008-01-01

    signalling pathways. The structure of rat FGF1 crystallized in the presence of SOS has been determined at 2.2 A resolution. SOS-mediated dimerization of FGF1 was observed, which was further supported by gel-filtration experiments. The major contributors to the sulfate-binding sites in rat FGF1 are Lys113...

  12. Photodissociation pathways and lifetimes of protonated peptides and their dimers

    DEFF Research Database (Denmark)

    Gopalan, Aravind; Klærke, Benedikte; Rajput, Jyoti

    2012-01-01

    rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis...

  13. Peroxynitrous Acid Dimer: Ab Initio Density Functional Study

    Science.gov (United States)

    Pathak, Rajeev

    2012-02-01

    Peroxynitrous acid (PNA) HOONO, isomeric to nitric acid, is a very strong oxidant. A novel dimeric hydrogen-bonded cluster of peroxynitrous acid (PNA-D) is proposed herein; ab inito quantum chemical investigations performed whereupon lead to several stable structures that have a direct bearing on the reactivity of the participating monomers, quantified in terms of the molecular electrostatic potential. The electron-correlation lending stability to PNA and its dimers is gauged through several density functionals namely B3LYP, B3PW91, M06-2X, M06-L, and φ-B97X, etc.; as well as from popular wave-function based second order Møller-Plesset (MP2) perturbation theory, using the basis sets 6-311++G(d,p) and 6-311++G(2d,2p). The infra-red vibrational spectra reveal spectral shifts and intensity redistribution after dimerization. While the lowest energy PNA-D has a perfect inversion symmetry; the other stable dimers emerge as combinations of monomers in different orientation.

  14. Synthesis and biological evaluation of gramicidin S dimers

    NARCIS (Netherlands)

    Grotenbreg, Gijsbert M.; Witte, Martin D.; Hooft, Peter A.V. van; Spalburg, Emile; Reiß, Philipp; Noort, Daan; Neeling, Albert J. de; Koert, Ulrich; Marel, Gijsbert A. van der; Overkleeft, Herman S.; Overhand, Mark

    2005-01-01

    The design and synthesis of analogues of the cyclic β-sheet peptide gramicidin S (GS), having additional functionalities in their turn regions, is reported. The monomeric GS analogues were transformed into dimers and their activities towards biological membranes, through antimicriobial and hemolytic

  15. Synthesis and Dimerization Behavior of Five Metallophthalocyanines in Different Solvents

    Directory of Open Access Journals (Sweden)

    Zhenhua Cheng

    2014-01-01

    Full Text Available Metallophthalocyanine (MPc has become one of the metal organic compounds with the largest production and the most widely application, because of its excellent performance in catalytic oxidation. However, aggregation of the MPc in solution, resulting in decreased solubility, greatly limits the performance of application. Studying the behavior of dimerization of MPcs can provide a theoretical basis for solving the problem of the low solubility. So five metallophthalocyanines (FePc, CoPc, NiPc, CuPc, and ZnPc were prepared with improved method and characterized. Dimerization of the five MPcs was measured by UV-Vis spectroscopy separately in N,N-dimethyl formamide (DMF and dimethylsulfoxide (DMSO. The red-shift of maximum absorption wavelength and deviations from Lambert-Beer law with increasing the concentration were observed for all the five MPcs. The dimerization equilibrium constants (K of the five MPcs in DMF were arranged in order of CoPc > ZnPc > CuPc > FePc > NiPc, while in DMSO they were arranged in order of ZnPc > CoPc > FePc > CuPc > NiPc. The type of the central metal and nature of the solvent affect the dimerization of the MPcs.

  16. Determination of the Tetramer-Dimer Equilibrium Constant of Rabbit ...

    African Journals Online (AJOL)

    ... derivatives of rabbit hemoglobin. The constant has been found to be the same for all the derivatives of rabbit hemoglobin, implying that the ligand bound on the heme has no significant effect on the tetramer-dimer dissociation of rabbit hemoglobin. African Journal of Educational Studies in Mathematics and Sciences Vol.

  17. Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction

    Directory of Open Access Journals (Sweden)

    Lukas P. Feilen

    2017-05-01

    Full Text Available Physiological function and pathology of the Alzheimer’s disease causing amyloid precursor protein (APP are correlated with its cytosolic adaptor Fe65 encompassing a WW and two phosphotyrosine-binding domains (PTBs. The C-terminal Fe65-PTB2 binds a large portion of the APP intracellular domain (AICD including the GYENPTY internalization sequence fingerprint. AICD binding to Fe65-PTB2 opens an intra-molecular interaction causing a structural change and altering Fe65 activity. Here we show that in the absence of the AICD, Fe65-PTB2 forms a homodimer in solution and determine its crystal structure at 2.6 Å resolution. Dimerization involves the unwinding of a C-terminal α-helix that mimics binding of the AICD internalization sequence, thus shielding the hydrophobic binding pocket. Specific dimer formation is validated by nuclear magnetic resonance (NMR techniques and cell-based analyses reveal that Fe65-PTB2 together with the WW domain are necessary and sufficient for dimerization. Together, our data demonstrate that Fe65 dimerizes via its APP interaction site, suggesting that besides intra- also intermolecular interactions between Fe65 molecules contribute to homeostatic regulation of APP mediated signaling.

  18. Family C 7TM receptor dimerization and activation

    DEFF Research Database (Denmark)

    Bonde, Marie Mi; Sheikh, Søren P; Hansen, Jakob Lerche

    2006-01-01

    to be fully defined. This review presents the biochemical support for family C 7TM receptor dimerization and discusses its importance for receptor biosynthesis, surface expression, ligand binding and activation, since lessons learnt here may well be applicable to the whole superfamily of 7TM receptors....

  19. Angle-Resolved Plasmonic Properties of Single Gold Nanorod Dimers

    Institute of Scientific and Technical Information of China (English)

    Jian Wu; Xuxing Lu; Qiannan Zhu; Junwei Zhao; Qishun Shen; Li Zhan; Weihai Ni

    2014-01-01

    Through wet-chemical assembly methods, gold nanorods were placed close to each other and formed a dimer with a gap distance*1 nm, and hence degenerated plasmonic dipole modes of individual nanorods coupled together to produce hybridized bonding and antibonding resonance modes. Previous studies using a condenser for illumination result in averaged signals over all excitation angles. By exciting an individual dimer obliquely at different angles, we demonstrate that these two new resonance modes are highly tunable and sensitive to the angle between the excitation polarization and the dimer orientation, which follows cos2u dependence. Moreover, for dimer structures with various structure angles, the resonance wavelengths as well as the refractive index sensitivities were found independent of the structure angle. Cal-culated angle-resolved plasmonic properties are in good agreement with the measurements. The assembled nanostructures investigated here are important for fundamental researches as well as potential applications when they are used as building blocks in plasmon-based optical and optoelectronic devices.

  20. Asymmetric electron capture in HCI collisions with rare gas dimers

    Science.gov (United States)

    Matsumoto, J.; Leredde, A.; Fléchard, X.; Shiromaru, H.; Rangama, J.; Zhou, C. L.; Iskandar, W.; Guillous, S.; Hennecart, D.; Mery, A.; Gervais, B.; Cassimi, A.

    2014-04-01

    Low-energy collisions between different rare gas dimers (Ar2, Ne2) and different projectiles (O3+, Ar9+, Xe20+) show that the weight of the different fragmentation processes, Coulomb explosion and Radiative Charge Transfer, strongly depends on the projectile charge state. This result is understood in term of impact parameter from which the electrons are captured on the projectile.

  1. TRF2 recruits ORC through TRFH domain dimerization.

    Science.gov (United States)

    Higa, Mitsunori; Kushiyama, Tatsunori; Kurashige, Seiichiro; Kohmon, Daisuke; Enokitani, Kouki; Iwahori, Satoko; Sugimoto, Nozomi; Yoshida, Kazumasa; Fujita, Masatoshi

    2017-01-01

    Telomeres are specialized chromatin structures that prevent the degradation and instability of the ends of linear chromosomes. While telomerase maintains long stretches of the telomeric repeat, the majority of telomeric DNA is duplicated by conventional DNA replication. A fundamental step in eukaryotic DNA replication involves chromatin binding of the origin recognition complex (ORC). In human cells, telomeric repeat binding factor 2 (TRF2) is thought to play a role in the recruitment of ORC onto telomeres. To better understand the mechanism of TRF2-mediated ORC recruitment, we utilized a lacO-LacI protein tethering system in U2OS cells and found that ectopically targeted TRF2, but not TRF1, can recruit ORC onto the lacO array. We further found that the TRF homology (TRFH) dimerization domain of TRF2, but not its mutant defective in dimerization, is sufficient for ORC and minichromosome maintenance (MCM) recruitment. Mutations impairing the dimerization also compromised ORC recruitment by full-length TRF2. Similar results were obtained using immunoprecipitation and GST pull-down assays. Together, these results suggest that dimerized TRF2 recruits ORC and stimulates pre-replication complex (pre-RC) formation at telomeres through the TRFH domain. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations

    NARCIS (Netherlands)

    De Jong, Djurre H.; Schafer, Lars V.; De Vries, Alex H.; Marrink, Siewert J.; Berendsen, Herman J. C.; Grubmueller, Helmut

    2011-01-01

    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices

  3. Scyphiphin D, a new iridoid glucoside dimer from Scyphiphora hydrophyllacea.

    Science.gov (United States)

    Zeng, Yan-Bo; Mei, Wen-Li; Wang, Hui; Li, Xiao-Na; Dai, Hao-Fu

    2010-11-01

    From the aerial parts of Scyphiphora hydrophyllacea Gaertn. F., a new iridoid glucoside dimer scyphiphin D (1) and a known iridoid glucoside geniposidic acid (2) were isolated. The structure of this new compound was determined on the basis of HR-FAB-MS, IR, (1)H and (13)C NMR (DEPT), and 2D NMR (HMQC, HMBC, COSY, ROESY) spectral data.

  4. (--AMPELOPSIN A : A DIMER RESVERATROL FROM Dryobalanops oblongifolia (dipterocarpaceae

    Directory of Open Access Journals (Sweden)

    Nanik Siti Aminah

    2010-06-01

    Full Text Available A dimer resveratrol compound named (--ampelopsin A was isolated from acetone extract of the stem bark of  Dryobalanops oblongifolia (Dipterocarpaceae. The structure of this compound was determined on the basis of NMR spectroscopic data.   Keywords: (--ampelopsin A, Dryobalanops oblongifolia, Dipterocarpaceae

  5. Construction of covalently coupled, concatameric dimers of 7TM receptors

    DEFF Research Database (Denmark)

    Terpager, Marie; Scholl, D Jason; Kubale, Valentina

    2009-01-01

    7TM receptors are easily fused to proteins such as G proteins and arrestin but because of the fact that their terminals are found on each side of the membrane they cannot be joined directly in covalent dimers. Here, we use an artificial connector comprising a transmembrane helix composed of Leu...

  6. Chemically distinct coupled Cu (II) dimers: Structure and ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 112; Issue 3. Chemically distinct coupled Cu(II) dimers: Structure and physicochemical properties. R Srinivasan R Venkatesan T M Rajendiran P Sambasiva Rao. Volume 112 Issue 3 June 2000 pp 359-359 ...

  7. Facile synthesis of dimer phase of coronene and its optical properties

    Energy Technology Data Exchange (ETDEWEB)

    Hayakawa, T.; Song, H.; Ishii, Y.; Kawasaki, S., E-mail: kawasaki.shinji@nitech.ac.jp [Nagoya Institute of Technology, Gokiso, Showa, Nagoya, Aichi (Japan)

    2016-07-06

    We synthesized very pure dimer phase of coronene by simple heat-treatment and subsequent sublimation purification. It was found that the dimer phase emits very bright red light under the irradiation of low energy ultra-violet light.

  8. Tricriticality for dimeric Coulomb molecular crystals in ground state

    Science.gov (United States)

    Travěnec, Igor; Šamaj, Ladislav

    2017-12-01

    We study the ground-state properties of a system of dimers. Each dimer consists in a pair of equivalent charges at a fixed distance, immersed in a neutralizing homogeneous background. All charges interact pairwisely by Coulomb potential. The dimer centers form a two-dimensional rectangular lattice with the aspect ratio α\\in [0, 1] and each dimer is allowed to rotate around its center. The previous numerical simulations, made for the more general Yukawa interaction, indicate that only two basic dimer configurations can appear: either all dimers are parallel or they have two different angle orientations within alternating (checkerboard) sublattices. As the dimer size increases, two second-order phase transitions, related to two kinds of the symmetry breaking in dimer’s orientations, were reported. In this paper, we use a recent analytic method based on an expansion of the interaction energy in Misra functions which converges quickly and provides an analytic derivation of the critical behaviour. Our main result is that there exists a specific aspect ratio of the rectangular lattice α^*=0.714 106 840 000 71\\ldots which divides the space of model’s phases onto two distinct regions. If the lattice aspect ratio α>α* , we recover both types of the second-order phase transitions and find that they are of mean-field type with the critical exponent β = 1/2 . If 0.711 535≤slantα<α* , the phase transition associated with the discontinuity of dimer’s angles on alternating sublattices becomes of first order. For α=α* , the first- and second-order phase transitions meet at the tricritical point, characterized by the different critical index β = 1/4 . Such phenomenon is known from literature about the Landau theory of one-component fields, but in our two-component version the scenario is more complicated: the component which is already in the symmetry-broken state at the tricritical point also interferes and exhibits unexpectedly the mean-field singular

  9. Designer interface peptide grafts target estrogen receptor alpha dimerization

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, S. [Laboratory of Computational Biophysics & Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174 (United States); Asare, B.K. [Department of Pharmacology and Toxicology, University of Buffalo, Buffalo, NY 14214 (United States); Biswas, P.K., E-mail: pbiswas@tougaloo.edu [Laboratory of Computational Biophysics & Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174 (United States); Rajnarayanan, R.V., E-mail: rajendra@buffalo.edu [Department of Pharmacology and Toxicology, University of Buffalo, Buffalo, NY 14214 (United States)

    2016-09-09

    The nuclear transcription factor estrogen receptor alpha (ERα), triggered by its cognate ligand estrogen, regulates a variety of cellular signaling events. ERα is expressed in 70% of breast cancers and is a widely validated target for anti-breast cancer drug discovery. Administration of anti-estrogen to block estrogen receptor activation is still a viable anti-breast cancer treatment option but anti-estrogen resistance has been a significant bottle-neck. Dimerization of estrogen receptor is required for ER activation. Blocking ERα dimerization is therefore a complementary and alternative strategy to combat anti-estrogen resistance. Dimer interface peptide “I-box” derived from ER residues 503–518 specifically blocks ER dimerization. Recently using a comprehensive molecular simulation we studied the interaction dynamics of ERα LBDs in a homo-dimer. Based on this study, we identified three interface recognition peptide motifs LDKITDT (ERα residues 479–485), LQQQHQRLAQ (residues 497–506), and LSHIRHMSNK (residues 511–520) and reported the suitability of using LQQQHQRLAQ (ER 497–506) as a template to design inhibitors of ERα dimerization. Stability and self-aggregation of peptide based therapeutics poses a significant bottle-neck to proceed further. In this study utilizing peptide grafted to preserve their pharmacophoric recognition motif and assessed their stability and potential to block ERα mediated activity in silico and in vitro. The Grafted peptides blocked ERα mediated cell proliferation and viability of breast cancer cells but did not alter their apoptotic fate. We believe the structural clues identified in this study can be used to identify novel peptidometics and small molecules that specifically target ER dimer interface generating a new breed of anti-cancer agents. - Highlights: • Designer peptide grafts retain core molecular recognition motif during MD simulations. • Designer peptide grafts with Poly-ALA helix form stable

  10. The use of {sup 99m}Tc-thymine to identify metastatic disease in dogs presenting the cutaneous form of canine transmissible venereal tumor; Uso da {sup 99m}Tc-timina na identificacao de metastases de tumor venereo transmissivel canino com apresentacao cutanea

    Energy Technology Data Exchange (ETDEWEB)

    Castelo-Branco, Paulo S.M. [Universidade Estacio de Sa, Rio de Janeiro, RJ (Brazil)]. E-mail: p.castelobranco@ig.com.br; Castro, Veronica; Sena, Priscila [Sociedade Uniao Internacional Protetora dos Animais (SUIPA), Rio de Janeiro, RJ (Brazil); Souza, Sergio A. Lopes de; Lopes, Flavia P.P. Lobo; Pereira, Joao Batista; Fonseca, Lea M. Barbosa da; Gutfilen, Bianca [Hospital Universitario Clementino Fraga Filho, Rio de Janeiro, RJ (Brazil). Dept. de Radiologia

    2008-08-15

    The venereal canine transmissible tumor (VCTT) is described in literature as a rare metastatic tumor. However accurate methods for verification of this affirmative are not available in the veterinary medicine routine. In this study, we evaluated the dissemination from VCTT with cutaneous presentation using the {sup 99m}Tc-Thymine scintigraphy. The labelled thymine was up taken by the three cases of VCTT. {sup 99m}Tc-Thymine is a promising imaging technique for non-invasive veterinarian evaluation of tumoral dissemination degree decurrent from the VCTT cases. (author)

  11. Repair of the three main types of bipyrimidine DNA photoproducts in human keratinocytes exposed to UVB and UVA radiations.

    Science.gov (United States)

    Courdavault, Sophie; Baudouin, Caroline; Charveron, Marie; Canguilhem, Bruno; Favier, Alain; Cadet, Jean; Douki, Thierry

    2005-07-12

    Induction of DNA damage by solar UV radiation is a key event in the development of skin cancers. Bipyrimidine photoproducts, including cyclobutane pyrimidine dimers (CPDs), (6-4) photoproducts (64 PPs) and their Dewar valence isomers, have been identified as major UV-induced DNA lesions. In order to identify the predominant and most persistent lesions, we studied the repair of the three types of photolesions in primary cultures of human keratinocytes. Specific and quantitative data were obtained using HPLC associated with tandem mass spectrometry. As shown in other cell types, 64 PPs are removed from UVB-irradiated keratinocytes much more efficiently than CPDs. In contrast, CPDs are still present in high amounts when cells recover their proliferation capacities after cell cycle arrest and elimination of a part of the population by apoptosis. The predominance of CPDs is still maintained when keratinocytes are exposed to a combination of UVB and UVA. Under these conditions, 64 PPs are converted into their Dewar valence isomers that are as efficiently repaired as their (6-4) precursors. Exposure of cells to pure UVA radiation generates thymine cyclobutane dimers that are slightly less efficiently repaired than CPDs produced upon UVB irradiation. Altogether, our results show that CPDs are the most frequent and the less efficiently repaired bipyrimidine photoproducts irrespectively of the applied UV treatment.

  12. Analysis of UV-induced mutation spectra in Escherichia coli by DNA polymerase {eta} from Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Santiago, Maria Jesus [Departamento de Genetica, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Cordoba (Spain); Alejandre-Duran, Encarna [Departamento de Genetica, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Cordoba (Spain); Ruiz-Rubio, Manuel [Departamento de Genetica, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Cordoba (Spain)]. E-mail: ge1rurum@uco.es

    2006-10-10

    DNA polymerase {eta} belongs to the Y-family of DNA polymerases, enzymes that are able to synthesize past template lesions that block replication fork progression. This polymerase accurately bypasses UV-associated cis-syn cyclobutane thymine dimers in vitro and therefore may contributes to resistance against sunlight in vivo, both ameliorating survival and decreasing the level of mutagenesis. We cloned and sequenced a cDNA from Arabidopsis thaliana which encodes a protein containing several sequence motifs characteristics of Pol{eta} homologues, including a highly conserved sequence reported to be present in the active site of the Y-family DNA polymerases. The gene, named AtPOLH, contains 14 exons and 13 introns and is expressed in different plant tissues. A strain from Saccharomyces cerevisiae, deficient in Pol{eta} activity, was transformed with a yeast expression plasmid containing the AtPOLH cDNA. The rate of survival to UV irradiation in the transformed mutant increased to similar values of the wild type yeast strain, showing that AtPOLH encodes a functional protein. In addition, when AtPOLH is expressed in Escherichia coli, a change in the mutational spectra is detected when bacteria are irradiated with UV light. This observation might indicate that AtPOLH could compete with DNA polymerase V and then bypass cyclobutane pyrimidine dimers incorporating two adenylates.

  13. Dimerization of MT1-MMP during cellular invasion detected by flourescence resonance energy transfer

    OpenAIRE

    Itoh, Yoshifumi; Palmisano, Ralf; Anilkumar, Narayanapanicker; Nagase, Hideaki; Miyawaki, Atsushi; Seiki, Motoharu

    2011-01-01

    Abstract Homo-dimerization of the membrane-bound collagenase MT1-MMP is crucial for its collagenolytic activity. However, it has not been clear if this dimerization is regulated during cellular invasion into 3D collagen matrices. To address this question, we established a fluorescence resonance energy transfer system to detect MT1-MMP dimerization and analysed the process in cells invading through 3D collagen. Our data indicates that dimerization occurrs dynamically and constantly ...

  14. Mixed Quantum/Classical Method for Nonadiabatic Quantum Dynamics in Explicit Solvent Models: The ππ*/nπ* Decay of Thymine in Water as a Test Case.

    Science.gov (United States)

    Cerezo, Javier; Liu, Yanli; Lin, Na; Zhao, Xian; Improta, Roberto; Santoro, Fabrizio

    2018-01-03

    We present a novel mixed quantum classical dynamical method to include solvent effects on internal conversion (IC) processes. All the solute degrees of freedom are represented by a wavepacket moving according to nonadiabatic quantum dynamics, while the motion of an explicit solvent model is described by an ensemble of classical trajectories. The mutual coupling of the solute and solvent dynamics is included within a mean-field framework and the quantum and classical equations of motions are solved simultaneously. As a test case we apply our method to the ultrafast ππ* → nπ* decay of thymine in water. Solvent dynamical response modifies IC yield already on the 50 fs time scale. This effect is due to water librational motions that stabilize the most populated state. Pure static disorder, that is, the existence of different solvent configurations when photoexcitation takes place, also has a remarkable impact on the dynamics.

  15. A first principles study of fluorescence quenching in rhodamine B dimers : how can quenching occur in dimeric species?

    NARCIS (Netherlands)

    Setiawan, Dani; Kazaryan, Andranik; Martoprawiro, Muhamad Abdulkadir; Filatov, Michael

    2010-01-01

    Rhodamine B (RhB) is widely used in chemistry and biology due to its high fluorescence quantum yield. In high concentrations, the quantum yield of fluorescence decreases considerably which is attributed to the formation of RhB dimers. In the present work, a possible mechanism of fluorescence

  16. Higher order expansions for the entropy of a dimer or a monomer-dimer system on d-dimensional lattices

    CERN Document Server

    Butera, Paolo; Pernici, Mario

    2013-01-01

    Recently an expansion as a power series in 1/d has been presented for the specific entropy of a complete dimer covering of a d-dimensional hypercubic lattice. This paper extends from 3 to 10 the number of terms known in the series. Likewise an expansion for the entropy, dependent on the dimer-density p, of a monomer-dimer system, involving a sum sum_k a_k(d) p^k, has been recently offered. We herein extend the number of the known expansion coefficients from 6 to 20 for the hyper-cubic lattices of general dimension d and from 6 to 24 for the hyper-cubic lattices of dimensions d 2. The computations of this paper have led us to make the following marvelous conjecture: "In the case of the hyper-cubic lattices, all the expansion coefficients, a_k(d), are positive"! This paper results from a simple melding of two disparate research programs: one computing to high orders the Mayer series coefficients of a dimer gas, the other studying the development of entropy from these coefficients. An effort is made to make thi...

  17. Evaluation of stability difference between asymmetric homochiral dimer in (S)-thalidomide crystal and symmetric heterochiral dimer in (RS)-thalidomide crystal

    Science.gov (United States)

    Suzuki, Toshiya; Tanaka, Masahito; Shiro, Motoo; Shibata, Norio; Osaka, Tetsuya; Asahi, Toru

    2010-03-01

    This article discusses differences in physicochemical properties such as solubility and melting point between (S)-thalidomide and (RS)-thalidomide based on crystal structures determined by X-ray diffraction experiments. Investigation of such differences is of great importance because thalidomide has attracted considerable attention again due to its wide-range bioactivity for intractable diseases. In this article, structures of hydrogen-bonded rings were compared between asymmetric homochiral dimers in (S)-thalidomide crystal and symmetric heterochiral dimers in (RS)-thalidomide crystal. The heterochiral dimer was evaluated to be more stable than the homochiral dimer by the energy calculations for hydrogen-bonded rings in those dimers. These results indicate that differences in physicochemical properties between enantiomeric and racemic thalidomides originate from the difference of structural stability between homochiral and heterochiral dimers.

  18. Dimerization of Receptor Protein-Tyrosine Phosphatase alpha in living cells

    Directory of Open Access Journals (Sweden)

    Gadella Theodorus WJ

    2001-06-01

    Full Text Available Abstract Background Dimerization is an important regulatory mechanism of single membrane-spanning receptors. For instance, activation of receptor protein-tyrosine kinases (RPTKs involves dimerization. Structural, functional and biochemical studies suggested that the enzymatic counterparts of RPTKs, the receptor protein-tyrosine phosphatases (RPTPs, are inhibited by dimerization, but whether RPTPs actually dimerize in living cells remained to be determined. Results In order to assess RPTP dimerization, we have assayed Fluorescence Resonance Energy Transfer (FRET between chimeric proteins of cyan- and yellow-emitting derivatives of green fluorescent protein, fused to RPTPα, using three different techniques: dual wavelength excitation, spectral imaging and fluorescence lifetime imaging. All three techniques suggested that FRET occurred between RPTPα -CFP and -YFP fusion proteins, and thus that RPTPα dimerized in living cells. RPTPα dimerization was constitutive, extensive and specific. RPTPα dimerization was consistent with cross-linking experiments, using a non-cell-permeable chemical cross-linker. Using a panel of deletion mutants, we found that the transmembrane domain was required and sufficient for dimerization. Conclusions We demonstrate here that RPTPα dimerized constitutively in living cells, which may be mediated by the transmembrane domain, providing strong support for the model that dimerization is involved in regulation of RPTPs.

  19. D-dimer: An Overview of Hemostasis and Fibrinolysis, Assays, and Clinical Applications.

    Science.gov (United States)

    Olson, John D

    2015-01-01

    D-dimer is the smallest fibrinolysis-specific degradation product found in the circulation. The origins, assays, and clinical use of D-dimer will be addressed. Hemostasis (platelet and vascular function, coagulation, fibrinolysis, hemostasis) is briefly reviewed. D-dimer assays are reviewed. The D-dimer is very sensitive to intravascular thrombus and may be markedly elevated in disseminated intravascular coagulation, acute aortic dissection, and pulmonary embolus. Because of its exquisite sensitivity, negative tests are useful in the exclusion venous thromboembolism. Elevations occur in normal pregnancy, rising two- to fourfold by delivery. D-dimer also rises with age, limiting its use in those >80 years old. There is a variable rise in D-dimer in active malignancy and indicates increased thrombosis risk in active disease. Elevated D-dimer following anticoagulation for a thrombotic event indicates increased risk of recurrent thrombosis. These and other issues are addressed. © 2015 Elsevier Inc. All rights reserved.

  20. Association of atoms into universal dimers using an oscillating magnetic field.

    Science.gov (United States)

    Langmack, Christian; Smith, D Hudson; Braaten, Eric

    2015-03-13

    In a system of ultracold atoms near a Feshbach resonance, pairs of atoms can be associated into universal dimers by an oscillating magnetic field with a frequency near that determined by the dimer binding energy. We present a simple expression for the transition rate that takes into account many-body effects through a transition matrix element of the contact. In a thermal gas, the width of the peak in the transition rate as a function of the frequency is determined by the temperature. In a dilute Bose-Einstein condensate of atoms, the width is determined by the inelastic scattering rates of a dimer with zero-energy atoms. Near an atom-dimer resonance, there is a dramatic increase in the width from inelastic atom-dimer scattering and from atom-atom-dimer recombination. The recombination contribution provides a signature for universal tetramers that are Efimov states consisting of two atoms and a dimer.

  1. Glycine transporter dimers: evidence for occurrence in the plasma membrane

    DEFF Research Database (Denmark)

    Bartholomäus, Ingo; Milan-Lobo, Laura; Nicke, Annette

    2008-01-01

    membrane based on hydrodynamic and native gel electrophoretic studies. Here, we used cysteine substitution and oxidative cross-linking to show that of GlyT1 and GlyT2 also form dimeric complexes within the plasma membrane. GlyT oligomerization at the cell surface was confirmed for both GlyT1 and GlyT2......Different Na(+)/Cl(-)-dependent neurotransmitter transporters of the SLC6a family have been shown to form dimers or oligomers in both intracellular compartments and at the cell surface. In contrast, the glycine transporters (GlyTs) GlyT1 and -2 have been reported to exist as monomers in the plasma...

  2. d -wave superconductivity in boson+fermion dimer models

    Science.gov (United States)

    Goldstein, Garry; Chamon, Claudio; Castelnovo, Claudio

    2017-05-01

    We present a slave-particle mean-field study of the mixed boson+fermion quantum dimer model introduced by Punk et al. [Proc. Natl. Acad. Sci. USA 112, 9552 (2015), 10.1073/pnas.1512206112] to describe the physics of the pseudogap phase in cuprate superconductors. Our analysis naturally leads to four charge e fermion pockets whose total area is equal to the hole doping p for a range of parameters consistent with the t -J model for high-temperature superconductivity. Here we find that the dimers are unstable to d -wave superconductivity at low temperatures. The region of the phase diagram with d -wave rather than s -wave superconductivity matches well with the appearance of the four fermion pockets. In the superconducting regime, the dispersion contains eight Dirac cones along the diagonals of the Brillouin zone.

  3. Radiative and rovibrational collisional relaxation of sodium dimer

    Science.gov (United States)

    Bayram, Burcin; Horton, Tim; McFarland, Jacob

    2016-05-01

    Radiative and rovibrational collisional relaxation of sodium dimer of the A1Σu+ (8,30) state have been measured by direct observation of the decay fluorescence. Sodium molecular vapor is created in a heatpipe oven at 600 K and excited using a 6-ns pulsed dye laser pumped by a Nd:YAG, operating at 532 nm. The preliminary lifetime measurement was done by directly acquiring lifetime data through boxcar averager from the stored oscilloscope trace of the fluorescence. Analysis of the exponential decay of the fluorescence allows us to obtain the radiative lifetime. By introducing the argon buffer gas and varying the pressure of the heatpipe, a collisional cross section between excited sodium dimer and ground state argon atom collision can be extracted using Stern-Volmer relation.

  4. Cytotoxic bibenzyl dimers from the stems of Dendrobium fimbriatum Hook.

    Science.gov (United States)

    Xu, Feng-Qing; Xu, Fang-Cheng; Hou, Bo; Fan, Wei-Wei; Zi, Cheng-Ting; Li, Yan; Dong, Fa-Wu; Liu, Yu-Qing; Sheng, Jun; Zuo, Zhi-Li; Hu, Jiang-Miao

    2014-11-15

    The bioassay-guided chemical investigation of the stems of Dendrobium fimbriatum Hook led to the isolation of seven first reported bibenzyl dimers with a linkage of a methylene moiety, fimbriadimerbibenzyls A-G (1-7), together with a new dihydrophenanthrene derivative (S)-2,4,5,9-tetrahydroxy-9,10-dihydrophenanthrene (8) and thirteen known compounds (9-21). The structure of the new compound was established by spectroscopic analysis. Biological evaluation of bibenzyl derivatives against five human cell lines indicated that seven of those compounds exhibited broad-spectrum and cytotoxic activities with IC50 values ranging from 2.2 to 21.2 μM. Those rare bibenzyl dimers exhibited cytotoxic activities in vitro and the cytotoxicity decreased as the number of oxygen-containing groups in the structure decreases. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Mechanically controlled quantum interference in individual π-stacked dimers.

    Science.gov (United States)

    Frisenda, Riccardo; Janssen, Vera A E C; Grozema, Ferdinand C; van der Zant, Herre S J; Renaud, Nicolas

    2016-12-01

    Recent observations of destructive quantum interference in single-molecule junctions confirm the role of quantum effects in the electronic conductance properties of molecular systems. These effects are central to a broad range of chemical and biological processes and may be beneficial for the design of single-molecule electronic components to exploit the intrinsic quantum effects that occur at the molecular scale. Here we show that destructive interference can be turned on or off within the same molecular system by mechanically controlling its conformation. Using a combination of ab initio calculations and single-molecule conductance measurements, we demonstrate the existence of a quasiperiodic destructive quantum-interference pattern along the breaking traces of π-stacked molecular dimers. The results demonstrate that it is possible to control the molecular conductance over more than one order of magnitude and with a sub-ångström resolution by exploiting the subtle structure-property relationship of π-stacked dimers.

  6. D-dimer measurements in acute aortic dissection

    Directory of Open Access Journals (Sweden)

    Vladyslava Bazylevska

    2016-07-01

    Full Text Available Acute aortic dissection (AAD is a medical emergency with significant morbidity and mortality. The diagnosis can be challenging due to the wide array of presenting symptoms and a broad differential diagnosis. Computed tomographic angiography is currently the gold standard for diagnosis of AAD. However, it carries the risk of contrast and radiation exposure and has a financial burden for patients. Multiple biomarkers have been evaluated as a screening tool for AAD. D-dimer has previously been suggested as a sole rule-out test for AAD. It is rapid and inexpensive, is widely available in the emergency rooms, and is highly sensitive for any thrombotic event. This review article evaluates the evidence for the use of D-dimer assays in the diagnosis of AAD, in differentiation of AAD from acute coronary syndromes, and in risk stratification of AAD patients.

  7. Data on dimer formation between importin α subtypes

    Directory of Open Access Journals (Sweden)

    Yoichi Miyamoto

    2016-06-01

    Full Text Available This article describes data related to the research article titled “Functional characterization of importin α8 as a classical nuclear localization signal receptor” [1]. A GST pull-down assay showed that both importin α1 and α8, which are classical nuclear localization signal (cNLS receptors, can form a dimer with importin α6, α7, or α8. Importin α8 has higher dimer-forming ability than importin α1. In addition, our data show that either importin α1 or importin α8 can form a heterodimer with importin α3, which exists in a preformed complex with cNLS substrates such as the conventional SV40TNLS or the p53 protein, resulting in the release of the cNLS substrates from importin α3.

  8. Emergence of a Dimer-Dimer Interaction in the Low-Energy Effective Quantum-Dimer Model of a Diamond-Like-Decorated Square-Lattice Heisenberg Antiferromagnets with Further Neighbor Couplings

    Science.gov (United States)

    Hirose, Yuhei; Oguchi, Akihide; Fukumoto, Yoshiyuki

    2017-12-01

    We study spin-1/2 Heisenberg antiferromagnets on a diamond-like-decorated square lattice perturbed by two kinds of further neighbor couplings. In our previous study [https://doi.org/10.7566/JPSJ.85.094002" xlink:type="simple">J. Phys. Soc. Jpn. 85, 094002 (2016)], the second-order effective Hamiltonian for the Heisenberg model perturbed by a further neighbor coupling was found to be a square-lattice quantum-dimer model with a finite hopping amplitude, t > 0, and no dimer-dimer interaction, v = 0. In this study, we introduce another kind of further neighbor coupling and show that it leads to an attractive interaction between dimers, which suggests the stabilization of the columnar phase of the square-lattice quantum-dimer model. The calculated v/t is presented as a function of the ratio of the two exchange parameters in the Heisenberg model.

  9. A New Hydroxychavicol Dimer from the Roots of Piper betle

    Directory of Open Access Journals (Sweden)

    Huei-Yu Tu

    2013-02-01

    Full Text Available A new hydroxychavicol dimer, 2-(g'-hydroxychavicol-hydroxychavicol (1, was isolated from the roots of Piper betle Linn. along with five known compounds, hydroxychavicol (2, aristololactam A II (3, aristololactam B II (4, piperolactam A (5 and cepharadione A (6. The structures of these isolated compounds were elucidated by spectroscopic methods. Compounds 1 and 2 exhibited inhibitory effects on the generation of superoxide anion and the release of elastase by human neutrophils.

  10. Dimerization and DNA recognition rules of mithramycin and its analogues

    OpenAIRE

    Weidenbach, Stevi; Hou, Caixia; Chen, Jhong-Min; Tsodikov, Oleg V.; Rohr, J?rgen

    2015-01-01

    The antineoplastic and antibiotic natural product mithramycin (MTM) is used against cancer-related hypercalcemia and, experimentally, against Ewing sarcoma and lung cancers. MTM exerts its cytotoxic effect by binding DNA as a divalent metal ion (Me2+)-coordinated dimer and disrupting the function of transcription factors. A precise molecular mechanism of action of MTM, needed to develop MTM analogues selective against desired transcription factors, is lacking. Although it is known that MTM bi...

  11. Plasmon excitations in the dimers formed by atom chains

    Science.gov (United States)

    Xue, Hong-jie; Hao, Da-peng; Zhang, Ming; Wang, Xiao-mei

    2017-02-01

    Based on the linear response theory in the random-phase approximation and the free-electron gas model, we study the plasmon excitations in the dimers formed by atom chains. With the help of energy absorption spectrum and charge distribution, the evolutions of longitudinal and transverse plasmon, and the effect of the system parameters such as size, atomic separation and electron filling on plasmon are obtained. In addition, the dipole, quadrupole, end and central plasmon are observed.

  12. A new phenylspirodrimane dimer from the fungus Stachybotrys chartarum.

    Science.gov (United States)

    Ding, Zhang-Gui; Ding, Jian-Hai; Zhao, Jiang-Yuan; Chunyu, Wei-Xun; Li, Ming-Gang; Gu, Shao-Jie; Wang, Fei; Wen, Meng-Liang

    2018-03-01

    A new phenylspirodrimane dimer, named stachartarin A (1), was isolated from cultures of the tin mine tailings-associated fungus Stachybotrys chartarum. Its structures were elucidated by means of spectroscopic methods. At the same time, the compound was tested for its cytotoxicity against HL-60, SMMC-7721, A-549, MCF-7, and SW480 cells. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Synthesis and anti-inflammatory activity of phenylbutenoid dimer analogs

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung Soo; Fang, Yuan Ying; Park, Hae Eil [Kangwon National University, Chuncheon (Korea, Republic of)

    2015-06-15

    Several phenylbutenoid dimer (PBD) analogs were synthesized and evaluated for their inhibitory activities against nitric oxide (NO) production and TNF-α release. The PBD analogs were synthesized via Diels–Alder and subsequent Schlosser reactions as key steps. Among the tested compounds, two analogs (8c, 8f) exhibited much stronger inhibitory activity against LPS-stimulated NO production and TNF-α release in RAW 264.7 cells than that of wogonin.

  14. On the photophysics and photochemistry of the water dimer

    Energy Technology Data Exchange (ETDEWEB)

    Segarra-Marti, Javier; Merchan, Manuela [Instituto de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, 46071 Valencia (Spain); Roca-Sanjuan, Daniel; Lindh, Roland [Department of Chemistry - Angstroem, Theoretical Chemistry Program, Uppsala University, Box 518, 75120 Uppsala (Sweden)

    2012-12-28

    The photochemistry of the water dimer irradiated by UV light is studied by means of the complete active space perturbation theory//complete active space self-consistent field (CASPT2//CASSCF) method and accurate computational approaches like as minimum energy paths. Both electronic structure computations and ab initio molecular dynamics simulations are carried out. The results obtained show small shifts relative to a single water molecule on the vertical excitation energies of the dimer due to the hydrogen bond placed between the water donor (W{sub D}) and the water acceptor (W{sub A}). A red-shift and a blue-shift are predicted for the W{sub D} and W{sub A}, respectively, supporting previous theoretical and experimental results. The photoinduced chemistry of the water dimer is described as a process occurring between two single water molecules in which the effect of the hydrogen bond plays a minor role. Thus, the photoinduced decay routes correspond to two photodissociation processes, one for each water molecule. The proposed mechanism for the decay channels of the lowest-lying excited states of the system is established as the photochemical production of a hydrogen-bonded H{sub 2}O Horizontal-Ellipsis HO species plus a hydrogen H atom.

  15. Protocadherin cis-dimer architecture and recognition unit diversity.

    Science.gov (United States)

    Goodman, Kerry M; Rubinstein, Rotem; Dan, Hanbin; Bahna, Fabiana; Mannepalli, Seetha; Ahlsén, Göran; Aye Thu, Chan; Sampogna, Rosemary V; Maniatis, Tom; Honig, Barry; Shapiro, Lawrence

    2017-11-14

    Clustered protocadherins (Pcdhs) mediate numerous neural patterning functions, including neuronal self-recognition and non-self-discrimination to direct self-avoidance among vertebrate neurons. Individual neurons stochastically express a subset of Pcdh isoforms, which assemble to form a stochastic repertoire of cis-dimers. We describe the structure of a PcdhγB7 cis-homodimer, which includes the membrane-proximal extracellular cadherin domains EC5 and EC6. The structure is asymmetric with one molecule contributing interface surface from both EC5 and EC6, and the other only from EC6. Structural and sequence analyses suggest that all Pcdh isoforms will dimerize through this interface. Site-directed mutants at this interface interfere with both Pcdh cis-dimerization and cell surface transport. The structure explains the known restrictions of cis-interactions of some Pcdh isoforms, including α-Pcdhs, which cannot form homodimers. The asymmetry of the interface approximately doubles the size of the recognition repertoire, and restrictions on cis-interactions among Pcdh isoforms define the limits of the Pcdh recognition unit repertoire.

  16. Self-discrimination of enantiomers in hydrogen-bonded dimers.

    Science.gov (United States)

    Alkorta, Ibon; Elguero, Jose

    2002-02-20

    The homochiral and heterochiral hydrogen-bonded (HB) dimers of a set of small model molecules (alpha-amino alcohols) have been studied by means of ab initio methods. The gas-phase calculations have been carried out with the hybrid HF/DFT B3LYP method and the 6-311++G** basis set. The electron density of the complexes has been analyzed using the atoms in molecules (AIM) methodology, which allows characterization of the HB interactions and additional intermolecular contacts. To take into account the water solvation effect, the polarized continuum model (PCM) method has been used to evaluate the Delta G(solv). The gas-phase results show that the heterochiral dimers are the most stable ones for each case studied, while in solution for several cases, the relative stability is reversed and the homochiral dimers become more stable. The AIM analysis shows the typical bond critical points characteristic of the HB and additional bond critical points denoting, in this case, destabilization of intermolecular interaction as CF(3)...F(3)C and CH(3)...H(3)C contacts.

  17. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Energy Technology Data Exchange (ETDEWEB)

    Storrs, Richard Wood [Univ. of California, Berkeley, CA (United States)

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by 31P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 Å of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an α-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  18. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Energy Technology Data Exchange (ETDEWEB)

    Storrs, R.W.

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by [sup 31]P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 [Angstrom] of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an [alpha]-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  19. Cockayne syndrome: varied requirement of transcription-coupled nucleotide excision repair for the removal of three structurally different adducts from transcribed DNA.

    Directory of Open Access Journals (Sweden)

    Nataliya Kitsera

    Full Text Available Hereditary defects in the transcription-coupled nucleotide excision repair (TC-NER pathway of damaged DNA cause severe neurodegenerative disease Cockayne syndrome (CS, however the origin and chemical nature of the underlying DNA damage had remained unknown. To find out, to which degree the structural properties of DNA lesions determine the extent of transcription arrest in human CS cells, we performed quantitative host cell reactivation analyses of expression vectors containing various synthetic adducts. We found that a single 3-(deoxyguanosin-N2-yl-2-acetylaminofluorene adduct (dG(N2-AAF constitutes an unsurmountable obstacle to transcription in both CS-A and CS-B cells and is removed exclusively by the CSA- and CSB-dependent pathway. In contrast, contribution of the CS proteins to the removal of two other transcription-blocking DNA lesions - N-(deoxyguanosin-8-yl-2-acetylaminofluorene (dG(C8-AAF and cyclobutane thymine-thymine (TT dimer - is only minor (TT dimer or none (dG(C8-AAF. The unique properties of dG(N2-AAF identify this adduct as a prototype for a new class of DNA lesions that escape the alternative global genome repair and could be critical for the CS pathogenesis.

  20. Qualitative point-of-care D-dimer testing compared with quantitative D-dimer testing in excluding pulmonary embolism in primary care

    NARCIS (Netherlands)

    Lucassen, W. A M; Erkens, P. M G; Geersing, G. J.; Büller, H. R.; Moons, K. G M; Stoffers, H. E J H; van Weert, H. C P M

    2015-01-01

    Background: General practitioners can safely exclude pulmonary embolism (PE) by using the Wells PE rule combined with D-dimer testing. Objective: To compare the accuracy of a strategy using the Wells rule combined with either a qualitative point-of-care (POC) D-dimer test performed in primary care

  1. Neutral dipole-dipole dimers: A new field in science

    Science.gov (United States)

    Kosower, Edward M.; Borz, Galina

    2018-03-01

    Dimer formation with dipole neutralization produces species such as low polarity water (LPW) compatible with hydrophobic surfaces (Phys. Chem. Chem. Phys. 2015, 17, 24895-24900) Dimerization and dipole neutralization occurs for N-methylacetamide on polyethylene, a behavior drastically different from its contortions in acetonitrile on AgBr:AgCl planar crystals (AgX) (ChemPhysChem 2014, 15, 3598-3607). The weak infrared absorption of the amide dimer on polyethylene is shown experimentally. Dimerization of palmitic acid is shown along with some of the many ramifications for intracellular systems. Polyoligomers of water are present on polyethylene surfaces. Some high resolution spectra of three of the polyoligomers of water are shown along with a mechanistic scheme for polyoligomer formation and dissolution. The structures of some of the oligomers are known from spectroscopic studies of water on AgX. The scope of the article begins with PE, generally accepted as hydrophobic. The IR of PE revealed not only that water was present but that it appeared in two forms, oligomers (O) and polyoligomers (PO). How did we recognize what they were? These species had been observed as especially strong "marker" peaks in the spectra1 of water placed on planar AgX, a platform developed by Katzir and his coworkers [6]. But there was a problem: the proximity to PE of oligomers with substantial (calculated) dipole moments and thus polarity, including cyclic hexamers of water (chair and boat forms), the cyclic pentamer, the books I and II, and the cyclic trimer [7a]. Another link was needed, a role perfectly fit by the already cited low polarity water (LPW). The choice was experimentally supported by the detection of low intensity absorption in the bending region.Some important generalities flow from these results. What other dimers might be present in the biological or chemical world? Palmitic acid dimer (PAD) would be a candidate for decreasing the polarity of the acid (PA). Another

  2. A potential new, stable state of the E-cadherin strand-swapped dimer in solution.

    Science.gov (United States)

    Schumann-Gillett, Alexandra; Mark, Alan E; Deplazes, Evelyne; O'Mara, Megan L

    2018-01-01

    E-cadherin is a transmembrane glycoprotein that facilitates inter-cellular adhesion in the epithelium. The ectodomain of the native structure is comprised of five repeated immunoglobulin-like domains. All E-cadherin crystal structures show the protein in one of three alternative conformations: a monomer, a strand-swapped trans homodimer and the so-called X-dimer, which is proposed to be a kinetic intermediate to forming the strand-swapped trans homodimer. However, previous studies have indicated that even once the trans strand-swapped dimer is formed, the complex is highly dynamic and the E-cadherin monomers may reorient relative to each other. Here, molecular dynamics simulations have been used to investigate the stability and conformational flexibility of the human E-cadherin trans strand-swapped dimer. In four independent, 100 ns simulations, the dimer moved away from the starting structure and converged to a previously unreported structure, which we call the Y-dimer. The Y-dimer was present for over 90% of the combined simulation time, suggesting that it represents a stable conformation of the E-cadherin dimer in solution. The Y-dimer conformation is stabilised by interactions present in both the trans strand-swapped dimer and X-dimer crystal structures, as well as additional interactions not found in any E-cadherin dimer crystal structures. The Y-dimer represents a previously unreported, stable conformation of the human E-cadherin trans strand-swapped dimer and suggests that the available crystal structures do not fully capture the conformations that the human E-cadherin trans homodimer adopts in solution.

  3. FT-IR and Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometries and atomic charges of uracil and 5-methyluracil (thymine)

    Science.gov (United States)

    Singh, J. S.

    2015-02-01

    FT-IR (400-4000 cm-1) and Raman spectra (200-4000 cm-1) of uracil and 5-methyluracil (thymine) have been recorded and analyzed. The optimized molecular geometries, atomic polar tensor (APT) charges and vibrational characteristics have been studied theoretically using restricted Hartree-Fock (RHF) and density functional theory (DFT) methods. Using the Becke's exchange in conjunction with Lee-Yang-Parr's correlation functional and Becke's three-parameter hybrid method (B3LYP), the ab initio and DFT calculations were carried out to study the optimized molecular fundamental vibrational frequencies for uracil and 5-methyluracil (thymine) by employing Gaussian-03 program. The fundamental vibrational frequencies along with their corresponding intensities in IR and Raman activities and depolarization ratios of the Raman lines have also been calculated using the RHF and DFT methods employing different basis sets. In quantum chemical calculations, most of the B3LYP/6-311++G∗∗ vibrational frequencies are in excellent agreement with the available experimental assignments and helped to propose in the reassignments of some missing frequencies in experimental study. Assuming under the Cs point group for both molecules, the distribution of normal mode of vibrations between the two species as planar (a‧) and non-planar (a″) for all 39 normal vibrational modes of 5-methyluracil are given by 26a‧ + 13a″, of which 30 modes (21a‧ + 9a″) correspond to the uracil moiety and 9 modes (5a‧ + 4a″) to the CH3 group. Consistent assignments have been made for the internal modes of CH3 group, especially for the anti-symmetric CH3 stretching and bending modes. A possible explanation could be the planarity of pyrimidine ring and non-planarity at carbon site of methyl group which might cause the splitting of frequencies including three components due to the substitution of CH3 group at the site of C5 atom on pyrimidine ring of uracil. The three non-equivalent CH bonds of CH3

  4. Complex Relationship between Ligand Binding and Dimerization in the Epidermal Growth Factor Receptor

    Directory of Open Access Journals (Sweden)

    Nicholas J. Bessman

    2014-11-01

    Full Text Available The epidermal growth factor receptor (EGFR plays pivotal roles in development and is mutated or overexpressed in several cancers. Despite recent advances, the complex allosteric regulation of EGFR remains incompletely understood. Through efforts to understand why the negative cooperativity observed for intact EGFR is lost in studies of its isolated extracellular region (ECR, we uncovered unexpected relationships between ligand binding and receptor dimerization. The two processes appear to compete. Surprisingly, dimerization does not enhance ligand binding (although ligand binding promotes dimerization. We further show that simply forcing EGFR ECRs into preformed dimers without ligand yields ill-defined, heterogeneous structures. Finally, we demonstrate that extracellular EGFR-activating mutations in glioblastoma enhance ligand-binding affinity without directly promoting EGFR dimerization, suggesting that these oncogenic mutations alter the allosteric linkage between dimerization and ligand binding. Our findings have important implications for understanding how EGFR and its relatives are activated by specific ligands and pathological mutations.

  5. Age- and sex-dependent reference intervals for D-dimer

    DEFF Research Database (Denmark)

    Haase, Christine; Joergensen, Maja; Ellervik, Christina

    2013-01-01

    A low D-dimer is commonly used to exclude venous thromboembolism in low risk patients. However, the reference intervals are poorly defined and D-dimer has been shown to increase by patient age. We aimed to establish age- and sex-dependent D-dimer reference intervals and to test the consequence of...... of different cut-off limits.......A low D-dimer is commonly used to exclude venous thromboembolism in low risk patients. However, the reference intervals are poorly defined and D-dimer has been shown to increase by patient age. We aimed to establish age- and sex-dependent D-dimer reference intervals and to test the consequence...

  6. Factors associated with D-dimer levels in HIV-infected individuals

    DEFF Research Database (Denmark)

    Borges, Alvaro H; O'Connor, Jemma L; Phillips, Andrew N

    2014-01-01

    with measured D-dimer levels were included (N = 9,848). Factors associated with D-dimer were identified by linear regression. Covariates investigated were: age, gender, race, body mass index, nadir and baseline CD4+ count, plasma HIV RNA levels, markers of inflammation (C-reactive protein [CRP], interleukin-6......BACKGROUND: Higher plasma D-dimer levels are strong predictors of mortality in HIV+ individuals. The factors associated with D-dimer levels during HIV infection, however, remain poorly understood. METHODS: In this cross-sectional study, participants in three randomized controlled trials...... viruses, was positively correlated with D-dimer. Other factors independently associated with higher D-dimer levels were black race, higher plasma HIV RNA levels, being off ART at baseline, and increased levels of CRP, IL-6 and cystatin C. In contrast, higher baseline CD4+ counts and higher high...

  7. Unexpected methyl migrations of ethanol dimer under synchrotron VUV radiation

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Weizhan; Hu, Yongjun, E-mail: yjhu@scnu.edu.cn, E-mail: lssheng@ustc.edu.cn; Li, Weixing; Guan, Jiwen [MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631 (China); Liu, Fuyi; Shan, Xiaobin; Sheng, Liusi, E-mail: yjhu@scnu.edu.cn, E-mail: lssheng@ustc.edu.cn [National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029 (China)

    2015-01-14

    While methyl transfer is well known to occur in the enzyme- and metal-catalyzed reactions, the methyl transfer in the metal-free organic molecules induced by the photon ionization has been less concerned. Herein, vacuum ultraviolet single photon ionization and dissociation of ethanol dimer are investigated with synchrotron radiation photoionization mass spectroscopy and theoretical methods. Besides the protonated clusters cation (C{sub 2}H{sub 5}OH) ⋅ H{sup +} (m/z = 47) and the β-carbon-carbon bond cleavage fragment CH{sub 2}O ⋅ (C{sub 2}H{sub 5}OH)H{sup +} (m/z = 77), the measured mass spectra revealed that a new fragment (C{sub 2}H{sub 5}OH) ⋅ (CH{sub 3}){sup +} (m/z = 61) appeared at the photon energy of 12.1 and 15.0 eV, where the neutral dimer could be vertically ionized to higher ionic state. Thereafter, the generated carbonium ions are followed by a Wagner-Meerwein rearrangement and then dissociate to produce this new fragment, which is considered to generate after surmounting a few barriers including intra- and inter-molecular methyl migrations by the aid of theoretical calculations. The appearance energy of this new fragment is measured as 11.55 ± 0.05 eV by scanning photoionization efficiency curve. While the signal intensity of fragment m/z = 61 starts to increase, the fragments m/z = 47 and 77 tend to slowly incline around 11.55 eV photon energy. This suggests that the additional fragment channels other than (C{sub 2}H{sub 5}OH) ⋅ H{sup +} and CH{sub 2}O ⋅ (C{sub 2}H{sub 5}OH)H{sup +} have also been opened, which consume some dimer cations. The present report provides a clear description of the photoionization and dissociation processes of the ethanol dimer in the range of the photon energy 12-15 eV.

  8. Bethe Ansatz Solutions of the Bose-Hubbard Dimer

    Directory of Open Access Journals (Sweden)

    Jon Links

    2006-12-01

    Full Text Available The Bose-Hubbard dimer Hamiltonian is a simple yet effective model for describing tunneling phenomena of Bose-Einstein condensates. One of the significant mathematical properties of the model is that it can be exactly solved by Bethe ansatz methods. Here we review the known exact solutions, highlighting the contributions of V.B. Kuznetsov to this field. Two of the exact solutions arise in the context of the Quantum Inverse Scattering Method, while the third solution uses a differential operator realisation of the su(2 Lie algebra.

  9. Stepwise "Dark Photoswitching" of Photochromic Dimers in a Junction

    DEFF Research Database (Denmark)

    Olsen, Stine Tetzschner; Hansen, Thorsten; Nielsen, Mogens Brøndsted

    2017-01-01

    Molecular photoswitches incorporated in a junction present a way to achieve light-controlled conductance switching by photoisomerization. Yet, the two isomers might also interconvert upon charging of the molecule if this results in a change in their relative energies. This behavior (current......-induced switching) has been termed dark photoswitching and was observed for the dihydroazulene–vinylheptafulvene couple in a junction. In this theoretical study, we expand this concept to dimeric structures containing two dihydroazulene units linked through meta- or para-phenylene bridges and anchored...

  10. Twisted-order parameter applied to dimerized ladders

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, J; Martin-Delgado, M A [Departamento de Fisica Teorica I, Universidad Complutense, 28040 Madrid (Spain); Sierra, G [Instituto de Fisica Teorica, C.S.I.C.-U.A.M., Madrid (Spain)

    2008-12-05

    We apply the twisted-order parameter (TOP) for dimerized quantum spin ladders to locate the critical points that separate gapped phases representing quantum spin liquids of various types. Using the density matrix renormalization group (DMRG), method, we find that the TOP is a good order parameter for these systems regardless of the number of legs. As a check, we reproduce with the DMRG and periodic boundary conditions the computations previously done with quantum Monte Carlo for one-dimensional S = 1/2, S = 1, S = 3/2 and S = 2 Heisenberg chains with alternating bonds.

  11. Graphite-Based Nanocomposite Electrochemical Sensor for Multiplex Detection of Adenine, Guanine, Thymine, and Cytosine: A Biomedical Prospect for Studying DNA Damage.

    Science.gov (United States)

    Ng, Khan Loon; Khor, Sook Mei

    2017-09-19

    Guanine (G), adenine (A), thymine (T), and cytosine (C) are the four basic constituents of DNA. Studies on DNA composition have focused especially on DNA damage and genotoxicity. However, the development of a rapid, simple, and multiplex method for the simultaneous measurement of the four DNA bases remains a challenge. In this study, we describe a graphite-based nanocomposite electrode (Au-rGO/MWCNT/graphite) that uses a simple electro-co-deposition approach. We successfully applied the developed sensor for multiplex detection of G, A, T, and C, using square-wave voltammetry. The sensor was tested using real animal and plant DNA samples in which the hydrolysis of T and C could be achieved with 8 mol L-1 of acid. The electrochemical sensor exhibited excellent sensitivity (G = 178.8 nA/μg mL-1, A = 92.9 nA/μg mL-1, T = 1.4 nA/μg mL-1, and C = 15.1 9 nA/μg mL-1), low limit of detection (G, A = 0.5 μg mL-1; T, C = 1.0 μg mL-1), and high selectivity in the presence of common interfering factors from biological matrixes. The reliability of the established method was assessed by method validation and comparison with the ultraperformance liquid chromatography technique, and a correlation of 103.7% was achieved.

  12. Excess-electron injection and transfer in terthiophene-modified DNA: terthiophene as a photosensitizing electron donor for thymine, cytosine, and adenine.

    Science.gov (United States)

    Park, Man Jae; Fujitsuka, Mamoru; Kawai, Kiyohiko; Majima, Tetsuro

    2012-02-13

    Excess-electron transfer (EET) in DNA has attracted wide attention owing to its close relation to DNA repair and nanowires. To clarify the dynamics of EET in DNA, a photosensitizing electron donor that can donate an excess electron to a variety of DNA sequences has to be developed. Herein, a terthiophene (3T) derivative was used as the photosensitizing electron donor. From the dyad systems in which 3T was connected to a single nucleobase, it was revealed that (1) 3T* donates an excess electron efficiently to thymine, cytosine, and adenine, despite adenine being a well-known hole conductor. The free-energy dependence of the electron-transfer rate was explained on the basis of the Marcus theory. From the DNA hairpins, it became clear that (1) 3T* can donate an excess electron not only to the adjacent nucleobase but also to the neighbor one nucleobase further along and so on. From the charge-injection rate, the possibilities of smaller β value and/or charge delocalization were discussed. In addition, EET through consecutive cytosine nucleobases was suggested. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Tuning the Sensitivity of Fluorescent Porphyrin Dimers to Viscosity and Temperature

    Science.gov (United States)

    Vyšniauskas, Aurimas; Ding, Dong; Qurashi, Maryam; Boczarow, Igor; Balaz, Milan; Anderson, Harry L.

    2017-01-01

    Abstract Conjugated porphyrin dimers have emerged as versatile viscosity‐sensitive fluorophores that are suitable for quantitative measurements of microscopic viscosity by ratiometric and fluorescence lifetime‐based methods, in a concentration‐independent manner. Here, we investigate the effect of extended conjugation in a porphyrin‐dimer structure on their ability to sense viscosity and temperature. We show that the sensitivity of the fluorescence lifetime to temperature is a unique property of only a few porphyrin dimers. PMID:28480989

  14. A crescent-shaped ALIX dimer targets ESCRT-III CHMP4 filaments.

    OpenAIRE

    Pires, Ricardo; Hartlieb, Bettina; Signor, Luca; Schoehn, Guy; Lata, Suman; Roessle, Manfred; Moriscot, Christine; Popov, Sergei; Hinz, Andreas; Jamin, Marc; Boyer, Veronique; Sadoul, Remy; Forest, Eric; Svergun, Dmitri I.; Göttlinger, Heinrich G.

    2009-01-01

    International audience; ALIX recruits ESCRT-III CHMP4 and is involved in membrane remodeling during endosomal receptor sorting, budding of some enveloped viruses, and cytokinesis. We show that ALIX dimerizes via the middle domain (ALIX(-V)) in solution. Structural modeling based on small angle X-ray scattering (SAXS) data reveals an elongated crescent-shaped conformation for dimeric ALIX lacking the proline-rich domain (ALIX(BRO1-V)). Mutations at the dimerization interface prevent dimerizati...

  15. Species A rotavirus NSP3 acquires its translation inhibitory function prior to stable dimer formation.

    Directory of Open Access Journals (Sweden)

    Hugo I Contreras-Treviño

    Full Text Available Species A rotavirus non-structural protein 3 (NSP3 is a translational regulator that inhibits or, under some conditions, enhances host cell translation. NSP3 binds to the translation initiation factor eIF4G1 and evicts poly-(A binding protein (PABP from eIF4G1, thus inhibiting translation of polyadenylated mRNAs, presumably by disrupting the effect of PABP bound to their 3'-ends. NSP3 has a long coiled-coil region involved in dimerization that includes a chaperone Hsp90-binding domain (HS90BD. We aimed to study the role in NSP3 dimerization of a segment of the coiled-coil region adjoining the HS90BD. We used a vaccinia virus system to express NSP3 with point mutations in conserved amino acids in the coiled-coil region and determined the effects of these mutations on translation by metabolic labeling of proteins as well as on accumulation of stable NSP3 dimers by non-dissociating Western blot, a method that separates stable NSP3 dimers from the monomer/dimerization intermediate forms of the protein. Four of five mutations reduced the total yield of NSP3 and the formation of stable dimers (W170A, K171E, R173E and R187E:K191E, whereas one mutation had the opposite effects (Y192A. Treatment with the proteasome inhibitor MG132 revealed that stable NSP3 dimers and monomers/dimerization intermediates are susceptible to proteasome degradation. Surprisingly, mutants severely impaired in the formation of stable dimers were still able to inhibit host cell translation, suggesting that NSP3 dimerization intermediates are functional. Our results demonstrate that rotavirus NSP3 acquires its function prior to stable dimer formation and remain as a proteasome target throughout dimerization.

  16. D-dimer as marker for microcirculatory failure: correlation with LOD and APACHE II scores.

    Science.gov (United States)

    Angstwurm, Matthias W A; Reininger, Armin J; Spannagl, Michael

    2004-01-01

    The relevance of plasma d-dimer levels as marker for morbidity and organ dysfunction in severely ill patients is largely unknown. In a prospective study we determined d-dimer plasma levels of 800 unselected patients at admission to our intensive care unit. In 91% of the patients' samples d-dimer levels were elevated, in some patients up to several hundredfold as compared to normal values. The highest mean d-dimer values were present in the patient group with thromboembolic diseases, and particularly in non-survivors of pulmonary embolism. In patients with circulatory impairment (r=0.794) and in patients with infections (r=0.487) a statistically significant correlation was present between d-dimer levels and the APACHE II score (PLOD, PLOD score. Taking all patients together, no correlations of d-dimer levels with single organ failure or with indicators of infection could be detected. In conclusion, d-dimer plasma levels strongly correlated with the severity of the disease and organ dysfunction in patients with circulatory impairment or infections suggesting that elevated d-dimer levels may reflect the extent of microcirculatory failure. Thus, a therapeutic strategy to improve the microcirculation in such patients may be monitored using d-dimer plasma levels.

  17. Radiation-induced tetramer-to-dimer transition of Escherichia coli lactose repressor

    Energy Technology Data Exchange (ETDEWEB)

    Goffinont, S. [Centre de Biophysique Moleculaire, CNRS, rue C. Sadron, 45071 Orleans (France); Davidkova, M. [Department of Radiation Dosimetry, Nuclear Physics Institute AS CR, Na Truhlarce 39/64, 18086, Prague 8 (Czech Republic); Spotheim-Maurizot, M., E-mail: spotheim@cnrs-orleans.fr [Centre de Biophysique Moleculaire, CNRS, rue C. Sadron, 45071 Orleans (France)

    2009-08-21

    The wild type lactose repressor of Escherichia coli is a tetrameric protein formed by two identical dimers. They are associated via a C-terminal 4-helix bundle (called tetramerization domain) whose stability is ensured by the interaction of leucine zipper motifs. Upon in vitro {gamma}-irradiation the repressor losses its ability to bind the operator DNA sequence due to damage of its DNA-binding domains. Using an engineered dimeric repressor for comparison, we show here that irradiation induces also the change of repressor oligomerisation state from tetramer to dimer. The splitting of the tetramer into dimers can result from the oxidation of the leucine residues of the tetramerization domain.

  18. Syntheses and optical and electrochemical properties of porphyrin dimers linked by metal ions.

    Science.gov (United States)

    Richeter, Sébastien; Jeandon, Christophe; Gisselbrecht, Jean-Paul; Ruppert, Romain; Callot, Henry J

    2002-05-29

    The preparation, isolation, and characterization of several new peripherally functionalized monomeric porphyrins and metalloporphyrins and of porphyrin dimers are described. These dimers are obtained by linking with metal ions two monomeric porphyrins bearing at their periphery an enaminoketone chelate fully conjugated with the aromatic ring. Porphyrin dimers linked by metal ions display large interactions in the ground state as evidenced by their electronic spectra and their electrochemical behavior. Compared to the monomeric analogue, these dimers show absorption spectra with intensified red-shifted Q-bands and their first oxidation potentials are substantially lowered and split into two distinct redox steps.

  19. Suppression of the singularly localized states in dimer quasiperiodic Fibonacci superlattices

    Science.gov (United States)

    Aziz, Z.; Bentata, S.; Djelti, R.; Sefir, Y.

    2010-05-01

    Using the transfer-matrix technique, we have numerically investigated the effect of introducing the dimer on the nature of the states across Dimer Fibonacci semiconductor superlattices on the miniband structure of the GaAs/Al xGa 1- xAs superlattices. By the introduction of the dimer model, the transmission spectra reveal the appearance of a miniband structure with a concomitant disappearance of the singularly localized states. This behavior is due to the interaction between the states of the dimer wells inside the potential and, therefore, the system is seen by the particle as two overlapped ordered structures.

  20. Experimental Observation of Strongly Bound Dimers of Sulfuric Acid: Application to Nucleation in the Atmosphere

    DEFF Research Database (Denmark)

    Petaja, Tuukka; Sipila, Mikko; Paasonen, Pauli

    2011-01-01

    Sulfuric acid is a key compound in atmospheric nucleation. Here we report on the observation of a close-to-collision-limited sulfuric acid dimer formation in atmospherically relevant laboratory conditions in the absence of measurable quantities of ammonia or organics. The observed dimer formation...... compound(s) with (a) concentration(s) high enough to prevent the dimer evaporation. Such a stabilizing compound should be abundant enough in any natural environment and would therefore not limit the formation of sulfuric acid dimers in the atmosphere....

  1. Binding capacities of human serum albumin monomer and dimer by continuous frontal affinity chromatography.

    Science.gov (United States)

    Nakano, N I; Shimamori, Y; Yamaguchi, S

    1982-03-19

    Human serum albumin monomer and dimer obtained by fractionation of a commercial preparation were immobilized on CH-Sepharose 4B by covalent coupling. For salicylic acid, warfarin, phenylbutazone, mefenamic acid, sulphamethizole and sulphonylureas, the binding capacities of the monomer and dimer were compared by continuous frontal affinity chromatography. The salicylate-binding capacities of both monomer and dimer were essentially retained upon immobilization. For these drugs, the dimer showed only about 10-30% less capacity per monomeric unit than that of the monomer, the reduction being associated for most drugs with the intrinsic binding constant rather than with the number of binding sites.

  2. Solid-phase synthesis of 2{sup '}-O-methoxyethyl oligonucleotides using dimeric phosphoramidate blocks

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Gi Weon; Kang, Yong Han [Dept. of Applied Chemistry, Hanyang University, Ansan (Korea, Republic of)

    2016-11-15

    This research focused on the method of using dimeric phosphoramidite blocks to synthesize oligonucleotides for development as oligonucleotide drugs. A 16-mer oligonucleotide with the randomly selected sequence of C*C*T*C*G*C *T*C*T*C*G*C*C* C*G*C was synthesized using CC, GC, and TC dimers, a combination of monomers and dimers, or only monomers as building blocks. Using dimer blocks in this synthetic method provided a significant decrease in critical impurities that had similar properties to the main product, which was confirmed by LC-MS and HPLC analysis.

  3. Modified field enhancement and extinction by plasmonic nanowire dimers due to nonlocal response

    DEFF Research Database (Denmark)

    Toscano, Giuseppe; Raza, Søren; Jauho, Antti-Pekka

    2012-01-01

    it in a wide frequency range against analytical results for the extinction cross section of a cylindrical plasmonic nanowire. Our main results concern more complex geometries, namely cylindrical and bow-tie nanowire dimers that can strongly enhance optical fields. For both types of dimers we find that nonlocal...... response can strongly affect both the field enhancement in between the dimers and their respective extinction cross sections. In particular, we give examples of blueshifted maximal field enhancements near hybridized plasmonic dimer resonances that are still large but nearly two times smaller than...

  4. Diagnostic implication of fibrin degradation products and D-dimer in aortic dissection

    Science.gov (United States)

    Dong, Jian; Duan, Xianli; Feng, Rui; Zhao, Zhiqing; Feng, Xiang; Lu, Qingsheng; Jing, Qing; Zhou, Jian; Bao, Junmin; Jing, Zaiping

    2017-03-01

    Fibrin degradation products (FDP) and D-dimer have been considered to be involved in many vascular diseases. In this study we aimed to explore the diagnostic implication of FDP and D-dimer in aortic dissection patients. 202 aortic dissection patients were collected as the case group, 150 patients with other cardiovascular diseases, including myocardial infarction (MI, n = 45), pulmonary infarction (n = 51) and abdominal aortic aneurysm (n = 54) were collected as non-dissection group, and 27 healthy people were in the blank control group. The FDP and D-dimer levels were detected with immune nephelometry. Logist regression analysis was performed to evaluate the influence of FDP and D-dimer for the aortic dissection patients. ROC curve was used to determine the diagnostic value of FDP and D-dimer. The FDP and D-dimer levels were significantly higher in aortic dissection patients than in non-dissection patients and the healthy controls. FDP and D-dimer were both the risk factors for patients with aortic dissection. From the ROC analysis, diagnostic value of FDP and D-dimer were not high to distinguish aortic dissection patients from the non-dissection patients. However FDP and D-dimer could be valuable diagnostic marker to differentiate aortic dissection patients and healthy controls with both AUC 0.863.

  5. Physicochemical Mechanism of Light-Driven DNA Repair by (6-4) Photolyases

    Science.gov (United States)

    Faraji, Shirin; Dreuw, Andreas

    2014-04-01

    DNA photolyases are light-activated enzymes that repair DNA damage induced by ultraviolet (UV) radiation. UV radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photolesions. Photolyases selectively bind to DNA and initiate the splitting of mutagenic pyrimidine dimers via photoinduced electron transfer from a flavin adenine dinucleotide anion (FADH-) to the lesion triggering its repair. This review discusses the consecutive steps of the repair process, from both experimental and theoretical points of view. It covers the following issues: the process of how photolyases accommodate the lesion into their binding pockets, excitation energy transfer between two involved catalytic cofactors, photoinduced electron transfer to the lesion, the splitting of the pyrimidine dimer radical anion, and the fate of the unstable radical species created after the splitting of the thymine dimer. In particular, mechanisms of the splitting and restoration of the original bases are described in detail, and the most probable repair pathways are outlined.

  6. Proteolysis of truncated hemolysin A yields a stable dimerization interface

    Energy Technology Data Exchange (ETDEWEB)

    Novak, Walter R.P.; Bhattacharyya, Basudeb; Grilley, Daniel P.; Weaver, Todd M. (Wabash); (UW)

    2017-02-21

    Wild-type and variant forms of HpmA265 (truncated hemolysin A) fromProteus mirabilisreveal a right-handed, parallel β-helix capped and flanked by segments of antiparallel β-strands. The low-salt crystal structures form a dimeric structureviathe implementation of on-edge main-chain hydrogen bonds donated by residues 243–263 of adjacent monomers. Surprisingly, in the high-salt structures of two variants, Y134A and Q125A-Y134A, a new dimeric interface is formedviamain-chain hydrogen bonds donated by residues 203–215 of adjacent monomers, and a previously unobserved tetramer is formed. In addition, an eight-stranded antiparallel β-sheet is formed from the flap regions of crystallographically related monomers in the high-salt structures. This new interface is possible owing to additional proteolysis of these variants after Tyr240. The interface formed in the high-salt crystal forms of hemolysin A variants may mimic the on-edge β-strand positioning used in template-assisted hemolytic activity.

  7. Peptide dimerization-dissociation rates from replica exchange molecular dynamics

    Science.gov (United States)

    Leahy, Cathal T.; Kells, Adam; Hummer, Gerhard; Buchete, Nicolae-Viorel; Rosta, Edina

    2017-10-01

    We show how accurate rates of formation and dissociation of peptide dimers can be calculated using direct transition counting (DTC) from replica-exchange molecular dynamics (REMD) simulations. First, continuous trajectories corresponding to system replicas evolving at different temperatures are used to assign conformational states. Second, we analyze the entire REMD data to calculate the corresponding rates at each temperature directly from the number of transition counts. Finally, we compare the kinetics extracted directly, using the DTC method, with indirect estimations based on trajectory likelihood maximization using short-time propagators and on decay rates of state autocorrelation functions. For systems with relatively low-dimensional intrinsic conformational dynamics, the DTC method is simple to implement and leads to accurate temperature-dependent rates. We apply the DTC rate-extraction method to all-atom REMD simulations of dimerization of amyloid-forming NNQQ tetrapetides in explicit water. In an assessment of the REMD sampling efficiency with respect to standard MD, we find a gain of more than a factor of two at the lowest temperature.

  8. Ankyrin-G Inhibits Endocytosis of Cadherin Dimers.

    Science.gov (United States)

    Cadwell, Chantel M; Jenkins, Paul M; Bennett, Vann; Kowalczyk, Andrew P

    2016-01-08

    Dynamic regulation of endothelial cell adhesion is central to vascular development and maintenance. Furthermore, altered endothelial adhesion is implicated in numerous diseases. Therefore, normal vascular patterning and maintenance require tight regulation of endothelial cell adhesion dynamics. However, the mechanisms that control junctional plasticity are not fully understood. Vascular endothelial cadherin (VE-cadherin) is an adhesive protein found in adherens junctions of endothelial cells. VE-cadherin mediates adhesion through trans interactions formed by its extracellular domain. Trans binding is followed by cis interactions that laterally cluster the cadherin in junctions. VE-cadherin is linked to the actin cytoskeleton through cytoplasmic interactions with β- and α-catenin, which serve to increase adhesive strength. Furthermore, p120-catenin binds to the cytoplasmic tail of cadherin and stabilizes it at the plasma membrane. Here we report that induced cis dimerization of VE-cadherin inhibits endocytosis independent of both p120 binding and trans interactions. However, we find that ankyrin-G, a protein that links membrane proteins to the spectrin-actin cytoskeleton, associates with VE-cadherin and inhibits its endocytosis. Ankyrin-G inhibits VE-cadherin endocytosis independent of p120 binding. We propose a model in which ankyrin-G associates with and inhibits the endocytosis of VE-cadherin cis dimers. Our findings support a novel mechanism for regulation of VE-cadherin endocytosis through ankyrin association with cadherin engaged in lateral interactions. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Predicting Product Distribution of Propene Dimerization in Nanoporous Materials.

    Science.gov (United States)

    Liu, Yifei Michelle; Smit, Berend

    2017-06-02

    In this work, a theoretical framework is developed to explain and predict changes in the product distribution of the propene dimerization reaction, which yields a mixture of C6 olefin isomers, resulting from the use of different porous materials as catalysts. The MOF-74 class of materials has shown promise in catalyzing the dimerization of propene with high selectivity for valuable linear olefin products. We show that experimentally observed changes in the product distribution can be explained in terms of the contribution of the pores to the free energy of formation, which are directly computed using molecular simulation. Our model is used to screen a library of 118 existing and hypothetical MOF and zeolite structures to study how product distribution can be tuned by changing pore size, shape, and composition of porous materials. Using these molecular descriptors, catalyst properties are identified that increase the selective reaction of linear olefin isomers, which are valued as industrial feedstocks. A pore size commensurate with the size of the desired linear products enhances linear conversion by sterically hindering the branched isomers. Another promising feature is the presence of open metal sites, which interact with the olefin π-bond to provide favorable binding sites for the linear isomers.

  10. Phosphate-Linked Silibinin Dimers (PLSd): New Promising Modified Metabolites.

    Science.gov (United States)

    Romanucci, Valeria; Gravante, Raffaele; Cimafonte, Martina; Marino, Cinzia Di; Mailhot, Gilles; Brigante, Marcello; Zarrelli, Armando; Fabio, Giovanni Di

    2017-08-11

    By exploiting the regioselective protection of the hydroxyl groups of silibinin along with the well-known phosphoramidite chemistry, we have developed an efficient strategy for the synthesis of new silibinin-modified species, which we have named Phosphate-Linked Silibinin Dimers (PLSd), in which the monomer units are linked by phosphodiester bonds. The antioxidant abilities of the new PLSd were estimated on HepG2 cells using DPPH free radical scavenging and xanthine/xanthine oxidase assays. The new phosphate-metabolites showed a higher anti-oxidant activity than the silibinin, as well as very low toxicity. The ability to scavenge reactive oxygen species (ROS) such as singlet oxygen () and hydroxyl radical () reveals that the two dimers are able to scavenge about two times more effectively than silibinin. Finally, solubility studies have shown that the PLSd present good water solubility (more than 20 mg·L-1) under circumneutral pH values, whereas the silibinin was found to be very poorly soluble (less than 0.4 mg·L-1) and not stable under alkaline conditions. Together, the above promising results warrant further investigation of the future potential of the PLSd as anti-oxidant metabolites within the large synthetic polyphenols field.

  11. Dimerization of a Viral SET Protein Endows its Function

    Energy Technology Data Exchange (ETDEWEB)

    H Wei; M Zhou

    2011-12-31

    Histone modifications are regarded as the most indispensible phenomena in epigenetics. Of these modifications, lysine methylation is of the greatest complexity and importance as site- and state-specific lysine methylation exerts a plethora of effects on chromatin structure and gene transcription. Notably, paramecium bursaria chlorella viruses encode a conserved SET domain methyltransferase, termed vSET, that functions to suppress host transcription by methylating histone H3 at lysine 27 (H3K27), a mark for eukaryotic gene silencing. Unlike mammalian lysine methyltransferases (KMTs), vSET functions only as a dimer, but the underlying mechanism has remained elusive. In this study, we demonstrate that dimeric vSET operates with negative cooperativity between the two active sites and engages in H3K27 methylation one site at a time. New atomic structures of vSET in the free form and a ternary complex with S-adenosyl homocysteine and a histone H3 peptide and biochemical analyses reveal the molecular origin for the negative cooperativity and explain the substrate specificity of H3K27 methyltransferases. Our study suggests a 'walking' mechanism, by which vSET acts all by itself to globally methylate host H3K27, which is accomplished by the mammalian EZH2 KMT only in the context of the Polycomb repressive complex.

  12. Intermolecular Coulombic Decay (ICD) Occuring in Triatomic Molecular Dimer

    Science.gov (United States)

    Iskandar, Wael; Gatton, Averell; Gaire, Bishwanath; Champenois, Elio; Larsen, Kirk; Shivaram, Niranjan; Moradmand, Ali; Severt, Travis; Williams, Joshua; Slaughter, Daniel; Weber, Thorsten

    2017-04-01

    For over two decades, the production of ICD process has been extensively investigated theoretically and experimentally in different systems bounded by a week force (ex. van-der-Waals or Hydrogen force). Furthermore, the ICD process has been demonstrated a strong implication in biological system (DNA damage and DNA repair mechanism) because of the production of genotoxic low energy electrons during the decay cascade. Studying large complex system such as triatomic molecular dimer may be helpful for further exploration of ``Auger electron driven cancer therapy''. The present experiment investigates the dissociation dynamics happened in collision between a photons and CO2 dimer. We will focus more specifically on the CO2++CO2+ fragmentation channel and the detection in coincidence of the two ionic fragments and the two electrons will be done using a COld Target Recoil Ion Momentum Spectroscopy (COLTRIMS). The measurements of the Kinetic Energy Release of the two fragments and the relative angular distribution of the electrons in the molecular frame reveal that the ICD is the only mechanism responsible for the production of this fragmentation channel.

  13. Comparative Molecular Dynamics Studies of Human DNA Polymerase η

    Science.gov (United States)

    2015-01-01

    High-energy ultraviolet radiation damages DNA through the formation of cyclobutane pyrimidine dimers, which stall replication. When the lesion is a thymine–thymine dimer (TTD), human DNA polymerase η (Pol η) assists in resuming the replication process by inserting nucleotides opposite the damaged site. We performed extensive molecular dynamics (MD) simulations to investigate the structural and dynamical effects of four different Pol η complexes with or without a TTD and with either dATP or dGTP as the incoming base. No major differences in the overall structures and equilibrium dynamics were detected among the four systems, suggesting that the specificity of this enzyme is due predominantly to differences in local interactions in the binding regions. Analysis of the hydrogen-bonding interactions between the enzyme and the DNA and dNTP provided molecular-level insights. Specifically, the TTD was observed to engage in more hydrogen-bonding interactions with the enzyme than its undamaged counterpart of two normal thymines. The resulting greater rigidity and specific orientation of the TTD are consistent with the experimental observation of higher processivity and overall efficiency at TTD sites than at analogous sites with two normal thymines. The similarities between the systems containing dATP and dGTP are consistent with the experimental observation of relatively low fidelity with respect to the incoming base. Moreover, Q38 and R61, two strictly conserved amino acids across the Pol η family, were found to exhibit persistent hydrogen-bonding interactions with the TTD and cation-π interactions with the free base, respectively. Thus, these simulations provide molecular level insights into the basis for the selectivity and efficiency of this enzyme, as well as the roles of the two most strictly conserved residues. PMID:26562587

  14. Anti-parallel dimer and tetramer formation of propylene carbonate

    Science.gov (United States)

    Tagawa, Ayana; Numata, Tomoko; Shikata, Toshiyuki

    2017-09-01

    Raman scattering and infrared (IR) absorption spectra of enantiopure (R)-propylene carbonate ((R)PC) and racemic propylene carbonate (PC) were recorded at room temperature, 25 °C, in benzene (Bz) solution and in the pure liquid state to investigate the presence of dimers and other higher order intermolecular associations. (R)PC and PC both demonstrated a strong C=O stretching vibrational band. The band exhibited changes in its shape and resonance wavenumber highly dependent on the concentrations of PCs, whereas a difference between the chirality of (R)PC and PC had little influence. In an extremely dilute condition, doubly split bands were observed at 1807 and 1820 cm-1 in both Raman and IR spectra, which are assigned to the characteristic bands of isolated monomeric PCs. An additional band appeared at 1795 cm-1 in a dilute to concentrated regime, and its magnitude strengthened with increasing concentrations accompanied with slight increasing in the magnitude of 1807 cm-1 band in Raman spectra, while an increase in the magnitude of 1807 cm-1 band was clearly greater than that of 1795 cm-1 band in IR spectra. The spectrum changes at 1795 and 1807 cm-1 were attributed to characteristics of anti-parallel dimer formation of PCs caused by strong dipole-dipole interactions between C=O groups. Moreover, another additional signal was clearly observed at 1780-1790 cm-1 in a concentrated regime, and became the primary signal in the pure liquid state with slight increasing in the intensity of 1795 cm-1 band in Raman spectra. On the other hand, in IR spectra the observed increasing of 1780-1790 cm-1 band was much less than that of 1795 cm-1 band. These newly found spectrum changes in the concentrated regime are attributed to the formation of anti-parallel tetramers of PCs based on the characteristics of band selection rule found in Raman and IR spectra. Equilibrium constants for the anti-parallel dimer (KD) and tetramer formation (KT) of PCs in Bz solution and in the pure

  15. Anti-parallel dimer and tetramer formation of propylene carbonate

    Directory of Open Access Journals (Sweden)

    Ayana Tagawa

    2017-09-01

    Full Text Available Raman scattering and infrared (IR absorption spectra of enantiopure (R-propylene carbonate ((RPC and racemic propylene carbonate (PC were recorded at room temperature, 25 °C, in benzene (Bz solution and in the pure liquid state to investigate the presence of dimers and other higher order intermolecular associations. (RPC and PC both demonstrated a strong C=O stretching vibrational band. The band exhibited changes in its shape and resonance wavenumber highly dependent on the concentrations of PCs, whereas a difference between the chirality of (RPC and PC had little influence. In an extremely dilute condition, doubly split bands were observed at 1807 and 1820 cm-1 in both Raman and IR spectra, which are assigned to the characteristic bands of isolated monomeric PCs. An additional band appeared at 1795 cm-1 in a dilute to concentrated regime, and its magnitude strengthened with increasing concentrations accompanied with slight increasing in the magnitude of 1807 cm-1 band in Raman spectra, while an increase in the magnitude of 1807 cm-1 band was clearly greater than that of 1795 cm-1 band in IR spectra. The spectrum changes at 1795 and 1807 cm-1 were attributed to characteristics of anti-parallel dimer formation of PCs caused by strong dipole-dipole interactions between C=O groups. Moreover, another additional signal was clearly observed at 1780-1790 cm-1 in a concentrated regime, and became the primary signal in the pure liquid state with slight increasing in the intensity of 1795 cm-1 band in Raman spectra. On the other hand, in IR spectra the observed increasing of 1780-1790 cm-1 band was much less than that of 1795 cm-1 band. These newly found spectrum changes in the concentrated regime are attributed to the formation of anti-parallel tetramers of PCs based on the characteristics of band selection rule found in Raman and IR spectra. Equilibrium constants for the anti-parallel dimer (KD and tetramer formation (KT of PCs in Bz solution and in

  16. Chemically induced contraction and stretching of a linear rotaxane dimer.

    Science.gov (United States)

    Jimenez-Molero, Maria Consuelo; Dietrich-Buchecker, Christiane; Sauvage, Jean-Pierre

    2002-03-15

    Copper(I)-induced assembly of two self-complementary identical units, which consist of a ring that incorporates a 1,10-phenanthroline group attached to a small filament containing a second 1,10-phenanthroline (phen) group, leads quantitatively to a doubly threaded complex. Each copper(I) center is four-coordinate and is located inside a ring and bound to a phen from the macrocyle. The two other coordination sites are occupied by a phen from the filament connected to the other ring. An X-ray structure of the dicopper(I) complex unambiguously demonstrates the doubly threaded nature of the system. The molecule has C(2) symmetry in the crystal. This is an extended form with a Cu small middle dot small middle dot small middle dotCu separation of 18.3 A and an overall length close to 40 A. Further synthetic work, which utilizes the two terminal phenolic functions of the previous dicopper(I) complex, gives rise to a more complex system in which both filaments have been prolonged in opposite directions by 2,2':6',2"-terpyridine (terpy) motifs and bulky stoppers. The organic backbone is that of a rotaxane dimer. Although redox cycling of Cu(I) to Cu(II) did not lead to intramolecular rearrangement, simple chemical reactions induced large conformational changes. The rotaxane dimer was set in motion as follows. The dicopper(I) complex, which is in an extended conformation, was demetallated by using KCN. From the free ligand, the dizinc complex was formed quantitatively at room temperature. (1)H NMR data show that a new conformation is obtained: each Zn(II) is five-coordinate (phen + terpy), and the molecule is in a contracted conformation. This process is reminiscent of biological muscles in the sense that the two filaments of this system can be moved along one another in a gliding motion that keeps the whole system together, but which converts a stretched compound (overall length approximately equal to 83 A) into a contracted species (overall length approximately equal to 65

  17. Synchronized oscillations of dimers in biphasic charged fd-virus suspensions

    Science.gov (United States)

    Kang, K.; Piao, S. H.; Choi, H. J.

    2016-08-01

    Micron-sized colloidal spheres that are dispersed in an isotropic-nematic biphasic host suspension of charged rods (fd-virus particles) are shown to spontaneously form dimers, which exhibit a synchronized oscillatory motion. Dimer formation is not observed in the monophase of isotropic and nematic suspensions. The synchronized oscillations of dimers are connected to the inhomogeneous state of the host suspension of charged rods (fd viruses) where nematic domains are in coexistence with isotropic regions. The synchronization of oscillations occurs in bulk states, in the absence of an external field. With a low field strength of an applied electric field, the synchronization is rather reduced, but it recovers again when the field is turned off. In this Rapid Communication, we report this observation as an example of the strange attractor, occurring in the mixture of PS (polystyrene) dimers in an isotropic-nematic coexistence biphasic fd-virus network. Furthermore, we highlight that the synchronization of PS-dimer oscillations is the result of a global bifurcation diagram, driven by a delicate balance between the short-attractive "twisted" interaction of PS dimers and long-ranged electrostatic repulsive interactions of charged fd rods. The interest is then in the local enhancement of "twist-nematic" elasticity in reorientation of the dimer oscillations. An analysis of image-time correlations is provided with the data movies and Fourier transforms of averaged orientations for the synchronized oscillations of dimers in the biphasic I -N coexistence concentration of charged fd-virus suspensions.

  18. Dynamics and kinetics of reversible homo-molecular dimerization of polycyclic aromatic hydrocarbons.

    Science.gov (United States)

    Mao, Qian; Ren, Yihua; Luo, K H; van Duin, Adri C T

    2017-12-28

    Physical dimerization of polycyclic aromatic hydrocarbons (PAHs) has been investigated via molecular dynamics (MD) simulation with the ReaxFF reactive force field that is developed to bridge the gap between the quantum mechanism and classical MD. Dynamics and kinetics of homo-molecular PAH collision under different temperatures, impact parameters, and orientations are studied at an atomic level, which is of great value to understand and model the PAH dimerization. In the collision process, the enhancement factors of homo-molecular dimerizations are quantified and found to be larger at lower temperatures or with smaller PAH instead of size independent. Within the capture radius, the lifetime of the formed PAH dimer decreases as the impact parameter increases. Temperature and PAH characteristic dependent forward and reverse rate constants of homo-molecular PAH dimerization are derived from MD simulations, on the basis of which a reversible model is developed. This model can predict the tendency of PAH dimerization as validated by pyrene dimerization experiments [H. Sabbah et al., J. Phys. Chem. Lett. 1(19), 2962 (2010)]. Results from this study indicate that the physical dimerization cannot be an important source under the typical flame temperatures and PAH concentrations, which implies a more significant role played by the chemical route.

  19. D-Dimer assay as a non invasive test for the diagnosis of left atrial ...

    African Journals Online (AJOL)

    Background: Systemic embolism is a serious and sometime fatal complication of rheumatic MS. Objective: We assessed the predictive power of D-Dimer level to predict occurrence of left atrial (LA) thrombi in patients with rheumatic mitral stenosis (MS). Methods: D-dimer levels were analyzed for 24 patients with rheumatic ...

  20. Dynamics and kinetics of reversible homo-molecular dimerization of polycyclic aromatic hydrocarbons

    Science.gov (United States)

    Mao, Qian; Ren, Yihua; Luo, K. H.; van Duin, Adri C. T.

    2017-12-01

    Physical dimerization of polycyclic aromatic hydrocarbons (PAHs) has been investigated via molecular dynamics (MD) simulation with the ReaxFF reactive force field that is developed to bridge the gap between the quantum mechanism and classical MD. Dynamics and kinetics of homo-molecular PAH collision under different temperatures, impact parameters, and orientations are studied at an atomic level, which is of great value to understand and model the PAH dimerization. In the collision process, the enhancement factors of homo-molecular dimerizations are quantified and found to be larger at lower temperatures or with smaller PAH instead of size independent. Within the capture radius, the lifetime of the formed PAH dimer decreases as the impact parameter increases. Temperature and PAH characteristic dependent forward and reverse rate constants of homo-molecular PAH dimerization are derived from MD simulations, on the basis of which a reversible model is developed. This model can predict the tendency of PAH dimerization as validated by pyrene dimerization experiments [H. Sabbah et al., J. Phys. Chem. Lett. 1(19), 2962 (2010)]. Results from this study indicate that the physical dimerization cannot be an important source under the typical flame temperatures and PAH concentrations, which implies a more significant role played by the chemical route.

  1. Fabrication and characterization of Au dimer antennas on glass pillars with enhanced plasmonic response

    DEFF Research Database (Denmark)

    Sadeghi, Pedram; Wu, Kaiyu; Rindzevicius, Tomas

    2017-01-01

    -difference time-domain (FDTD) and finite-element method (FEM) simulations. Additionally, measured spectra are accompanied by dark-field microscopy images of the dimers, showing the pronounced change in color. Placing nanoantennas on nanopillars with a height comparable to the in-plane dimer dimensions results...

  2. Intravenous immunoglobulin G (IVIg): Properties of dimeric and sialylated IgG

    NARCIS (Netherlands)

    Guhr, T.

    2013-01-01

    This thesis describes the properties of the IgG dimer and sialylated IgG fraction in IVIg. Both fractions have been suggested to contribute to the immune modulating effects of IVIg in the treatment of autoimmune and inflammatory diseases. Taken together we can conclude that the IgG dimer fraction is

  3. A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy

    NARCIS (Netherlands)

    Franken, Linda; Oostergetel, Gerrit; Pijning, Tjaard; Puri, Pranav; Arkhipova, Valentina Ivanovna; Boekema, Egbert; Poolman, Berend; Guskov, Albert

    2017-01-01

    Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we report the cryo-electron microscopy study on 100S

  4. CONFORMATIONAL FLEXIBILITY OF AQUEOUS MONOMERIC AND DIMERIC INSULIN - A MOLECULAR-DYNAMICS STUDY

    NARCIS (Netherlands)

    MARK, AE; BERENDSEN, HJC; VANGUNSTEREN, WF

    1991-01-01

    A series of molecular dynamics simulations have been used to investigate the nature of monomeric and dimeric insulin in aqueous solution. It is shown that in the absence of crystal contacts both monomeric and dimeric insulin have a high degree of intrinsic flexibility. Neither of the two monomer

  5. A crescent-shaped ALIX dimer targets ESCRT-III CHMP4 filaments.

    Science.gov (United States)

    Pires, Ricardo; Hartlieb, Bettina; Signor, Luca; Schoehn, Guy; Lata, Suman; Roessle, Manfred; Moriscot, Christine; Popov, Sergei; Hinz, Andreas; Jamin, Marc; Boyer, Veronique; Sadoul, Remy; Forest, Eric; Svergun, Dmitri I; Göttlinger, Heinrich G; Weissenhorn, Winfried

    2009-06-10

    ALIX recruits ESCRT-III CHMP4 and is involved in membrane remodeling during endosomal receptor sorting, budding of some enveloped viruses, and cytokinesis. We show that ALIX dimerizes via the middle domain (ALIX(-V)) in solution. Structural modeling based on small angle X-ray scattering (SAXS) data reveals an elongated crescent-shaped conformation for dimeric ALIX lacking the proline-rich domain (ALIX(BRO1-V)). Mutations at the dimerization interface prevent dimerization and induce an open elongated monomeric conformation of ALIX(-V) as determined by SAXS modeling. ALIX dimerizes in vivo and dimeric ALIX colocalizes with CHMP4B upon coexpression. We show further that ALIX dimerization affects HIV-1 budding. C-terminally truncated activated CHMP4B retaining the ALIX binding site forms linear, circular, and helical filaments in vitro, which can be bridged by ALIX. Our data suggest that dimeric ALIX represents the active form that interacts with ESCRT-III CHMP4 polymers and functions as a scaffolding protein during membrane remodeling processes.

  6. Evidence for the dimerization-mediated catalysis of methionine sulfoxide reductase A from Clostridium oremlandii.

    Science.gov (United States)

    Lee, Eun Hye; Lee, Kitaik; Kwak, Geun-Hee; Park, Yeon Seung; Lee, Kong-Joo; Hwang, Kwang Yeon; Kim, Hwa-Young

    2015-01-01

    Clostridium oremlandii MsrA (CoMsrA) is a natively selenocysteine-containing methionine-S-sulfoxide reductase and classified into a 1-Cys type MsrA. CoMsrA exists as a monomer in solution. Herein, we report evidence that CoMsrA can undergo homodimerization during catalysis. The monomeric CoMsrA dimerizes in the presence of its substrate methionine sulfoxide via an intermolecular disulfide bond between catalytic Cys16 residues. The dimeric CoMsrA is resolved by the reductant glutaredoxin, suggesting the relevance of dimerization in catalysis. The dimerization reaction occurs in a concentration- and time-dependent manner. In addition, the occurrence of homodimer formation in the native selenoprotein CoMsrA is confirmed. We also determine the crystal structure of the dimeric CoMsrA, having the dimer interface around the two catalytic Cys16 residues. A central cone-shaped hole is present in the surface model of dimeric structure, and the two Cys16 residues constitute the base of the hole. Collectively, our biochemical and structural analyses suggest a novel dimerization-mediated mechanism for CoMsrA catalysis that is additionally involved in CoMsrA regeneration by glutaredoxin.

  7. Synthesis and Diels–Alder cycloaddition reaction of norbornadiene and benzonorbornadiene dimers

    Directory of Open Access Journals (Sweden)

    Bilal Nişancı

    2009-08-01

    Full Text Available Dimeric forms of norbornadiene and benzonorbornadiene were synthesized starting with known monobromide derivatives. The Diels–Alder cycloaddition reaction of dimers with TCNE and PTAD was investigated and new norbornenoid polycyclics were obtained. All compounds were characterized properly using NMR spectroscopy.

  8. High D-dimer levels increase the likelihood of pulmonary embolism

    NARCIS (Netherlands)

    Tick, L. W.; Nijkeuter, M.; Kramer, M. H. H.; Hovens, M. M. C.; Büller, H. R.; Leebeek, F. W. G.; Huisman, M. V.

    2008-01-01

    Objective. To determine the utility of high quantitative D-dimer levels in the diagnosis of pulmonary embolism. Methods. D-dimer testing was performed in consecutive patients with suspected pulmonary embolism. We included patients with suspected pulmonary embolism with a high risk for venous

  9. Predicting the effect of ions on the conformation of the H-NS dimerization domain

    NARCIS (Netherlands)

    Vreede, J.; Dame, R.T.

    2012-01-01

    The histone-like nucleoid structuring protein (H-NS) is a DNA-organizing protein in bacteria. It contains a DNA-binding domain and a dimerization domain, connected by a flexible linker region. Dimerization occurs through the formation of a helical bundle, including a coiled-coil interaction motif.

  10. Genetic predictors of fibrin D-dimer levels in healthy adults

    NARCIS (Netherlands)

    N.L. Smith (Nicholas); J.E. Huffman (Jennifer E.); D.P. Strachan (David); J. Huang (Jian); A. Dehghan (Abbas); S. Trompet (Stella); L.M. Lopez (Lorna M.); S.Y. Shin (So Youn); J. Baumert (Jens); V. Vitart (Veronique); J.C. Bis (Joshua); S.H. Wild (Sarah); A. Rumley (Ann); Q. Yang (Qiong Fang); A.G. Uitterlinden (André); D.J. Stott (David. J.); G. Davies (Gareth); A.M. Carter (Angela M.); B. Thorand (Barbara); O. Polašek (Ozren); B. McKnight (Barbara); H. Campbell (Harry); A.R. Rudnicka (Alicja); M.H. Chen (Min-hsin); B.M. Buckley (Brendan M.); S.E. Harris (Sarah); A. Peters (Annette); D. Pulanic (Drazen); T. Lumley (Thomas); A.J.M. de Craen (Anton J.M.); D.C. Liewald (David C.); C. Gieger (Christian); I. Ford (Ian); A.J. Gow (Alan J.); M. Luciano (Michelle); D.J. Porteous (David J.); X. Guo (Xiuqing); N. Sattar (Naveed); A. Tenesa (Albert); M. Cushman (Mary Ann); P.E. Slagboom (Eline); P.M. Visscher (Peter M.); T.D. Spector (Tim); T. Illig (Thomas); I. Rudan (Igor); E.G. Bovill (Edwin G.); A.F. Wright (Alan); W.L. McArdle (Wendy); G.H. Tofler (Geoffrey); A. Hofman (Albert); R.G.J. Westendorp (Rudi); J.M. Starr (John); P.J. Grant (Peter J.); M. Karakas (Mahir); N.D. Hastie (Nicholas D.); B.M. Psaty (Bruce); J.F. Wilson (James); G.D.O. Lowe (Gordon); C.J. O'Donnell (Christopher); J.C.M. Witteman (Jacqueline); J.W. Jukema (Jan Wouter); I.J. Deary (Ian); N. Soranzo (Nicole); W. Koenig (Wolfgang); C. Hayward (Caroline)

    2011-01-01

    textabstractBACKGROUND: Fibrin fragment D-dimer, one of several peptides produced when crosslinked fibrin is degraded by plasmin, is the most widely used clinical marker of activated blood coagulation. To identity genetic loci influencing D-dimer levels, we performed the first large-scale,

  11. Diphenylamino Radical Dimer as a Color Center in a Molecular Crystal

    NARCIS (Netherlands)

    Wiersma, Douwe A.; Lichtenbelt, Jan H.; Kommandeur, Jan

    1969-01-01

    Radical pairs of diphenylamino (DPA) can be formed in a single crystal of tetraphenylhydrazine (TPH) by uv photolysis. The structure of these radical dimers can be elucidated by ESR measurements. These studies show that eight configurationally different dimers occur, which fall into two classes with

  12. Analytic expression for three-body recombination rates into deep dimers

    DEFF Research Database (Denmark)

    Fedorov, D. V.; Mikkelsen, Mathias; Jensen, A. S.

    2015-01-01

    We investigate three-body recombination rates into deep dimers in cold atomic gases with large scattering length within hyper-spherical adiabatic zero-range approach. We derive closed analytic expressions for the rates for one- and two-species gases. Although the deep dimers are beyond the zero...

  13. The use of D-dimer in specific clinical conditions: a narrative review

    NARCIS (Netherlands)

    Bruinstroop, E.; van de Ree, M. A.; Huisman, M. V.

    2009-01-01

    The use of D-dimer in combination with a clinical decision rule has been widely investigated in pulmonary embolism and deep venous thrombosis. Although it has been shown to be safe in excluding venous thromboembolism, the clinician is often faced with specific situations in which the use of D-dimer

  14. A Model for Dimerization of the SOX Group E Transcription Factor Family.

    Directory of Open Access Journals (Sweden)

    Sarah N Ramsook

    Full Text Available Group E members of the SOX transcription factor family include SOX8, SOX9, and SOX10. Preceding the high mobility group (HMG domain in each of these proteins is a thirty-eight amino acid region that supports the formation of dimers on promoters containing tandemly inverted sites. The purpose of this study was to obtain new structural insights into how the dimerization region functions with the HMG domain. From a mutagenic scan of the dimerization region, the most essential amino acids of the dimerization region were clustered on the hydrophobic face of a single, predicted amphipathic helix. Consistent with our hypothesis that the dimerization region directly contacts the HMG domain, a peptide corresponding to the dimerization region bound a preassembled HMG-DNA complex. Sequence conservation among Group E members served as a basis to identify two surface exposed amino acids in the HMG domain of SOX9 that were necessary for dimerization. These data were combined to make a molecular model that places the dimerization region of one SOX9 protein onto the HMG domain of another SOX9 protein situated at the opposing site of a tandem promoter. The model provides a detailed foundation for assessing the impact of mutations on SOX Group E transcription factors.

  15. DFT molecular simulations of solvated glucose dimers: explicit vs. implicit water

    Science.gov (United States)

    The behavior of Glucose dimers in solution is investigated at the DFT level of theory via optimization and constant energy DFT molecular dynamics. The effect of the solvent on the dimer is treated two different ways: using the implicit solvation method COSMO alone to treat the bulk water behavior an...

  16. Synchronized oscillations of dimers in biphasic charged fd-virus suspensions.

    Science.gov (United States)

    Kang, K; Piao, S H; Choi, H J

    2016-08-01

    Micron-sized colloidal spheres that are dispersed in an isotropic-nematic biphasic host suspension of charged rods (fd-virus particles) are shown to spontaneously form dimers, which exhibit a synchronized oscillatory motion. Dimer formation is not observed in the monophase of isotropic and nematic suspensions. The synchronized oscillations of dimers are connected to the inhomogeneous state of the host suspension of charged rods (fd viruses) where nematic domains are in coexistence with isotropic regions. The synchronization of oscillations occurs in bulk states, in the absence of an external field. With a low field strength of an applied electric field, the synchronization is rather reduced, but it recovers again when the field is turned off. In this Rapid Communication, we report this observation as an example of the strange attractor, occurring in the mixture of PS (polystyrene) dimers in an isotropic-nematic coexistence biphasic fd-virus network. Furthermore, we highlight that the synchronization of PS-dimer oscillations is the result of a global bifurcation diagram, driven by a delicate balance between the short-attractive "twisted" interaction of PS dimers and long-ranged electrostatic repulsive interactions of charged fd rods. The interest is then in the local enhancement of "twist-nematic" elasticity in reorientation of the dimer oscillations. An analysis of image-time correlations is provided with the data movies and Fourier transforms of averaged orientations for the synchronized oscillations of dimers in the biphasic I-N coexistence concentration of charged fd-virus suspensions.

  17. Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer

    Science.gov (United States)

    Filizola, Marta; Wang, Simon X.; Weinstein, Harel

    2006-08-01

    Based on the growing evidence that G-protein coupled receptors (GPCRs) form homo- and hetero-oligomers, models of GPCR signaling are now considering macromolecular assemblies rather than monomers, with the homo-dimer regarded as the minimal oligomeric arrangement required for functional coupling to the G-protein. The dynamic mechanisms of such signaling assemblies are unknown. To gain some insight into properties of GPCR dimers that may be relevant to functional mechanisms, we study their current structural prototype, rhodopsin. We have carried out nanosecond time-scale molecular dynamics (MD) simulations of a rhodopsin dimer and compared the results to the monomer simulated in the same type of bilayer membrane model composed of an equilibrated unit cell of hydrated palmitoyl-oleoyl-phosphatidyl choline (POPC). The dynamic representation of the homo-dimer reveals the location of structural changes in several regions of the monomeric subunits. These changes appear to be more pronounced at the dimerization interface that had been shown to be involved in the activation process [Proc Natl Acad Sci USA 102:17495, 2005]. The results are consistent with a model of GPCR activation that involves allosteric modulation through a single GPCR subunit per dimer.

  18. Age-Adjusted D-Dimer in the Prediction of Pulmonary Embolism: Does a Normal Age-Adjusted D-Dimer Rule Out PE?

    Directory of Open Access Journals (Sweden)

    Jacob Ortiz

    2017-01-01

    Full Text Available Risk assessment for pulmonary embolism (PE currently relies on physician judgment, clinical decision rules (CDR, and D-dimer testing. There is still controversy regarding the role of D-dimer testing in low or intermediate risk patients. The objective of the study was to define the role of clinical decision rules and D-dimer testing in patients suspected of having a PE. Records of 894 patients referred for computed tomography pulmonary angiography (CTPA at a University medical center were analyzed. The clinical decision rules overall had an ROC of approximately 0.70, while signs of DVT had the highest ROC (0.80. A low probability CDR coupled with a negative age-adjusted D-dimer largely excluded PE. The negative predictive value (NPV of an intermediate CDR was 86–89%, while the addition of a negative D-dimer resulted in NPVs of 94%. Thus, in patients suspected of having a PE, a low or intermediate CDR does not exclude PE; however, in patients with an intermediate CDR, a normal age-adjusted D-dimer increases the NPV.

  19. Mechanism for Controlling the Dimer-Monomer Switch and Coupling Dimerization to Catalysis of the Severe Acute Respiratory Syndrome Coronavirus 3C-Like Protease

    Energy Technology Data Exchange (ETDEWEB)

    Shi,J.; Sivaraman, J.; Song, J.

    2008-01-01

    Unlike 3C protease, the severe acute respiratory syndrome coronavirus (SARS-CoV) 3C-like protease (3CLpro) is only enzymatically active as a homodimer and its catalysis is under extensive regulation by the unique extra domain. Despite intense studies, two puzzles still remain: (i) how the dimer-monomer switch is controlled and (ii) why dimerization is absolutely required for catalysis. Here we report the monomeric crystal structure of the SARS-CoV 3CLpro mutant R298A at a resolution of 1.75 Angstroms . Detailed analysis reveals that Arg298 serves as a key component for maintaining dimerization, and consequently, its mutation will trigger a cooperative switch from a dimer to a monomer. The monomeric enzyme is irreversibly inactivated because its catalytic machinery is frozen in the collapsed state, characteristic of the formation of a short 310-helix from an active-site loop. Remarkably, dimerization appears to be coupled to catalysis in 3CLpro through the use of overlapped residues for two networks, one for dimerization and another for the catalysis.

  20. X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases

    Energy Technology Data Exchange (ETDEWEB)

    Prokofev, I. I.; Lashkov, A. A., E-mail: alashkov83@gmail.com; Gabdulkhakov, A. G.; Balaev, V. V.; Seregina, T. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation); Mironov, A. S. [State Research Institute of Genetics and Selection of Industrial Microorganisms (Russian Federation); Betzel, C. [University of Hamburg (Germany); Mikhailov, A. M. [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation)

    2016-11-15

    In many types of human tumor cells and infectious agents, the demand for pyrimidine nitrogen bases increases during the development of the disease, thus increasing the role of the enzyme uridine phosphorylase in metabolic processes. The rational use of uridine phosphorylase and its ligands in pharmaceutical and biotechnology industries requires knowledge of the structural basis for the substrate specificity of the target enzyme. This paper summarizes the results of the systematic study of the three-dimensional structure of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae in complexes with substrates of enzymatic reactions—uridine, phosphate anion, thymidine, uracil, and thymine. These data, supplemented with the results of molecular modeling, were used to consider in detail the structural basis for the substrate specificity of uridine phosphorylases. It was shown for the first time that the formation of a hydrogen-bond network between the 2′-hydroxy group of uridine and atoms of the active-site residues of uridine phosphorylase leads to conformational changes of the ribose moiety of uridine, resulting in an increase in the reactivity of uridine compared to thymidine. Since the binding of thymidine to residues of uridine phosphorylase causes a smaller local strain of the β-N1-glycosidic bond in this the substrate compared to the uridine molecule, the β-N1-glycosidic bond in thymidine is more stable and less reactive than that in uridine. It was shown for the first time that the phosphate anion, which is the second substrate bound at the active site, interacts simultaneously with the residues of the β5-strand and the β1-strand through hydrogen bonding, thus securing the gate loop in a conformation.

  1. Simultaneous determination of adenine guanine and thymine at multi-walled carbon nanotubes incorporated with poly(new fuchsin) composite film

    Energy Technology Data Exchange (ETDEWEB)

    Tang Ching; Yogeswaran, Umasankar [Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, No.1, Section 3, Chung-Hsiao East Road, Taipei 106, Taiwan (China); Chen, S.-M. [Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, No.1, Section 3, Chung-Hsiao East Road, Taipei 106, Taiwan (China)], E-mail: smchen78@ms15.hinet.net

    2009-03-16

    A composite film (MWCNTs-PNF) which contains multi-walled carbon nanotubes (MWCNTs) along with the incorporation of poly(new fuchsin) (PNF) has been synthesized on glassy carbon electrode (GCE), gold (Au) and indium tin oxide (ITO) by potentiostatic methods. The presence of MWCNTs in the composite film enhances surface coverage concentration ({gamma}) of PNF to {approx}176.5%, and increases the electron transfer rate constant (k{sub s}) to {approx}346%. The composite film also exhibits promising enhanced electrocatalytic activity towards the mixture of biochemical compounds such as adenine (AD), guanine (GU) and thymine (THY). The surface morphology of the composite film deposited on ITO has been studied using scanning electron microscopy and atomic force microscopy. These two techniques reveal that the PNF incorporated on MWCNTs. Electrochemical quartz crystal microbalance study reveals the enhancement in the functional properties of MWCNTs and PNF. The electrocatalytic responses of analytes at MWCNTs and MWCNTs-PNF films were measured using both cyclic voltammetry (CV) and differential pulse voltammetry (DPV). From electrocatalysis studies, well separated voltammetric peaks have been obtained at the composite film for AD, GU and THY, with the peak separation of 320.3 and 132.7 mV between GU-AD and AD-THY respectively. The sensitivity of the composite film towards AD, GU and THY in DPV technique is 218.18, 12.62 and 78.22 mA M{sup -1} cm{sup -2} respectively, which are higher than MWCNTs film. Further, electroanalytical studies of AD, GU and THY present in single-strand deoxyribonucleic acid (ssDNA) have been carried out using semi-derivative CV and DPV.

  2. Detectability of H2-Ar and H2-Ne Dimers in Jovian Atmospheres

    Directory of Open Access Journals (Sweden)

    Young-Key Minn

    1997-12-01

    Full Text Available The detection of jovian hydrogen-hydrogen dimers through the clear telluric 2-micron window(Kim et al. 1995, Trafton et al. 1997 suggests possibility to detect noble gases in the form of dimer with hydrogen in jovian atmospheres. Since noble gases do not have spectral structures in the infrared, it has been difficult to derive their abundances in the atmospheres of jovian planets. If there is a significant component of noble gases other than helium in the jovian atmospheres. it might be detected through its dimer spectrum with hydrogen molecule. The relatively sharp spectral structures of hydrogen-argon and hydrogen-neon dimers compared with those of hydrogen-hydrogen dimers are useful for the detection, if an adequate signal-to-noise (S/N is obtained. If we use a large telescope, such as the Keck telescope, with a long exposure time (>24 hours, then H2-Ar spectral structure may be detected.

  3. Structure of the dimeric form of CTP synthase from Sulfolobus solfataricus

    DEFF Research Database (Denmark)

    Lauritsen, Iben; Willemoës, Martin; Jensen, Kaj Frank

    2011-01-01

    CTP synthase catalyzes the last committed step in de novo pyrimidine-nucleotide biosynthesis. Active CTP synthase is a tetrameric enzyme composed of a dimer of dimers. The tetramer is favoured in the presence of the substrate nucleotides ATP and UTP; when saturated with nucleotide, the tetramer...... completely dominates the oligomeric state of the enzyme. Furthermore, phosphorylation has been shown to regulate the oligomeric states of the enzymes from yeast and human. The crystal structure of a dimeric form of CTP synthase from Sulfolobus solfataricus has been determined at 2.5 Å resolution....... A comparison of the dimeric interface with the intermolecular interfaces in the tetrameric structures of Thermus thermophilus CTP synthase and Escherichia coli CTP synthase shows that the dimeric interfaces are almost identical in the three systems. Residues that are involved in the tetramerization of S...

  4. Changes in fibrin D-dimer, fibrinogen, and protein S during pregnancy

    DEFF Research Database (Denmark)

    Hansen, Anette Tarp; Andreasen, Birgitte Horst; Salvig, Jannie Dalby

    2010-01-01

    Background. Pregnancy is a hypercoagulable state with a 5- to 10- fold higher risk of venous thromboembolism. Existing reference intervals for fibrin D-dimer (D-dimer), functional fibrinogen (fibrinogen) and protein S, free antigen (protein S) are based on non-pregnant patients and reference...... intervals for pregnant patients are warranted. Objectives. The aim of the present study was to contribute to the establishment of reference intervals for D-dimer, fibrinogen and protein S during pregnancy and to discuss the use of the analyses during pregnancy. Methods. We included 55 healthy pregnant women...... in gestational week 11–17, with normal current pregnancy. Blood samples were collected in gestational weeks 11–17, 21–27 and 34–37. The three plasma parameters D-dimer, fibrinogen and protein S were analysed by STA-R Evolution®. Results. A significant rise in D-dimer was found from first to second trimester (p...

  5. Three new sesquiterpene lactone dimers from Carpesium macrocephalum.

    Science.gov (United States)

    Zhang, Jian-Ping; Xu, Xi-Ke; Ye, Ji; Yang, Yong-Xun; Gao, Shuang; Li, Hui-Liang; Zhang, Wei-Dong

    2016-04-01

    Three new sesquiterpene lactone dimers (SLDs), carpedilactones E-G (1-3), together with two known monomeric units, ivalin (4) and alantolactone (5), were isolated from the acetonic extract of Carpesium macrocephalum. Their chemical structures were elucidated by IR, UV, HR-ESI-MS, NMR 1D and 2D experiments, and the absolute configuration of 1-3 was resolved according to the (1)H NMR and CD spectrographic features of 1,3-/2,4-linked SLDs. Furthermore, 1 was unambiguously confirmed by Cu-Kα X-ray crystallographic analysis. Additionally, compounds 1 and 2 were revealed with potent cytotoxicities against human colon cancer HCT116 cells with IC50 values of 2.27 and 3.30 μM, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Restricted dislocation motion in crystals of colloidal dimer particles.

    Science.gov (United States)

    Gerbode, Sharon J; Lee, Stephanie H; Liddell, Chekesha M; Cohen, Itai

    2008-08-01

    At high area fractions, monolayers of colloidal dimer particles form a degenerate crystal (DC) structure in which the particle lobes occupy triangular lattice sites while the particles are oriented randomly along any of the three lattice directions. We report that dislocation glide in DCs is blocked by certain particle orientations. The mean number of lattice constants between such obstacles is Z[over](exp)=4.6+/-0.2 in experimentally observed DC grains and Z[over](sim)=6.18+/-0.01 in simulated monocrystalline DCs. Dislocation propagation beyond these obstacles is observed to proceed through dislocation reactions. We estimate that the energetic cost of dislocation pair separation via such reactions in an otherwise defect free DC grows linearly with final separation, hinting that the material properties of DCs may be dramatically different from those of 2-D crystals of spheres.

  7. Dimerization of Carboxylic Acids: An Equation of State Approach

    DEFF Research Database (Denmark)

    Tsivintzelis, Ioannis; Kontogeorgis, Georgios; Panayiotou, Costas

    2017-01-01

    The association term of the nonrandom hydrogen bonding theory, which is an equation of state model, is extended to describe the dimerization of carboxylic acids in binary mixtures with inert solvents and in systems of two different acids. Subsequently, the model is applied to describe the excess...... enthalpies and the vapor-liquid equilibrium of relevant binary mixtures containing low molecular weight organic acids. The model sheds light on the interplay of intermolecular interactions through the calculation of the various contributions to the mixing enthalpies, namely from hydrogen bonding and non......-hydrogen bonding (dipolar, induced polar or dispersive) interactions. According to model predictions, the acid molecules are so strongly associated that the addition of inert solvents to carboxylic acids with small carbon numbers at ambient temperature does not dramatically alter their degree of association...

  8. Amorphous Silica-Promoted Lysine Dimerization: a Thermodynamic Prediction

    Science.gov (United States)

    Kitadai, Norio; Nishiuchi, Kumiko; Nishii, Akari; Fukushi, Keisuke

    2017-08-01

    It has long been suggested that mineral surfaces played a crucial role in the abiotic polymerization of amino acids that preceded the origin of life. Nevertheless, it remains unclear where the prebiotic process took place on the primitive Earth, because the amino acid-mineral interaction and its dependence on environmental conditions have yet to be understood adequately. Here we examined experimentally the adsorption of L-lysine (Lys) and its dimer (LysLys) on amorphous silica over a wide range of pH, ionic strength, adsorbate concentration, and the solid/water ratio, and determined the reaction stoichiometries and the equilibrium constants based on the extended triple-layer model (ETLM). The retrieved ETLM parameters were then used, in combination with the equilibrium constant for the peptide bond formation in bulk water, to calculate the Lys-LysLys equilibrium in the presence of amorphous silica under various aqueous conditions. Results showed that the silica surface favors Lys dimerization, and the influence varies greatly with changing environmental parameters. At slightly alkaline pH (pH 9) in the presence of a dilute NaCl (1 mM), the thermodynamically attainable LysLys from 0.1 mM Lys reached a concentration around 50 times larger than that calculated without silica. Because of the versatility of the ETLM, which has been applied to describe a wide variety of biomolecule-mineral interactions, future experiments with the reported methodology are expected to provide a significant constraint on the plausible geological settings for the condensation of monomers to polymers, and the subsequent chemical evolution of life.

  9. Amorphous Silica-Promoted Lysine Dimerization: a Thermodynamic Prediction

    Science.gov (United States)

    Kitadai, Norio; Nishiuchi, Kumiko; Nishii, Akari; Fukushi, Keisuke

    2018-03-01

    It has long been suggested that mineral surfaces played a crucial role in the abiotic polymerization of amino acids that preceded the origin of life. Nevertheless, it remains unclear where the prebiotic process took place on the primitive Earth, because the amino acid-mineral interaction and its dependence on environmental conditions have yet to be understood adequately. Here we examined experimentally the adsorption of L-lysine (Lys) and its dimer (LysLys) on amorphous silica over a wide range of pH, ionic strength, adsorbate concentration, and the solid/water ratio, and determined the reaction stoichiometries and the equilibrium constants based on the extended triple-layer model (ETLM). The retrieved ETLM parameters were then used, in combination with the equilibrium constant for the peptide bond formation in bulk water, to calculate the Lys-LysLys equilibrium in the presence of amorphous silica under various aqueous conditions. Results showed that the silica surface favors Lys dimerization, and the influence varies greatly with changing environmental parameters. At slightly alkaline pH (pH 9) in the presence of a dilute NaCl (1 mM), the thermodynamically attainable LysLys from 0.1 mM Lys reached a concentration around 50 times larger than that calculated without silica. Because of the versatility of the ETLM, which has been applied to describe a wide variety of biomolecule-mineral interactions, future experiments with the reported methodology are expected to provide a significant constraint on the plausible geological settings for the condensation of monomers to polymers, and the subsequent chemical evolution of life.

  10. Intermolecular potential energy surface for CS2 dimer.

    Science.gov (United States)

    Farrokhpour, Hossein; Mombeini, Zainab; Namazian, Mansoor; Coote, Michelle L

    2011-04-15

    A new four-dimensional intermolecular potential energy surface for CS(2) dimer is obtained by ab initio calculation of the interaction energies for a range of configurations and center-of-mass separation distances for the first time. The calculations were performed using the supermolecular approach at the Møller-Plesset second-order perturbation (MP2) level of theory with the augmented correlation consistent basis sets (aug-cc-pVxZ, x = D, T) and corrected for the basis-set superposition error using the full counterpoise correction method. A two-point extrapolation method was used to extrapolate the calculated energy points to the complete basis set limit. The effect of using the higher levels of theory, quadratic configuration interaction containing single, double, and perturbative triple excitations QCISD(T) and coupled cluster singles, doubles and perturbative triples excitations CCSD(T), on the shape of potential energy surface was investigated. It is shown that the MP2 level of theory apparently performs extremely poorly for describing the intermolecular potential energy surface, overestimating the total energy by a factor of nearly 1.73 in comparison with the QCISD(T) and CCSD(T) values. The value of isotropic dipole-dipole dispersion coefficient (C(6) ) of CS(2) fluid was obtained from the extrapolated MP2 potential energy surface. The MP2 extrapolated energy points were fitted to well-known analytical potential functions using two different methods to represent the potential energy surface analytically. The most stable configuration of the dimer was determined at R = 6.23 au, α = 90°, β = 90°, and γ = 90°, with a well depth of 3.980 kcal mol(-1) at the MP2 level of theory. Finally, the calculated second virial coefficients were compared with experimental values to test the quality of the presented potential energy surface. Copyright © 2010 Wiley Periodicals, Inc.

  11. Resonant multiphoton fragmentation spectrum of niobium dimer cation.

    Science.gov (United States)

    Aydin, M; Lombardi, John R

    2009-03-26

    Resonant multiphoton fragmentation spectra of niobium dimer cation (Nb2(+)) have been obtained by utilizing laser vaporization of a Nb metal target. Ions are mass-selected with a time-of-flight mass spectrometer followed by a mass gate and then fragmented with a pulsed dye laser, and the resulting fragment ions are detected with a second time-of-flight reflectron mass spectrometer and multichannel plate. Photon resonances are detected by monitoring ion current as a function of fragmentation laser wavelength. A rich but complex spectrum of the cation is obtained. The bands display a characteristic multiplet structure that may be interpreted as due to transitions from the ground state X4Sigma(Omega g)- to several excited states, (B/D)4Pi(Omega u) and 4Sigma(Omega u)-. The ground state X4sigma(+/-1/2g)- is derived from the electron configuration pi(u)4 1sigma(g)2 2sigma(g)1 delta(g)2. The two spin-orbit components are split by 145 cm(-1) due to a strong second-order isoconfigurational spin-orbit interaction with the low-lying 2Sigma(+/-1/2g)+ state. The vibrational frequencies of the ground state and the excited-state of Nb2(+) are identified as well as molecular spin-orbit constants (A(SO)) in the excited state. The electronic structure of niobium dimer cation was investigated using density functional theory. For the electronic ground state, the predicted spectroscopic properties were in good agreement with experiment. Calculations on excited states reveal congested manifolds of quartet and doublet electronic states in the range 0-30,000 cm(-1), reflecting the multitude of possible electronic promotions among the 4d- and 5s-based molecular orbitals. Comparisons are drawn between Nb2(+) and the prevalent isoelectronic molecules V2(+)/NbV(+)/Nb2/V2/NbV2.

  12. Structure of dimeric mitochondrial ATP synthase: Novel F0 bridging features and the structural basis of mitochondrial cristae biogenesis

    National Research Council Canada - National Science Library

    Fernando Minauro-Sanmiguel; Stephan Wilkens; José J. García

    2005-01-01

    .... How two ATP synthase complexes dimerize to promote cristae formation is unknown. Here we resolved the structure of the dimeric F 1 F 0 ATP synthase complex isolated from bovine heart mitochondria by transmission electron microscopy...

  13. Structural insights into lipid-dependent reversible dimerization of human GLTP

    Energy Technology Data Exchange (ETDEWEB)

    Samygina, Valeria R.; Ochoa-Lizarralde, Borja [CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio (Spain); Popov, Alexander N. [European Synchrotron Radiation Facility, 38043 Grenoble (France); Cabo-Bilbao, Aintzane; Goni-de-Cerio, Felipe [CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio (Spain); Molotkovsky, Julian G. [Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997 (Russian Federation); Patel, Dinshaw J. [Memorial Sloan–Kettering Cancer Center, New York, NY 10021 (United States); Brown, Rhoderick E., E-mail: reb@umn.edu [University of Minnesota, Austin, MN 55912 (United States); Malinina, Lucy, E-mail: reb@umn.edu [CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio (Spain)

    2013-04-01

    It is shown that dimerization is promoted by glycolipid binding to human GLTP. The importance of dimer flexibility in wild-type protein is manifested by point mutation that ‘locks’ the dimer while diversifying ligand/protein adaptations. Human glycolipid transfer protein (hsGLTP) forms the prototypical GLTP fold and is characterized by a broad transfer selectivity for glycosphingolipids (GSLs). The GLTP mutation D48V near the ‘portal entrance’ of the glycolipid binding site has recently been shown to enhance selectivity for sulfatides (SFs) containing a long acyl chain. Here, nine novel crystal structures of hsGLTP and the SF-selective mutant complexed with short-acyl-chain monoSF and diSF in different crystal forms are reported in order to elucidate the potential functional roles of lipid-mediated homodimerization. In all crystal forms, the hsGLTP–SF complexes displayed homodimeric structures supported by similarly organized intermolecular interactions. The dimerization interface always involved the lipid sphingosine chain, the protein C-terminus (C-end) and α-helices 6 and 2, but the D48V mutant displayed a ‘locked’ dimer conformation compared with the hinge-like flexibility of wild-type dimers. Differences in contact angles, areas and residues at the dimer interfaces in the ‘flexible’ and ‘locked’ dimers revealed a potentially important role of the dimeric structure in the C-end conformation of hsGLTP and in the precise positioning of the key residue of the glycolipid recognition centre, His140. ΔY207 and ΔC-end deletion mutants, in which the C-end is shifted or truncated, showed an almost complete loss of transfer activity. The new structural insights suggest that ligand-dependent reversible dimerization plays a role in the function of human GLTP.

  14. Functional roles of the dimer-interface residues in human ornithine decarboxylase.

    Directory of Open Access Journals (Sweden)

    Chien-Yun Lee

    Full Text Available Ornithine decarboxylase (ODC catalyzes the decarboxylation of ornithine to putrescine and is the rate-limiting enzyme in the polyamine biosynthesis pathway. ODC is a dimeric enzyme, and the active sites of this enzyme reside at the dimer interface. Once the enzyme dissociates, the enzyme activity is lost. In this paper, we investigated the roles of amino acid residues at the dimer interface regarding the dimerization, protein stability and/or enzyme activity of ODC. A multiple sequence alignment of ODC and its homologous protein antizyme inhibitor revealed that 5 of 9 residues (residues 165, 277, 331, 332 and 389 are divergent, whereas 4 (134, 169, 294 and 322 are conserved. Analytical ultracentrifugation analysis suggested that some dimer-interface amino acid residues contribute to formation of the dimer of ODC and that this dimerization results from the cooperativity of these interface residues. The quaternary structure of the sextuple mutant Y331S/Y389D/R277S/D332E/V322D/D134A was changed to a monomer rather than a dimer, and the Kd value of the mutant was 52.8 µM, which is over 500-fold greater than that of the wild-type ODC (ODC_WT. In addition, most interface mutants showed low but detectable or negligible enzyme activity. Therefore, the protein stability of these interface mutants was measured by differential scanning calorimetry. These results indicate that these dimer-interface residues are important for dimer formation and, as a consequence, are critical for enzyme catalysis.

  15. Lactococcus lactis YfiA is necessary and sufficient for ribosome dimerization.

    Science.gov (United States)

    Puri, Pranav; Eckhardt, Thomas H; Franken, Linda E; Fusetti, Fabrizia; Stuart, Marc C A; Boekema, Egbert J; Kuipers, Oscar P; Kok, Jan; Poolman, Bert

    2014-01-01

    Dimerization and inactivation of ribosomes in Escherichia coli is a two-step process that involves the binding of ribosome modulation factor (RMF) and hibernation promotion factor (HPF). Lactococcus lactis MG1363 expresses a protein, YfiA(L) (l) , which associates with ribosomes in the stationary phase of growth and is responsible for dimerization of ribosomes. We show that full-length YfiA(L) (l) is necessary and sufficient for ribosome dimerization in L. lactis but also functions heterologously in vitro with E. coli ribosomes. Deletion of the yfiA gene has no effect on the growth rate but diminishes the survival of L. lactis under energy-starving conditions. The N-terminal domain of YfiA(L) (l) is homologous to HPF from E. coli, whereas the C-terminal domain has no counterpart in E. coli. By assembling ribosome dimers in vitro, we could dissect the roles of the N- and C-terminal domains of YfiA(L) (l) . It is concluded that the dimerization and inactivation of ribosomes in L. lactis and E. coli differ in several cellular and molecular aspects. In addition, two-dimensional maps of dimeric ribosomes from L. lactis obtained by single particle electron microscopy show a marked structural difference in monomer association in comparison to the ribosome dimers in E. coli. © 2013 John Wiley & Sons Ltd.

  16. Thermal entanglement in an orthogonal dimer-plaquette chain with alternating Ising-Heisenberg coupling

    Science.gov (United States)

    Paulinelli, H. G.; de Souza, S. M.; Rojas, Onofre

    2013-07-01

    In this paper we explore the entanglement in an orthogonal dimer-plaquette Ising-Heisenberg chain, assembled between plaquette edges, also known as orthogonal dimer plaquettes. The quantum entanglement properties involving an infinite chain structure are quite important, not only because the mathematical calculation is cumbersome but also because real materials are well represented by infinite chains. Using the local gauge symmetry of this model, we are able to map onto a simple spin-1 like Ising and spin-1/2 Heisenberg dimer model with single effective ion anisotropy. Thereafter this model can be solved using the decoration transformation and transfer matrix approach. First, we discuss the phase diagram at zero temperature of this model, where we find five ground states, one ferromagnetic, one antiferromagnetic, one triplet-triplet disordered and one triplet-singlet disordered phase, beside a dimer ferromagnetic-antiferromagnetic phase. In addition, we discuss the thermodynamic properties such as entropy, where we display the residual entropy. Furthermore, using the nearest site correlation function it is possible also to analyze the pairwise thermal entanglement for both orthogonal dimers. Additionally, we discuss the threshold temperature of the entangled region as a function of Hamiltonian parameters. We find a quite interesting thin reentrance threshold temperature for one of the dimers, and we also discuss the differences and similarities for both dimers.

  17. Morphological and physiological retinal degeneration induced by intravenous delivery of vitamin A dimers in rabbits

    Directory of Open Access Journals (Sweden)

    Jackie Penn

    2015-02-01

    Full Text Available The eye uses vitamin A as a cofactor to sense light and, during this process, some vitamin A molecules dimerize, forming vitamin A dimers. A striking chemical signature of retinas undergoing degeneration in major eye diseases such as age-related macular degeneration (AMD and Stargardt disease is the accumulation of these dimers in the retinal pigment epithelium (RPE and Bruch’s membrane (BM. However, it is not known whether dimers of vitamin A are secondary symptoms or primary insults that drive degeneration. Here, we present a chromatography-free method to prepare gram quantities of the vitamin A dimer, A2E, and show that intravenous administration of A2E to the rabbit results in retinal degeneration. A2E-damaged photoreceptors and RPE cells triggered inflammation, induced remolding of the choroidal vasculature and triggered a decline in the retina’s response to light. Data suggest that vitamin A dimers are not bystanders, but can be primary drivers of retinal degeneration. Thus, preventing dimer formation could be a preemptive strategy to address serious forms of blindness.

  18. Accuracy of D-Dimers to Rule Out Venous Thromboembolism Events across Age Categories

    Directory of Open Access Journals (Sweden)

    G. Der Sahakian

    2010-01-01

    Full Text Available Background. Strategies combining pretest clinical assessment and D-dimers measurement efficiently and safely rule out venous thromboembolism events (VTE in low- and intermediate-risk patients. Objectives. As process of ageing is associated with altered concentrations of coagulation markers including an increase in D-dimers levels, we investigated whether D-dimers could reliably rule out VTE across age categories. Method. We prospectively assessed the test performance in 1,004 patients visiting the emergency department during the 6-month period with low or intermediate risk of VTE who also received additional diagnostic procedures. Results. 67 patients had VTE with D-dimers levels above the threshold, and 3 patients displayed D-dimers levels below the threshold. We observed that specificity of D-dimers test decreased in an age-dependent manner. However, sensitivity and negative predictive value remained at very high level in each age category including older patients. Conclusion. We conclude that, even though D-dimers level could provide numerous false positive results in elderly patients, its high sensitivity could reliably help physicians to exclude the diagnosis of VTE in every low- and intermediate-risk patient.

  19. The Dimer Interface of the Membrane Type 1 Matrix Metalloproteinase Hemopexin Domain

    Science.gov (United States)

    Tochowicz, Anna; Goettig, Peter; Evans, Richard; Visse, Robert; Shitomi, Yasuyuki; Palmisano, Ralf; Ito, Noriko; Richter, Klaus; Maskos, Klaus; Franke, Daniel; Svergun, Dmitri; Nagase, Hideaki; Bode, Wolfram; Itoh, Yoshifumi

    2011-01-01

    Homodimerization is an essential step for membrane type 1 matrix metalloproteinase (MT1-MMP) to activate proMMP-2 and to degrade collagen on the cell surface. To uncover the molecular basis of the hemopexin (Hpx) domain-driven dimerization of MT1-MMP, a crystal structure of the Hpx domain was solved at 1.7 Å resolution. Two interactions were identified as potential biological dimer interfaces in the crystal structure, and mutagenesis studies revealed that the biological dimer possesses a symmetrical interaction where blades II and III of molecule A interact with blades III and II of molecule B. The mutations of amino acids involved in the interaction weakened the dimer interaction of Hpx domains in solution, and incorporation of these mutations into the full-length enzyme significantly inhibited dimer-dependent functions on the cell surface, including proMMP-2 activation, collagen degradation, and invasion into the three-dimensional collagen matrix, whereas dimer-independent functions, including gelatin film degradation and two-dimensional cell migration, were not affected. These results shed light on the structural basis of MT1-MMP dimerization that is crucial to promote cellular invasion. PMID:21193411

  20. Dimer rotation on the carbon-induced Si(001)-c(4×4) structure

    Science.gov (United States)

    Peng, G. W.; Sun, Y. Y.; Huan, A. C. H.; Feng, Y. P.

    2006-09-01

    We present first-principles results identifying the reaction pathways for Si dimer rotations on the carbon-induced Si(001)-c(4×4) surface. The nudged elastic band calculations show that the recently proposed rotated dimer model [Phys. Rev. Lett. 94, 076102 (2005)] can be obtained from the refined missing dimer model by dimer rotation with small energy barriers. It is found that the energy barrier is sensitive to the rotation directions of Si dimers. The energy barrier along the minimum energy path (MEP) is 0.82eV . Three stable configurations are identified along the MEP, one of which with a single rotated dimer is more stable than all existing models and its energy is lower than that of the rotated dimer model, the previously most stable structure, by 0.25eV per c(4×4) cell. The stabilization mechanism of the new stable structure is analyzed. We propose a possible method to search for new stable structures based on the existing models by mapping out the reaction paths in the phase configuration.

  1. Ribosome dimerization is essential for the efficient regrowth of Bacillus subtilis.

    Science.gov (United States)

    Akanuma, Genki; Kazo, Yuka; Tagami, Kazumi; Hiraoka, Hirona; Yano, Koichi; Suzuki, Shota; Hanai, Ryo; Nanamiya, Hideaki; Kato-Yamada, Yasuyuki; Kawamura, Fujio

    2016-03-01

    Ribosome dimers are a translationally inactive form of ribosomes found in Escherichia coli and many other bacterial cells. In this study, we found that the 70S ribosomes of Bacillus subtilis dimerized during the early stationary phase and these dimers remained in the cytoplasm until regrowth was initiated. Ribosome dimerization during the stationary phase required the hpf gene, which encodes a homologue of the E. coli hibernation-promoting factor (Hpf). The expression of hpf was induced at an early stationary phase and its expression was observed throughout the rest of the experimental period, including the entire 6 h of the stationary phase. Ribosome dimerization followed the induction of hpf in WT cells, but the dimerization was impaired in cells harbouring a deletion in the hpf gene. Although the absence of ribosome dimerization in these Hpf-deficient cells did not affect their viability in the stationary phase, their ability to regrow from the stationary phase decreased. Thus, following the transfer of stationary-phase cells to fresh LB medium, Δhpf mutant cells grew slower than WT cells. This observed lag in growth of Δhpf cells was probably due to a delay in restoring their translational activity. During regrowth, the abundance of ribosome dimers in WT cells decreased with a concomitant increase in the abundance of 70S ribosomes and growth rate. These results suggest that the ribosome dimers, by providing 70S ribosomes to the cells, play an important role in facilitating rapid and efficient regrowth of cells under nutrient-rich conditions.

  2. D-dimer and histamine in early stage bacteremia: A prospective controlled cohort study.

    Science.gov (United States)

    Schwameis, Michael; Steiner, Margarete Maria; Schoergenhofer, Christian; Lagler, Heimo; Buchtele, Nina; Jilma-Stohlawetz, Petra; Boehm, Thomas; Jilma, Bernd

    2015-12-01

    Plasma histamine levels and D-dimer predict disease severity and mortality in advanced septic shock. We hypothesized that increased plasma histamine levels parallel coagulation activation and yield prognostic significance already at a very early stage of bacteremia. This prospective controlled cohort study enrolled 72 consecutive non-surgical non-ICU-ward inpatients with newly culture-diagnosed bacteremia and a Pitt Bacteremia score ≤2 to determine the extent of histamine and D-dimer release and their predictive role on outcome at the earliest stage of blood stream infection. Age-matched healthy adults served as internal controls (n=36). A binominal logistic regression and a Cox proportional hazards regression analysis were performed to ascertain the effects of D-dimer and histamine on in-hospital mortality. In contrast to plasma histamine, D-dimer levels were significantly higher within hours of culture-proven bacteremia. In-hospital mortality occurred in 17%. Histamine levels were neither associated with D-dimer level (r=0.04; p>0.05) nor with ICU admissions (r=0.06; p>0.05) and outcome (crude OR 0.8, 95% CI 0.3-1.9; p=0.6). In contrast, early-elevated D-dimer levels predicted mortality: the odds to die increased with the D-dimer level, and was 12.6 (crude OR, 95% CI 3-52; p=0.001) in patients with a D-dimer ≥4μg/mL (n=13). Histamine levels are elevated in only few patients (4%) with newly diagnosed bacteremia. Our findings suggest that D-dimer, but not plasma histamine, could be a promising marker of lethality already at a very early stage of blood stream infection. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  3. Hydrogen bond induced HF elimination from photoionized fluorophenol dimers in the gas phase.

    Science.gov (United States)

    Chatterjee, Piyali; Ghosh, Arup K; Chakraborty, Tapas

    2017-02-28

    In this paper, we report finding of a remarkable chemical effect of hydrogen bonding, elimination of hydrogen fluoride (HF) from the hydrogen bonded dimers of 2-fluorophenol (2-FP) and 3-fluorophenol (3-FP), in a supersonic jet expansion upon multi-photon ionization using 4th harmonic wavelength (266 nm) of a Q-switched Nd:YAG laser, and the reaction has been probed by time-of-flight mass spectrometry. No HF elimination is observed to occur by such means from the monomer of 3-FP, but it occurs with a small yield from the monomer of 2-FP. On the other hand, upon dimerization the reaction is triggered on for 3-FP, and for 2-FP it becomes so facile that no intact dimer cation survives and only the HF eliminated product ion appears in the mass spectra. Electronic structure calculation shows that in the cationic ground (D0) state, although the reaction for 2-FP dimer is exothermic, the associated barrier is significantly high (2.75 eV) and for its occurrence, absorption of three photons (2+1 type) is required. However, the reaction is predicted barrierless in the intermediate S1 state of this dimer, and HF loss dimer cation mass peak could appear in the mass spectrum due to an effective two-photon (1+1) ionization process. In the case of 3-FP dimer, the energy barriers both in S1 (neutral) and D0 (ionic) states are high, and it is suggested that for occurrence of HF elimination, dimer cation needs to absorb an additional photon. For facilitation of HF loss from this dimer cation, a rearrangement of the geometry and formation of an intermediate adduct have been suggested, and it is argued that the latter could be produced by nucleophilic attack of the neutral moiety at the ortho site of the cationic counterpart.

  4. D-dimer levels and cerebral infarction in critically ill cancer patients.

    Science.gov (United States)

    Ryu, Jeong-Am; Bang, Oh Young; Lee, Geun-Ho

    2017-08-30

    D-dimer levels have been used in the diagnosis of a variety of thrombosis-related diseases. In this study, we evaluated whether measuring D-dimer levels can help to diagnose cerebral infarction (CI) in critically ill cancer patients. We retrospectively evaluated all cancer patients who underwent brain magnetic resonance imaging (MRI) between March 2010 and February 2014 at the medical oncology intensive care unit (ICU) of Samsung Medical Center. Brain MRI scanning was performed when CI was suspected due to acute neurological deficits. We compared D-dimer levels between patients ultimately diagnosed as having or not having CI and analyzed diffusion-weighted imaging (DWI) lesion patterns. A total of 88 patients underwent brain MRI scanning due to clinical suspicion of CI; altered mental status and unilateral hemiparesis were the most common neurological deficits. CI was ultimately diagnosed in 43 (49%) patients. According to the DWI patterns, multiple arterial infarctions (40%) were more common than single arterial infarctions (9%). Cryptogenic stroke etiologies were more common (63%) than determined etiologies. There was no significant difference in D-dimer levels between patients with and without CI (P = 0.319). Although D-dimer levels were not helpful in diagnosing CI, D-dimer levels were associated with cryptogenic etiologies in critically ill cancer patients; D-dimer levels were higher in the cryptogenic etiology group than in the determined etiology group or the non-infarction group (P = 0.001). In multivariate analysis, elevated D-dimer levels (> 8.89 μg/mL) were only associated with cryptogenic stroke (adjusted OR 5.46; 95% confidence interval, 1.876-15.857). Abnormal D-dimer levels may support the diagnosis of cryptogenic stroke in critically ill cancer patients.

  5. Dimerization of the Glucan Phosphatase Laforin Requires the Participation of Cysteine 329

    Science.gov (United States)

    Sánchez-Martín, Pablo; Raththagala, Madushi; Bridges, Travis M.; Husodo, Satrio; Gentry, Matthew S.; Sanz, Pascual; Romá-Mateo, Carlos

    2013-01-01

    Laforin, encoded by a gene that is mutated in Lafora Disease (LD, OMIM 254780), is a modular protein composed of a carbohydrate-binding module and a dual-specificity phosphatase domain. Laforin is the founding member of the glucan-phosphatase family and regulates the levels of phosphate present in glycogen. Multiple reports have described the capability of laforin to form dimers, although the function of these dimers and their relationship with LD remains unclear. Recent evidence suggests that laforin dimerization depends on redox conditions, suggesting that disulfide bonds are involved in laforin dimerization. Using site-directed mutagenesis we constructed laforin mutants in which individual cysteine residues were replaced by serine and then tested the ability of each protein to dimerize using recombinant protein as well as a mammalian cell culture assay. Laforin-Cys329Ser was the only Cys/Ser mutant unable to form dimers in both assays. We also generated a laforin truncation lacking the last three amino acids, laforin-Cys329X, and this truncation also failed to dimerize. Interestingly, laforin-Cys329Ser and laforin-Cys329X were able to bind glucans, and maintained wild type phosphatase activity against both exogenous and biologically relevant substrates. Furthermore, laforin-Cys329Ser was fully capable of participating in the ubiquitination process driven by a laforin-malin complex. These results suggest that dimerization is not required for laforin phosphatase activity, glucan binding, or for the formation of a functional laforin-malin complex. Cumulatively, these results suggest that cysteine 329 is specifically involved in the dimerization process of laforin. Therefore, the C329S mutant constitutes a valuable tool to analyze the physiological implications of laforin’s oligomerization. PMID:23922729

  6. Spontaneous dimerization, critical lines, and short-range correlations in a frustrated spin-1 chain

    Science.gov (United States)

    Chepiga, Natalia; Affleck, Ian; Mila, Frédéric

    2016-11-01

    We report on a detailed investigation of the spin-1 J1-J2-J3 Heisenberg model, a frustrated model with nearest-neighbor coupling J1, next-nearest neighbor coupling J2, and a three-site interaction J3[(Si -1.Si) (Si.Si +1) +H .c . ] previously studied in [Phys. Rev. B 93, 241108(R) (2016), 10.1103/PhysRevB.93.241108]. Using density matrix renormalization group (DMRG) and exact diagonalizations, we show that the phase boundaries between the Haldane phase, the next-nearest neighbor Haldane phase, and the dimerized phase can be very accurately determined by combining the information deduced from the dimerization, the ground-state energy, the entanglement spectrum and the Berry phase. By a careful investigation of the finite-size spectrum, we also show that the transition between the next-nearest neighbor Haldane phase and the dimerized phase is in the Ising universality class all along the critical line. Furthermore, we justify the conformal embedding of the SU (2) 2 Wess-Zumino-Witten conformal field theory in terms of a boson and an Ising field, and we explicitly derive a number of consequences of this embedding for the spectrum along the SU (2) 2 transition line between the Haldane phase and the dimerized phase. We also show that the solitons along the first-order transition line between the Haldane phase and the dimerized phase carry a spin-1/2, while the domain walls between different dimerization domains inside the dimerized phase carry a spin 1. Finally, we show that short-range correlations change character in the Haldane and dimerized phases through disorder and Lifshitz lines, as well as through the development of short-range dimer correlations in the Haldane phase, leading to a remarkably rich phase diagram.

  7. Disulphide bridges of phospholipase C of Chlamydomonas reinhardtii modulates lipid interaction and dimer stability.

    Directory of Open Access Journals (Sweden)

    Mayanka Awasthi

    Full Text Available BACKGROUND: Phospholipase C (PLC is an enzyme that plays pivotal role in a number of signaling cascades. These are active in the plasma membrane and triggers cellular responses by catalyzing the hydrolysis of membrane phospholipids and thereby generating the secondary messengers. Phosphatidylinositol-PLC (PI-PLC specifically interacts with phosphoinositide and/or phosphoinositol and catalyzes specific cleavage of sn-3- phosphodiester bond. Several isoforms of PLC are known to form and function as dimer but very little is known about the molecular basis of the dimerization and its importance in the lipid interaction. PRINCIPAL FINDINGS: We herein report that, the disruption of disulphide bond of a novel PI-specific PLC of C. reinhardtii (CrPLC can modulate its interaction affinity with a set of phospholipids and also the stability of its dimer. CrPLC was found to form a mixture of higher oligomeric states with monomer and dimer as major species. Dimer adduct of CrPLC disappeared in the presence of DTT, which suggested the involvement of disulphide bond(s in CrPLC oligomerization. Dimer-monomer equilibrium studies with the isolated fractions of CrPLC monomer and dimer supported the involvement of covalent forces in the dimerization of CrPLC. A disulphide bridge was found to be responsible for the dimerization and Cys7 seems to be involved in the formation of the disulphide bond. This crucial disulphide bond also modulated the lipid affinity of CrPLC. Oligomers of CrPLC were also captured in in vivo condition. CrPLC was mainly found to be localized in the plasma membrane of the cell. The cell surface localization of CrPLC may have significant implication in the downstream regulatory function of CrPLC. SIGNIFICANCE: This study helps in establishing the role of CrPLC (or similar proteins in the quaternary structure of the molecule its affinities during lipid interactions.

  8. Hydrogen bond induced HF elimination from photoionized fluorophenol dimers in the gas phase

    Science.gov (United States)

    Chatterjee, Piyali; Ghosh, Arup K.; Chakraborty, Tapas

    2017-02-01

    In this paper, we report finding of a remarkable chemical effect of hydrogen bonding, elimination of hydrogen fluoride (HF) from the hydrogen bonded dimers of 2-fluorophenol (2-FP) and 3-fluorophenol (3-FP), in a supersonic jet expansion upon multi-photon ionization using 4th harmonic wavelength (266 nm) of a Q-switched Nd:YAG laser, and the reaction has been probed by time-of-flight mass spectrometry. No HF elimination is observed to occur by such means from the monomer of 3-FP, but it occurs with a small yield from the monomer of 2-FP. On the other hand, upon dimerization the reaction is triggered on for 3-FP, and for 2-FP it becomes so facile that no intact dimer cation survives and only the HF eliminated product ion appears in the mass spectra. Electronic structure calculation shows that in the cationic ground (D0) state, although the reaction for 2-FP dimer is exothermic, the associated barrier is significantly high (2.75 eV) and for its occurrence, absorption of three photons (2+1 type) is required. However, the reaction is predicted barrierless in the intermediate S1 state of this dimer, and HF loss dimer cation mass peak could appear in the mass spectrum due to an effective two-photon (1+1) ionization process. In the case of 3-FP dimer, the energy barriers both in S1 (neutral) and D0 (ionic) states are high, and it is suggested that for occurrence of HF elimination, dimer cation needs to absorb an additional photon. For facilitation of HF loss from this dimer cation, a rearrangement of the geometry and formation of an intermediate adduct have been suggested, and it is argued that the latter could be produced by nucleophilic attack of the neutral moiety at the ortho site of the cationic counterpart.

  9. Antiviral activity of α-helical stapled peptides designed from the HIV-1 capsid dimerization domain

    Directory of Open Access Journals (Sweden)

    Cowburn David

    2011-05-01

    Full Text Available Abstract Background The C-terminal domain (CTD of HIV-1 capsid (CA, like full-length CA, forms dimers in solution and CTD dimerization is a major driving force in Gag assembly and maturation. Mutations of the residues at the CTD dimer interface impair virus assembly and render the virus non-infectious. Therefore, the CTD represents a potential target for designing anti-HIV-1 drugs. Results Due to the pivotal role of the dimer interface, we reasoned that peptides from the α-helical region of the dimer interface might be effective as decoys to prevent CTD dimer formation. However, these small peptides do not have any structure in solution and they do not penetrate cells. Therefore, we used the hydrocarbon stapling technique to stabilize the α-helical structure and confirmed by confocal microscopy that this modification also made these peptides cell-penetrating. We also confirmed by using isothermal titration calorimetry (ITC, sedimentation equilibrium and NMR that these peptides indeed disrupt dimer formation. In in vitro assembly assays, the peptides inhibited mature-like virus particle formation and specifically inhibited HIV-1 production in cell-based assays. These peptides also showed potent antiviral activity against a large panel of laboratory-adapted and primary isolates, including viral strains resistant to inhibitors of reverse transcriptase and protease. Conclusions These preliminary data serve as the foundation for designing small, stable, α-helical peptides and small-molecule inhibitors targeted against the CTD dimer interface. The observation that relatively weak CA binders, such as NYAD-201 and NYAD-202, showed specificity and are able to disrupt the CTD dimer is encouraging for further exploration of a much broader class of antiviral compounds targeting CA. We cannot exclude the possibility that the CA-based peptides described here could elicit additional effects on virus replication not directly linked to their ability to bind

  10. An artemisinin-derived dimer has highly potent anti-cytomegalovirus (CMV and anti-cancer activities.

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    Ran He

    Full Text Available We recently reported that two artemisinin-derived dimers (dimer primary alcohol 606 and dimer sulfone 4-carbamate 832-4 are significantly more potent in inhibiting human cytomegalovirus (CMV replication than artemisinin-derived monomers. In our continued evaluation of the activities of artemisinins in CMV inhibition, twelve artemisinin-derived dimers and five artemisinin-derived monomers were used. Dimers as a group were found to be potent inhibitors of CMV replication. Comparison of CMV inhibition and the slope parameter of dimers and monomers suggest that dimers are distinct in their anti-CMV activities. A deoxy dimer (574, lacking the endoperoxide bridge, did not have any effect on CMV replication, suggesting a role for the endoperoxide bridge in CMV inhibition. Differences in anti-CMV activity were observed among three structural analogs of dimer sulfone 4-carbamate 832-4 indicating that the exact placement and oxidation state of the sulfur atom may contribute to its anti-CMV activity. Of all tested dimers, artemisinin-derived diphenyl phosphate dimer 838 proved to be the most potent inhibitor of CMV replication, with a selectivity index of approximately 1500, compared to our previously reported dimer sulfone 4-carbamate 832-4 with a selectivity index of about 900. Diphenyl phosphate dimer 838 was highly active against a Ganciclovir-resistant CMV strain and was also the most active dimer in inhibition of cancer cell growth. Thus, diphenyl phosphate dimer 838 may represent a lead for development of a highly potent and safe anti-CMV compound.

  11. A 4% efficient organic solar cell using a fluorinated fused subphthalocyanine dimer as an electron acceptor

    Energy Technology Data Exchange (ETDEWEB)

    Verreet, Bregt; Heremans, Paul [IMEC, Kapeldreef 75, B-3001 Leuven (Belgium); ESAT, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Leuven (Belgium); Rand, Barry P.; Cheyns, David; Hadipour, Afshin; Aernouts, Tom [IMEC, Kapeldreef 75, B-3001 Leuven (Belgium); Medina, Anais; Claessens, Christian G. [Departamento de Quimica Organica, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Torres, Tomas [Departamento de Quimica Organica, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); IMDEA-Nanociencia, Facultad de Ciencias, Ciudad Universitaria de Cantoblanco, 28049 Madrid (Spain)

    2011-07-15

    Planar bilayer organic solar cells with a fluorinated fused subphthalocyanine dimer (FSubPcDimer) as an acceptor and chloroboron (III) subphthalocyanine (SubPc) as a donor obtain a 60% higher J{sub sc} compared to cells using C{sub 60} as an acceptor, resulting in a power conversion efficiency of 4%. This is obtained thanks to the important contribution to the photocurrent of the low-bandgap FSubPcDimer. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  12. Propagation of light in serially coupled plasmonic nanowire dimer: Geometry dependence and polarization control

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Danveer; Raghuwanshi, Mohit; Pavan Kumar, G. V. [Photonics and Optical Nanoscopy Laboratory, Department of Physics and Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008 (India)

    2012-09-10

    We experimentally studied plasmon-polariton-assisted light propagation in serially coupled silver nanowire (Ag-NW) dimers and probed their dependence on bending-angle between the nanowires and polarization of incident light. From the angle-dependence study, we observed that obtuse angles between the nanowires resulted in better transmission than acute angles. From the polarization studies, we inferred that light emission from junction and distal ends of Ag-NW dimers can be systematically controlled. Further, we applied this property to show light routing and polarization beam splitting in obtuse-angled Ag-NW dimer. The studied geometry can be an excellent test-bed for plasmonic circuitry.

  13. Characterization of topological phases of dimerized Kitaev chain via edge correlation functions

    Science.gov (United States)

    Wang, Yucheng; Miao, Jian-Jian; Jin, Hui-Ke; Chen, Shu

    2017-11-01

    We study analytically topological properties of a noninteracting modified dimerized Kitaev chain and an exactly solvable interacting dimerized Kitaev chain under open boundary conditions by analyzing two introduced edge correlation functions. The interacting dimerized Kitaev chain at the symmetry point Δ =t and the chemical potential μ =0 can be exactly solved by applying two Jordan-Wigner transformations and a spin rotation, which permits us to calculate the edge correlation functions analytically. We demonstrate that the two edge correlation functions can be used to characterize the trivial, Su-Schrieffer-Heeger-like topological and topological superconductor phases of both the noninteracting and interacting systems and give their phase diagrams.

  14. Identification of two conformationally trapped n-propanol-water dimers in a supersonic expansion

    Science.gov (United States)

    Mead, Griffin J.; Alonso, Elena R.; Finneran, Ian A.; Carroll, P. Brandon; Blake, Geoffrey A.

    2017-05-01

    Two conformers of the n-propanol-water dimer have been observed in a supersonic expansion using chirped-pulse Fourier-transform microwave (CPFTMW) spectroscopy. Structural assignments reveal the n-propanol sub-unit is conformationally trapped, with its methyl group in both Gauche and Trans orientations. Despite different carbon backbone conformations, both dimers display the same water-donor/alcohol-acceptor hydrogen bonding motif. This work builds upon other reported alcohol-water dimers and upon previous work detailing the trapping of small molecules into multiple structural minima in rare gas supersonic expansions.

  15. Aberrant phenotypes of transgenic mice expressing dimeric human erythropoietin

    Directory of Open Access Journals (Sweden)

    Yun Seong-Jo

    2012-01-01

    Full Text Available Abstract Background Dimeric human erythropoietin (dHuEPO peptides are reported to exhibit significantly higher biological activity than the monomeric form of recombinant EPO. The objective of this study was to produce transgenic (tg mice expressing dHuEPO and to investigate the characteristics of these mice. Methods A dHuEPO-expressing vector under the control of the goat beta-casein promoter, which produced a dimer of human EPO molecules linked by a 2-amino acid peptide linker (Asp-Ile, was constructed and injected into 1-cell fertilized embryos by microinjection. Mice were screened using genomic DNA samples obtained from tail biopsies. Blood samples were obtained by heart puncture using heparinized tubes, and hematologic parameters were assessed. Using the microarray analysis tool, we analyzed differences in gene expression in the spleens of tg and control mice. Results A high rate of spontaneous abortion or death of the offspring was observed in the recipients of dHuEPO embryos. We obtained 3 founder lines (#4, #11, and #47 of tg mice expressing the dHuEPO gene. However, only one founder line showed stable germline integration and transmission, subsequently establishing the only transgenic line (#11. We obtained 2 F1 mice and 3 F2 mice from line #11. The dHuEPO protein could not be obtained because of repeated spontaneous abortions in the tg mice. Tg mice exhibited symptoms such as short lifespan and abnormal blood composition. The red blood cell count, white blood cell count, and hematocrit levels in the tg mice were remarkably higher than those in the control mice. The spleens of the tg mice (F1 and F2 females were 11- and -21-fold larger than those of the control mice. Microarray analysis revealed 2,672 spleen-derived candidate genes; more genes were downregulated than upregulated (849/764. Reverse transcriptase-polymerase chain reaction (RT-PCR and quantitative real-time PCR (qRT-PCR were used for validating the results of the microarray

  16. CO dimer: new potential energy surface and rovibrational calculations.

    Science.gov (United States)

    Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker

    2013-08-15

    The spectrum of CO dimer was investigated by solving the rovibrational Schrödinger equation on a new potential energy surface constructed from coupled-cluster ab initio points. The Schrödinger equation was solved with a Lanczos algorithm. Several 4D (rigid monomer) global ab initio potential energy surfaces (PESs) were made using a previously reported interpolating moving least-squares (IMLS) fitting procedure specialized to describe the interaction of two linear fragments. The potential has two nonpolar minima giving rise to a complicated set of energy level stacks, which are very sensitive to the shapes and relative depths of the two wells. Although the CO dimer has defied previous attempts at an accurate purely ab initio description our best surface yields results in good agreement with experiment. Root-mean-square (rms) fitting errors of less than 0.1 cm(-1) were obtained for each of the fits using 2226 ab initio data at different levels. This allowed direct assessment of the quality of various levels of ab initio theory for prediction of spectra. Our tests indicate that standard CCSD(T) is slow to converge the interaction energy even when sextuple zeta bases as large as ACV6Z are used. The explicitly correlated CCSD(T)-F12b method was found to recover significantly more correlation energy (from singles and doubles) at the CBS limit. Correlation of the core-electrons was found to be important for this system. The best PES was obtained by extrapolation of calculations at the CCSD(T)(AE)-F12b/CVnZ-F12 (n = 3,4) levels. The calculated energy levels were compared to 105 J ≤ 10 levels from experiment. The rms error for 68 levels with J ≤ 6 is only 0.29 cm(-1). The calculated energy levels were assigned stack labels using several tools. New stacks were found. One of them, stack y1, has an energy lower than many previously known stacks and may be observable.

  17. Discrete Dipole Approximation Simulation of Nearly Touching Plasmonic Au Dimers and Influence of Particle Shape Assembly on Optical Response.

    Science.gov (United States)

    Xu, Xi-Bin; Wang, Yu-Ying; Yi, Zao; Li, Xi-Bo; Luo, Jiang-Shan; Luo, Bing-Chi; Yi, You-Gen; Tang, Yong-Jian

    2016-01-01

    The method Discrete Dipole Approximation (DDA) is used to calculate the extinction spectra and field distribution of three types of dimers. In the paper we provide a systematic analysis of the optical response of different nanoscopic dimer structures with relatively small gap distances. A description is given about how the energy and excitation cross sections of dimer plasmons depend on nanoparticle separation. Resonance peaks of dimers show red-shift compared with single nanoparticle. Dimers formed by different single particle display distinct optical response. Interaction junctions in dimers can serve as hot spots for field enhancement. Field distribution in gaps made of two flat planes is nearly continuous. Changing gaps between two particles in dimers can tune the resonance wavelength effectively as well as different particle ensembles. Existence of sharp corners can attract and change field distribution. It is not effective volume but the effective cross-section that dominates the extinction efficiency.

  18. Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model

    Science.gov (United States)

    Zhao, Song-Feng; Huang, Fang; Wang, Guo-Li; Zhou, Xiao-Xin

    2016-03-01

    We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov–Popov–Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province

  19. Dimerization-Dependent Green and Yellow Fluorescent Proteins

    Science.gov (United States)

    Alford, Spencer C.; Ding, Yidan; Simmen, Thomas; Campbell, Robert E.

    2012-01-01

    Dimerization-dependent fluorescent proteins (ddFP) are a recently introduced class of genetically encoded reporters that can be used for the detection of protein interactions in live cells. The progenitor of this class of tools was a red fluorescent ddFP (ddRFP) derived from a homodimeric variant of Discosoma red fluorescent protein. Here, we describe the engineering and application of an expanded palette of ddFPs, which includes green (ddGFP) and yellow (ddYFP) variants. These optimized variants offer several advantages relative to ddRFP including increased in vitro contrast and brightness for ddGFP and increased brightness and a lowered pKa for ddYFP. We demonstrate that both variants are useful as biosensors for protease activity in live cells. Using the ddGFP tool, we generated a highly effective indicator of endomembrane proximity that can be used to image the mitochondria-associated membrane (MAM) interface of endoplasmic reticulum (ER) and mitochondria. PMID:23656278

  20. Roughness effect on the efficiency of dimer antenna based biosensor

    Directory of Open Access Journals (Sweden)

    D. Barchiesi

    2012-09-01

    Full Text Available The fabrication process of nanodevices is continually improved. However, most of the nanodevices, such as biosensors present rough surfaces with mean roughness of some nanometers even if the deposition rate of material is more controlled. The effect of roughness on performance of biosensors was fully addressed for plane biosensors and gratings, but rarely addressed for biosensors based on Local Plasmon Resonance. The purpose of this paper is to evaluate numerically the influence of nanometric roughness on the efficiency of a dimer nano-biosensor (two levels of roughness are considered. Therefore, we propose a general numerical method, that can be applied to any other nanometric shape, to take into account the roughness in a three dimensional model. The study focuses on both the far-field, which corresponds to the experimental detected data, and the near-field, responsible for exciting and then detecting biological molecules. The results suggest that the biosensor efficiency is highly sensitive to the surface roughness. The roughness can produce important shifts of the extinction efficiency peak and a decrease of its amplitude resulting from changes in the distribution of near-field and absorbed electric field intensities.