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Sample records for pyrimidine dimers

  1. Biological consequences of cyclobutane pyrimidine dimers

    NARCIS (Netherlands)

    Vink, A.A.; Roza, L.

    2001-01-01

    In the skin many molecules may absorb ultraviolet (UV) radiation upon exposure. In particular, cellular DNA strongly absorbs shorter wavelength solar UV radiation, resulting in various types of DNA damage. Among the DNA photoproducts produced the cyclobutane pyrimidine dimers (CPDs) are predominant.

  2. [Retarded excision of pyrimidine dimers in human unstimulated lymphocytes].

    Science.gov (United States)

    Snopov, S A; Roza, L; de Gruijl, F R

    2006-01-01

    Using immuno-labelling of cyclobutane pyrimidine dimers (CPDs) in nuclei of peripheral lymphocytes after their UVC-irradiation and cultivation, we have found that within the first four hours of cultivation the CPD-specific fluorescent signal from cell nuclei increased. Earlier, a similar increase in binding of antibody specific for pyrimidine (6-4) pyrimidone photoproducts to undenatured DNA isolated from UV-irradiated Chinese hamster ovary cells was reported (Mitchell et al., 1986). Our experiments showed that nucleotide excision repair enzyme might induce such of DNA modification in lymphocyte nuclei that increased specific antibody binding to DNA fragments with lesions. We suggest that enzymatic formation of open structures in DNA predominated qualitatively over dual-incision and excision of these fragments, and resulted in the enhanced exposure of the pyrimidine dimers in nuclei to specific antibodies. The results evidence that nucleotid excision repair in unstimualted human lymphocytes being deficient in dual incision and removal of UV-induced DNA lesions appear to be capable of performing chromatin relaxation and pre-incision uncoiling of DNA fragments with lesions.

  3. Ultraviolet light-induced cyclobutane pyrimidine dimers in rabbit eyes.

    Science.gov (United States)

    Mallet, Justin D; Rochette, Patrick J

    2011-01-01

    Sunlight exposure of the eye leads to pathologies including photokeratitis, cortical cataracts, pterygium, actinic conjunctivitis and age-related macular degeneration. It is well established that exposure to ultraviolet (UV) radiations leads to DNA damage, mainly cyclobutane pyrimidine dimers (CPDs). CPD formation is the principal factor involved in skin cancer. However, the exact mechanism by which sunlight induces ocular pathologies is not well understood. To shed light on this issue, we quantified the CPD formation onto DNA of rabbit ocular cells following UVB exposure. We found that CPDs were induced only in the structures of the ocular anterior chamber (cornea, iris and lens) and were more concentrated in the corneal epithelium. Residual UVB that pass through the cornea are completely absorbed by the anterior layers of the iris. CPDs were also detected in the central portion of the lens that is not protected by the iris (pupil). By determining the UV-induced DNA damage formation in eyes, we showed that anterior ocular structures are a reliable physical barrier that protects the subjacent structures from the toxic effects of UV. Although the corneal epithelium is the structure where most of the CPDs were detected, no cancer is related to solar exposure.

  4. Photoreactivation of pyrimidine dimers in DNA from thyroid cells of the teleost, Poecilia formosa

    Energy Technology Data Exchange (ETDEWEB)

    Achey, P.M.; Woodhead, A.D.; Setlow, R.B.

    1979-01-01

    We have developed and used a simple technique to estimate the quantity of pyrimidine dimers in unlabeled cellular DNA. DNA is extracted from cells, treated with an endonuclease specific for dimers, and its molecular weight estimated by its electrophoretic mobility on alkaline agarose slab gels. The technique is used to show that cells from thyroid tissue of the fish Poecilia formosa have photoreactivating activity towards dimmers in the cellular DNA.

  5. Removal of pyrimidine dimers in UV-irradiated spores of Dictyostelium discoideum during germination

    Energy Technology Data Exchange (ETDEWEB)

    Okaichi, K.; Tano, K.; Ohnishi, T.; Nozu, K.

    1985-06-01

    The spores of Dictyostelium discoideum TW-8 (radC) are about twice as sensitive to UV than the parental strain NC-4 spores at a 10% survival level. Ultraviolet irradiation apparently suppressed the emergence of amoebae from swollen TW-8 spores as compared with NC-4 spores, though the conversion of spores into swollen spores was not affected by UV irradiation in either strain. About 85% removal of pyrimidine dimers was detected in UV-irradiated NC-4 spores at 200 J/m/sup 2/ during spore germination for 9 h, but no removal of pyrimidine dimers was detected in TW-8 spores under the same conditions. The removal of pyrimidine dimers from the NC-4 spores began at around 2 h germination when the spores have become swollen. The number of enzyme-sensitive sites (ESS) detected by Micrococcus luteus endonuclease in the DNA of UV-irradiated NC-4 spores also began to decrease at about 2 h into germination. The decrease in ESS, however, was hardly detectable in UV-irradiated TW-8 spores at any step during germination. Cycloheximide inhibited both decrease in the number of pyrimidine dimers, and decrease in the number of ESS of UV-irradiated NC-4 spores. It is suggested that UV-specific endonuclease is newly synthesized in swollen spores of NC-4. (author).

  6. Excision of pyrimidine dimers from nuclear deoxyribonucleic acid in ultraviolet-irradiated Dictyostelium discoideum

    Energy Technology Data Exchange (ETDEWEB)

    Clark, J.M.; Deering, R.A.

    1987-02-01

    A sensitive endonuclease assay was used to study the fate of pyrimidine dimers introduced by ultraviolet irradiation into the nuclear deoxyribonucleic acid of the cellular slime mold Dictyostellium discoideum. Analysis of the frequency of T4 endonuclease V-induced single-strand breaks by alkaline sucrose gradient sedimentation showed that strain NC4 (rad/sup +/) removed >98% of the dimers induced by irradiation at 40 J/m/sup 2/ (254 nm) within 215 min after irradiation. HPS104 (radC44), a mutant sensitive to ultraviolet irradiation, removed 91% under these conditions, although at a significantly slower rate than NC4: only 8% were removed during the 10- to 15- min period immediately after irradiation, whereas NC4 excised 64% during this interval. HPS104 thus appears to be deficient in the activity(ies) responsible for rapidly incising ultraviolet-irradiated nuclear deoxyribonucleic acid at the sites of pyrimidine dimers.

  7. 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.

  8. Enhanced DNA repair of cyclobutane pyrimidine dimers changes the biological response to UV-B radiation

    Energy Technology Data Exchange (ETDEWEB)

    Yarosh, Daniel B

    2002-11-30

    The goal of DNA repair enzyme therapy is the same as that for gene therapy: to rescue a defective proteome/genome by introducing a substitute protein/DNA. The danger of inadequate DNA repair is highlighted in the genetic disease xeroderma pigmentosum. These patients are hypersensitive to sunlight and develop multiple cutaneous neoplasms very early in life. The bacterial DNA repair enzyme T4 endonuclease V was shown over 25 years ago to be capable of reversing the defective repair in xeroderma pigmentosum cells. This enzyme, packaged in an engineered delivery vehicle, has been shown to traverse the stratum corneum, reach the nuclei of living cells of the skin, and enhance the repair of UV-induced cyclobutane pyrimidine dimers (CPD). In such a system, changes in DNA repair, mutagenesis, and cell signaling can be studied without manipulation of the genome.

  9. UVA-induced cyclobutane pyrimidine dimers in DNA: a direct photochemical mechanism?

    Science.gov (United States)

    Mouret, Stéphane; Philippe, Coralie; Gracia-Chantegrel, Jocelyne; Banyasz, Akos; Karpati, Szilvia; Markovitsi, Dimitra; Douki, Thierry

    2010-04-07

    The carcinogenic action of UVA radiation is commonly attributed to DNA oxidation mediated by endogenous photosensitisers. Yet, it was recently shown that cyclobutane pyrimidine dimers (CPD), well known for their involvement in UVB genotoxicity, are produced in larger yield than oxidative lesions in UVA-irradiated cells and skin. In the present work, we gathered mechanistic information on this photoreaction by comparing formation of all possible bipyrimidine photoproducts upon UVA irradiation of cells, purified genomic DNA and dA(20):dT(20) oligonucleotide duplex. We observed that the distribution of photoproducts, characterized by the sole formation of CPD and the absence of (6-4) photoproducts was similar in the three types of samples. The CPD involving two thymines represented 90% of the amount of photoproducts. Moreover, the yields of formation of the DNA lesions were similar in cells and isolated DNA. In addition, the effect of the wavelength of the incident photons was found to be the same in isolated DNA and cells. This set of data shows that UVA-induced cyclobutane pyrimidine dimers are formed via a direct photochemical mechanism, without mediation of a cellular photosensitiser. This is possible because the double-stranded structure increases the capacity of DNA bases to absorb UVA photons, as evidenced in the case of the oligomer dA(20):dT(20). These results emphasize the need to consider UVA in the carcinogenic effects of sunlight. An efficient photoprotection is needed that can only be complete by completely blocking incident photons, rather than by systemic approaches such as antioxidant supplementation.

  10. Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics.

    Science.gov (United States)

    Goto, Noriko; Bazar, Gyorgy; Kovacs, Zoltan; Kunisada, Makoto; Morita, Hiroyuki; Kizaki, Seiichiro; Sugiyama, Hiroshi; Tsenkova, Roumiana; Nishigori, Chikako

    2015-07-02

    Ultraviolet (UV) radiation causes cellular DNA damage, among which cyclobutane pyrimidine dimers (CPDs) are responsible for a variety of genetic mutations. Although several approaches have been developed for detection of CPDs, conventional methods require time-consuming steps. Aquaphotomics, a new approach based on near-infrared spectroscopy (NIRS) and multivariate analysis that determines interactions between water and other components of the solution, has become an effective method for qualitative and quantitative parameters measurement in the solutions. NIR spectral patterns of UVC-irradiated and nonirradiated DNA solutions were evaluated using aquaphotomics for detection of UV-induced CPDs. Groups of UV-irradiated and nonirradiated DNA samples were classified (87.5% accuracy) by soft independent modeling of class analogy (SIMCA). A precise regression model calculated from NIR water spectral patterns based on UVC doses (r Val = 0.9457) and the concentration of cis-syn cyclobutane thymine dimers (cis-syn TTs; r Val = 0.9993) was developed using partial least squares regression (PLSR), while taking advantage of water spectral patterns, particularly around 1400-1500 nm. Our results suggested that, in contrast to DNA, the formation of cis-syn TTs increased the strongly hydrogen bonded water. Additionally, NIRS could qualitatively and quantitatively detect cis-syn TTs in isolated DNA aqueous solutions upon UVC exposure.

  11. Pyrimidine dimer formation and germination of UV-irradiated spores of Dictyostelium discoideum NC-4 and. gamma. s-13

    Energy Technology Data Exchange (ETDEWEB)

    Nozu, K.; Ohnishi, T.; Okaichi, K. (Nara Medical Univ., Kashihara (Japan))

    1982-04-01

    Survival, UV-photoproducts and germination of UV-irradiated spores of Dictyostelium discoideum were studied on two strains, NC-4 and ..gamma..s-13. The spores of NC-4 are about 35 times more resistant to UV than ..gamma..s-13 spores at 10% survival. Pyrimidine dimers were formed in UV-irradiated spores in both strains. No photoproducts other than pyrimidine dimers were detected. The formation of pyrimidine dimers in spores was about 2% in both strains at 800 J/m/sup 2/. In the germination of spores, the conversion of spores into swollen spores was not affected by UV in both strains, but the emergence of amoebae from the swollen spores was suppressed, which was more distinctive in ..gamma..s-13 spores than in NC-4 spores. The emerged amoebae from the UV-irradiated NC-4 spores were viable, while those from the ..gamma..s-13 spores were inviable even when they succeeded in emergence.

  12. Wavelength-dependent ultraviolet induction of cyclobutane pyrimidine dimers in the human cornea.

    Science.gov (United States)

    Mallet, Justin D; Rochette, Patrick J

    2013-08-01

    Exposition to ultraviolet (UV) light is involved in the initiation and the progression of skin cancer. The genotoxicity of UV light is mainly attributed to the induction of cyclobutane pyrimidine dimers (CPDs), the most abundant DNA damage generated by all UV types (UVA, B and C). The human cornea is also exposed to the harmful UV radiations, but no UV-related neoplasm has been reported in this ocular structure. The probability that a specific DNA damage leads to a mutation and eventually to cellular transformation is influenced by its formation frequency. To shed light on the genotoxic effect of sunlight in the human eye, we have analyzed CPD induction in the cornea and the iris following irradiation of ex vivo human eyes with UVA, B or C. The extent of CPD induction was used to establish the penetrance of the different UV types in the human cornea. We show that UVB- and UVC-induced CPDs are concentrated in the corneal epithelium and do not penetrate deeply beyond this corneal layer. On the other hand, UVA wavelengths penetrate deeper and induce CPDs in the entire cornea and in the first layers of the iris. Taken together, our results are undoubtedly an important step towards better understanding the consequences of UV exposure to the human eye.

  13. Apigenin prevents ultraviolet-B radiation induced cyclobutane pyrimidine dimers formation in human dermal fibroblasts.

    Science.gov (United States)

    Britto, S Mary; Shanthakumari, D; Agilan, B; Radhiga, T; Kanimozhi, G; Prasad, N Rajendra

    2017-09-01

    Exposure to solar ultraviolet-B (UVB) radiation leads to the formation of cyclobutane pyrimidine dimers (CPDs). We investigated the protective effect of apigenin against UVB-induced CPDs formation in human dermal fibroblasts cells (HDFa). For this purpose, HDFa cells were treated with apigenin (15μM) prior to UVB irradiation (20mJ/cm(2)); DNA damage and subsequent molecular end points were observed. Exposure to UVB radiation increased significant CPDs formation in HDFa cells and the frequencies of CPDs were reduced by treatment with apigenin (15μM). UVB-induced CPDs downregulates the expression of nucleotide excision repair (NER) genes such as xeroderma pigmentosum complementation group C, B, G and F (XPC, XPB, XPG and XPF), transcription factor II human (TFIIH) and excision repair cross-complementation group 1 (ERCC1) in HDFa cells. Conversely, apigenin treatment restored UVB-induced loss of NER proteins in HDFa cells, which indicates its preventive effect against CPDs formation. Besides, single low dose UVB-exposure induced nuclear fragmentation, apoptotic frequency and apoptotic proteins expression (Bax and Caspase-3) have been prevented by the apigenin pretreatment. Furthermore, apigenin exhibits strong UV absorbance property and showed 10.08 SPF value. Thus, apigenin can protect skin cells against UVB-induced CPDs formation probably through its sunscreen effect. Hence, apigenin can be considered as an effective protective agent against UV induced skin damages. Copyright © 2017 Elsevier B.V. All rights reserved.

  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. Light-induced activation of class II cyclobutane pyrimidine dimer photolyases.

    Science.gov (United States)

    Okafuji, Asako; Biskup, Till; Hitomi, Kenichi; Getzoff, Elizabeth D; Kaiser, Gebhard; Batschauer, Alfred; Bacher, Adelbert; Hidema, Jun; Teranishi, Mika; Yamamoto, Kazuo; Schleicher, Erik; Weber, Stefan

    2010-05-04

    Light-induced activation of class II cyclobutane pyrimidine dimer (CPD) photolyases of Arabidopsis thaliana and Oryza sativa has been examined by UV/Vis and pulsed Davies-type electron-nuclear double resonance (ENDOR) spectroscopy, and the results compared with structure-known class I enzymes, CPD photolyase and (6-4) photolyase. By ENDOR spectroscopy, the local environment of the flavin adenine dinucleotide (FAD) cofactor is probed by virtue of proton hyperfine couplings that report on the electron-spin density at the positions of magnetic nuclei. Despite the amino-acid sequence dissimilarity as compared to class I enzymes, the results indicate similar binding motifs for FAD in the class II photolyases. Furthermore, the photoreduction kinetics starting from the FAD cofactor in the fully oxidized redox state, FAD(ox), have been probed by UV/Vis spectroscopy. In Escherichia coli (class I) CPD photolyase, light-induced generation of FADH from FAD(ox), and subsequently FADH(-) from FADH, proceeds in a step-wise fashion via a chain of tryptophan residues. These tryptophans are well conserved among the sequences and within all known structures of class I photolyases, but completely lacking from the equivalent positions of class II photolyase sequences. Nevertheless, class II photolyases show photoreduction kinetics similar to those of the class I enzymes. We propose that a different, but also effective, electron-transfer cascade is conserved among the class II photolyases. The existence of such electron transfer pathways is supported by the observation that the catalytically active fully reduced flavin state obtained by photoreduction is maintained even under oxidative conditions in all three classes of enzymes studied in this contribution.

  16. Kinetics and mechanism of electron-induced splitting of a cyclobutane pyrimidine dimer with or without an electron acceptor

    Institute of Scientific and Technical Information of China (English)

    YAN; Liqin(晏利琴); SONG; Qinhua(宋钦华); HEI; Xiaoming(黑晓明); WANG; Wenfeng(王文锋); GUO; Qingxiang(郭庆祥)

    2003-01-01

    Utilizing a pulse radiolysis equipment with time-resolved optical detector, kinetic processes of electron-induced splitting of cis-syn 1,3-dimethyluracil cyclobutane dimer (DMUD) in aqueous solution were investigated in the presence or absence of riboflavin (RF) or flavin adenine dinucleotide (FAD). It has been observed that the cyclobutane pyrimidine dimer reacting with hydrated electron splits spontaneously to give a monomer and a monomer radical anion, and the anion transfers one electron to RF or FAD. From the buildup kinetics of radical species, the rate constants of electron transfer from the monomer radical anion to RF and FAD have been determined. On the basis of comparison of the interactions between DMUD and hydrated electron in the presence and absence of RF or FAD, a chain reaction process in the absence of RF or FAD has been demonstrated.

  17. 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...

  18. Inducible removal of UV-induced pyrimidine dimers from transcriptionally active and inactive genes of Saccharomyces cerevisiae.

    Science.gov (United States)

    Waters, R; Zhang, R; Jones, N J

    1993-05-01

    The prior UV irradiation of alpha haploid Saccharomyces cerevisiae with a UV dose of 25 J/m2 substantially increases the repairability of damage subsequently induced by a UV dose of 70 J/m2 given 1 h after the first irradiation. This enhancement of repair is seen at both the MAT alpha and HML alpha loci, which are, respectively, transcriptionally active and inactive in alpha haploid cells. The presence in the medium of the protein synthesis inhibitor, cycloheximide in the period between the two irradiations eliminated this effect. Enhanced repair still occurred if cycloheximide was present only after the final UV irradiation. This indicated that the first result is not due to cycloheximide merely blocking the synthesis of repair enzymes associated with a hypothetical rapid turnover of such molecules. The enhanced repairability is not the result of changes in chromatin accessibility without protein synthesis, merely caused by the repair of the damage induced by the prior irradiation. The data clearly show that a UV-inducible removal of pyrimidine dimers has occurred which involves the synthesis of new proteins. The genes known to possess inducible promoters, and which are involved in excision are RAD2, RAD7, RAD16 and RAD23. Studies with the rad7 and rad16 mutants which are defective in the ability to repair HML alpha and proficient in the repair of MAT alpha showed that in rad7, preirradiation enhanced the repair at MAT alpha, whereas in rad16 this increased repair of MAT alpha was absent. The preirradiation did not modify the inability to repair HML alpha in either strain. Thus RAD16 has a role in this inducible repair.(ABSTRACT TRUNCATED AT 250 WORDS)

  19. Rapid deamination of cyclobutane pyrimidine dimer photoproducts at TCG sites in a translationally and rotationally positioned nucleosome in vivo.

    Science.gov (United States)

    Cannistraro, Vincent J; Pondugula, Santhi; Song, Qian; Taylor, John-Stephen

    2015-10-30

    Sunlight-induced C to T mutation hot spots in skin cancers occur primarily at methylated CpG sites that coincide with sites of UV-induced cyclobutane pyrimidine dimer (CPD) formation. The C and 5-methyl-C in CPDs are not stable and deaminate to U and T, respectively, which leads to the insertion of A by the DNA damage bypass polymerase η, thereby defining a probable mechanism for the origin of UV-induced C to T mutations. Deamination rates for T(m)CG CPDs have been found to vary 12-fold with rotational position in a nucleosome in vitro. To determine the influence of nucleosome structure on deamination rates in vivo, we determined the deamination rates of CPDs at TCG sites in a stably positioned nucleosome within the FOS promoter in HeLa cells. A procedure for in vivo hydroxyl radical footprinting with Fe-EDTA was developed, and, together with results from a cytosine methylation protection assay, we determined the translational and rotational positions of the TCG sites. Consistent with the in vitro observations, deamination was slower for one CPD located at an intermediate rotational position compared with two other sites located at outside positions, and all were much faster than for CPDs at non-TCG sites. Photoproduct formation was also highly suppressed at one site, possibly due to its interaction with a histone tail. Thus, it was shown that CPDs of TCG sites deaminate the fastest in vivo and that nucleosomes can modulate both their formation and deamination, which could contribute to the UV mutation hot spots and cold spots.

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

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    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.

  1. Fully functional global genome repair of (6-4) photoproducts and compromised transcription-coupled repair of cyclobutane pyrimidine dimers in condensed mitotic chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Komura, Jun-ichiro, E-mail: junkom@med.tohoku.ac.jp [Department of Cell Biology, Tohoku University Graduate School of Medicine, Sendai 980-8575 (Japan); Ikehata, Hironobu [Department of Cell Biology, Tohoku University Graduate School of Medicine, Sendai 980-8575 (Japan); Mori, Toshio [Radioisotope Research Center, Nara Medical University, Kashihara, Nara 634-8521 (Japan); Ono, Tetsuya [Department of Cell Biology, Tohoku University Graduate School of Medicine, Sendai 980-8575 (Japan)

    2012-03-10

    During mitosis, chromatin is highly condensed, and activities such as transcription and semiconservative replication do not occur. Consequently, the condensed condition of mitotic chromatin is assumed to inhibit DNA metabolism by impeding the access of DNA-transacting proteins. However, about 40 years ago, several researchers observed unscheduled DNA synthesis in UV-irradiated mitotic chromosomes, suggesting the presence of excision repair. We re-examined this subject by directly measuring the removal of UV-induced DNA lesions by an ELISA and by a Southern-based technique in HeLa cells arrested at mitosis. We observed that the removal of (6-4) photoproducts from the overall genome in mitotic cells was as efficient as in interphase cells. This suggests that global genome repair of (6-4) photoproducts is fully functional during mitosis, and that the DNA in mitotic chromatin is accessible to proteins involved in this mode of DNA repair. Nevertheless, not all modes of DNA repair seem fully functional during mitosis. We also observed that the removal of cyclobutane pyrimidine dimers from the dihydrofolate reductase and c-MYC genes in mitotic cells was very slow. This suggests that transcription-coupled repair of cyclobutane pyrimidine dimers is compromised or non-functional during mitosis, which is probably the consequence of mitotic transcriptional repression. -- Highlights: Black-Right-Pointing-Pointer Global genome repair of (6-4) photoproducts is fully active in mitotic cells. Black-Right-Pointing-Pointer DNA in condensed mitotic chromatin does not seem inaccessible or inert. Black-Right-Pointing-Pointer Mitotic transcriptional repression may impair transcription-coupled repair.

  2. 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.

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

    Science.gov (United States)

    Vreeswijk, Maaike P G; Meijers, Caro M; Giphart-Gassler, Micheline; Vrieling, Harry; van Zeeland, Albert A; Mullenders, Leon H F; Loenen, Wil A M

    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 (6-4 PP). 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 6-4 PP 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.

  4. 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

  5. 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.

  6. Self-assembling of cytosine nucleoside into triply-bound dimers in acid media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, X-rays diffractometry, and theoretical calculations.

    Science.gov (United States)

    Armentano, Donatella; De Munno, Giovanni; Di Donna, Leonardo; Sindona, Giovanni; Giorgi, Gianluca; Salvini, Laura; Napoli, Anna

    2004-02-01

    Electrospray tandem mass spectrometry (ESI-MS/MS) is used to evaluate the assembling of cytosine and thymine nucleosides in the gas phase, through the formation of hydrogen bonded supermolecules. Mixtures of cytidine analogues and homologues deliver in the gas phase proton-bound heterodimers stabilized by multiple interactions, as proven by the kinetics of their dissociation into the corresponding protonated monomers. Theoretical calculations, performed on initial structures of methylcytosine homodimers available in the literature, converged to a minimized structure whereby the two pyrimidine rings interact through the formation of three hydrogen bonds of similar energy. The crystallographic data here reported show the equivalency of the two interacting pyrimidines which is attributable to the presence of an inversion center. Thymine and uracil pyrimidyl nucleosides form, by ESI, gaseous proton-bound dimers. The kinetic of their dissociation into the related protonated monomers shows that the nucleobases are weekly interacting through a single hydrogen bond. The minimized structure of the protonated heterodimer formed by thymine and N-1-methylthymine confirmed the existence of mainly one hydrogen bond which links the two nucleobases through the O4 oxygens. No crystallographic data exists on thymine proton-bound species, nor have we been able to obtain these aggregates in the solid phase. The gaseous phase, under high vacuum conditions, seems therefore a suitable environment where vanishing structures produced by ESI can be studied with a good degree of approximation.

  7. Synthesis, Dimeric Crystal Structure, and Biological Activities of N-(4-Methyl-6-oxo-1,6-dihydro-pyrimidin-2-yl)-N-(2-trifluoromethyl-phenyl)-guanidine

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The title compound, N-(4-methyl-6-oxo-1,6-dihydro-pyrimidin-2-yl)-N′-(2-trifluoromethyl-phenyl)-guanidine, was synthesized and its structure was confirmed by using IR, MS, 1H NMR, and elemental analysis. The single crystal structure of the title compound was determined by X-ray diffraction. The preliminary biological test showed that the synthesized compound has a weak herbicidal activity.

  8. The acrylonitrile dimer ion: A study of its dissociation via self-catalysis, self-protonation and cyclization into the pyrimidine radical cation

    NARCIS (Netherlands)

    Ervasti, H.K.; Jobst, K.J.; Burgers, P.C.; Ruttink, P.J.A.; Terlouw, J.K.

    2007-01-01

    Large energy barriers prohibit the rearrangement of solitary acrylonitrile ions, CH2CHCN+, into their more stable hydrogen-shift isomers CH2CCNH+ or CHCH–CNH+. This prompted us to examine if these isomerizations occur by self-catalysis in acrylonitrile dimer ions. Such ions, generated by chemical

  9. 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.

  10. Inducible nucleotide excision repair (NER) of UV-induced cyclobutane pyrimidine dimers in the cell cycle of the budding yeast Saccharomyces cerevisiae: evidence that inducible NER is confined to the G1 phase of the mitotic cell cycle.

    Science.gov (United States)

    Scott, A D; Waters, R

    1997-03-18

    We previously reported on an inducible component of nucleotide excision repair in Saccharomyces cerevisiae that is controlled by the RAD16 gene. Here we describe a study of this event at the MAT alpha and HML alpha mating-type loci and on the transcribed (TS) and nontranscribed (NTS) strands of the RAD16 gene. Events were examined at various stages of the mitotic cycle in cells synchronised by centrifugal elutriation. Repair of cyclobutane pyrimidine dimers (CPDs) following a single UV dose does not vary significantly in different stages of the mitotic cell cycle. CPDs are removed more rapidly from the transcriptionally active MAT alpha locus than from the silent HML alpha locus, and the TS of RAD16 is repaired faster than the NTS in all stages of the cycle following a single UV irradiation. Enhanced excision of CPDs at MAT alpha and HML alpha can be induced only in the G1 and early S stages of the cell cycle. Here prior irradiation of cells with 25 J/m2 enhances the removal of CPDs following a second UV dose of 70 J/m2. The level of enhancement of repair does not differ significantly between MAT alpha and HML alpha in G1. Enhanced removal of CPDs is absent when cells receive the inducing dose in late S or G2/M. Repair of CPDs in both strands of RAD16 is similarly enhanced only if cells receive the initial irradiation in G1 and early S. The level of enhanced removal of CPDs is not significantly different in the TS and NTS of RAD16 either in asynchronous cells or in cells preirradiated in G1 and early S. It has been shown by others that UV-induced expression of RAD16 remains at high levels if cells are held in G1 by treatment with alpha factor. Therefore the increase in RAD16 transcript levels in G1 may be responsible for the ability to enhance NER solely in this stage of the cell cycle.

  11. Pyrimidine-pyridine ring interconversion

    NARCIS (Netherlands)

    Plas, van der H.C.

    2003-01-01

    This chapter discusses the pyrimidine-to-pyridine ring transformation and pyridine-to-pyrimidine ring transformation. In nucleophile-induced pyrimidine-to-pyridine rearrangements, two types of reactions can be distinguished depending on the structure of the nucleophile: (1) reactions in which the ni

  12. The acrylonitrile dimer ion

    Science.gov (United States)

    Ervasti, Henri K.; Jobst, Karl J.; Burgers, Peter C.; Ruttink, Paul J. Ae; Terlouw, Johan K.

    2007-04-01

    Large energy barriers prohibit the rearrangement of solitary acrylonitrile ions, CH2CHCN+, into their more stable hydrogen-shift isomers CH2CCNH+ or CHCH-CNH+. This prompted us to examine if these isomerizations occur by self-catalysis in acrylonitrile dimer ions. Such ions, generated by chemical ionization experiments of acrylonitrile with an excess of carbon dioxide, undergo five dissociations in the [mu]s time frame, as witnessed by peaks at m/z 53, 54, 79, 80 and 105 in their metastable ion mass spectrum. Collision experiments on these product ions, deuterium labeling, and a detailed computational analysis using the CBS-QB3 model chemistry lead to the following conclusions: (i) the m/z 54 ions are ions CH2CHCNH+ generated by self-protonation in ion-dipole stabilized hydrogen-bridged dimer ions [CH2CHCN...H-C(CN)CH2]+ and [CH2CHCN...H-C(H)C(H)CN]+; the proton shifts in these ions are associated with a small reverse barrier; (ii) dissociation of the H-bridged ions into CH2CCNH+ or CHCH-CNH+ by self-catalysis is energetically feasible but kinetically improbable: experiment shows that the m/z 53 ions are CH2CHCN+ ions, generated by back dissociation; (iii) the peaks at m/z 79, 80 and 105 correspond with the losses of HCN, C2H2 and H, respectively. The calculations indicate that these ions are generated from dimer ions that have adopted the (much more stable) covalently bound "head-to-tail" structure [CH2CHCN-C(H2)C(H)CN]+; experiments indicate that the m/z 79 (C5H5N) and m/z 105 (C6H6N2) ions have linear structures but the m/z 80 (C4H4N2) ions consist of ionized pyrimidine in admixture with its stable pyrimidine-2-ylidene isomer. Acrylonitrile is a confirmed species in interstellar space and our study provides experimental and computational evidence that its dimer radical cation yields the ionized prebiotic pyrimidine molecule.

  13. Purine and pyrimidine metabolism.

    Science.gov (United States)

    Zöllner, N

    1982-09-01

    The pathways of purine biosynthesis and degradation have been elucidated during the last 30 years; the regulation of the mechanisms involved is not yet fully understood, particularly with respect to quantitative aspects. Research into inborn errors of purine metabolism has provided valuable insights into purine synthesis and salvage pathways. Nutrition experiments using purine-free formula diets and supplements with defined purine sources permit precise descriptions of the influence of various dietary purines on uric acid formation. Supplements of dietary purines produce dose-proportional increases in plasma uric acid concentrations, uric acid pool size and renal uric acid excretion. The magnitude of these increases depends on the type of purine compound administered, which may limit the value of food tables for human dietetics. Purine content of food must be related not only to weight but also to energy and to protein, particularly if new foodstuffs or a vegetarian diet are ingested. Dietary purines appear to influence the biosynthesis of pyrimidines. In contrast to dietary purines, pyrimidines in the diet, if administered as nucleosides or nucleotides, are utilized in animals for the synthesis of nucleic acids. Much further work is necessary for a better understanding of the inter-relationships of purine and pyrimidine metabolism.

  14. A Search for Interstellar Pyrimidine

    CERN Document Server

    Kuan, Y J; Charnley, S B; Kisiel, Z; Ehrenfreund, P; Huang, H C; Kuan, Yi-Jehng; Yan, Chi-Hung; Charnley, Steven B.; Kisiel, Zbigniew; Ehrenfreund, Pascale; Huang, Hui-Chun

    2003-01-01

    We have searched three hot molecular cores for submillimeter emission from the nucleic acid building-block pyrimidine. We obtain upper limits to the total pyrimidine (beam-averaged) column densities towards Sgr B2(N), Orion KL and W51 e1/e2 of 1.7E+14 cm^{-2}, 2.4E+14 cm^{-2} and 3.4E+14 cm^{-2}, respectively. The associated upper limits to the pyrimidine fractional abundances lie in the range (0.3-3)E-10. Implications of this result for interstellar organic chemistry, and for the prospects of detecting nitrogen heterocycles in general, are briefly discussed.

  15. 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 c...

  16. Universality in bosonic dimer-dimer scattering

    Energy Technology Data Exchange (ETDEWEB)

    Deltuva, A. [Centro de Fisica Nuclear, Universidade de Lisboa, P-1649-003 Lisboa (Portugal)

    2011-08-15

    Bosonic dimer-dimer scattering is studied near the unitary limit using momentum-space equations for the four-particle transition operators. The impact of the Efimov effect on the dimer-dimer scattering observables is explored, and a number of universal relations is established with high accuracy. The rate for the creation of Efimov trimers via dimer-dimer collisions is calculated.

  17. Pyrimidine as antiinflammatory agent: A review

    Directory of Open Access Journals (Sweden)

    Amir M

    2007-01-01

    Full Text Available Pyrimidine nucleus exhibited remarkable pharmacological activities. Literature indicates that compounds having pyrimidine nucleus have wide range of therapeutic uses that include antiinflammatory, antibacterial, anticancer, antiviral, antiHIV, antimalarial, antihypertensive, sedatives and hypnotics, anticonvulsant and antihistaminic. The present review provides a broad view of the antiinflammatory activity possessed by compounds having a pyrimidine nucleus.

  18. 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.

  19. Polyurethane Foams with Pyrimidine Rings

    Directory of Open Access Journals (Sweden)

    Kania Ewelina

    2014-09-01

    Full Text Available Oligoetherols based on pyrimidine ring were obtained upon reaction of barbituric acid with glycidol and alkylene carbonates. These oligoetherols were then used to obtain polyurethane foams in the reaction of oligoetherols with isocyanates and water. The protocol of foam synthesis was optimized by the choice of proper kind of oligoetherol and synthetic composition. The thermal resistance was studied by dynamic and static methods with concomitant monitoring of compressive strength. The polyurethane foams have similar physical properties as the classic ones except their enhanced thermal resistance. They stand long-time heating even at 200°C. Moreover thermal exposition of foams results generally in increase of their compressive strength.

  20. 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...

  1. N-(Pyrimidin-2-ylaniline

    Directory of Open Access Journals (Sweden)

    Edura Badaruddin

    2009-04-01

    Full Text Available There are two molecules in the asymmetric unit of the title compound, C10H9N3, with inter-ring dihedral angles of 31.1 (1 and 35.3 (1°. The bridging C—N—C bond angles are 128.2 (1 and 129.1 (1°. In the crystal, the two independent molecules are linked into a dimer by two N—H...N hydrogen bonds.

  2. 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.

  3. Genetic factors influencing pyrimidine-antagonist chemotherapy

    NARCIS (Netherlands)

    Maring, JG; Groen, HJM; Wachters, FM; Uges, DRA; de Vries, EGE

    2005-01-01

    Pyrimidine antagonists, for example, 5-fluorouracil (5-FU), cytarabine (ara-C) and gemcitabine (dFdC), are widely used in chemotherapy regimes for colorectal, breast, head and neck, non-small-cell lung cancer, pancreatic cancer and leukaemias. Extensive metabolism is a prerequisite for conversion of

  4. Enzymology of Pyrimidine Metabolism and Neurodegeneration.

    Science.gov (United States)

    Vincenzetti, Silvia; Polzonetti, Valeria; Micozzi, Daniela; Pucciarelli, Stefania

    2016-01-01

    It is well known that disorders of pyrimidine pathways may lead to neurological, hematological, immunological diseases, renal impairments, and association with malignancies. Nucleotide homeostasis depends on the three stages of pyrimidine metabolism: de novo synthesis, catabolism and recycling of these metabolites. Cytidine and uridine, in addition to be used as substrates for pyrimidine nucleotide salvaging, also act as the precursors of cytidine triphosphate used in the biosynthetic pathway of both brain's phosphatidylcholine and phosphatidylethanolamine via the Kennedy cycle. The synthesis in the brain of phosphatidylcholine and other membrane phosphatides can utilize, in addition to glucose, three compounds present in the blood stream: choline, uridine, and a polyunsaturated fatty acids like docosahexaenoic acid. Some authors, using rat models, found that oral administration of two phospholipid precursors such as uridine and omega-3 fatty acids, along with choline from the diet, can increase the amount of synaptic membrane generated by surviving striatal neurons in rats with induced Parkinson's disease. Other authors found that in hypertensive rat fed with uridine and choline, cognitive deficit resulted improved. Uridine has also been recently considered as a neuroactive molecule, because of its involvement in important neurological functions by improving memory, sleep disorders, anti-epileptic effects, as well as neuronal plasticity. Cytidine and uridine are uptaken by the brain via specific receptors and successively salvaged to the corresponding nucleotides. The present review is devoted to the enzymology of pyrimidine pathways whose importance has attracted the attention of several researchers investigating on the mechanisms underlying the physiopathology of brain.

  5. Protein dimerization. Inside job.

    Science.gov (United States)

    Metzger, H

    1994-04-01

    In a sophisticated combination of genetic engineering and organic synthesis, a general method for dimerizing recombinant intracellular proteins has been devised; the usefulness of the method should now be testable.

  6. Prebiotic syntheses of purines and pyrimidines.

    Science.gov (United States)

    Basile, B; Lazcano, A; Oró, J

    1984-01-01

    The work done in many laboratories during the last two decades has confirmed that hydrogen cyanide and cyanoacetylene are the two major precursors for the prebiotic synthesis of purines and pyrimidines, respectively. Although several different pathways for the synthesis of purines have been described, they are all variations of the initial mechanism proposed by Oró and Kimball, where hydrogen cyanide leads first to the formation of a 4,5-di-substituted imidazole derivative, and then to the closing of the purine ring with a C1 compound. A number of experiments have shown that purines and pyrimidines can also be obtained from methane, ammonia (nitrogen), and water mixtures, provided an activating source of energy (radiation, electric discharges, etc.) is available. However, in this case the yields are lower by about two orders of magnitude because of the intermediate formation of hydrogen cyanide and cyanoacetylene. The latter two compounds have been found in interstellar space, Titan and other bodies of the solar system. They were probably present in the primordial parent bodies from the solar nebula in concentrations of 10(-2) to 10(-3) M as inferred from recent calculations by Miller and coworkers obtained for the Murchison meteorite. These concentrations should have been sufficient to generate relatively large amounts of purine and pyrimidine bases on the primitive Earth.

  7. A previously undescribed pathway for pyrimidine catabolism.

    Science.gov (United States)

    Loh, Kevin D; Gyaneshwar, Prasad; Markenscoff Papadimitriou, Eirene; Fong, Rebecca; Kim, Kwang-Seo; Parales, Rebecca; Zhou, Zhongrui; Inwood, William; Kustu, Sydney

    2006-03-28

    The b1012 operon of Escherichia coli K-12, which is composed of seven unidentified ORFs, is one of the most highly expressed operons under control of nitrogen regulatory protein C. Examination of strains with lesions in this operon on Biolog Phenotype MicroArray (PM3) plates and subsequent growth tests indicated that they failed to use uridine or uracil as the sole nitrogen source and that the parental strain could use them at room temperature but not at 37 degrees C. A strain carrying an ntrB(Con) mutation, which elevates transcription of genes under nitrogen regulatory protein C control, could also grow on thymidine as the sole nitrogen source, whereas strains with lesions in the b1012 operon could not. Growth-yield experiments indicated that both nitrogens of uridine and thymidine were available. Studies with [(14)C]uridine indicated that a three-carbon waste product from the pyrimidine ring was excreted. After trimethylsilylation and gas chromatography, the waste product was identified by mass spectrometry as 3-hydroxypropionic acid. In agreement with this finding, 2-methyl-3-hydroxypropionic acid was released from thymidine. Both the number of available nitrogens and the waste products distinguished the pathway encoded by the b1012 operon from pyrimidine catabolic pathways described previously. We propose that the genes of this operon be named rutA-G for pyrimidine utilization. The product of the divergently transcribed gene, b1013, is a tetracycline repressor family regulator that controls transcription of the b1012 operon negatively.

  8. Crystal structures of 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(naphthalen-1-yl)acetamide and 2-[(4,6-di­amino­pyrimidin-2-yl)sulfan­yl]-N-(4-fluoro­phen­yl)acetamide

    Science.gov (United States)

    Subasri, S.; Kumar, Timiri Ajay; Sinha, Barij Nayan; Jayaprakash, Venkatesan; Viswanathan, Vijayan; Velmurugan, Devadasan

    2017-01-01

    The title compounds, C16H15N5OS, (I), and C12H12FN5OS, (II), are [(di­amino­pyrimidine)­sulfan­yl]acetamide derivatives. In (I), the pyrimidine ring is inclined to the naphthalene ring system by 55.5 (1)°, while in (II), the pyrimidine ring is inclined to the benzene ring by 58.93 (8)°. In (II), there is an intra­molecular N—H⋯N hydrogen bond and a short C—H⋯O contact. In the crystals of (I) and (II), mol­ecules are linked by pairs of N—H⋯N hydrogen bonds, forming inversion dimers with R 2 2(8) ring motifs. In the crystal of (I), the dimers are linked by bifurcated N—H⋯(O,O) and C—H⋯O hydrogen bonds, forming layers parallel to (100). In the crystal of (II), the dimers are linked by N—H⋯O hydrogen bonds, also forming layers parallel to (100). The layers are linked by C—H⋯F hydrogen bonds, forming a three-dimensional architecture.

  9. Superbackscattering nanoparticle dimers.

    Science.gov (United States)

    Liberal, Iñigo; Ederra, Iñigo; Gonzalo, Ramón; Ziolkowski, Richard W

    2015-07-10

    The theory and design of superbackscattering nanoparticle dimers are presented. We analytically derive the optimal configurations and the upper bound of their backscattering cross-sections. In particular, it is demonstrated that electrically small nanoparticle dimers can enhance the backscattering by a factor of 6.25 with respect to single dipolar particles. We demonstrate that optimal designs approaching this theoretical limit can be found by using a simple circuit model. The study of practical implementations based on plasmonic and high-permittivity particles has been also addressed. Moreover, the numerical examples reveal that the dimers can attain close to a fourfold enhancement of the single nanoparticle response even in the presence of high losses.

  10. Neutral pyrimidine C-H donor as anion receptor

    Institute of Scientific and Technical Information of China (English)

    袁迎雪; 吴娜娜; 韩逸飞; 宋相志; 王洪波

    2016-01-01

    Anion receptors including pyrimidine subunit were designed and synthesized and their binding abilities with various anions were investigated by fluorescence and 1H NMR titration experiments. DFT calculations provided some information for anion recognition. It is confirmed that both of two new pyrimidine anion receptors have the selectivity for Cl−.

  11. Superbackscattering Nanoparticle Dimers

    CERN Document Server

    Liberal, Iñigo; Gonzalo, Ramón; Ziolkoski, Richard W

    2015-01-01

    The theory and design of superbackscattering nanoparticle dimers are presented. We analytically derive the optimal configurations and the upper bound of their backscattering cross-sections. In particular, it is demonstrated that electrically small nanoparticle dimers can enhance the backscattering by a factor of 6.25 with respect to single dipolar particles. We demonstrate that optimal designs approaching this theoretical limit can be found by using a simple circuit model. The study of practical implementations based on plasmonic and high-permittivity particles reveal that fourfold enhancement factors might be attainable even with realistic losses.

  12. Alkane dimers interaction

    DEFF Research Database (Denmark)

    Ferrighi, Lara; Madsen, Georg Kent Hellerup; Hammer, Bjørk

    2010-01-01

    The interaction energies of a series of n-alkane dimers, from methane to decane, have been investigated with Density Functional Theory (DFT), using the MGGA-M06-L density functional. The results are compared both to the available wavefunction-based values as well as to dispersion corrected DFT...

  13. Pyrimidine biosynthetic pathway of Baccillus subtilis.

    Science.gov (United States)

    Potvin, B W; Kelleher, R J; Gooder, H

    1975-08-01

    Biochemical and genetic data were obtained from a series of 51 Pyr- strains of Bacillus subtilis. The observed enzymatic deficiencies allowed the mutants to be placed into 12 clases, some of which represent defects in more than one of the six known pyrimidine biosynthetic enzymes. Mapping analysis by transformation has shown that all the Pyr- mutations are located in a single small area of the B. subtilis genome. A correlation of the biochemical defects and the genetic data has been made. Those mutations conferring similar enzymatic deficiencies were found to be contiguous on the B. subtilis map. Regulatory aspects of the pyrimidine pathway have also been investigated and are compared to previously reported results from other organisms. Evidence is presented which bears upon the possible physical association of the first three enzymes and the association of at least some of the enzymes of this pathway with particulate elements of the cell. A model for the organization of the enzymes is presented with dihydroorotate dehydrogenase as the central enzyme in a proposed aggregate.

  14. 6-(3,5-Dimethylbenzyl-5-ethyl-1-[(2-phenylethoxymethyl]pyrimidine-2,4(1H,3Hdione

    Directory of Open Access Journals (Sweden)

    Nasser R. El-Brollosy

    2012-04-01

    Full Text Available In the title pyrimidine derivative, C24H28N2O3, the uracil unit is essentially planar with an r.m.s. deviation of 0.0054 (1 Å for the eight non-H atoms. The pyrimidine ring is tilted by a dihedral angle of 77.08 (7° with respect to the aromatic ring of the 3,5-dimethylbenzyl substituent, whereas it is nearly parallel to the benzene ring of the phenethoxymethyl unit, with a dihedral angle of 8.17 (8°. An intramolecular C—H...O hydrogen bond generates an S(6 ring motif. In the crystal, molecules are linked by a pair of amide–uracil N—H...O hydrogen bonds into an inversion R22(8 dimer. These dimers are stacked along the b axis through π–π interactions with a centroid–centroid distance of 3.9517 (8 Å. Weak C—H...π interactions are also present.

  15. Synthesis and crystal structure of N-(4-chloro­phen­yl)-5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidin-2-amine

    Science.gov (United States)

    Repich, Hlib; Orysyk, Svitlana; Savytskyi, Pavlo; Pekhnyo, Vasyl

    2017-01-01

    The title compound, C13H12ClN5, was synthesized by the cyclization of 1-(4,6-di­methyl­pyrimidin-2-yl)-4-phenyl­thio­semicarbazide in the presence of Ni(NO3)2. The mol­ecular structure of the compound is essentially planar. In the crystal, mol­ecules form dimers via pairs of N—H⋯N hydrogen bonds between the H atom of the exocyclic amino group and the N atom at the 4-position of the triazole ring. The resulting dimers are packed into layers which are connected by π-stacking inter­actions between the aromatic systems of the pyrimidine and benzene nuclei, and between the triazole cores. PMID:28083130

  16. Structural Insight into the Core of CAD, the Multifunctional Protein Leading De Novo Pyrimidine Biosynthesis.

    Science.gov (United States)

    Moreno-Morcillo, María; Grande-García, Araceli; Ruiz-Ramos, Alba; Del Caño-Ochoa, Francisco; Boskovic, Jasminka; Ramón-Maiques, Santiago

    2017-06-06

    CAD, the multifunctional protein initiating and controlling de novo biosynthesis of pyrimidines in animals, self-assembles into ∼1.5 MDa hexamers. The structures of the dihydroorotase (DHO) and aspartate transcarbamoylase (ATC) domains of human CAD have been previously determined, but we lack information on how these domains associate and interact with the rest of CAD forming a multienzymatic unit. Here, we prove that a construct covering human DHO and ATC oligomerizes as a dimer of trimers and that this arrangement is conserved in CAD-like from fungi, which holds an inactive DHO-like domain. The crystal structures of the ATC trimer and DHO-like dimer from the fungus Chaetomium thermophilum confirm the similarity with the human CAD homologs. These results demonstrate that, despite being inactive, the fungal DHO-like domain has a conserved structural function. We propose a model that sets the DHO and ATC complex as the central element in the architecture of CAD. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Synthesis of novel chiral compounds of purine and pyrimidine bases

    Institute of Scientific and Technical Information of China (English)

    汪毓海; 陈庆华

    1999-01-01

    The physiologically active groups such as purine and pyrimidine bases are introduced to the asymmetric ynthesis. The optically pure compounds bearing purine and pyrimidine bases (5a—5e) were prepared via the asymetric Michael addition reaction of purines and pyrimidines as Michael donators with the chiral source 5-(R)-[(1R, 2S, 5R)-menthyloxy]-2(5H)-furanone (3a), which was prepared from the natural chiral auxiliary (-)-menthol. The synthetic method was studied in detail and the new compounds were identified on the basis of their analytical data and spectroscopic data, such as [α]D20, IR, UV, 1H NMR, 13C NMR and MS. The absolute configuration of 5a was established by X-ray crystallography. The results provided an efficient synthetic route to chiral purines and pyrimidine analogues, and offered chiral sources for further research on the physiologically active compounds of chiral nucleotides.

  18. Synthesis of Polyfunctionally Substituted Fused Pyrimidine Derivatives as Antimicrobial Agents

    Institute of Scientific and Technical Information of China (English)

    EISSA, Abd EI-Monem Mohamed Farag

    2008-01-01

    A variety of pyrimidine derivatives 2--4 and annulated pyrimidine derivatives 5-17 have been synthesized via a sequence of heterocyclization reaction of readily available 6-naphthyl-4-oxo-2-thioxo-1,2,3,4-tetrahydroprimi-dine-5-carbonitrile (1) with different acidic and basic reagents. The new compounds were synthesized with the aim of study of their antimicrobial activity. The structures of all synthesized compounds were elucidated by elemental analysis and spectroscopic studies.

  19. Ethyl 4-(1,3-benzodioxol-5-yl)-6-methyl-2-sulfanylidene-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

    Science.gov (United States)

    Nayak, Susanta K; Venugopala, K N; Govender, Thavendran; Kruger, Hendrik G; Maguire, Glenn E M; Row, Tayur N Guru

    2011-11-01

    In the title compound, C(15)H(16)N(2)O(4)S, the dihedral angles between the planes of the benzodioxole and ester groups and the plane of the six-membered tetra-hydro-pyrimidine ring are 89.5 (1) and 20.2 (1)°, respectively. Inter-molecular N-H⋯S hydrogen bonds assemble the mol-ecules into dimers, which are further connected via N-H⋯O inter-actions into chains parallel to [010]. Weak C-H⋯S and C-H⋯π inter-actions enhance the stability of the crystal structure.

  20. Low-energy positron scattering by pyrimidine

    Energy Technology Data Exchange (ETDEWEB)

    Barbosa, Alessandra Souza; Pastega, Diego F.; Bettega, Márcio H. F., E-mail: bettega@fisica.ufpr.br [Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná (Brazil)

    2015-12-28

    This work reports elastic integral and differential cross sections for positron collisions with pyrimidine, for energies up to 20 eV. The cross sections were computed with the Schwinger multichannel method in the static plus polarization approximation. We also employed the Born closure procedure to account for the long range potential due to the permanent dipole moment of the molecule. Our results are compared with the experimental total cross section of Zecca et al. [J. Phys. B 43, 215204 (2010)], the experimental grand-total, quasi-elastic integral and differential cross section of Palihawadana et al. [Phys. Rev. A 88, 12717 (2013)]. We also compare our results with theoretical integral and differential cross sections obtained by Sanz et al. [Phys. Rev. A 88, 62704 (2013)] with the R-matrix and the independent atom model with screening-corrected additivity rule methods, and with the results computed by Franz and Gianturco [Phys. Rev. A 88, 042711 (2013)] using model correlation-polarization potentials. The agreement between the theory and the experiment is encouraging.

  1. Electronic structure of alloxan and its dimers: QM/QD simulations and quantum chemical topology analysis.

    Science.gov (United States)

    Allehyani, Basmah H; Elroby, Shaaban A; Aziz, Saadalluh G; Hilal, Rifaat H

    2015-01-01

    This study aims to identify the origin of the extra stability of alloxan, a biologically active pyrimidine. To achieve this goal, detailed DFT computations and quantum dynamics simulations have been performed to establish the most stable conformation and the global minimum structure on the alloxan potential energy surface. The effects of the solvent, basis set, and DFT method have been examined to validate the theoretical model adopted throughout the work. Two non-covalent intermolecular dimers of alloxan, the H-bonded and dipolar dimers, have been investigated at the ωB97X-D and M06-2X levels of theory using the triple zeta 6-311++G** to establish their relative stability. Quantum chemical topology features and natural bond orbital analysis (NBO) have been performed to identify and characterize the forces that govern the structures and underlie the extra stability of alloxan.

  2. Dynamics of a bouncing dimer

    CERN Document Server

    Dorbolo, S; Tsimring, L S; Kudrolli, A

    2005-01-01

    We investigate the dynamics of a dimer bouncing on a vertically oscillated plate. The dimer, composed of two spheres rigidly connected by a light rod, exhibits several modes depending on initial and driving conditions. The first excited mode has a novel horizontal drift in which one end of the dimer stays on the plate during most of the cycle, while the other end bounces in phase with the plate. The speed and direction of the drift depend on the aspect ratio of the dimer. We employ event-driven simulations based on a detailed treatment of frictional interactions between the dimer and the plate in order to elucidate the nature of the transport mechanism in the drift mode.

  3. Privileged substructure-based diversity-oriented synthesis pathway for diverse pyrimidine-embedded polyheterocycles

    DEFF Research Database (Denmark)

    Kim, Heejun; Thanh Tung, Truong; Park, Seung Bum

    2013-01-01

    A new diversity-oriented synthesis pathway for the fabrication of a pyrimidine-embedded polyheterocycles library was developed for potential interactions with diverse biopolymers. Five different pyrimidine-embedded core skeletons were synthesized from ortho-alkynylpyrimidine carbaldehydes...

  4. Uptake and incorporation of pyrimidines in Euglena gracilis.

    Science.gov (United States)

    Wasternack, C H

    1976-08-01

    In photoorganotrophically grown cells of Euglena gracilis the uptake and incorporation degree of 12 different pyrimidines were tested. The rate of uptake of pyrimidines has distinct maxima in the late log phase and in the stationary phase of cell multiplication. The kinetics of uptake are linear in the first 2 h, do not show saturation at various concentrations and increase with the concetrations. No accumulation of the pyrimidines at various concentrations could be observed in the first 2 h of incubation. Membrane inhibitors as uranyl acetate inhibit the uptake of the reference substance alpha-AIB, which is wellknown transported by an active transport mechanism, but have no effect on uptake rate of uracil and cytosine. It could not be observed an energy requirement tested in temperature dependence and with electron transport inhibitors. Uptake of uridine, uracil, barbituric acid and alpha-AIB is inhibited by cycloheximide in a different manner after 5 - 10 min.

  5. Significance and Biological Importance of Pyrimidine in the Microbial World

    Directory of Open Access Journals (Sweden)

    Vinita Sharma

    2014-01-01

    Full Text Available Microbes are unique creatures that adapt to varying lifestyles and environment resistance in extreme or adverse conditions. The genetic architecture of microbe may bear a significant signature not only in the sequences position, but also in the lifestyle to which it is adapted. It becomes a challenge for the society to find new chemical entities which can treat microbial infections. The present review aims to focus on account of important chemical moiety, that is, pyrimidine and its various derivatives as antimicrobial agents. In the current studies we represent more than 200 pyrimidines as antimicrobial agents with different mono-, di-, tri-, and tetrasubstituted classes along with in vitro antimicrobial activities of pyrimidines derivatives which can facilitate the development of more potent and effective antimicrobial agents.

  6. Universal dimer-dimer scattering in lattice effective field theory

    CERN Document Server

    Elhatisari, Serdar; Lee, Dean; Meißner, Ulf-G; Rupak, Gautam

    2016-01-01

    We consider two-component fermions with short-range interactions and large scattering length. This system has universal properties that are realized in many different fields including atomic, nuclear and particle physics. In the limit of large fermion-fermion scattering length $a_\\mathrm{ff}$ and zero range interaction, all properties of the system scale proportionally with the only length scale $a_\\mathrm{ff}$. We consider the case where there are bound dimers and calculate the scattering phase shifts for the two-dimer system near threshold using lattice effective field theory. From the scattering phase shifts, we extract the universal dimer-dimer scattering length $a_\\mathrm{dd}/a_\\mathrm{ff}=0.645(89)$ and effective range $r_\\mathrm{dd}/a_\\mathrm{ff}=-0.413(79)$.

  7. Collisional properties of weakly bound heteronuclear dimers

    NARCIS (Netherlands)

    Marcelis, B.; Kokkelmans, S.J.J.M.F.; Shlyapnikov, G.V.; Petrov, D.S.

    2008-01-01

    We consider collisional properties of weakly bound heteronuclear molecules (dimers) formed in a two-species mixture of atoms with a large mass difference. We focus on dimers containing light fermionic atoms as they manifest collisional stability due to an effective dimer-dimer repulsion originating

  8. Nucleotide metabolism in Lactococcus lactis: Salvage pathways of exogenous pyrimidines

    DEFF Research Database (Denmark)

    Martinussen, Jan; Andersen, Paal Skytt; Hammer, Karin

    1994-01-01

    By measuring enzyme activities in crude extracts and studying the effect of toxic analogs (5-fluoropyrimidines) on cell growth, the metabolism of pyrimidines in Lactococcus lactis was analyzed. Pathways by which uracil, uridine, deoxyuridine, cytidine, and deoxycytidine are metabolized in L. lact...

  9. Intramolecular inverse electron demand Diels-Alder reactions of pyrimidines.

    NARCIS (Netherlands)

    Frissen, A.E.

    1990-01-01

    This thesis deals with the intramolecular inverse electron demand Diels-Alder reaction of pyrimidines. The main objective of the study was to investigate the synthetic applicability of this reaction and to get more insight in the electronic and steric effects which determine the reactivity of compou

  10. Annellation of Triazole and Tetrazole Systems onto Pyrrolo[2,3-d]pyrimidines: Synthesis of Tetrazolo[1,5-c]-pyrrolo[3,2-e]-pyrimidines and Triazolo[1,5-c]pyrrolo-[3,2-e]pyrimidines as Potential Antibacterial Agents

    Directory of Open Access Journals (Sweden)

    Rina D. Shah

    2002-07-01

    Full Text Available Syntheses of several novel 4-chloropyrrolo[2,3-d]pyrimidines (1, 4-hydrazinopyrrolo[2,3-d]pyrimidines (2 and 3-amino-4-iminopyrrolo[2,3-d]pyrimidines (7 and their use in the synthesis of tetrazolo[1,5-c]pyrrolo[3,2-e]pyrimidines (3 and triazolo[1,5-c]pyrrolo[3,2-e]pyrimidines (4 required for biological screening are reported.

  11. Crystal structure of (S-5,7-diphenyl-4,7-dihydrotetrazolo[1,5-a]pyrimidine

    Directory of Open Access Journals (Sweden)

    Ivy K. Price

    2015-04-01

    Full Text Available The title compound, C16H13N5, was synthesized by coupling aminotetrazole with chalcone in the presence of an amine organocatalyst derived from chincona alkaloid. There are two molecules, A and B, in the asymmetric unit. In molecule A, the dihedral angles between the partly hydrogenated pyrimidine ring system (r.m.s. deviation = 0.056 Å and the sp2- and sp3-bonded phenyl groups are 33.32 (11 and 86.53 (11°, respectively. The equivalent data for molecule B are 0.049 Å, and 27.05 (10 and 85.27 (11°, respectively. In the crystal, A+B dimers linked by pairs of N—H...N hydrogen bonds generate R22(8 loops. The dimers are linked by aromatic π–π stacking interactions [shortest centroid–centroid separation = 3.5367 (15 Å], which results in a three-dimensional network.

  12. 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.

  13. A novel and convenient synthesis of thiazolo[3,2-a]pyrimidin-7-ones and pyrido[1,2-a]pyrimidin-2-ones using Vilsmeier reagent

    Institute of Scientific and Technical Information of China (English)

    Yi Yi Weng; Lei Ming Ying; Qi Xu Chen; Wei Ke Su

    2012-01-01

    A novel route for the synthesis of thiazolo[3,2-a]pyrimidin-7-ones and pyrido[1,2-a]pyrimidin-2-ones from acetylated 2-aminothiazoles and 2-aminopyridines under Vilsmeier conditions has been developed.The plausible mechanism has also been proposed.

  14. Novel pyrimidine-2,4-dione-1,2,3-triazole and furo[2,3-d]pyrimidine-2-one-1,2,3-triazole hybrids as potential anti-cancer agents: Synthesis, computational and X-ray analysis and biological evaluation.

    Science.gov (United States)

    Gregorić, Tomislav; Sedić, Mirela; Grbčić, Petra; Tomljenović Paravić, Andrea; Kraljević Pavelić, Sandra; Cetina, Mario; Vianello, Robert; Raić-Malić, Silvana

    2017-01-05

    Regioselective 1,4-disubstituted 1,2,3-triazole tethered pyrimidine-2,4-dione derivatives (5-23) were successfully prepared by the copper(I)-catalyzed click chemistry. While known palladium/copper-cocatalyzed method based on Sonogashira cross-coupling followed by the intramolecular 5-endo-dig ring closure generated novel 6-alkylfuro[2,3-d]pyrimidine-2-one-1,2,3-triazole hybrids (24b-37b), a small library of their 5-alkylethynyl analogs (24a-37a) was synthesized and described for the first time by tandem terminal alkyne dimerization and subsequent 5-endo-trig cyclization, which was additionally corroborated with computational and X-ray crystal structure analyses. The nature of substituents on alkynes and thereof homocoupled 1,3-diynes predominantly influenced the ratio of the formed products in both pathways. In vitro antiproliferative activity of prepared compounds evaluated on five human cancer cell lines revealed that N,N-1,3-bis-(1,2,3-triazole)-5-bromouracil (5-7) and 5,6-disubstituted furo[2,3-d]pyrimidine-2-one-1,2,3-triazole 34a hybrids exhibited the most pronounced cytostatic acitivities against hepatocellular carcinoma (HepG2) and cervical carcinoma (HeLa) cells with higher potencies than the reference drug 5-fluorouracil. Cytostatic effect of pyrimidine-2,4-dione-1,2,3-triazole hybrid 7 in HepG2 cells could be attributed to the Wee-1 kinase inhibition and abolishment of sphingolipid signaling mediated by acid ceramidase and sphingosine kinase 1. Importantly, this compound proved to be a non-mitochondrial toxicant, which makes it a promising candidate for further lead optimization and development of a new and more efficient agent for the treatment of hepatocellular carcinoma.

  15. Thiamin Pyrimidine Biosynthesis in Candida albicans: A Remarkable Reaction between Histidine and Pyridoxal Phosphate

    Energy Technology Data Exchange (ETDEWEB)

    Lai, Rung-Yi; Huang, Siyu; Fenwick, Michael K.; Hazra, Amrita; Zhang, Yang; Rajashankar, Kanagalaghatta; Philmus, Benjamin; Kinsland, Cynthia; Sanders, Jennie Mansell; Ealick, Steven E.; Begley, Tadhg P. (Cornell); (TAM)

    2012-06-26

    In Saccharomyces cerevisiae, thiamin pyrimidine is formed from histidine and pyridoxal phosphate (PLP). The origin of all of the pyrimidine atoms has been previously determined using labeling studies and suggests that the pyrimidine is formed using remarkable chemistry that is without chemical or biochemical precedent. Here we report the overexpression of the closely related Candida albicans pyrimidine synthase (THI5p) and the reconstitution and preliminary characterization of the enzymatic activity. A structure of the C. albicans THI5p shows PLP bound at the active site via an imine with Lys62 and His66 in close proximity to the PLP. Our data suggest that His66 of the THI5 protein is the histidine source for pyrimidine formation and that the pyrimidine synthase is a single-turnover enzyme.

  16. Tetraoxane-pyrimidine nitrile hybrids as dual stage antimalarials.

    Science.gov (United States)

    Oliveira, Rudi; Guedes, Rita C; Meireles, Patrícia; Albuquerque, Inês S; Gonçalves, Lídia M; Pires, Elisabete; Bronze, Maria Rosário; Gut, Jiri; Rosenthal, Philip J; Prudêncio, Miguel; Moreira, Rui; O'Neill, Paul M; Lopes, Francisca

    2014-06-12

    The use of artemisinin or other endoperoxides in combination with other drugs is a strategy to prevent development of resistant strains of Plasmodium parasites. Our previous work demonstrated that hybrid compounds, comprising endoperoxides and vinyl sulfones, were capable of high activity profiles comparable to artemisinin and chloroquine while acting through two distinct mechanisms of action: oxidative stress and falcipain inhibition. In this study, we adapted this approach to a novel class of falcipain inhibitors: peptidomimetic pyrimidine nitriles. Pyrimidine tetraoxane hybrids displayed potent nanomolar activity against three strains of Plasmodium falciparum and falcipain-2, combined with low cytotoxicity. In vivo, a decrease in parasitemia and an increase in survival of mice infected with Plasmodium berghei was observed when compared to control. All tested compounds combined good blood stage activity with significant effects on liver stage parasitemia, a most welcome feature for any new class of antimalarial drug.

  17. 5-Benzothiazole substituted pyrimidine derivatives as HCV replication (replicase) inhibitors.

    Science.gov (United States)

    Arasappan, Ashok; Bennett, Frank; Girijavallabhan, Vinay; Huang, Yuhua; Huelgas, Regina; Alvarez, Carmen; Chen, Lei; Gavalas, Stephen; Kim, Seong-Heon; Kosinski, Aneta; Pinto, Patrick; Rizvi, Razia; Rossman, Randall; Shankar, Bandarpalle; Tong, Ling; Velazquez, Francisco; Venkatraman, Srikanth; Verma, Vishal A; Kozlowski, Joseph; Shih, Neng-Yang; Piwinski, John J; MacCoss, Malcolm; Kwong, Cecil D; Clark, Jeremy L; Fowler, Anita T; Geng, Feng; Kezar, Hollis S; Roychowdhury, Abhijit; Reynolds, Robert C; Maddry, Joseph A; Ananthan, Subramaniam; Secrist, John A; Li, Cheng; Chase, Robert; Curry, Stephanie; Huang, Hsueh-Cheng; Tong, Xiao; Njoroge, F George

    2012-05-01

    Based on a previously identified HCV replication (replicase) inhibitor 1, SAR efforts were conducted around the pyrimidine core to improve the potency and pharmacokinetic profile of the inhibitors. A benzothiazole moiety was found to be the optimal substituent at the pyrimidine 5-position. Due to potential reactivity concern, the 4-chloro residue was replaced by a methyl group with some loss in potency and enhanced rat in vivo profile. Extensive investigations at the C-2 position resulted in identification of compound 16 that demonstrated very good replicon potency, selectivity and rodent plasma/target organ concentration. Inhibitor 16 also demonstrated good plasma levels and oral bioavailability in dogs, while monkey exposure was rather low. Chemistry optimization towards a practical route to install the benzothiazole moiety resulted in an efficient direct C-H arylation protocol.

  18. Pyrimidine Nucleobase Radical Reactivity in DNA and RNA.

    Science.gov (United States)

    Greenberg, Marc M

    2016-11-01

    Nucleobase radicals are major products of the reactions between nucleic acids and hydroxyl radical, which is produced via the indirect effect of ionizing radiation. The nucleobase radicals also result from hydration of cation radicals that are produced via the direct effect of ionizing radiation. The role that nucleobase radicals play in strand scission has been investigated indirectly using ionizing radiation to generate them. More recently, the reactivity of nucleobase radicals resulting from formal hydrogen atom or hydroxyl radical addition to pyrimidines has been studied by independently generating the reactive intermediates via UV-photolysis of synthetic precursors. This approach has provided control over where the reactive intermediates are produced within biopolymers and facilitated studying their reactivity. The contributions to our understanding of pyrimidine nucleobase radical reactivity by this approach are summarized.

  19. Pyrimidine nucleobase radical reactivity in DNA and RNA

    Science.gov (United States)

    Greenberg, Marc M.

    2016-11-01

    Nucleobase radicals are major products of the reactions between nucleic acids and hydroxyl radical, which is produced via the indirect effect of ionizing radiation. The nucleobase radicals also result from hydration of cation radicals that are produced via the direct effect of ionizing radiation. The role that nucleobase radicals play in strand scission has been investigated indirectly using ionizing radiation to generate them. More recently, the reactivity of nucleobase radicals resulting from formal hydrogen atom or hydroxyl radical addition to pyrimidines has been studied by independently generating the reactive intermediates via UV-photolysis of synthetic precursors. This approach has provided control over where the reactive intermediates are produced within biopolymers and facilitated studying their reactivity. The contributions to our understanding of pyrimidine nucleobase radical reactivity by this approach are summarized.

  20. Structural basis for sequence specific DNA binding and protein dimerization of HOXA13.

    Directory of Open Access Journals (Sweden)

    Yonghong Zhang

    Full Text Available The homeobox gene (HOXA13 codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of genes during embryonic morphogenesis. Here we present the NMR structure of HOXA13 homeodomain (A13DBD bound to an 11-mer DNA duplex. A13DBD forms a dimer that binds to DNA with a dissociation constant of 7.5 nM. The A13DBD/DNA complex has a molar mass of 35 kDa consistent with two molecules of DNA bound at both ends of the A13DBD dimer. A13DBD contains an N-terminal arm (residues 324 - 329 that binds in the DNA minor groove, and a C-terminal helix (residues 362 - 382 that contacts the ATAA nucleotide sequence in the major groove. The N370 side-chain forms hydrogen bonds with the purine base of A5* (base paired with T5. Side-chain methyl groups of V373 form hydrophobic contacts with the pyrimidine methyl groups of T5, T6* and T7*, responsible for recognition of TAA in the DNA core. I366 makes similar methyl contacts with T3* and T4*. Mutants (I366A, N370A and V373G all have decreased DNA binding and transcriptional activity. Exposed protein residues (R337, K343, and F344 make intermolecular contacts at the protein dimer interface. The mutation F344A weakens protein dimerization and lowers transcriptional activity by 76%. We conclude that the non-conserved residue, V373 is critical for structurally recognizing TAA in the major groove, and that HOXA13 dimerization is required to activate transcription of target genes.

  1. Synthesis and biological evaluation of some New pyrimidine derivatives

    Directory of Open Access Journals (Sweden)

    Firyal Weli Askar

    2017-06-01

    Full Text Available New pyrimidine derivatives comprising azo, schiff's bases, chalcones, and chromene ring moieties were prepared.The newly synthesized compounds have been established on the basis of their m.p., TLC, FT-IR, UV-Vis ,¹H-NMR data and element analysis. These compounds were screened for their antimicrobial and in vitro antioxidant properties. The results of this investigation revealed that these compounds are potent antimicrobial and antioxidant agent.

  2. Synthesis and Antibacterial Activity of Chalcones and Pyrimidine-2-ones

    OpenAIRE

    2005-01-01

    Some new chalcones have been prepared by Claisen-schmidt condensation of ketone and different aromatic aldehydes. These chalcones on condensation with urea in presence of acid gave Pyrimidine-2-ones. The synthesized compounds have been characterized by elemental analysis, IR and 1H NMR spectral data. They have been screened for their antibacterial activity against Gram positive bacteria B. subtillis & S. aureus and Gram negative bacteria E. coli & S. typhi.

  3. Kinetics of DNA tile dimerization.

    Science.gov (United States)

    Jiang, Shuoxing; Yan, Hao; Liu, Yan

    2014-06-24

    Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

  4. NMR Structural Studies on Alamethicin Dimers

    Institute of Scientific and Technical Information of China (English)

    李星

    2003-01-01

    15N labeled alamethicin dimer was synthesized. The structure and dynamics of alamethicin dimers were studied with nuclear magnetic resonance (NMR) spectroscopy. The data from 15N-labeled alamethicin dimer suggest little differences in conformation between the dimer and monomer in the Aib1-Pro14 region. Significant difference in the conformation of the C-terminus are manifest in the NH chemical shifts in the Val15-Pho20 region.

  5. Indolizines and pyrrolo[1,2-c]pyrimidines decorated with a pyrimidine and a pyridine unit respectively

    Directory of Open Access Journals (Sweden)

    Marcel Mirel Popa

    2015-06-01

    Full Text Available The three possible structural isomers of 4-(pyridylpyrimidine were employed for the synthesis of new pyrrolo[1,2-c]pyrimidines and new indolizines, by 1,3-dipolar cycloaddition reaction of their corresponding N-ylides generated in situ from their corresponding cycloimmonium bromides. In the case of 4-(3-pyridylpyrimidine and 4-(4-pyridylpyrimidine the quaternization reactions occur as expected at the pyridine nitrogen atom leading to pyridinium bromides and consequently to new indolizines via the corresponding pyridinium N-ylides. However, in the case of 4-(2-pyridylpyrimidine the steric hindrance directs the reaction to the pyrimidinium N-ylides and, subsequently, to the formation of the pyrrolo[1,2-c]pyrimidines. The new pyrrolo[1,2-c]pyrimidines and the new indolizines were structurally characterized through NMR spectroscopy. The X-ray structures of two of the starting materials, 4-(2-pyridylpyrimidine and 4-(4-pyridylpyrimidine, are also reported.

  6. Rubidium dimers in paraffin-coated cells

    CERN Document Server

    Acosta, V M; Windes, D; Corsini, E; Ledbetter, M P; Karaulanov, T; Auzinsh, M; Rangwala, S A; Kimball, D F Jackson; Budker, D

    2010-01-01

    Measurements were made to determine the density of rubidium dimer vapor in paraffin-coated cells. The number density of dimers and atoms in similar paraffin-coated and uncoated cells was measured by optical spectroscopy. Due to the relatively low melting point of paraffin, a limited temperature range of 43-80 deg C was explored, with the lower end corresponding to a dimer density of less than 10^7 cm^(-3). With one-minute integration time, a sensitivity to dimer number density of better than 10^6 cm^(-3) was achieved. No significant difference in dimer density was observed between the cells.

  7. An efficient synthesis of pyrazolo[1,5-a]pyrimidines and evaluation of their antimicrobial activity

    Indian Academy of Sciences (India)

    SOMESHWAR DESHMUKH; KUNAL DINGORE; VISHWAS GAIKWAD; MADHUKAR JACHAK

    2016-09-01

    A series of new pyrazolo[1,5-a]pyrimidine derivatives has been synthesized by using 7-hydrazinyl- 5-methylpyrazolo[1,5-a]pyrimidine-3-carbonitrile 1 and 7-amino-5-methylpyrazolo[1,5-a]pyrimidine-3-carbonitrile 2 as precursors. The pyrazolo[3,4-d] pyrimidines 3a–b have been synthesized by a three-step reactionstarting with 1. Compound 1 was utilized for the synthesis of dioxopyrrolidindolinylamio-pyrazolo-pyrimidines 4a–b, and dioxoisoindolin-pyrazolo-pyrimidines 4c–d. Also, compounds 4a-d were synthesized using deepeutectic solvents (DES). This method using DES provides several advantages such as benign environment, high yield, scalable and simple work-up procedure. Similarly, the cyclocondensation of 2 with α-acetyl- γ -butyrolactone afforded pyrazolo-pyrido-pyrimidine 5 and dihydrofuro-pyrido-pyrazolo-pyrimidine 6. All synthesized compounds were screened for antimicrobial activity.

  8. Fiber optic D dimer biosensor

    Science.gov (United States)

    Glass, Robert S.; Grant, Sheila A.

    1999-01-01

    A fiber optic sensor for D dimer (a fibrinolytic product) can be used in vivo (e.g., in catheter-based procedures) for the diagnosis and treatment of stroke-related conditions in humans. Stroke is the third leading cause of death in the United States. It has been estimated that strokes and stroke-related disorders cost Americans between $15-30 billion annually. Relatively recently, new medical procedures have been developed for the treatment of stroke. These endovascular procedures rely upon the use of microcatheters. These procedures could be facilitated with this sensor for D dimer integrated with a microcatheter for the diagnosis of clot type, and as an indicator of the effectiveness, or end-point of thrombolytic therapy.

  9. Mechanism of FGF receptor dimerization and activation

    Science.gov (United States)

    Sarabipour, Sarvenaz; Hristova, Kalina

    2016-01-01

    Fibroblast growth factors (fgfs) are widely believed to activate their receptors by mediating receptor dimerization. Here we show, however, that the FGF receptors form dimers in the absence of ligand, and that these unliganded dimers are phosphorylated. We further show that ligand binding triggers structural changes in the FGFR dimers, which increase FGFR phosphorylation. The observed effects due to the ligands fgf1 and fgf2 are very different. The fgf2-bound dimer structure ensures the smallest separation between the transmembrane (TM) domains and the highest possible phosphorylation, a conclusion that is supported by a strong correlation between TM helix separation in the dimer and kinase phosphorylation. The pathogenic A391E mutation in FGFR3 TM domain emulates the action of fgf2, trapping the FGFR3 dimer in its most active state. This study establishes the existence of multiple active ligand-bound states, and uncovers a novel molecular mechanism through which FGFR-linked pathologies can arise.

  10. DNA repair mechanism by photolyase: electron transfer path from the photolyase catalytic cofactor FADH(-) to DNA thymine dimer.

    Science.gov (United States)

    Medvedev, D; Stuchebrukhov, A A

    2001-05-21

    Photolyase is an enzyme that catalyses photorepair of thymine dimers in UV damaged DNA by electron transfer reaction. The structure of the photolyase/DNA complex is unknown at present. Using crystal structure coordinates of the substrate-free enzyme from E. coli, we have recently built a computer molecular model of a thymine dimer docked to photolyase catalytic site and studied molecular dynamics of the system. In this paper, we present analysis of the electronic coupling and electron transfer pathway between the catalytic cofactor FADH(-) and the pyrimidine dimer by the method of interatomic tunneling currents. Electronic structure is treated in the extended Hückel approximation. The root mean square transfer matrix element is about 6 cm(-1), which is consistent with the experimentally determined rate of transfer. We find that electron transfer mechanism responsible for the repair utilizes an unusual folded conformation of FADH(-) in photolyases, in which the isoalloxazine ring of the flavin and the adenine are in close proximity, and the peculiar features of the docked orientation of the dimer. The tunneling currents show explicitly that despite of the close proximity between the donor and acceptor complexes, the electron transfer mechanism between the flavin and the thymine bases is not direct, but indirect, with the adenine acting as an intermediate. These calculations confirm the previously made conclusion based on an indirect evidence for such mechanism.

  11. 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.

  12. Palladium-catalyzed regioselective arylation of imidazo[1,2-a]pyrimidine.

    Science.gov (United States)

    Li, Wenjie; Nelson, Dorian P; Jensen, Mark S; Hoerrner, R Scott; Javadi, Gary J; Cai, Dongwei; Larsen, Robert D

    2003-12-11

    Imidazo[1,2-a]pyrimidine can be arylated at the 3-position with aryl bromides in the presence of base and a catalytic amount of palladium. This provides an efficient one-step synthesis of 3-arylimidazo[1,2-a]pyrimidines from the unsubstituted heterocycle. [reaction: see text

  13. Carbon-Carbon Bond Cleavage Reaction: Synthesis of Multisubstituted Pyrazolo[1,5-a]pyrimidines.

    Science.gov (United States)

    Saikia, Pallabi; Gogoi, Sanjib; Boruah, Romesh C

    2015-07-02

    A new carbon-carbon bond cleavage reaction was developed for the efficient synthesis of multisubstituted pyrazolo[1,5-a]pyrimidines. This base induced reaction of 1,3,5-trisubstituted pentane-1,5-diones and substituted pyrazoles afforded good yields of the pyrazolo[1,5-a]pyrimidines.

  14. 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

  15. 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 synthes

  16. Influence of exogenous silicon on UV-B radiation-induced cyclobutane pyrimidine dimmers in soybean leaves and its alleviation mechanism.

    Science.gov (United States)

    Chen, Jiana; Zhang, Mingcai; Eneji, A Egrinya; Li, Jianmin

    2016-06-01

    The DNA is particularly sensitive to UV-B radiation and can readily be damaged by UV-B stress, resulting to the formation of photoproducts like cyclobutane pyrimidine dimers (CPDs). Silicon has multifarious benefits to plants, especially under biotic and abiotic stress. In this study, we used soybean seedlings to determine whether silicon could alleviate damage to DNA caused by UV-B stress. Silicon significantly reduced the accumulation of CPDs, lessening the damage of UV-B stress to the seedlings by the following three mechanisms: (1) increasing the concentration of UV-B absorbing compounds to reduce damage; (2) strengthening the antioxidant capacity of plants represented by higher levels of non-enzymatic antioxidants and (3) increasing the photolyase gene expression, thus accelerating photorepair.

  17. Synthesis of steroidal dimers: Selective amine catalysed steroidal dimerization

    Indian Academy of Sciences (India)

    Shamsuzzaman; Mohd Gulfam Aalam; Tabassum Siddiqui

    2011-07-01

    Some new dimeric steroids namely cholest-5-en-3-spiro-[6',5'-oxa]-5'-cholest-3'-one (2), cholest-5-en-7-spiro-[4',5'-oxa]-5'-cholest-7'-one (4a) and 3-substitutedcholest-5-en-7-spiro-[4',5'-oxa]-3'-substituted-5'-cholestan-7'-ones (4b, c) are synthesized starting from cholest-5-en-3-one (1), cholest-5-en-7-one (3a) and 3-substituted-cholest-5-en-7-ones (3b, c) respectively by using DMAP and xylene. All the synthesized compounds were characterized by using IR, MS and 1H, 13C NMR spectral and elemental analysis.

  18. Dimerization of Human Growth Hormone by Zinc

    Science.gov (United States)

    Cunningham, Brian C.; Mulkerrin, Michael G.; Wells, James A.

    1991-08-01

    Size-exclusion chromatography and sedimentation equilibrium studies demonstrated that zinc ion (Zn2+) induced the dimerization of human growth hormone (hGH). Scatchard analysis of 65Zn2+ binding to hGH showed that two Zn2+ ions associate per dimer of hGH in a cooperative fashion. Cobalt (II) can substitute for Zn2+ in the hormone dimer and gives a visible spectrum characteristic of cobalt coordinated in a tetrahedral fashion by oxygen- and nitrogen-containing ligands. Replacement of potential Zn2+ ligands (His18, His21, and Glu174) in hGH with alanine weakened both Zn2+ binding and hGH dimer formation. The Zn2+-hGH dimer was more stable than monomeric hGH to denaturation in guanidine-HCl. Formation of a Zn2+-hGH dimeric complex may be important for storage of hGH in secretory granules.

  19. Dimer models and Calabi-Yau algebras

    CERN Document Server

    Broomhead, Nathan

    2008-01-01

    In this thesis we study dimer models, as introduced in string theory, which give a way of writing down a class of non-commutative `superpotential' algebras. Some examples are 3-dimensional Calabi-Yau algebras, as defined by Ginzburg, and some are not. We consider two types of `consistency' condition on dimer models, and show that a `geometrically consistent' model is `algebraically consistent'. Finally we prove that the algebras obtained from algebraically consistent dimer models are 3-dimensional Calabi-Yau algebras.

  20. On Dimer Models and Closed String Theories

    OpenAIRE

    Sarkar, Tapobrata

    2007-01-01

    We study some aspects of the recently discovered connection between dimer models and D-brane gauge theories. We argue that dimer models are also naturally related to closed string theories on non compact orbifolds of $\\BC^2$ and $\\BC^3$, via their twisted sector R charges, and show that perfect matchings in dimer models correspond to twisted sector states in the closed string theory. We also use this formalism to study the combinatorics of some unstable orbifolds of $\\BC^2$.

  1. Dimerization of norbornene on zeolite catalysts

    Institute of Scientific and Technical Information of China (English)

    N. G. Grigor’eva; S. V. Bubennov; L. M. Khalilov; B. I. Kutepov

    2015-01-01

    The high activity and selectivity of H‐Beta and H‐ZSM‐12 zeolites in the dimerization of norbornene was established. The norbornene conversion reached 100%in chlorinated paraffin and argon gas medium, with a selectivity of dimer formation of 88%–98%. Four stereo‐isomers of the bis‐2,2’‐norbornylidene structure were identified in the dimer fraction, with the (Z)‐anti‐bis‐2,2’‐norbornylidene prevailing over the others.

  2. Inhibition of arenavirus by A3, a pyrimidine biosynthesis inhibitor.

    Science.gov (United States)

    Ortiz-Riaño, Emilio; Ngo, Nhi; Devito, Stefanie; Eggink, Dirk; Munger, Joshua; Shaw, Megan L; de la Torre, Juan Carlos; Martínez-Sobrido, Luis

    2014-01-01

    Arenaviruses merit significant interest as important human pathogens, since several of them cause severe hemorrhagic fever disease that is associated with high morbidity and significant mortality. Currently, there are no FDA-licensed arenavirus vaccines available, and current antiarenaviral therapy is limited to an off-labeled use of the nucleoside analog ribavirin, which has limited prophylactic efficacy. The pyrimidine biosynthesis inhibitor A3, which was identified in a high-throughput screen for compounds that blocked influenza virus replication, exhibits a broad-spectrum antiviral activity against negative- and positive-sense RNA viruses, retroviruses, and DNA viruses. In this study, we evaluated the antiviral activity of A3 against representative Old World (lymphocytic choriomeningitis virus) and New World (Junin virus) arenaviruses in rodent, monkey, and human cell lines. We show that A3 is significantly more efficient than ribavirin in controlling arenavirus multiplication and that the A3 inhibitory effect is in part due to its ability to interfere with viral RNA replication and transcription. We document an additive antiarenavirus effect of A3 and ribavirin, supporting the potential combination therapy of ribavirin and pyrimidine biosynthesis inhibitors for the treatment of arenavirus infections.

  3. Synthesis and characterization of novel Schiff bases containing pyrimidine unit

    Directory of Open Access Journals (Sweden)

    Jumbad H. Tomma

    2014-01-01

    Full Text Available The work involves synthesis of novel Schiff base derivatives containing a pyrimidine unit starting with chalcones. 4-Aminoacetophenone was reacted with 4-nitrobenzaldehyde or 4-chlorobenzaldehyde in basic medium giving chalcones, [I]a and [I]b, respectively, by Claisen-Schemidt reaction. The chalcones [I]a and [I]b were reacted with urea in HCl medium giving oxopyrimidines, [II]a and [II]b. They were also reacted with thiourea in basic medium to give thioxopyrimidines, [III]a and [III]b. The novel mono and bis Schiff bases, [VIII]na, [VIII]nb, [IX]na, [IX]nb, [X]na, [X]nb, [XI]na, and [XI]nb were synthesized by the reaction of pyrimidine derivatives; oxopyrimdines, [II]a and [II]b and thioxopyrimidines, [III]a and [III]b with 4-(4′-n-alkoxybenzoloxybenzaldehyde [VI] and polymethylene-α,ω-bis-4-oxybenzaldehydes [VII]m, respectively, in dry benzene using drops of glacial acetic acid as a catalyst. The synthesized compounds were characterized by melting points, elemental analysis, FTIR, and 1H NMR spectroscopy.

  4. 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.

  5. Sputtering of dimers off a silicon surface

    Energy Technology Data Exchange (ETDEWEB)

    Nietiadi, Maureen L. [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Rosandi, Yudi [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Department of Physics, Universitas Padjadjaran, Jatinangor, Sumedang 45363 (Indonesia); Kopnarski, Michael [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Institut fuer Oberflaechen- und Schichtanalytik IFOS GmbH, Trippstadter Strasse 120, D-67663 Kaiserslautern (Germany); Urbassek, Herbert M., E-mail: urbassek@rhrk.uni-kl.de [Physics Department, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany); Research Center OPTIMAS, University Kaiserslautern, Erwin-Schroedinger-Strasse, D-67663 Kaiserslautern (Germany)

    2012-10-15

    We present experimental and molecular-dynamics simulation results of the sputtering of a Si surface by 2 keV Ar ions. Results on both the monomer and dimer distributions are presented. In simulation, these distributions follow a generalized Thompson law with power exponent n=2 and n=3, respectively. The experimental data, obtained via plasma post-ionization in an SNMS (secondary neutral mass spectrometry) apparatus, show good agreement with respect to the dimer fraction, and the relative energy distributions of dimers and monomers. The consequences for the dimer sputtering mechanism are discussed.

  6. Catabolism of pyrimidines in yeast: a tool to understand degradation of anticancer drugs

    DEFF Research Database (Denmark)

    Andersen, G; Merico, A; Björnberg, O;

    2006-01-01

    The pyrimidine catabolic pathway is of crucial importance in cancer patients because it is involved in degradation of several chemotherapeutic drugs, such as 5-fluorouracil; it also is important in plants, unicellular eukaryotes, and bacteria for the degradation of pyrimidine-based biocides....../antibiotics. During the last decade we have developed a yeast species, Saccharomyces kluyveri, as a model and tool to study the genes and enzymes of the pyrimidine catabolic pathway. In this report, we studied degradation of uracil and its putative degradation products in 38 yeasts and showed that this pathway...

  7. Stopping power for electrons in pyrimidine in the energy range 20-3000 eV.

    Science.gov (United States)

    Colmenares, R; Sanz, A G; Fuss, M C; Blanco, F; García, G

    2014-01-01

    In this work, we present new experimental electron energy loss distribution functions for pyrimidine (C4H4N2) measured for the incident energy range 30-2000 eV. Theoretical total and elastic cross sections for electron scattering from pyrimidine were calculated using the screening-corrected additivity rule (IAM-SCAR) method. Based on the mean energy loss observed in the experiment and the theoretical integral inelastic cross section, the stopping power for electrons in pyrimidine is calculated in the energy range 20-3000 eV.

  8. Catabolism of pyrimidines in yeast: A tool to understand degradation of anticancer drugs

    DEFF Research Database (Denmark)

    Andersen, Gorm; Merico, A.; Bjornberg, O.

    2006-01-01

    The pyrimidine catabolic pathway is of crucial importance in cancer patients because it is involved in degradation of several chemotherapeutic drugs, such as 5-fluorouracil; it also is important in plants, unicellular eukaryotes, and bacteria for the degradation of pyrimidine-based biocides....../antibiotics. During the last decade we have developed a yeast species, Saccharomyces kluyveri, as a model and tool to study the genes and enzymes of the pyrimidine catabolic pathway. In this report, we studied degradation of uracil and its putative degradation products in 38 yeasts and showed that this pathway...

  9. An Efficient, Clean, and Catalyst-Free Synthesis of Fused Pyrimidines Using Sonochemistry

    Directory of Open Access Journals (Sweden)

    M. Mamaghani

    2014-01-01

    Full Text Available In this report, synthesis of indenopyrido[2,3-d]pyrimidine and pyrimido[4,5-b]quinoline derivatives was investigated via one-pot three-component reaction between 6-amino-2-(alkylthio-pyrimidin-4(3Hone, 1,3-indanedione, or 1,3-cyclohexadione and arylaldehyde under ultrasonic irradiation in ethylene glycol as solvent at 65°C. In these reactions fused pyrimidine derivatives were synthesized with high to excellent yields (82–97% and short reaction times (10–33 min.

  10. An Efficient, Clean, and Catalyst-Free Synthesis of Fused Pyrimidines Using Sonochemistry

    OpenAIRE

    2014-01-01

    In this report, synthesis of indenopyrido[2,3-d]pyrimidine and pyrimido[4,5-b]quinoline derivatives was investigated via one-pot three-component reaction between 6-amino-2-(alkylthio)-pyrimidin-4(3H)one, 1,3-indanedione, or 1,3-cyclohexadione and arylaldehyde under ultrasonic irradiation in ethylene glycol as solvent at 65°C. In these reactions fused pyrimidine derivatives were synthesized with high to excellent yields (82–97%) and short reaction times (10–33 min).

  11. Mahler Measure, Eisenstein Series and Dimers

    NARCIS (Netherlands)

    Stienstra, J.

    2007-01-01

    This note reveals a mysterious link between the partition function of certain dimer models on 2-dimensional tori and the L-function of their spectral curves. It also relates the partition function in certain families of dimer models to Eisenstein series. http://www.arxiv.org/abs/math.NT/0502197

  12. Dimeric assembly of enterocyte brush border enzymes

    DEFF Research Database (Denmark)

    Danielsen, E M

    1994-01-01

    temperature (20 degrees C) reduced the rate of, but did not prevent, dimerization. Maltase-glucoamylase (EC 3.2.1.20) only appeared as a dimer when extracted and analyzed under low salt conditions, suggesting a weak association between the two subunits. This finding is consistent with the electronmicroscopic...

  13. Potassium Hexacyanoferrate (III-Catalyzed Dimerization of Hydroxystilbene: Biomimetic Synthesis of Indane Stilbene Dimers

    Directory of Open Access Journals (Sweden)

    Jing-Shan Xie

    2015-12-01

    Full Text Available Using potassium hexacyanoferrate (III–sodium acetate as oxidant, the oxidative coupling reaction of isorhapontigenin and resveratrol in aqueous acetone resulted in the isolation of three new indane dimers 4, 6, and 7, together with six known stilbene dimers. Indane dimer 5 was obtained for the first time by direct transformation from isorhapontigenin. The structures and relative configurations of the dimers were elucidated using spectral analysis, and their possible formation mechanisms were discussed. The results indicate that this reaction could be used as a convenient method for the semi-synthesis of indane dimers because of the mild conditions and simple reaction products.

  14. Statistical transmutation in doped quantum dimer models.

    Science.gov (United States)

    Lamas, C A; Ralko, A; Cabra, D C; Poilblanc, D; Pujol, P

    2012-07-06

    We prove a "statistical transmutation" symmetry of doped quantum dimer models on the square, triangular, and kagome lattices: the energy spectrum is invariant under a simultaneous change of statistics (i.e., bosonic into fermionic or vice versa) of the holes and of the signs of all the dimer resonance loops. This exact transformation enables us to define the duality equivalence between doped quantum dimer Hamiltonians and provides the analytic framework to analyze dynamical statistical transmutations. We investigate numerically the doping of the triangular quantum dimer model with special focus on the topological Z(2) dimer liquid. Doping leads to four (instead of two for the square lattice) inequivalent families of Hamiltonians. Competition between phase separation, superfluidity, supersolidity, and fermionic phases is investigated in the four families.

  15. Universal four-Boson states in ultracold molecular gases: resonant effects in dimer-dimer collisions.

    Science.gov (United States)

    D'Incao, J P; von Stecher, J; Greene, Chris H

    2009-07-17

    We study the manifestations of universal four-body physics in ultracold dimer-dimer collisions. We show that resonant features associated with three-body Efimov physics and dimer-dimer scattering lengths are universally related. The emergence of universal four-boson states allows for the tunability of the dimer-dimer interaction, thus enabling the future study of ultracold molecular gases with both attractive and repulsive interactions. Moreover, our study of the interconversion between dimers and Efimov trimers shows that B2+B2-->B3+B rearrangement reactions can provide an efficient trimer formation mechanism. Our analysis of the temperature dependence of this reaction provides an interpretation of the available experimental data and sheds light on the possible experimental realization of rearrangement processes in ultracold gases.

  16. 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

    An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers...... 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...... and insulin stability and function, we engineered a covalently linked insulin dimer in which two monomers were linked by a disulfide bond. The structure of this covalent dimer was identical to the self-association dimer of human insulin. Importantly, this covalent dimer was capable of further oligomerization...

  17. Synthesis and comparing the antibacterial activities of pyrimidine derivatives

    Indian Academy of Sciences (India)

    B ANDREWS; K KOMATHI; S MOHAN

    2017-03-01

    A series of 10 derivatives of 5-(5-amino-1,3,4-thiadiazole-2-yl)-3,4-dihydro-6-methyl-4-phenylpyrimidin-2(1H)-one and 10 derivatives of 3,4-dihydro-5-(5-mercapto-4H-1,2,4-triazol-3-yl)-6-methyl-4-phenyl pyrimidin-2(1H)-one have been synthesized. Among the synthesized derivatives, triazole substitutedcompounds have shown higher antibacterial inhibition when compared to the thiadiazole derivatives. All the structures of the newly synthesized compounds have been characterized by IR, 1H and 13C NMR, GC-MS and CHN analysis. Most of the compounds have shown promising antibacterial activity when compared with the standard drug ciprofloxacin.

  18. New insights on pyrimidine signalling within the arterial vasculature

    DEFF Research Database (Denmark)

    Haanes, Kristian Agmund; Spray, Stine; Syberg, Susanne;

    2016-01-01

    and relaxation in the coronary circulation and to establish whether P2Y receptors have different functions along the mouse coronary vascular tree. We tested stable pyrimidine analogues on isolated coronary arteries from P2Y2 and P2Y6 receptor KO mice in a myograph setup. In larger diameter segments of the left...... descending coronary artery (LAD) (lumen diameter~150μm) P2Y6 is the predominant contractile receptor for both UTP (uridine triphosphate) and UDP (uridine diphosphate) induced contraction. In contrast, P2Y2 receptors mediate endothelial-dependent relaxation. However, in smaller diameter LAD segments (lumen...... diameter~50μm), the situation is opposite, with P2Y2 being the contractile receptor and P2Y6 functioning as a relaxant receptor along with P2Y2. Immunohistochemistry was used to confirm smooth muscle and endothelial localization of the receptors. In vivo measurements of blood pressure in WT mice revealed...

  19. 1,4-Bis(pyrimidin-2-ylsulfanylbutane

    Directory of Open Access Journals (Sweden)

    Muhammad Akbar

    2010-11-01

    Full Text Available The –SCH2CH2CH2CH2S– portion of the title compound, C12H14N2S2, adopts an extended zigzag conformation. The angles at the tetrahedral carbon atoms are marginally increased [113.63 (12° and 111.38 (17° for S—C—C and C—C—C respectively] from the idealized tetrahedral angle. The molecule lies on an inversion center located at the mid-point of the butyl chain. In the crystal, there is a π–π stacking interaction between inversion-related pyrimidine rings with mean interplanar spacing of 3.494 (2 Å.

  20. Bis(pyrimidine-2-carboxylato-κ2N,Ocopper(II

    Directory of Open Access Journals (Sweden)

    Bing-Yu Zhang

    2008-01-01

    Full Text Available The title compound, [Cu(C5H3N2O22], was prepared in a water–ethanol solution containing 2-cyanopyrimidine, malonic acid and copper(II nitrate trihydrate. The CuII ion, located on an inversion center, is chelated by two pyrimidine-2-carboxylate anions in a CuO2N2 square-planar geometry. The uncoordinated carboxylate O atom and pyrimidine N atoms are linked to adjacent pyrimidine rings via weak C—H...O and C—H...N hydrogen bonding. π–π Stacking is observed between nearly parallel pyrimidine rings, the centroid-to-centroid separation being 3.8605 (13 Å.

  1. divalent metal complexes of 4-amino-n-pyrimidin-2-ylbenzene ...

    African Journals Online (AJOL)

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    use of metal complexes as chemotherapeutic drugs has become a vibrant and growing area of ..... through the pyrimidine nitrogen atom [17]. ... binding can take place by the acceptance of a one pair of electron from the donor nitrogen atom.

  2. Absorption and Intermediary Metabolism of Purines and Pyrimidines in Lactating Dairy Cows

    DEFF Research Database (Denmark)

    Nielsen, Charlotte Stentoft; Røjen, Betina Amdisen; Jensen, Søren Krogh

    2015-01-01

    About 20 % of ruminal microbial N in dairy cows derives from purines and pyrimidines; however, their intermediary metabolism and contribution to the overall N metabolism has sparsely been described. In the present study, the postprandial patterns of net portal-drained viscera (PDV) and hepatic...... metabolism were assessed to evaluate purine and pyrimidine N in dairy cows. Blood was sampled simultaneously from four veins with eight hourly samples from four multi-catheterised Holstein cows. Quantification of twenty purines and pyrimidines was performed with HPLC–MS/MS, and net fluxes were estimated...... across the PDV, hepatic tissue and total splanchnic tissue (TSP). Concentration differences between veins of fifteen purine and pyrimidine nucleosides (NS), bases (BS) and degradation products (DP) were different from zero (P≤ 0·05), resulting in the net PDV releases of purine NS (0·33–1·3 mmol...

  3. Synthesis of 2-Arylimidazo[1,2-a]pyrimidines in Ionic Liquids

    Institute of Scientific and Technical Information of China (English)

    Dan Qian XU; Bao You LIU; Zhen Yuan XU

    2003-01-01

    Room temperature ionic liquids were used as a "green" recyclable alternative toconventional solvents in the synthesis of pharmaceutically useful compounds 2-arylimidazo[1, 2-a]pyrimidines through Tschotschibabin reaction of α-bromoacetophenones with 2-aminopyfinidinein good yields.

  4. The pyrimidine operon pyrRPB-carA from Lactococcus lactis

    DEFF Research Database (Denmark)

    Martinussen, Jan; Schallert, J.; Andersen, Birgit;

    2001-01-01

    The four genes pyrR, pyrP, pyrB, and carA were found to constitute an operon in Lactococcus lactis subsp, lactis MG1363. The functions of the different genes were established by mutational analysis. The first gene in the operon is the pyrimidine regulatory gene, pyrR, which is responsible...... for the regulation of the expression of the pyrimidine biosynthetic genes leading to UMP formation. The second gene encodes a membrane-bound high-affinity uracil permease, required for utilization of exogenous uracil. The last two genes in the operon, pyrB and carA, encode pyrimidine biosynthetic enzymes; aspartate....... The expression of the pyrimidine biosynthetic genes including the pyrRPB-carA operon is subject to control at the transcriptional level, most probably by an attenuator mechanism in which PyrR acts as the regulatory protein....

  5. Synthesis and evaluation of chalcone analogues based pyrimidines as angiotensin converting enzyme inhibitors.

    Science.gov (United States)

    Bukhari, S N A; Butt, A M; Amjad, M W B; Ahmad, W; Shah, V H; Trivedi, A R

    2013-11-01

    Hypertension is a widespread and frequently progressive ailment that imparts a foremost threat for cardiovascular and renal disorders. Mammoth efforts are needed for the synthesis of innovative antihypertensive agents to combat this lethal disease. Chalcones have shown antihypertensive activity through inhibition of Angiotensin Converting Enzyme (ACE). Hence, a series of chalcone analogues is synthesized and used as precursor for the synthesis of novel series of pyrimidines. Precursor chalcones were prepared by reacting aldehydes and ketones in presence of sodium hydroxide followed by synthesis of corresponding pyrimidines by reaction with urea in presence of potassium hydroxide. Both groups were then evaluated for their effects on ACE. The results depicted that pyrimidines were more active than chalcones with methoxy (C5 and P5) substitution showing best results to inhibit ACE. Given that chalcone analogues and pyrimidines show a potential as the angiotensin converting enzyme inhibitors.

  6. The 3-ureidopropionase of Caenorhabditis elegans, an enzyme involved in pyrimidine degradation.

    Science.gov (United States)

    Janowitz, Tim; Ajonina, Irene; Perbandt, Markus; Woltersdorf, Christian; Hertel, Patrick; Liebau, Eva; Gigengack, Ulrike

    2010-10-01

    Pyrimidines are important metabolites in all cells. Levels of cellular pyrimidines are controlled by multiple mechanisms, with one of these comprising the reductive degradation pathway. In the model invertebrate Caenorhabditis elegans, two of the three enzymes of reductive pyrimidine degradation have previously been characterized. The enzyme catalysing the final step of pyrimidine breakdown, 3-ureidopropionase (β-alanine synthase), had only been identified based on homology. We therefore cloned and functionally expressed the 3-ureidopropionase of C. elegans as hexahistidine fusion protein. The purified recombinant enzyme readily converted the two pyrimidine degradation products: 3-ureidopropionate and 2-methyl-3-ureidopropionate. The enzyme showed a broad pH optimum between pH 7.0 and 8.0. Activity was highest at approximately 40 °C, although the half-life of activity was only 65 s at that temperature. The enzyme showed clear Michaelis-Menten kinetics, with a K(m) of 147 ± 26 μM and a V(max) of 1.1 ± 0.1 U·mg protein(-1). The quaternary structure of the recombinant enzyme was shown to correspond to a dodecamer by 'blue native' gel electrophoresis and gel filtration. The organ specific and subcellular localization of the enzyme was determined using a translational fusion to green fluorescent protein and high expression was observed in striated muscle cells. With the characterization of the 3-ureidopropionase, the reductive pyrimidine degradation pathway in C. elegans has been functionally characterized.

  7. Ultraviolet irradiation of DNA complexed with. alpha. /. beta. -type small, acid-soluble proteins from spores of Bacillus or Clostridium species makes spore photoproduct but not thymine dimers

    Energy Technology Data Exchange (ETDEWEB)

    Nicholson, W.L.; Setlow, B.; Setlow, P. (Univ. of Connecticut Health Center, Farmington (United States))

    1991-10-01

    UV irradiation of complexes of DNA and an {alpha}/{beta}-type small, acid-soluble protein (SASP) from Bacillus subtilis spores gave decreasing amounts of pyrimidine dimers and increasing amounts of spore photoproduct as the SASP/DNA ratio was increased. The yields of pyrimidine dimers and spore photoproduct were < 0.2% and 8% of total thymine, respectively, when DNA saturated with SASP was irradiated at 254 nm with 30 kJ/m{sup 2}; in the absence of SASP the yields were reversed - 4.5% and 0.3%, respectively. Complexes of DNA with {alpha}/{beta}-type SASP from Bacillus cereus, Bacillus megaterium, or Clostridium bifermentans spores also gave spore photoproduct upon UV irradiation. However, incubation of these SASPs with DNA under conditions preventing complex formation or use of mutant SASPs that do not form complexes did not affect the photoproducts formed in vitro. These results suggest that the UV photochemistry of bacterial spore DNA in vivo is due to the binding of {alpha}/{beta}-type SASP, a binding that is known to cause a change in DNA conformation in vitro from the B form to the A form. The yields of spore photoproduct in vitro were significantly lower than in vivo, perhaps because of the presence of substances other than SASP in spores. It is suggested that as these factors diffuse out in the first minutes of spore germination, spore photoproduct yields become similar to those observed for irradiation of SASP/DNA complexes in vitro.

  8. Pyrimidine non-nucleoside analogs: A direct synthesis of a novel class of N-substituted amino and N-sulfonamide derivatives of pyrimidines.

    Science.gov (United States)

    Elgemeie, Galal H; Salah, Ali M; Abbas, Nermeen S; Hussein, Hoda A; Mohamed, Reham A

    2017-03-04

    A convenient method for the regioselective synthesis of pyrimidine non-nucleoside analogs was developed. This study reports a novel and efficient method for the synthesis of a new type of N-substituted amino methylsulfanylpyrimidines and the corresponding pyrazolo[3,4-d]pyrimidines. This series of compounds was designed through the reaction of dimethyl N-cyanodithioiminocarbonate with 2-cyano-N'-(thiophen-2-yl-, furan-2-yl- and pyridin-4-ylmethylene)acetohydrazide and N'-(2-cyanoacetyl)arylsulfonohydrazides. The scope and limitation of the method are demonstrated. The antibacterial and antifungal activities of the synthesized compounds were also evaluated.

  9. Quantum dimer model for the pseudogap metal

    Science.gov (United States)

    Punk, Matthias; Allais, Andrea; Sachdev, Subir

    2015-01-01

    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. PMID:26195771

  10. 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.

  11. Effect of the cyclobutane cytidine dimer on the properties of Escherichia coli DNA photolyase.

    Science.gov (United States)

    Murphy, Anar K; Tammaro, Margaret; Cortazar, Frank; Gindt, Yvonne M; Schelvis, Johannes P M

    2008-11-27

    Cyclobutane pyrimidine dimer (CPD) photolyases are structure specific DNA-repair enzymes that specialize in the repair of CPDs, the major photoproducts that are formed upon irradiation of DNA with ultraviolet light. The purified enzyme binds a flavin adenine dinucleotide (FAD), which is in the neutral radical semiquinone (FADH(*)) form. The CPDs are repaired by a light-driven, electron transfer from the anionic hydroquinone (FADH(-)) singlet excited state to the CPD, which is followed by reductive cleavage of the cyclobutane ring and subsequent monomerization of the pyrimidine bases. CPDs formed between two adjacent thymidine bases (TT) are repaired with greater efficiency than those formed between two adjacent cytidine bases (CC). In this paper, we investigate the changes in Escherichia coli photolyase that are induced upon binding to DNA containing CC lesions using resonance Raman, UV-vis absorption, and transient absorption spectroscopies, spectroelectrochemistry, and computational chemistry. The binding of photolyase to a CC lesion modifies the energy levels of FADH(*), the rate of charge recombination between FADH(-) and Trp(306)(*), and protein-FADH(*) interactions differently than binding to a TT lesion. However, the reduction potential of the FADH(-)/FADH(*) couple is modified in the same way with both substrates. Our calculations show that the permanent electric dipole moment of CC is stronger (12.1 D) and oriented differently than that of TT (8.7 D). The possible role of the electric dipole moment of the CPD in modifying the physicochemical properties of photolyase as well as in affecting CPD repair will be discussed.

  12. Quantitative analysis of cyclic dimer fatty acid content in the dimerization product by proton NMR spectroscopy.

    Science.gov (United States)

    Park, Kyun Joo; Kim, Minyoung; Seok, Seunghwan; Kim, Young-Wun; Kim, Do Hyun

    2015-01-01

    In this work, (1)H NMR is utilized for the quantitative analysis of a specific cyclic dimer fatty acid in a dimer acid mixture using the pseudo-standard material of mesitylene on the basis of its structural similarity. Mesitylene and cyclic dimer acid levels were determined using the signal of the proton on the cyclic ring (δ=6.8) referenced to the signal of maleic acid (δ=6.2). The content of the cyclic dimer fatty acid was successfully determined through the standard curve of mesitylene and the reported equation. Using the linearity of the mesitylene curve, the cyclic dimer fatty acid in the oil mixture was quantified. The results suggest that the proposed method can be used to quantify cyclic compounds in mixtures to optimize the dimerization process.

  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. A New Dimeric Phthalide from Angelica sinensis

    Institute of Scientific and Technical Information of China (English)

    Ling YI; Ping LI; Zhi Ming BI

    2006-01-01

    A new dimeric phthalide named Z, Z'-3.3'a, 7.7'a-diligustilide was isolated from the roots of Angelica sinensis. Its structure was determined using spectroscopic methods and X-ray crystallographic diffraction analysis.

  15. Synthesis of pyrazolo[1,5-a]pyrimidine derivatives and their antifungal activities against phytopathogenic fungi in vitro.

    Science.gov (United States)

    Zhang, Jin; Peng, Ju-Fang; Bai, Yu-Bin; Wang, Ping; Wang, Tao; Gao, Jin-Ming; Zhang, Zun-Ting

    2016-11-01

    5,6-Diarylpyrazolo[1,5-a]pyrimidines (3) and 6,7-diarylpyrazolo[1,5-a]pyrimidines (4) were chemoselectively synthesized by the condensation of isoflavone (1) and 3-aminopyrazole (2). 5,6-Diarylpyrazolo[1,5-a]pyrimidines (3) were obtained via microwave irradiation, and 6,7-diarylpyrazolo[1,5-a]pyrimidines (4) were obtained via conventional heating. In addition, the pyrimidine derivatives 3 and 4 were evaluated against five phytopathogenic fungi (Cytospora sp., Colletotrichum gloeosporioides, Botrytis cinerea, Alternaria solani, and Fusarium solani) using the mycelium growth rate method. Some of them were effective in inhibiting the growth of the five phytopathogenic fungi. For instance, 6,7-diarylpyrazolo[1,5-a]pyrimidines (4j) inhibited the growth of A. solani with an [Formula: see text] value of 17.11 [Formula: see text], and 6,7-diarylpyrazolo[1,5-a]pyrimidines (4h) inhibited the growth of both Cytospora sp. and F. solani with [Formula: see text] values of 27.32 and 21.04 [Formula: see text], respectively. A chemoselective synthesis of 5,6-pyrazolo[1,5-a]pyrimidines 3 derivatives in excellent yields was performed under microwave irradiation and 6,7-pyrazolo[1,5-a]pyrimidines 4 were also prepared using heating method. The antifungal properties of 3 and 4 were tested against Cytospora sp., Colletotrichum gloeosporioides, Botrytis cinerea, Alternaria solani, and Fusarium solani.

  16. Designing Stable Antiparallel Coiled Coil Dimers

    Institute of Scientific and Technical Information of China (English)

    曾宪纲; 周海梦

    2001-01-01

    The history of antiparallel coiled coil dimer design is briefly reviewed and the main principles governing the successful designs are explained. They include analysis of the inter-subunit electrostatic repulsion for determining partners for dimerization and of the buried polar interaction for determining the relative orientation of the partners. A theory is proposed to explain the lack of antiparallel coiled coil homodimers in nature.

  17. Formation of Cystine Slipknots in Dimeric Proteins

    OpenAIRE

    Mateusz Sikora; Marek Cieplak

    2013-01-01

    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 dim...

  18. Role of Rydberg states in the photostability of heterocyclic dimers: the case of pyrazole dimer.

    Science.gov (United States)

    Zilberg, Shmuel; Haas, Yehuda

    2012-11-26

    A new route for the nonradiative decay of photoexcited, H-bonded, nitrogen-containing, heterocyclic dimers is offered and exemplified by a study of the pyrazole dimer. In some of these systems the N(3s) Rydberg state is the lowest excited singlet state. This state is formed by direct light absorption or by nonradiative transition from the allowed ππ* state. An isomer of this Rydberg state is formed by H atom transfer to the other component of the dimer. The newly formed H-bonded radical pair is composed of two radicals (a H-adduct of pyrazole, a heterocyclic analogue of the NH(4) radical) and the pyrazolium π-radical. It is calculated to have a shallow local minimum and is the lowest point on the PES of the H-pyrazole/pyrazolium radical pair. This species can cross back to the ground state of the original dimer through a relatively small energy gap and compete with the H-atom loss channel, known for the monomer. In both Rydberg dimers, an electron occupies a Rydberg orbital centered mostly on one of the two components of the dimer. This Rydberg Center Shift (RCS) mechanism, proposed earlier (Zilberg, S.; Kahan, A.; Haas, Y. Phys. Chem. Chem. Phys. 2012, 14, 8836), leads to deactivation of the electronically excited dimer while keeping it intact. It, thus, may explain the high photostability of the pyrazole dimer as well as other heterocyclic dimers.

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

    DEFF Research Database (Denmark)

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

    2002-01-01

    M. The disappearance of adhesive dimers was counterbalanced by an increase in Trp156-dependent lateral dimers. Increasing the calcium concentration to a normal level rapidly restored the original balance between adhesive and lateral dimers. We also present evidence that E-cadherin dimers in vivo have a short lifetime...

  20. Adsorption of dimeric surfactants in lamellar silicates

    Energy Technology Data Exchange (ETDEWEB)

    Balcerzak, Mateusz; Pietralik, Zuzanna [Department of Macromolecular Physics, Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland); Domka, Ludwik [Department of Metalorganic Chemistry, Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznań (Poland); Skrzypczak, Andrzej [Institute of Chemical Technology, Poznań University of Technology, Berdychowo 4, 60-965 Poznań (Poland); Kozak, Maciej, E-mail: mkozak@amu.edu.pl [Department of Macromolecular Physics, Faculty of Physics, A. Mickiewicz University, Umultowska 85, 61-614 Poznań (Poland)

    2015-12-01

    Highlights: • The intercalation of dimeric surfactants changed the morphology of MMT samples. • XRD indicated structures formed by surfactant molecules in interlayer space. • The four-step thermal decomposition of dimeric surfactant, confirms intercalation. - Abstract: The adsorption of different types of cationic surfactants in lamellar silicates changes their surface character from hydrophilic to hydrophobic. This study was undertaken to obtain lamellar silicates modified by a series of novel dimeric (gemini) surfactants of different length alkyl chains and to characterise these organophilised materials. Synthetic sodium montmorillonite SOMASIF® ME 100 (M) and enriched bentonite of natural origin (Nanoclay – hydrophilic bentonite®) were organophilised with dimeric (gemini) surfactants (1,1′-(1,4-butanediyl)bis(alkoxymethyl)imidazolium dichlorides). As a result of surfactant molecule adsorption in interlamellar space, the d-spacing (d{sub 001}) increased from 0.97 nm (for the anhydrous structure) to 2.04 nm. A Fourier transform infrared spectroscopy (FTIR) analysis of the modified systems reveals bands assigned to the stretching vibrations of the CH{sub 2} and CH{sub 3} groups and the scissoring vibrations of the NH group from the structure of the dimeric surfactants. Thermogravimetric (TG) and derivative thermogravimetric (DTG) studies imply a four-stage process of surfactant decomposition. Scanning electron microscopy (SEM) images provide information on the influence of dimeric surfactant intercalation into the silicate structures. Particles of the modified systems show a tendency toward the formation of irregularly shaped agglomerates.

  1. De novo pyrimidine biosynthesis in the oomycete plant pathogen Phytophthora infestans.

    Science.gov (United States)

    García-Bayona, Leonor; Garavito, Manuel F; Lozano, Gabriel L; Vasquez, Juan J; Myers, Kevin; Fry, William E; Bernal, Adriana; Zimmermann, Barbara H; Restrepo, Silvia

    2014-03-10

    The oomycete Phytophthora infestans, causal agent of the tomato and potato late blight, generates important economic and environmental losses worldwide. As current control strategies are becoming less effective, there is a need for studies on oomycete metabolism to help identify promising and more effective targets for chemical control. The pyrimidine pathways are attractive metabolic targets to combat tumors, virus and parasitic diseases but have not yet been studied in Phytophthora. Pyrimidines are involved in several critical cellular processes and play structural, metabolic and regulatory functions. Here, we used genomic and transcriptomic information to survey the pyrimidine metabolism during the P. infestans life cycle. After assessing the putative gene machinery for pyrimidine salvage and de novo synthesis, we inferred genealogies for each enzymatic domain in the latter pathway, which displayed a mosaic origin. The last two enzymes of the pathway, orotate phosphoribosyltransferase and orotidine-5-monophosphate decarboxylase, are fused in a multi-domain enzyme and are duplicated in some P. infestans strains. Two splice variants of the third gene (dihydroorotase) were identified, one of them encoding a premature stop codon generating a non-functional truncated protein. Relative expression profiles of pyrimidine biosynthesis genes were evaluated by qRT-PCR during infection in Solanum phureja. The third and fifth genes involved in this pathway showed high up-regulation during biotrophic stages and down-regulation during necrotrophy, whereas the uracil phosphoribosyl transferase gene involved in pyrimidine salvage showed the inverse behavior. These findings suggest the importance of de novo pyrimidine biosynthesis during the fast replicative early infection stages and highlight the dynamics of the metabolism associated with the hemibiotrophic life style of pathogen.

  2. Photochemistry of Pyrimidine in Astrophysical Ices: Formation of Nucleobases and Other Prebiotic Species

    Science.gov (United States)

    Nuevo, Michel; Sandford, Scott A.; Materese, Christopher K.; Milam, Stefanie N.

    2012-01-01

    Nucleobases are N-heterocycles that are the informational subunits of DNA and RNA. They are divided into two molecular groups: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites, and their extraterrestrial origin confirmed by isotopic measurements. Although no N-heterocycles have ever been observed in the ISM, the positions of the 6.2- m interstellar emission features suggest a population of such molecules is likely to be present. However, laboratory experiments have shown that the ultraviolet (UV) irradiation of pyrimidine in ices of astrophysical relevance such as H2O, NH3, CH3OH, CH4, CO, or combinations of these at low temperature (less than or equal to 20 K) leads to the formation of several pyrimidine derivatives including the nucleobases uracil and cytosine, as well as precursors such as 4(3H)-pyrimidone and 4-aminopyrimidine. Quantum calculations on the formation of 4(3H)-pyrimidone and uracil from the irradiation of pyrimidine in pure H2O ices are in agreement with their experimental formation pathways.10 In those residues, other species of prebiotic interest such as urea as well as the amino acids glycine and alanine could also be identified. However, only very small amounts of pyrimidine derivatives containing CH3 groups could be detected, suggesting that the addition of methyl groups to pyrimidine is not an efficient process. For this reason, the nucleobase thymine was not observed in any of the samples. In this work, we study the formation of nucleobases and other photo-products of prebiotic interest from the UV irradiation of pyrimidine in ices containing H2O, NH3, CH3OH, and CO, mixed in astrophysical proportions.

  3. N-(4-Meth-oxy-phen-yl)-6-methyl-2-phenyl-5-{[4-(tri-fluoro-meth-yl)anilino]meth-yl}pyrimidin-4-amine.

    Science.gov (United States)

    Cieplik, Jerzy; Pluta, Janusz; Bryndal, Iwona; Lis, Tadeusz

    2013-11-27

    The title compound, C26H23F3N4O, crystallizes with two symmetry-independent mol-ecules in the asymmetric unit, denoted A and B, which differ mainly in the rotation of the meth-oxy-phenyl ring. The -CF3 group of mol-ecule B is disordered by rotation, with the F atoms split over two sets of sites; the occupancy factor for the major component is 0.853 (4). The dihedral angles between the pyrimidine ring and the attached phenyl, meth-oxy-phenyl and tri-fluoro-methyl-phenyl rings are 8.1 (2), 37.5 (2) and 70.7 (2)°, respectively, in mol-ecule A, and 9.3 (2), 5.3 (2) and 79.7 (2)° in mol-ecule B. An intra-molecular N-H⋯N hydrogen bond occurs in each mol-ecule. In the crystal, two crystallographically independent mol-ecules associate into a dimer via a pair of N-H⋯N hydrogen bonds, with a resulting R 2 (2)(12) ring motif and π-π stacking inter-actions [centroid-centroid distance = 3.517 (4) Å] between the pyrimidine rings. For the A mol-ecules, there are inter-molecular C-H⋯O hydrogen bonds between an aryl C atom of meth-oxy-phenyl ring and a meth-oxy O atom of an adjacent mol-ecule. A similar inter-action is lacking in the B mol-ecules.

  4. Fenarimol, a Pyrimidine-Type Fungicide, Inhibits Brassinosteroid Biosynthesis

    Directory of Open Access Journals (Sweden)

    Keimei Oh

    2015-07-01

    Full Text Available The plant steroid hormone brassinosteroids (BRs are important signal mediators that regulate broad aspects of plant growth and development. With the discovery of brassinoazole (Brz, the first specific inhibitor of BR biosynthesis, several triazole-type BR biosynthesis inhibitors have been developed. In this article, we report that fenarimol (FM, a pyrimidine-type fungicide, exhibits potent inhibitory activity against BR biosynthesis. FM induces dwarfism and the open cotyledon phenotype of Arabidopsis seedlings in the dark. The IC50 value for FM to inhibit stem elongation of Arabidopsis seedlings grown in the dark was approximately 1.8 ± 0.2 μM. FM-induced dwarfism of Arabidopsis seedlings could be restored by brassinolide (BL but not by gibberellin (GA. Assessment of the target site of FM in BR biosynthesis by feeding BR biosynthesis intermediates indicated that FM interferes with the side chain hydroxylation of BR biosynthesis from campestanol to teasterone. Determination of the binding affinity of FM to purified recombinant CYP90D1 indicated that FM induced a typical type II binding spectrum with a Kd value of approximately 0.79 μM. Quantitative real-time PCR analysis of the expression level of the BR responsive gene in Arabidopsis seedlings indicated that FM induces the BR deficiency in Arabidopsis.

  5. Potential formation of three pyrimidine bases in interstellar regions

    CERN Document Server

    Majumdar, Liton; Das, Ankan; Chakrabarti, Sandip K

    2015-01-01

    Work on the chemical evolution of pre-biotic molecules remains incomplete since the major obstacle is the lack of adequate knowledge of rate coefficients of various reactions which take place in interstellar conditions. In this work, we study the possibility of forming three pyrimidine bases, namely, cytosine, uracil and thymine in interstellar regions. Our study reveals that the synthesis of uracil from cytosine and water is quite impossible under interstellar circumstances. For the synthesis of thymine, reaction between uracil and :CH2 is investigated. Since no other relevant pathways for the formation of uracil and thymine were available in the literature, we consider a large gas-grain chemical network to study the chemical evolution of cytosine in gas and ice phases. Our modeling result shows that cytosine would be produced in cold, dense interstellar conditions. However, presence of cytosine is yet to be established. We propose that a new molecule, namely, C4N3OH5 could be observable in the interstellar ...

  6. 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

    An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers...

  7. 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....

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

    Directory of Open Access Journals (Sweden)

    Tine N Vinther

    Full Text Available An ingenious system evolved to facilitate insulin binding to the insulin receptor as a monomer and at the same time ensure sufficient stability of insulin during storage. Insulin dimer is the cornerstone of this system. Insulin dimer is relatively weak, which ensures dissociation into monomers in the circulation, and it is stabilized by hexamer formation in the presence of zinc ions during storage in the pancreatic β-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 and insulin stability and function, we engineered a covalently linked insulin dimer in which two monomers were linked by a disulfide bond. The structure of this covalent dimer was identical to the self-association dimer of human insulin. Importantly, this covalent dimer was capable of further oligomerization to form the structural equivalent of the classical hexamer. The covalently linked dimer neither bound to the insulin receptor, nor induced a metabolic response in vitro. However, it was extremely thermodynamically stable and did not form amyloid fibrils when subjected to mechanical stress, underlining the importance of oligomerization for insulin stability.

  9. Lead optimization through VLAK protocol: new annelated pyrrolo-pyrimidine derivatives as antitumor agents.

    Science.gov (United States)

    Lauria, Antonino; Patella, Chiara; Abbate, Ilenia; Martorana, Annamaria; Almerico, Anna Maria

    2012-09-01

    The chemometric protocol VLAK was applied to predict improvement of the biological activity of pyrrolo-pyrimidine derivatives as anticancer agents, by using the NCI ACAM Database as depository of antitumor drugs with a known mechanism of action. Among the selected compounds two of these showed a good increase in the antitumor activity. These new pyrrolo-pyrimidine compounds were demonstrated effective against the full panels of NCI DTP tumour human cell lines. The derivative 8-[3-(piperidino)propyl]-4,10-dimethyl-9-phenyl-6-(methylsulfanyl)-3,4-dihydropyrimido[1,2-c]pyrrolo[3,2-e]pyrimidin-2(8H)-one reveled efficacious against the leukemia subpanel, in particular the RPMI cell line resulted the most sensitive (pGI(50) = 6.68). Moreover the derivative 7-(3-Chloropropyl)-9-methyl-5-(methylsulfanyl)-8-phenyl-3H-imidazo[1,2-c]pyrrolo[3,2-e]pyrimidin-2(7H)-one showed a good antitumor activity against the leukemia subpanel with a low cytotoxic activity, above all against the HCT11 human tumour cell line. The VLAK protocol revealed a good method to design new molecules with good antitumor activity, starting from low active compounds. Moreover this protocol focused on the pyrrolo-pyrimidine derivatives as useful starting point for further development to obtain more potent antitumor agents.

  10. Chemical modification of the third strand: differential effects on purine and pyrimidine triple helix formation.

    Science.gov (United States)

    Mills, Martin; Arimondo, Paola B; Lacroix, Laurent; Garestier, Thérèse; Klump, Horst; Mergny, Jean-Louis

    2002-01-08

    DNA triple helices offer exciting perspectives toward oligonucleotide-directed control of gene expression. Oligonucleotide analogues are routinely used with modifications in either the backbone or the bases to form more stable triple-helical structures or to prevent their degradation in cells. In this article, different chemical modifications are tested in a model system, which sets up a competition between the purine and pyrimidine motifs. For most modifications, the DeltaH degrees of purine triplex formation is close to zero, implying a nearly temperature-independent affinity constant. In contrast, the pyrimidine triplex is strongly favored at lower temperatures. The stabilization induced by modifications previously known to be favorable to the pyrimidine motif was quantified. Interestingly, modifications favorable to the GT motif (propynyl-U and dU replacing T) were also discovered. In a system where two third strands compete for triplex formation, replacement of the GA or GT strand by a pyrimidine strand may be observed at neutral pH upon lowering the temperature. This purine-to-pyrimidine triplex conversion depends on the chemical nature of the triplex-forming strands and the stability of the corresponding triplexes.

  11. Synthesis, crystal structure, characterization and antifungal activity of pyrazolo[1,5-a]pyrimidines derivatives

    Science.gov (United States)

    Zhang, Jin; Peng, Ju-Fang; Wang, Tao; Wang, Ping; Zhang, Zun-Ting

    2016-09-01

    Under microwave radiation, isomers 2-(pyrazolo[1,5-a]pyrimidin-5-yl)phenols (3) and 2-(pyrazolo[1,5-a]pyrimidin-7-yl)phenols (4) were simultaneously obtained by the condensation of chromones and 3-aminopyrazoles. These two isomers were fully characterized by IR, 1H NMR, 13C NMR and HRMS. In addition, a representative product 5-chloro-2-(2-methyl-pyrazolo[1,5-a] pyrimidin-5-yl)phenol (3e) was further conformed by the single crystal X-ray diffraction. The antifungal abilities of the obtained products 3 and 4 were evaluated against five phytopathogenic fungi (Cytospora sp., Colletotrichum gloeosporioides, Botrytis cinerea, Alternaria solani and Fusarium solani). The results revealed that 2-(pyrazolo[1,5-a]pyrimidin-5-yl)phenol (3a) and 4-chloro-2-(2-methylpyrazolo[1,5-a]pyrimidin-7-yl)phenol (4e) exhibited good antifungal abilities against Colletotrichum gloeosporioides with the IC50 values of 24.90 and 28.28 μg/mL, respectively.

  12. Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides

    Science.gov (United States)

    Stairs, Shaun; Nikmal, Arif; Bučar, Dejan-Krešimir; Zheng, Shao-Liang; Szostak, Jack W.; Powner, Matthew W.

    2017-05-01

    Understanding prebiotic nucleotide synthesis is a long standing challenge thought to be essential to elucidating the origins of life on Earth. Recently, remarkable progress has been made, but to date all proposed syntheses account separately for the pyrimidine and purine ribonucleotides; no divergent synthesis from common precursors has been proposed. Moreover, the prebiotic syntheses of pyrimidine and purine nucleotides that have been demonstrated operate under mutually incompatible conditions. Here, we tackle this mutual incompatibility by recognizing that the 8-oxo-purines share an underlying generational parity with the pyrimidine nucleotides. We present a divergent synthesis of pyrimidine and 8-oxo-purine nucleotides starting from a common prebiotic precursor that yields the β-ribo-stereochemistry found in the sugar phosphate backbone of biological nucleic acids. The generational relationship between pyrimidine and 8-oxo-purine nucleotides suggests that 8-oxo-purine ribonucleotides may have played a key role in primordial nucleic acids prior to the emergence of the canonical nucleotides of biology.

  13. Adaptive Reprogramming of De Novo Pyrimidine Synthesis Is a Metabolic Vulnerability in Triple-Negative Breast Cancer.

    Science.gov (United States)

    Brown, Kristin K; Spinelli, Jessica B; Asara, John M; Toker, Alex

    2017-04-01

    Chemotherapy resistance is a major barrier to the treatment of triple-negative breast cancer (TNBC), and strategies to circumvent resistance are required. Using in vitro and in vivo metabolic profiling of TNBC cells, we show that an increase in the abundance of pyrimidine nucleotides occurs in response to chemotherapy exposure. Mechanistically, elevation of pyrimidine nucleotides induced by chemotherapy is dependent on increased activity of the de novo pyrimidine synthesis pathway. Pharmacologic inhibition of de novo pyrimidine synthesis sensitizes TNBC cells to genotoxic chemotherapy agents by exacerbating DNA damage. Moreover, combined treatment with doxorubicin and leflunomide, a clinically approved inhibitor of the de novo pyrimidine synthesis pathway, induces regression of TNBC xenografts. Thus, the increase in pyrimidine nucleotide levels observed following chemotherapy exposure represents a metabolic vulnerability that can be exploited to enhance the efficacy of chemotherapy for the treatment of TNBC.Significance: The prognosis for patients with TNBC with residual disease after chemotherapy is poor. We find that chemotherapy agents induce adaptive reprogramming of de novo pyrimidine synthesis and show that this response can be exploited pharmacologically, using clinically approved inhibitors of de novo pyrimidine synthesis, to sensitize TNBC cells to chemotherapy. Cancer Discov; 7(4); 391-9. ©2017 AACR.See related article by Mathur et al., p. 380This article is highlighted in the In This Issue feature, p. 339.

  14. Substrate specificity of pyrimidine nucleoside phosphorylases of NP-II family probed by X-ray crystallography and molecular modeling

    Science.gov (United States)

    Balaev, V. V.; Lashkov, A. A.; Prokofev, I. I.; Gabdulkhakov, A. G.; Seregina, T. A.; Mironov, A. S.; Betzel, C.; Mikhailov, A. M.

    2016-09-01

    Pyrimidine nucleoside phosphorylases, which are widely used in the biotechnological production of nucleosides, have different substrate specificity for pyrimidine nucleosides. An interesting feature of these enzymes is that the three-dimensional structure of thymidine-specific nucleoside phosphorylase is similar to the structure of nonspecific pyrimidine nucleoside phosphorylase. The three-dimensional structures of thymidine phosphorylase from Salmonella typhimurium and nonspecific pyrimidine nucleoside phosphorylase from Bacillus subtilis in complexes with a sulfate anion were determined for the first time by X-ray crystallography. An analysis of the structural differences between these enzymes demonstrated that Lys108, which is involved in the phosphate binding in pyrimidine nucleoside phosphorylase, corresponds to Met111 in thymidine phosphorylases. This difference results in a decrease in the charge on one of the hydroxyl oxygens of the phosphate anion in thymidine phosphorylase and facilitates the catalysis through SN2 nucleophilic substitution. Based on the results of X-ray crystallography, the virtual screening was performed for identifying a potent inhibitor (anticancer agent) of nonspecific pyrimidine nucleoside phosphorylase, which does not bind to thymidine phosphorylase. The molecular dynamics simulation revealed the stable binding of the discovered compound—2-pyrimidin-2-yl-1H-imidazole-4-carboxylic acid—to the active site of pyrimidine nucleoside phosphorylase.

  15. Pyrimidine pool imbalance induced by BLM helicase deficiency contributes to genetic instability in Bloom syndrome.

    Science.gov (United States)

    Chabosseau, Pauline; Buhagiar-Labarchède, Géraldine; Onclercq-Delic, Rosine; Lambert, Sarah; Debatisse, Michelle; Brison, Olivier; Amor-Guéret, Mounira

    2011-06-28

    Defects in DNA replication are associated with genetic instability and cancer development, as illustrated in Bloom syndrome. Features of this syndrome include a slowdown in replication speed, defective fork reactivation and high rates of sister chromatid exchange, with a general predisposition to cancer. Bloom syndrome is caused by mutations in the BLM gene encoding a RecQ helicase. Here we report that BLM deficiency is associated with a strong cytidine deaminase defect, leading to pyrimidine pool disequilibrium. In BLM-deficient cells, pyrimidine pool normalization leads to reduction of sister chromatid exchange frequency and is sufficient for full restoration of replication fork velocity but not the fork restart defect, thus identifying the part of the Bloom syndrome phenotype because of pyrimidine pool imbalance. This study provides new insights into the molecular basis of control of replication speed and the genetic instability associated with Bloom syndrome. Nucleotide pool disequilibrium could be a general phenomenon in a large spectrum of precancerous and cancer cells.

  16. Thiolated pyrimidine nucleotides may interfere thiol groups concentrated at lipid rafts of HIV-1 infected cells.

    Science.gov (United States)

    Kanizsai, Szilvia; Ongrádi, Joseph; Aradi, János; Nagy, Károly

    2014-12-01

    Upon HIV infection, cells become activated and cell surface thiols are present in increased number. Earlier we demonstrated in vitro anti-HIV effect of thiolated pyrimidine nucleotide UD29, which interferes thiol function. To further analyse the redox processes required for HIV-1 entry and infection, toxicity assays were performed using HIV-1 infected monolayer HeLaCD4-LTR/ β-gal cells and suspension H9 T cells treated with several thiolated nucleotide derivatives of UD29. Selective cytotoxicity of thiolated pyrimidines on HIV-1 infected cells were observed. Results indicate that thiolated pyrimidine derivates may interfere with -SH (thiol) groups concentrated in lipid rafts of cell membrane and interacts HIV-1 infected (activated) cells resulting in a selective cytotoxicity of HIV-1 infected cells, and reducing HIV-1 entry.

  17. Nucleobases and Other Prebiotic Species from the UV Irradiation of Pyrimidine in Astrophysical Ices

    Science.gov (United States)

    Sandford, Scott; Materese, Christopher; Nuevo, Michel

    2012-01-01

    Nucleobases are aromatic N-heterocycles that constitute the informational subunits of DNA and RNA and are divided into two families: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites and their extraterrestrial origin confirmed by isotope measurement. Although no N-heterocycles have been individually identified in the ISM, the 6.2-micron interstellar emission feature seen towards many astronomical objects suggests a population of such molecules is likely present. We report on a study of the formation of pyrimidine-based molecules, including nucleobases and other species of prebiotic interest, from the ultraviolet (UV) irradiation of pyrimidine in low temperature ices containing H2O, NH3, C3OH, and CH4, to simulate the astrophysical conditions under which prebiotic species may be formed in the Solar System.

  18. Transport of pyrimidine nucleosides in cells of Escherichia coli K 12.

    Science.gov (United States)

    Mygind, B; Munch-Petersen

    1975-11-15

    1. The transport of pyrimidine mucleosides into cells of Escherichis coli has been investigated in mutant strains which cannot metabolize these nucleosides. Such cells transport and concentrate purimidine mucleosides several hindredfold. 2. The transport is inhibited by energy poisons and by sulfhydryl reagents. 3. Pyrimidine mucleosides compete mutually for transport. Adenosine is also a strong competitor while guanosine and inosine are weak competitors. 4. The rate of pyrimidine mucleoside transport is shown to be under control of the cytR and deoR gene products, which are also known to regulate the synthesis of nucleoside-catabolizing enzymes. The transport system is repressed by growth on glucose, as is the synthesis of the enzymes.

  19. Microwave assisted synthesis and antimicrobial activity of some novel pyrimidine derivatives

    Directory of Open Access Journals (Sweden)

    S. J. VAGHASIA

    2007-02-01

    Full Text Available The synthesis of thiazolo [5,4-d]pyrimidines can be achieved from different 5-thiazolidinones, 2-butyl-1H-imidazole-5-carbaldehyde and thiourea using microwave irradiation within 5 min. The structures of the products were supported by FTIR, PMR and mass spectral data. The in vitro antimicrobial activity of the synthesized thiazolo [5,4-d]pyrimidines 1a-j, having substituents at the 1- and 3-positions, were determined by the cup-plate method against several standard strains chosen to define the spectrum and potency of the new compounds. The antimicrobial activities of the thiazolo [5,4-d]pyrimidines 1a-j are compared with those of known chosen standard drugs, viz. ampicillin, chloramphenicol, ciprofloxacin, norfloxacin and griseofulvin.

  20. Synthesis and Antimicrobial Studies of Pyrimidine Pyrazole Heterocycles

    Directory of Open Access Journals (Sweden)

    Rakesh Kumar

    2014-01-01

    Full Text Available Prompted from the diversity of the wider use and being an integral part of genetic material, an effort was made to synthesize pyrimidine pyrazole derivatives of pharmaceutical interest by oxidative cyclization of chalcones with satisfactory yield and purity. A novel series of 1,3-dimethyl-6-hydroxy-2,4-dioxo-5-(1′-phenyl-3′-aryl-1H-pyrazol-5′-yl-1,2,3,4-tetrahydropyrimidines (5a–d and 1,3-diaryl-6-hydroxy-4-oxo-2-thioxo-5-(1′-phenyl-3′-aryl-1H-pyrazol-5′-yl-1,2,3,4-tetrahydropyrimidines (5e–l has been synthesized. The structures of these compounds were established on the basis of FT-IR, 1H NMR, 13C NMR, and mass spectral analysis. All the synthesized compounds were screened for their antimicrobial activity against bacteria and fungi. Among all the compounds, 5g was found to be the most active as its MIC was 31.25 µg/mL against S. aureus and B. cereus. The compounds 5h, 5c, and 5e also possess antibacterial activity with MIC values as 62.50, 125.00, and 500.00 µg/mL, respectively. The compounds 5c and 5j were found to have antifungal activity against Aspergillus spp. As antifungal drugs lag behind the antibacterial drugs, therefore we tried in vitro combination of these two compounds with standard antifungal drugs (polyene and azole against Aspergillus spp. The combination of ketoconazole with 5c and 5j showed synergy at 1 : 8 (6.25 : 50.00 µg/mL and 1 : 4 (25 : 100 µg/mL against A. fumigatus (ITCC 4517 and A. fumigatus (VPCI 190/96, respectively.

  1. Ethyl 6-methyl-2-sulfanyl-idene-4-[4-(trifluoro-meth-yl)phen-yl]-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate.

    Science.gov (United States)

    Nayak, Susanta K; Venugopala, K N; Govender, Thavendran; Kruger, Hendrik G; Maguire, Glenn E M; Row, T N Guru

    2011-07-01

    The title compound, C(15)H(15)F(3)N(2)O(2)S, adopts a conformation with an intra-molecular C-H⋯π inter-action. The dihedral angles between the planes of the 4-(trifluoro-meth-yl)phenyl and ester groups with the plane of the six-membered tetra-hydro-pyrimidine ring are 81.8 (1) and 16.0 (1)°, respectively. In the crystal structure, inter-molecular N-H⋯S hydrogen bonds link pairs of mol-ecules into dimers and N-H⋯O inter-actions generate hydrogen-bonded mol-ecular chains along the crystallographic a axis.

  2. Geometric Reid's recipe for dimer models

    CERN Document Server

    Bocklandt, Raf; Velez, Alexander Quintero

    2013-01-01

    Crepant resolutions of three-dimensional toric Gorenstein singularities are derived equivalent to noncommutative algebras arising from consistent dimer models. By choosing a special stability parameter and hence a distinguished crepant resolution $Y$, this derived equivalence generalises the Fourier-Mukai transform relating the $G$-Hilbert scheme and the skew group algebra $\\CC[x,y,z]\\ast G$ for a finite abelian subgroup of $\\SL(3,\\CC)$. We show that this equivalence sends the vertex simples to pure sheaves, except for the zero vertex which is mapped to the dualising complex of the compact exceptional locus. This generalises results of Cautis-Logvinenko and Cautis-Craw-Logvinenko to the dimer setting, though our approach is different in each case. We also describe some of these pure sheaves explicitly and compute the support of the remainder, providing a dimer model analogue of results from Logvinenko.

  3. Partition-DFT on the Water Dimer

    CERN Document Server

    Gómez, Sara; Restrepo, Albeiro; Wasserman, Adam

    2016-01-01

    As is well known, the ground-state symmetry group of the water dimer switches from its equilibrium $C_{s}$-character to $C_{2h}$-character as the distance between the two oxygen atoms of the dimer decreases below $R_{\\rm O-O}\\sim 2.5$ \\AA{}. For a range of $R_{\\rm O-O}$ between 1 and 5 \\AA{}, and for both symmetries, we apply Partition Density Functional Theory (PDFT) to find the unique monomer densities that sum to the correct dimer densities while minimizing the sum of the monomer energies. We calculate the work involved in deforming the isolated monomer densities and find that it is slightly larger for the $C_s$ geometry for all $R_{\\rm O-O}$. We discuss how the PDFT densities and the corresponding partition potentials support the orbital-interaction picture of hydrogen-bond formation.

  4. 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.)

  5. Kosterlitz Thouless Universality in Dimer Models

    CERN Document Server

    Chandrasekharan, S; Chandrasekharan, Shailesh; Strouthos, Costas G.

    2003-01-01

    Using the monomer-dimer representation of strongly coupled U(N) lattice gauge theories with staggered fermions, we study finite temperature chiral phase transitions in (2+1) dimensions. A new cluster algorithm allows us to compute monomer-monomer and dimer-dimer correlations at zero monomer density (chiral limit) accurately on large lattices. This makes it possible to show convincingly, for the first time, that these models undergo a finite temperature phase transition which belongs to the Kosterlitz-Thouless universality class. We find that this universality class is unaffected even in the large N limit. This shows that the mean field analysis often used in this limit breaks down in the critical region.

  6. Poly[tetrakis(selenocyanato-κNbis(methanol-κOtris(μ-pyrimidine-κ2N:N′dicobalt(II

    Directory of Open Access Journals (Sweden)

    Mario Wriedt

    2010-07-01

    Full Text Available In the title compound, [Co2(NCSe4(C4H4N23(CH3OH2]n, the CoII ion is coordinated by three N-bonded pyrimidine ligands, two N-bonded selenocyanate anions and one O-bonded methanol molecule in an octahedral coordination mode. The asymmetric unit consists of one CoII ion, one pyrimidine ligand, two selenocyanate anions and one methanol molecule in general positions as well as one pyrimidine ligand located around a twofold rotation axis. In the crystal structure, the pyrimidine ligands bridge [Co(CNSe2(CH3OH] units into zigzag-like chains, which are further connected by pyrimidine ligands into layers parallel to (010.

  7. Breakdown of the regulatory control of pyrimidine biosynthesis in human breast cancer cells.

    Science.gov (United States)

    Sigoillot, Frederic D; Sigoillot, Severine M; Guy, Hedeel I

    2004-04-20

    The activity of the de novo pyrimidine biosynthetic pathway in the MCF7 breast cancer cells was 4.4-fold higher than that in normal MCF10A breast cells. Moreover, while pyrimidine biosynthesis in MCF10A was tightly regulated, increasing as the culture matured and subsequently down-regulated in confluency, the biosynthetic rate in MCF7 cells remained elevated and invariant in all growth phases. The flux through the pathway is regulated by carbamoyl phosphate synthetase, a component of the multifunctional protein, CAD. The intracellular CAD concentration was 3.5- to 4-fold higher in MCF7 cells, an observation that explains the high rate of pyrimidine biosynthesis but cannot account for the lack of growth-dependent regulation. In MCF10A cells, up-regulation of the pathway in the exponential growth phase resulted from MAP kinase phosphorylation of CAD Thr456. The pathway was subsequently down-regulated by dephosphorylation of P approximately Thr456 and the phosphorylation of CAD by PKA. In contrast, the CAD P approximately Thr456 was persistently phosphorylated in MCF7 cells, while the PKA site remained unphosphorylated and consequently the activity of the pathway was elevated in all growth phases. In support of this interpretation, inhibition of MAP kinase in MCF7 cells decreased CAD P approximately Thr456, increased PKA phosphorylation and decreased pyrimidine biosynthesis. Conversely, transfection of MCF10A with constructs that elevated MAP kinase activity increased CAD P approximately Thr456 and the pyrimidine biosynthetic rate. The differences in the CAD phosphorylation state responsible for unregulated pyrimidine biosynthesis in MCF7 cells are likely to be a consequence of the elevated MAP kinase activity and the antagonism between MAP kinase- and PKA-mediated phosphorylations.

  8. Erwinia amylovora pyrC mutant causes fire blight despite pyrimidine auxotrophy.

    Science.gov (United States)

    Ramos, L S; Sinn, J P; Lehman, B L; Pfeufer, E E; Peter, K A; McNellis, T W

    2015-06-01

    Erwinia amylovora bacteria cause fire blight disease, which affects apple and pear production worldwide. The Erw. amylovora pyrC gene encodes a predicted dihydroorotase enzyme involved in pyrimidine biosynthesis. Here, we discovered that the Erw. amylovora pyrC244::Tn5 mutant was a uracil auxotroph. Unexpectedly, the Erw. amylovora pyrC244::Tn5 mutant grew as well as the wild-type in detached immature apple and pear fruits. Fire blight symptoms caused by the pyrC244::Tn5 mutant in immature apple and pear fruits were attenuated compared to those caused by the wild-type. The pyrC244::Tn5 mutant also caused severe fire blight symptoms in apple tree shoots. A plasmid-borne copy of the wild-type pyrC gene restored prototrophy and symptom induction in apple and pear fruit to the pyrC244::Tn5 mutant. These results suggest that Erw. amylovora can obtain sufficient pyrimidine from the host to support bacterial growth and fire blight disease development, although de novo pyrimidine synthesis by Erw. amylovora is required for full symptom development in fruits. Significance and impact of the study: This study provides information about the fire blight host-pathogen interaction. Although the Erwinia amylovora pyrC mutant was strictly auxotrophic for pyrimidine, it grew as well as the wild-type in immature pear and apple fruits and caused severe fire blight disease in apple trees. This suggests that Erw. amylovora can obtain sufficient pyrimidines from host tissue to support growth and fire blight disease development. This situation contrasts with findings in some human bacterial pathogens, which require de novo pyrimidine synthesis for growth in host blood, for example.

  9. 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.

  10. 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.

  11. Photon Propagation through Linearly Active Dimers

    Directory of Open Access Journals (Sweden)

    José Delfino Huerta Morales

    2017-06-01

    Full Text Available We provide an analytic propagator for non-Hermitian dimers showing linear gain or losses in the quantum regime. In particular, we focus on experimentally feasible realizations of the PT -symmetric dimer and provide their mean photon number and second order two-point correlation. We study the propagation of vacuum, single photon spatially-separable, and two-photon spatially-entangled states. We show that each configuration produces a particular signature that might signal their possible uses as photon switches, semi-classical intensity-tunable sources, or spatially entangled sources to mention a few possible applications.

  12. Refined conformal spectra in the dimer model

    CERN Document Server

    Rasmussen, Jorgen

    2012-01-01

    Working with Lieb's transfer matrix for the dimer model, we point out that the full set of dimer configurations may be partitioned into disjoint subsets (sectors) closed under the action of the transfer matrix. These sectors are labelled by an integer or half-integer quantum number we call the variation index. In the continuum scaling limit, each sector gives rise to a representation of the Virasoro algebra. We determine the corresponding conformal partition functions and their finitizations, and observe an intriguing link to the Ramond and Neveu-Schwarz sectors of the critical dense polymer model as described by a conformal field theory with central charge c=-2.

  13. The use of pyr-mutations to modify pyrimidine pools in Lactococci

    DEFF Research Database (Denmark)

    Hansen, Steen Lyders Lerche; Martinussen, Jan; Hammer, Karin

    1999-01-01

    . By combining the two described mutations, with a cdd mutation, we will be able to construct strains in which pyrimidine pools can be manipulated by adding different pyrimidine-sources at variable concentrations to the growth media. Since nucleotides are central metabolites, many physiological parameters may......The specific engineering of organisms used for startercultures has become an effective way of improving and developing new products in the dairy industry. In order to obtain strains with specific characteristics, it is imperative to have a good understanding of the central biochemical pathways...

  14. The use of Pyr-mutants to modify pyrimidine metabolism in lactococci

    DEFF Research Database (Denmark)

    Hansen, Steen Lyders Lerche; Martinussen, Jan; Hammer, Karin

    1998-01-01

    . By combining the two described mutations, with a cdd mutation, we will be able to construct strains in which pyrimidine pools can be manipulated by adding different pyrimidine-sources at variable concentrations to the growth media. Since nucleotides are central metabolites, many physiological parameters may......The specific engineering of organisms used for startercultures has become an effective way of improving and developing new products in the dairy industry. In order to obtain strains with specific characteristics, it is imperative to have a good understanding of the central biochemical pathways...

  15. Nucleobases and other Prebiotic Species from the Ultraviolet Irradiation of Pyrimidine in Astrophysical Ices

    Science.gov (United States)

    Sandford, S. A.; Nuevo, M.; Materese, C. K.; Milam, S. N.

    2012-01-01

    Nucleobases are N-heterocycles that are the informational subunits of DNA and RNA, and are divided into two families: pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in meteorites and their extraterrestrial origin confirmed by isotope measurement. Although no Nheterocycles have ever been observed in the ISM, the positions of the 6.2-m interstellar emission features suggest a population of such molecules is likely to be present. In this work we study the formation of pyrimidine-based molecules, including nucleobases, as well as other species of prebiotic interest, from the ultraviolet (UV) irradiation of pyrimidine in combinations of H2O, NH3, CH3OH, and CH4 ices at low temperature, in order to simulate the astrophysical conditions under which prebiotic species may be formed in the interstellar medium and icy bodies of the Solar System. Experimental: Gas mixtures are prepared in a glass mixing line (background pressure approx. 10(exp -6)-10(exp -5) mbar). Relative proportions between mixture components are determined by their partial pressures. Gas mixtures are then deposited on an aluminum foil attached to a cold finger (15-20 K) and simultaneously irradiated with an H2 lamp emitting UV photons (Lyman and a continuum at approx.160 nm). After irradiation samples are warmed to room temperature, at which time the remaining residues are recovered to be analyzed with liquid and gas chromatographies. Results: These experiments showed that the UV irradiation of pyrimidine mixed in these ices at low temperature leads to the formation of several photoproducts derived from pyrimidine, including the nucleobases uracil and cytosine, as well as their precursors 4(3H)-pyrimidone and 4-aminopyrimidine (Fig. 1). Theoretical quantum calculations on the formation of 4(3H)-pyrimidone and uracil from the irradiation of pyrimidine in pure H2O ices are in agreement with their experimental formation pathways. In

  16. Design,Synthesis,and Hypnotic Activity of Pyrazolo[1,5-a]pyrimidine Derivatives

    Institute of Scientific and Technical Information of China (English)

    Song Qing WANG; Lin FANG; Xiu Jie LIU; Kang ZHAO

    2004-01-01

    On the basis of the Zaleplon structure, novel pyrazolo[1,5-a]pyrimidines were designed and prepared for studies on their hypnotic activity.This paper reported the synthesis of twelve new 5-methyl-7-substituted-pyrazolo[1,5-a]pyrimidine-3-carbonitrile derivatives by using simple starting materials such as propane dinitrile and triethyl orthoformate.The structures of the derived target compounds were confirmed by their IR and 1H-NMR spectroscopic data.The preliminary pharmacological evaluations indicated that some compounds showed hypnotic activity, while derivative 1c was the most potent one.

  17. Heteroaryl ethers by oxidative palladium catalysis of pyridotriazol-1-yloxy pyrimidines with arylboronic acids.

    Science.gov (United States)

    Bardhan, Sujata; Wacharasindhu, Sumrit; Wan, Zhao-Kui; Mansour, Tarek S

    2009-06-18

    The oxidative palladium-catalyzed cross-coupling of pyrimidines containing pyridotriazol-1-yloxy (OPt) as either a urea or an amide functional group with arylboronic acids in the presence of Cs(2)CO(3) in DME containing 0.6-1.0% H(2)O is described for the preparation of heteroaryl ethers. The bromo substitution in the case of 3-(5-bromo-pyrimidin-2-yloxy)-3H-[1,2,3]triazolo[4,5-b]pyridine 1 could serve as a handle for further elaborations such as Suzuki coupling for attaching varied aryl groups.

  18. Design, synthesis and cytotoxic activity of some novel compounds containing pyrazolo[3,4-]pyrimidines nucleus

    Indian Academy of Sciences (India)

    Manal M Kandeel; Sameha M Roshdy; Eman K A Abdelall; Mohamed A Abdelgawad; Phoebe F Lamie

    2013-09-01

    Novel pyrazolo[3,4-]pyrimidines were designed and synthesized as antitumour agents against human breast cancer adenoma (MCF-7). Molecular modelling and pharmacological screening were performed against breast cancer cell line and also certain synthetic pathways were developed in order to introduce functionality onto C6 and N5 positions of pyrimidine moiety. Surprisingly, all the test compounds showed IC50 lower than that of the standard olomoucine I, especially compounds 4b, 8a, 10b, 11a and b, which showed IC50 between 0.009 and 0.004 M.

  19. A p-quinodimethane-bridged porphyrin dimer.

    Science.gov (United States)

    Zeng, Wangdong; Ishida, Masatoshi; Lee, Sangsu; Sung, Young Mo; Zeng, Zebing; Ni, Yong; Chi, Chunyan; Kim, Dongho; Wu, Jishan

    2013-12-01

    A p-quinodimethane (p-QDM)-bridged porphyrin dimer 1 has been prepared for the first time. An unexpected Michael addition reaction took place when we attempted to synthesize compound 1 by reaction of the cross-conjugated keto-linked porphyrin dimers 8a and 8b with alkynyl/aryl Grignard reagents. Alternatively, compound 1 could be successfully prepared by intramolecular Friedel-Crafts alkylation of the diol-linked porphyrin dimer 14 with concomitant oxidation in air. Compound 1 shows intense one-photon absorption (OPA, λ(max)=955 nm, ε=45400 M(-1) cm(-1)) and a large two-photon absorption (TPA) cross-section (σ((2))(max)=2080 GM at 1800 nm) in the near-infrared (NIR) region due to its extended π-conjugation and quinoidal character. It also exhibits a short singlet excited-state lifetime of 25 ps. The cyclic voltammogram of 1 displays multiple redox waves with a small electrochemical energy gap of 0.86 eV. The ground-state geometry, electronic structure, and optical properties of 1 have been further studied by density functional theory (DFT) calculations and compared with those of the keto-linked dimer 8b. This research has revealed that incorporation of a p-QDM unit into the porphyrin framework had a significant impact on its optical and electronic properties, leading to a novel NIR OPA and TPA chromophore.

  20. Geometric Reid's recipe for dimer models

    NARCIS (Netherlands)

    Bocklandt, R.; Craw, A.; Quintero Vélez, A.

    2015-01-01

    Crepant resolutions of three-dimensional toric Gorenstein singularities are derived equivalent to noncommutative algebras arising from consistent dimer models. By choosing a special stability parameter and hence a distinguished crepant resolution Y, this derived equivalence generalises the Fourier-M

  1. The Diamagnetic Susceptibility of the Tubulin Dimer

    Directory of Open Access Journals (Sweden)

    Wim Bras

    2014-01-01

    Full Text Available An approximate value of the diamagnetic anisotropy of the tubulin dimer, Δχdimer, has been determined assuming axial symmetry and that only the α-helices and β-sheets contribute to the anisotropy. Two approaches have been utilized: (a using the value for the Δχα for an α-helical peptide bond given by Pauling (1979 and (b using the previously determined anisotropy of fibrinogen as a calibration standard. The Δχdimer≈4×10-27 JT−2 obtained from these measurements are similar to within 20%. Although Cotton-Mouton measurements alone cannot be used to estimate Δχ directly, the value we measured, CMdimer=1.41±0.03×10-8 T−2cm2mg−1, is consistent with the above estimate for Δχdimer. The method utilized for the determination of the tubulin dimer diamagnetic susceptibility is applicable to other proteins and macromolecular assemblies as well.

  2. A new lignan dimer from Mallotus philippensis.

    Science.gov (United States)

    Mai, Nguyen Thi; Cuong, Nguyen Xuan; Thao, Nguyen Phuong; Nam, Nguyen Hoai; Khoi, Nguyen Huu; Minh, Chau Van; Heyden, Yvan Vander; Thuan, Ngo Thi; Tuyen, Nguyen Van; Quetin-Leclercq, Joëlle; Kiem, Phan Van

    2010-03-01

    A new lignan dimer, bilariciresinol (1), was isolated from the leaves of Mallotus philippensis, along with platanoside (2), isovitexin (3), dihydromyricetin (4), bergenin (5), 4-O-galloylbergenin (6), and pachysandiol A (7). Their structures were elucidated by spectroscopic experiments including 1D and 2D NMR and FTICR-MS.

  3. Synthesis of novel 15-membered macrolide dimers

    Institute of Scientific and Technical Information of China (English)

    Shu Tao Ma; Rui Xin Ma; Rui Qing Xian; Bo Jiao

    2009-01-01

    A series of novel dimers of 15-memhered macrolides was synthesized and evaluated. The directs exhibited excellent activity against erythromycin-susceptible S. pneumonia, but did not show any improved activity against erythromycin-resistant S. pneumoniae encoded by erm gene.

  4. Amplitude enhancement by a gold dimer

    Science.gov (United States)

    Hong, Xin; Wang, Jingxin; Jin, Zheng

    2016-10-01

    The unique optical properties such as brightness, non-bleaching, good bio-compatibility make gold particles ideal label candidates for molecular probes. Due to the strongly enhanced field, aggregation of gold nanoparticles finds themselves plenty of applications in bio-imaging. But limited by its small cross-section associated with nanometer sized particle, it is a big challenge to employ it in a single molecular detection. The field enhancement results from the effect of plasmonic coupling between two closely attached gold nanoparticle under the right excitation condition. With the aim to apply the gold dimer probe to find the molecules in our recently established optical detection method, we compared of the amplitude enhancement by the dimer relative to a single particle. The amplitude distribution under a highly focused illumination objective was calculated, whose results suggest that at the optimized excitation condition, the local field can be enhanced 190 fold. In consequence, experimental detection was carried out. Gold dimers were linked together by the hybridization of two single chain DNAs. Dimer and single particle probes were mixed together in one detection. Overwhelming contrast between these two kinds of probes were clearly exhibited in the experimental detection image. This method can provide a way to a high specific detection in early diagnosis.

  5. Structure of the nucleotide complex of PyrR, the pyr attenuation protein from Bacillus caldolyticus, suggests dual regulation by pyrimidine and purine nucleotides.

    Science.gov (United States)

    Chander, Preethi; Halbig, Kari M; Miller, Jamie K; Fields, Christopher J; Bonner, Heather K S; Grabner, Gail K; Switzer, Robert L; Smith, Janet L

    2005-03-01

    PyrR is a protein that regulates the expression of genes and operons of pyrimidine nucleotide biosynthesis (pyr genes) in many bacteria. PyrR acts by binding to specific sequences on pyr mRNA and causing transcriptional attenuation when intracellular levels of uridine nucleotides are elevated. PyrR from Bacillus subtilis has been purified and extensively studied. In this work, we describe the purification to homogeneity and characterization of recombinant PyrR from the thermophile Bacillus caldolyticus and the crystal structures of unliganded PyrR and a PyrR-nucleotide complex. The B. caldolyticus pyrR gene was previously shown to restore normal regulation of the B. subtilis pyr operon in a pyrR deletion mutant. Like B. subtilis PyrR, B. caldolyticus PyrR catalyzes the uracil phosphoribosyltransferase reaction but with maximal activity at 60 degrees C. Crystal structures of B. caldolyticus PyrR reveal a dimer similar to the B. subtilis PyrR dimer and, for the first time, binding sites for nucleotides. UMP and GMP, accompanied by Mg2+, bind specifically to PyrR active sites. Nucleotide binding to PyrR is similar to other phosphoribosyltransferases, but Mg2+ binding differs. GMP binding was unexpected. The protein bound specific sequences of pyr RNA 100 to 1,000 times more tightly than B. subtilis PyrR, depending on the RNA tested and the assay method; uridine nucleotides enhanced RNA binding, but guanosine nucleotides antagonized it. The new findings of specific GMP binding and its antagonism of RNA binding suggest cross-regulation of the pyr operon by purines.

  6. The Renaissance of Metal-Pyrimidine Nucleobase Coordination Chemistry.

    Science.gov (United States)

    Lippert, Bernhard; Sanz Miguel, Pablo J

    2016-08-16

    The significance of metal ions for the function and properties of DNA and RNA, long seen primarily under biological aspects and medicinal uses, has recently gained a renewed momentum. This is a consequence of the advent of novel applications in the fields of materials science, biotechnology, and analytical sensor chemistry that relate to the designed incorporation of transition metal ions into nucleic acid base pairs. Ag(+) and Hg(2+) ions, binding to pyrimidine (pym) nucleobases, represent major players in this development. Interestingly, these metal ions were the ones that some 60 years ago started the field! At the same time, the mentioned metal ions had demonstrated a "special relationship" with the pym nucleobases cytosine, thymine, and uracil! Parallel work conducted with oligonucleotides and model nucleobases fostered numerous significant details of these interactions, in particular when X-ray crystallography was involved, correcting earlier views occasionally. Our own activities during the past three to four decades have focused on, among others, the coordination chemistry of transition and main-group metal ions with pym model nucleobases, with an emphasis on Pt(II) and Pd(II). It has always been our goal to deduce, if possible, the potential relevance of our findings for biological processes. It is interesting to put our data, in particular for trans-a2Pt(II) (a = NH3 or amine), into perspective with those of other metal ions, notably Ag(+) and Hg(2+). Irrespective of major differences in kinetics and lability/inertness between d(8) and d(10) metal ions, there is also a lot of similarity in structural aspects as a result of the preferred linear coordination geometry of these species. Moreover, the apparent clustering of metal ions to the pym nucleobases, which is presumably essential for the formation of nanoclusters on oligonucleotide scaffolds, is impressively reflected in model systems, as are reasons for inter-nucleobase cross-links containing more

  7. 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.

  8. rac-(4R,17S,18R,26R-Ethyl 4′-methoxycarbonyl-5′′-(4-methoxyphenyl-1′-methyl-2,3′′-dioxo-2′′,3′′-dihydroindoline-3-spiro-2′-pyrrolidine-3′-spiro-2′′-thiazolo[3,2-a]pyrimidine-6′′-carboxylate

    Directory of Open Access Journals (Sweden)

    Xiao-Fang Li

    2009-02-01

    Full Text Available In the title compound, C30H30N4O7S, the two spiro junctions link a planar 2-oxindole ring [with a mean deviation from the plane of 0.0319 (3 Å, a pyrrolidine ring in an envelope conformation and a thiazolo[3,2-a]pyrimidine system. Two molecules are connected into a dimer by two N—H...O hydrogen bonds, forming an R22(8 graph-set motif. The title compound has four stereogenic centers and appears as a racemic mixture of one single diastereoisomer (RSRR/SRSS.

  9. The Photochemistry of Pyrimidine in Pure H2O Ice Subjected to Different Radiation Environments and the Formation of Uracil

    Science.gov (United States)

    Nuevo, M.; Chen, Y.-J.; Materese. C. K..; Hu, W.-J.; Qiu, J.-M.; Wu, S.-R.; Fung, H.-S.; Sandford, S. A.; Chu, C.-C.; Yih, T.-S.; Wu, R.; Ip, W.-H.

    2013-01-01

    Nucleobases are N-heterocycles which are the informational subunits of DNA and RNA. They include pyrimidine bases (uracil, cytosine, and thymine) and purine bases (adenine and guanine). Nucleobases have been detected in several meteorites, although no Nheterocycles have been observed in space to data. Laboratory experiments showed that the ultraviolet (UV) irradiation of pyrimidine in pure H2O ice at low temperature (<=20 K) leads to the formation of pyrimidine derivatives including the nucleobase uracil and its precursor 4(3H)-pyrimidone. These results were confirmed by quantum chemical calculations. When pyrimidine is mixed with combinations of H2O, NH3, CH3OH, and CH4 ices under similar conditions, uracil and cytosine are formed. In the present work we study the formation of 4(3H)-pyrimidone and uracil from the irradiation of pyrimidine in H2O ice with high-energy UV photons (Lyman , He I, and He II lines) provided by a synchrotron source. The photo-destruction of pyrimidine in these H2O ices as well as the formation yields for 4(3H)-pyrimidone and uracil are compared with our previous results in order to study the photo-stability of pyrimidine and the production efficiency of uracil as a function of the photon energy.

  10. Novel inhibitors of Mycobacterium tuberculosis growth based on modified pyrimidine nucleosides and their analogues

    Science.gov (United States)

    Shmalenyuk, E. R.; Kochetkov, S. N.; Alexandrova, L. A.

    2013-09-01

    The review summarizes data on the synthesis and antituberculosis activity of pyrimidine nucleoside derivatives and their analogues. Enzymes from M. tuberculosis as promising targets for prototypes of new-generation drugs are considered. Nucleosides as inhibitors of drug-resistant M. tuberculosis strains are characterized. The bibliography includes 101 references.

  11. Synthesis and anti-inflammatory activity of imidazo [1,2-a] pyrimidine derivatives

    Institute of Scientific and Technical Information of China (English)

    Jin Pei Zhou; Yi Wei Ding; Hui Bin Zhang; Lian Xu; Yue Dai

    2008-01-01

    A series of imidazo [1,2-a] pyrimidine derivatives substituted adjacently with two aryls at positions 2 and 3 were designed and synthesized in order to improve their anti-inflammatory activities. Biological tests suggested that these compounds have antiinflammatory activities with COX-2 selectivity to some extent.

  12. Ring transformations in reactions of pyrimidine and N-alkyl-pyridinium salts with nucleophiles

    NARCIS (Netherlands)

    Oostveen, E.A.

    1977-01-01

    Paper IOn treatment with liquid ammonia at -33°C, the quaternary pyrimidinium salts, i.e. 1-methylpyrimidinium methyl sulfate, 1,2-dimethylpyrimidinium iodide, 1,4,6-trimethyl-pyrimidinium iodide and 1,2,4,6-tetramethylpyrimidinium iodide demethylate yielding pyrimidine. 2-methyl-, 4,6-dimethyl- and

  13. Blockage of the pyrimidine biosynthetic pathway affects riboflavin production in Ashbya gossypii.

    Science.gov (United States)

    Silva, Rui; Aguiar, Tatiana Q; Domingues, Lucília

    2015-01-10

    The Ashbya gossypii riboflavin biosynthetic pathway and its connection with the purine pathway have been well studied. However, the outcome of genetic alterations in the pyrimidine pathway on riboflavin production by A. gossypii had not yet been assessed. Here, we report that the blockage of the de novo pyrimidine biosynthetic pathway in the recently generated A. gossypii Agura3 uridine/uracil auxotrophic strain led to improved riboflavin production on standard agar-solidified complex medium. When extra uridine/uracil was supplied, the production of riboflavin by this auxotroph was repressed. High concentrations of uracil hampered this (and the parent) strain growth, whereas excess uridine favored the A. gossypii Agura3 growth. Considering that the riboflavin and the pyrimidine pathways share the same precursors and that riboflavin overproduction may be triggered by nutritional stress, we suggest that overproduction of riboflavin by the A. gossypii Agura3 may occur as an outcome of a nutritional stress response and/or of an increased availability in precursors for riboflavin biosynthesis, due to their reduced consumption by the pyrimidine pathway.

  14. Quantifying the effects of halogen bonding by haloaromatic donors on the acceptor pyrimidine.

    Science.gov (United States)

    Ellington, Thomas L; Reves, Peyton L; Simms, Briana L; Wilson, Jamey L; Watkins, Davita L; Tschumper, Gregory S; Hammer, Nathan I

    2017-02-28

    The effects of intermolecular interactions by a series of haloaromatic halogen bond donors on the normal modes and chemical shifts of the acceptor pyrimidine are investigated by Raman and NMR spectroscopies and electronic structure computations. Halogen bond interactions with pyrimidine's nitrogen atoms shift normal modes to higher energy and shift 1H and 13C NMR peaks upfield in adjacent nuclei. This perturbation of vibrational normal modes is reminiscent of the effects of hydrogen bonded networks of water, methanol, or silver on pyrimidine. The unexpected observation of vibrational red shifts and downfield 13C NMR shifts in some complexes suggests that other intermolecular forces such as pi-interactions are competing with halogen bonding. Natural bond orbital analyses indicate a wide range of charge transfer from pyrimidine to different haloaromatic donors is possible and computed halogen bond binding energies can be larger than a typical hydrogen bond. These results emphasize the importance in strategic selection of substituents and electron withdrawing groups in developing supramolecular structures based on halogen bonding.

  15. beta-Ureidopropionase deficiency: an inborn error of pyrimidine degradation associated with neurological abnormalities.

    NARCIS (Netherlands)

    Kuilenburg, A.B.P. van; Meinsma, R.; Beke, E.; Assmann, B.; Ribes, A.; Lorente, I.; Busch, R.; Mayatepek, E.; Abeling, N.G.G.M.; Cruchten, A.C. van; Stroomer, A.E.; Lenthe, H. van; Zoetekouw, L.; Kulik, W.; Hoffmann, G.F.; Voit, T.; Wevers, R.A.; Rutsch, F.; Gennip, A.H. van

    2004-01-01

    beta-Ureidopropionase deficiency is an inborn error of the pyrimidine degradation pathway, affecting the cleavage of N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyric acid. In this study, we report the elucidation of the genetic basis underlying a beta-ureidopropionase deficiency in four p

  16. Rapid and efficient synthesis of fused heterocyclic pyrimidines under ultrasonic irradiation.

    Science.gov (United States)

    Mosslemin, Mohammad Hossein; Nateghi, Mohammad Reza

    2010-01-01

    Some fused heterocyclic pyrimidines have been synthesized in high yields using ultrasound irradiation in a one-pot, three-component and efficient process by condensation reaction of barbituric acids, aldehydes and a series of enamines in water. Prominent among the advantages of this new method are operational simplicity, good yields in short reaction times and easy work-up procedures employed.

  17. Formation of Nucleobases from the UV Irradiation of Pyrimidine in Astrophysical Ice Analogs

    Science.gov (United States)

    Sandford, Scott A.; Nuevo, Michel; Materese, Christopher K.

    2014-01-01

    Nucleobases are the informational subunits of DNA and RNA. They consist of Nheterocycles that belong to either the pyrimidine-base group (uracil, cytosine, and thymine) or the purinebase group (adenine and guanine). Several nucleobases, mostly purine bases, have been detected in meteorites [1-3], with isotopic signatures consistent with an extraterrestrial origin [4]. Uracil is the only pyrimidine-base compound formally reported in meteorites [2], though the presence of cytosine cannot be ruled out [5,6]. However, the actual process by which the uracil was made and the reasons for the non-detection of thymine in meteorites have yet to be fully explained. Although no N-heterocycles have ever been observed in the ISM [7,8], the positions of the 6.2-µm interstellar emission features suggest a population of such molecules is likely to be present [9]. In this work we study the formation of pyrimidine-based molecules, including the three nucleobases uracil, cytosine, and thymine from the ultraviolet (UV) irradiation of pyrimidine in ices consisting of several combinations of H(sub2)O, NH(sub3), CH(sub3)OH, and CH(sub4) at low temperature, in order to simulate the astrophysical conditions under which prebiotic species may be formed in the interstellar medium, in the protosolar nebula, and on icy bodies of the Solar System.

  18. The pyrimidine nucleotide biosynthetic pathway modulates production of biofilm determinants in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Marco Garavaglia

    Full Text Available Bacteria are often found in multicellular communities known as biofilms, which constitute a resistance form against environmental stresses. Extracellular adhesion and cell aggregation factors, responsible for bacterial biofilm formation and maintenance, are tightly regulated in response to physiological and environmental cues. We show that, in Escherichia coli, inactivation of genes belonging to the de novo uridine monophosphate (UMP biosynthetic pathway impairs production of curli fibers and cellulose, important components of the bacterial biofilm matrix, by inhibiting transcription of the csgDEFG operon, thus preventing production of the biofilm master regulator CsgD protein. Supplementing growth media with exogenous uracil, which can be converted to UMP through the pyrimidine nucleotide salvage pathway, restores csgDEFG transcription and curli production. In addition, however, exogenous uracil triggers cellulose production, particularly in strains defective in either carB or pyrB genes, which encode enzymes catalyzing the first steps of de novo UMP biosynthesis. Our results indicate the existence of tight and complex links between pyrimidine metabolism and curli/cellulose production: transcription of the csgDEFG operon responds to pyrimidine nucleotide availability, while cellulose production is triggered by exogenous uracil in the absence of active de novo UMP biosynthesis. We speculate that perturbations in the UMP biosynthetic pathways allow the bacterial cell to sense signals such as starvation, nucleic acids degradation, and availability of exogenous pyrimidines, and to adapt the production of the extracellular matrix to the changing environmental conditions.

  19. Inhibition of pyrimidine biosynthesis pathway suppresses viral growth through innate immunity.

    Directory of Open Access Journals (Sweden)

    Marianne Lucas-Hourani

    Full Text Available Searching for stimulators of the innate antiviral response is an appealing approach to develop novel therapeutics against viral infections. Here, we established a cell-based reporter assay to identify compounds stimulating expression of interferon-inducible antiviral genes. DD264 was selected out of 41,353 compounds for both its immuno-stimulatory and antiviral properties. While searching for its mode of action, we identified DD264 as an inhibitor of pyrimidine biosynthesis pathway. This metabolic pathway was recently identified as a prime target of broad-spectrum antiviral molecules, but our data unraveled a yet unsuspected link with innate immunity. Indeed, we showed that DD264 or brequinar, a well-known inhibitor of pyrimidine biosynthesis pathway, both enhanced the expression of antiviral genes in human cells. Furthermore, antiviral activity of DD264 or brequinar was found strictly dependent on cellular gene transcription, nuclear export machinery, and required IRF1 transcription factor. In conclusion, the antiviral property of pyrimidine biosynthesis inhibitors is not a direct consequence of pyrimidine deprivation on the virus machinery, but rather involves the induction of cellular immune response.

  20. An efficient and green preparation of 5-aminophosphonate substituted pyrimidine nucleosides under solvent-free conditions

    Institute of Scientific and Technical Information of China (English)

    Xin Ying Zhang; Ying Ying Qu; Xue Sen Fan

    2010-01-01

    An environmentally benign and highly efficient one-pot preparation of α-aminophosphonates under solvent-free conditions was developed.By employing this method,5-aminophosphonate substituted pyrimidine nucleosides were synthesized in good to excellent yields starting from 5-formyl-2'-deoxyuridine,aniline and dimethylphosphite.

  1. An Efficient and Facile Methodology for Bromination of Pyrimidine and Purine Nucleosides with Sodium Monobromoisocyanurate (SMBI

    Directory of Open Access Journals (Sweden)

    Roger Stromberg

    2013-10-01

    Full Text Available An efficient and facile strategy has been developed for bromination of nucleosides using sodium monobromoisocyanurate (SMBI. Our methodology demonstrates bromination at the C-5 position of pyrimidine nucleosides and the C-8 position of purine nucleosides. Unprotected and also several protected nucleosides were brominated in moderate to high yields following this procedure.

  2. Antimicrobial activity of new 4,6-disubstituted pyrimidine, pyrazoline, and pyran derivatives.

    Science.gov (United States)

    Ramiz, Mahmoud M M; El-Sayed, Wael A; El-Tantawy, Asmaa I; Abdel-Rahman, Adel A-H

    2010-05-01

    A number of new 2,6-didisubstituted pyrimidine, pyrazoline, and pyran derivatives were synthesized starting from their chalcone derivative. The synthesized compounds displayed different degrees of antimicrobial activity against Bscillus subtilis (Gram-positive), Pseudomonas aeruginosa (Gram-negative), and Streptomyces species (Actinomycetes).

  3. Tumour radiosensitization with the halogenated pyrimidines 5'-bromo-and 5'-iododeoxyuridine

    Energy Technology Data Exchange (ETDEWEB)

    Epstein, A.H.; Cook, J.A.; Goffman, T. (National Cancer Inst., Bethesda, MD (United States)); Glatstein, E. (Texas Univ., Dallas, TX (United States). Southwestern Medical Center)

    1993-02-01

    The authors review studies of the use of iododeoxyuridine (IdUrd) and bromodeoxyuridine as radiosensitizers and attempt to correlate the clinical outcome for patients treated with radiation and IdUrd with the extent of halogenated pyrimidine cellular uptake and incorporation. (U.K.).

  4. A second pathway to degrade pyrimidine nucleic acid precursors in eukaryotes

    DEFF Research Database (Denmark)

    Andersen, Gorm; Bjornberg, Olof; Polakova, Silvia;

    2008-01-01

    Pyrimidine bases are the central precursors for RNA and DNA, and their intracellular pools are determined by de novo, salvage and catabolic pathways. In eukaryotes, degradation of uracil has been believed to proceed only via the reduction to dihydrouracil. Using a yeast model, Saccharomyces kluyv...

  5. Inwerking van stikstofhoudende nucleofielen op enige 15N-gemerkte pyrimidine- en chinazolinederivaten

    NARCIS (Netherlands)

    Kroon, A.P.

    1974-01-01

    In this thesis an investigation is described on the mechanism of aminations of pyrimidine- and quinazoline derivatives with nitrogen containing bases.In the introduction a survey is given of investigations, reported in the literature, concerning σ-complex formation on azahetarenes and their derivati

  6. 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.

  7. A Nove Asymmetric ent—Kauranoid Dimer from Isodon enanderianus

    Institute of Scientific and Technical Information of China (English)

    纳智; 黎胜红; 等

    2002-01-01

    Further investigation on the aerial parts of Isodon enanderianus afforded a novel asymmetric ent-kauranoid dimer,enanderi-nanin J(1).The structure of the dimer was elucidated by means of spectroscopic methods (including 2D NMR tecniques ),Enanderinanin J was a dimer of xerophilusin A and probably formed by [4+2] cycloaddition.

  8. A Novel Asymmetric ent-Kauranoid Dimer from Isodon enanderianus

    Institute of Scientific and Technical Information of China (English)

    NA,Zhi(纳智); LI,Sheng-Hong(黎胜红); XIANG,Wei(项伟); ZHAO,Ai-Hua(赵爱华); LI,Chao-Ming(李朝明); SUN,Han-Dong(孙汉董)

    2002-01-01

    Further investigation on the aerial parts of Isodon enanderianus afforded a novel asymmetric ent-kauranoid dimer, enanuderinaninJ (1). The structure of the dimer was elucidated by means of spectroscopic methods (including 2D NMR techniques ). Enanderinanin J was a dimer of xerophilusin A and probably formed by [ 4 + 2] cycloaddition.

  9. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair.

    Science.gov (United States)

    Du, Fengxia; Zhang, Minjie; Li, Xiaohua; Yang, Caiyun; Meng, Hao; Wang, Dong; Chang, Shuang; Xu, Ye; Price, Brendan; Sun, Yingli

    2014-10-03

    The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

  10. The reaction of the acrylonitrile ion CH 2dbnd CH-C tbnd N rad + with HCN: Proton-transport catalysis vs formation of ionized pyrimidine

    Science.gov (United States)

    Ervasti, Henri K.; Jobst, Karl J.; Gerbaux, Pascal; Burgers, Peter C.; Ruttink, Paul J. A.; Terlouw, Johan K.

    2009-11-01

    The CBS-QB3 model chemistry predicts that the title ion-molecule reaction, of potential interest in astrochemistry, yields a stable head-to-tail dimer, [HC dbnd N-CH 2C(H)C tbnd N] rad + ( D1). Cyclization of D1 into ionized pyrimidine seems possible, but the initiating 1,2-H shift is close in energy to back-dissociation into CH 2dbnd C(H)CN rad + ( AN) + HCN. Less energy demanding is formation of the H-bridged isomers [CH 2dbnd C(CN)H--N tbnd CH] rad + and [HC tbnd N--HC(H) dbnd C(H)CN] rad +, whose HCN component may catalyze isomerization of AN into CH 2dbnd C dbnd C dbnd NH rad + ( AN1) and CH dbnd C(H)C dbnd NH rad + ( AN2) respectively. Tandem mass spectrometry based experiments using 15N/ 13C labelling show that cyclization of D1 does not occur and that AN1 is the predominant reaction product instead.

  11. Cyclic M2(RL)2 coordination complexes of 5-(3-[N-tert-Butyl-N-aminoxyl]phenyl)pyrimidine with paramagnetic transition metal dications.

    Science.gov (United States)

    Baskett, Martha; Lahti, Paul M; Paduan-Filho, Armando; Oliveira, Nei F

    2005-09-19

    5-(3-(N-tert-Butyl-N-aminoxyl)phenyl)pyrimidine (RL = 3NITPhPyrim) forms isostructural cyclic M2(RL)2 cyclic dimers with M(hfac)2 (M = Mn, Co, Cu; hfac = hexafluoroacetylacetonate). Mn2(hfac)4(RL)2 exhibits strong antiferromagnetic Mn-RL exchange, with weak ferromagnetic exchange (0.7 cm(-1)) between Mn-RL units that is consistent with a spin polarization exchange mechanism. The magnetic moment of Co2(hfac)4(RL)2 at higher temperatures is consistent with strongly antiferromagnetic exchange within the Co-NIT units and tends toward zero below 50 K at lower magnetic fields. Cu2(hfac)4(RL)2 shows more complex behavior, with no high-temperature plateau in chiT(T) up to 300 K but a monotonic decrease down to about 100 K. The Cu(II)-nitroxide bonds decrease by 0.2-0.3 A over the same temperature range, corresponding to a change of nitroxide coordination from axial to equatorial. This thermally reversible Jahn-Teller distortion leads to a thermally induced spin state conversion from a high-spin, paramagnetic state at higher temperature to a low-spin state at lower temperature. This spin state conversion is accompanied by a reversible solid-state thermochromic change between dull yellow-brown at room temperature and green at 77 K.

  12. The enzymology of cytosolic pyrimidine 5'-nucleotidases: functional analysis and physiopathological implications.

    Science.gov (United States)

    Magni, Giulio; Amici, Adolfo; Orsomando, Giuseppe

    2013-01-01

    In mammals, cellular 5'-nucleotidase (5'-NT) activity (EC 3.1.3.5) encompasses a number of genetically and structurally distinct enzyme forms, either membrane-bound or soluble, mainly cytosolic, that are characterized by broad specificity towards nucleoside 5'-monophosphate substrates differing in base (purine/pyrimidine) and/or sugar (oxy/deoxy-ribose) moieties. In particular, among the cytosolic 5'-NTs active towards pyrimidine nucleotides are cN-III and cdN, ubiquitously distributed in mammalian tissues and treated as a single entity in the early days. cN-III was first linked to a genetic defect , hereditary pyrimidine nucleotidase deficiency, associated to a nonspherocyt ic hemolytic anemia disorder of still unclear mechanism but metabolically characterized by abnormally high levels of pyrimidine compounds and ribonucleoproteins in erythrocytes, as evidenced by occurrence of basophilic stippling on blood smearings. Since the first review on pyrimidine-specific nucleotidases (Amici, A.; Magni, G., Arch. Biochem. Biophys., 2002, 397(2), 184- 190), excellent overviews on the topic appeared in the literature. In the present contribution, the major findings on these two enzymatic proteins, cN-III and cdN, will be described with particular emphasis on the relationships between their structure and function, as well as on their roles in normal and pathological conditions. The catalytic mechanism of both specific hydrolytic and phosphotransferase activities, possessed by both enzymes, will be discussed also in the light of recent solution of both cN-III and cdN three-dimensional structures. This review also focuses on possible therapeutic approaches involving cellular 5'-NTs in detoxifying common antiviral and antineoplastic drugs.

  13. Medicinal attributes of pyrazolo[1,5-a]pyrimidine based scaffold derivatives targeting kinases as anticancer agents

    Directory of Open Access Journals (Sweden)

    Nasser S.M. Ismail

    2016-12-01

    Full Text Available Pyrazolo pyrimidines are fused heterocyclic ring systems which known as bioisosteres of adenine, that are necessary for every aspect of cell life. Pyrazolo[1,5-a]pyrimidines derivatives have been explored for their inhibitory activity towards a variety of protein kinase enzymes and their function as anticancer agents. This review to the best of our knowledge is the first assemblage on synthesis and medicinal aspects including structure activity relationships of pyrazolo[1,5-a]pyrimidines reported to date.

  14. Construction of a ferritin dimer by breaking its symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, B; Uenuma, M; Uraoka, Y; Yamashita, I [Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192 (Japan); CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan)

    2010-11-05

    Ferritin has a mono-dispersed structure and biomineralization properties that allow it to form various kinds of nanoparticles and play an important role in modern nanotechnology. Independent nanoparticles synthesized in ferritin are valuable, but moreover a pair of nanoparticles can bring new properties different from those of the independent nanoparticles. In this study, by breaking ferritin's symmetry, we successfully produced ferritin dimers which provide real protein frameworks for nanoparticle dimer formation. Identical nickel hydro-oxide nanoparticle dimers were produced by simply biomineralizing ferritin dimers. The method presented here can produce multi-functional ferritin dimers with different kinds of nanoparticles.

  15. 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......Introduction. D-dimer levels increase throughout pregnancy, hampering the usefulness of the conventional threshold for dismissing thromboembolism. This study investigates the biological fluctuation of D-dimer in normal pregnancy. Methods. A total of 801 healthy women with expected normal...... normal pregnancy, repeated D-dimer measurements are of no clinical use in the evaluation of thromboembolic events during pregnancy....

  16. 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.

  17. Calcium-dependent Dimerization of Human Soluble Calcium Activated Nucleotidase: Characterization of the Dimer Interface

    Energy Technology Data Exchange (ETDEWEB)

    Yang,M.; Horii, K.; Herr, A.; Kirley, T.

    2006-01-01

    Mammals express a protein homologous to soluble nucleotidases used by blood-sucking insects to inhibit host blood clotting. These vertebrate nucleotidases may play a role in protein glycosylation. The activity of this enzyme family is strictly dependent on calcium, which induces a conformational change in the secreted, soluble human nucleotidase. The crystal structure of this human enzyme was recently solved; however, the mechanism of calcium activation and the basis for the calcium-induced changes remain unclear. In this study, using analytical ultracentrifugation and chemical cross-linking, we show that calcium or strontium induce noncovalent dimerization of the soluble human enzyme. The location and nature of the dimer interface was elucidated using a combination of site-directed mutagenesis and chemical cross-linking, coupled with crystallographic analyses. Replacement of Ile{sup 170}, Ser{sup 172}, and Ser{sup 226} with cysteine residues resulted in calcium-dependent, sulfhydryl-specific intermolecular cross-linking, which was not observed after cysteine introduction at other surface locations. Analysis of a super-active mutant, E130Y, revealed that this mutant dimerized more readily than the wild-type enzyme. The crystal structure of the E130Y mutant revealed that the mutated residue is found in the dimer interface. In addition, expression of the full-length nucleotidase revealed that this membrane-bound form can also dimerize and that these dimers are stabilized by spontaneous oxidative cross-linking of Cys{sup 30}, located between the single transmembrane helix and the start of the soluble sequence. Thus, calcium-mediated dimerization may also represent a mechanism for regulation of the activity of this nucleotidase in the physiological setting of the endoplasmic reticulum or Golgi.

  18. 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.

  19. 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.

  20. 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.

  1. Immunoglobulin Free Light Chain Dimers in Human Diseases

    Directory of Open Access Journals (Sweden)

    Batia Kaplan

    2011-01-01

    Full Text Available Immunoglobulin free light chain (FLC kappa (κ and lambda (λ isotypes exist mainly in monomeric and dimeric forms. Under pathological conditions, the level of FLCs as well as the structure of monomeric and dimeric FLCs and their dimerization properties might be significantly altered. The abnormally high fractions of dimeric FLCs were demonstrated in the serum of patients with multiple myeloma (MM and primary systemic amyloidosis (AL, as well as in the serum of anephric patients. The presence of tetra- and trimolecular complexes formed due to dimer-dimer and dimer-monomer interactions was detected in the myeloma serum. Analysis of the amyloidogenic light chains demonstrated mutations within the dimer interface, thus raising the possibility that these mutations are responsible for amyloidogenicity. Increased κ monomer and dimer levels, as well as a high κ/λ monomer ratio, were typically found in the cerebrospinal fluid from patients with multiple sclerosis (MS. In many MS cases, the elevation of κ FLCs was accompanied by an abnormally high proportion of λ dimers. This review focuses on the disease-related changes of the structure and level of dimeric FLCs, and raises the questions regarding their formation, function, and role in the pathogenesis and diagnosis of human diseases.

  2. Entanglement and decoherence in a quantum dimer

    Institute of Scientific and Technical Information of China (English)

    Hou Xi-Wen; Hui Zi; Ding Rui-Min; Chen Xiao-Yang; Gao Yu

    2006-01-01

    The dynamical properties of quantum entanglement in an integrable quantum dimer are studied in terms of the reduced-density linear entropy with various coupling parameters and total boson numbers. The characteristic time of decoherence process in the early-time evolution of the linear entropy is obtained, indicating that the characteristic time and the corresponding entropy exhibit a maximum near the position of the corresponding classical separatrix energy.

  3. Path integrals for dimerized quantum spin systems

    Energy Technology Data Exchange (ETDEWEB)

    Foussats, Adriana, E-mail: afoussats@gmail.co [Facultad de Ciencias Exactas, Ingenieria y Agrimensura and Instituto de Fisica Rosario (UNR-CONICET), Av. Pellegrini 250, 2000 Rosario (Argentina); Greco, Andres [Facultad de Ciencias Exactas, Ingenieria y Agrimensura and Instituto de Fisica Rosario (UNR-CONICET), Av. Pellegrini 250, 2000 Rosario (Argentina); Muramatsu, Alejandro [Institut fuer Theoretische Physik III, Universitaet Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart (Germany)

    2011-01-11

    Dimerized quantum spin systems may appear under several circumstances, e.g. by a modulation of the antiferromagnetic exchange coupling in space, or in frustrated quantum antiferromagnets. In general, such systems display a quantum phase transition to a Neel state as a function of a suitable coupling constant. We present here two path-integral formulations appropriate for spin S=1/2 dimerized systems. The first one deals with a description of the dimers degrees of freedom in an SO(4) manifold, while the second one provides a path-integral for the bond-operators introduced by Sachdev and Bhatt. The path-integral quantization is performed using the Faddeev-Jackiw symplectic formalism for constrained systems, such that the measures and constraints that result from the algebra of the operators is provided in both cases. As an example we consider a spin-Peierls chain, and show how to arrive at the corresponding field-theory, starting with both an SO(4) formulation and bond-operators.

  4. Powerful methods to establish chromosomal markers in Lactococcus lactis: an analysis of pyrimidine salvage pathway mutants obtained by positive selections

    DEFF Research Database (Denmark)

    Martinussen, Jan; Hammer, Karin

    1995-01-01

    phosphoribosyltransferase (upp), uridindcytidine kinase (udk), pyrimidine nucleoside phosphorylase (pdp), cytidine/deoxycytidine deaminase (dd), thymidine kinase (tdk) and purine nucleoride phosphorylase (pup). Based on an analysis of the mutants obtained, the pathways by which L. lactis metabolizes uracil...

  5. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair

    Energy Technology Data Exchange (ETDEWEB)

    Du, Fengxia [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); Zhang, Minjie [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Li, Xiaohua; Yang, Caiyun [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); Meng, Hao; Wang, Dong; Chang, Shuang [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Xu, Ye [Department of Radiation Oncology, Division of Genomic Stability, Dana Farber Cancer Institute, Harvard Medical School, MA 02134 (United States); Price, Brendan, E-mail: Brendan_Price@dfci.harvard.edu [Department of Radiation Oncology, Division of Genomic Stability, Dana Farber Cancer Institute, Harvard Medical School, MA 02134 (United States); Sun, Yingli, E-mail: sunyl@big.ac.cn [Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101 (China)

    2014-10-03

    Highlights: • ATM phosphorylates the opposite strand of the dimer in response to DNA damage. • The PETPVFRLT box of ATM plays a key role in its dimer dissociation in DNA repair. • The dephosphorylation of ATM is critical for dimer re-formation after DNA repair. - Abstract: The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

  6. MspA nanopores from subunit dimers.

    Directory of Open Access Journals (Sweden)

    Mikhail Pavlenok

    Full Text Available Mycobacterium smegmatis porin A (MspA forms an octameric channel and represents the founding member of a new family of pore proteins. Control of subunit stoichiometry is important to tailor MspA for nanotechnological applications. In this study, two MspA monomers were connected by linkers ranging from 17 to 62 amino acids in length. The oligomeric pore proteins were purified from M. smegmatis and were shown to form functional channels in lipid bilayer experiments. These results indicated that the peptide linkers did not prohibit correct folding and localization of MspA. However, expression levels were reduced by 10-fold compared to wild-type MspA. MspA is ideal for nanopore sequencing due to its unique pore geometry and its robustness. To assess the usefulness of MspA made from dimeric subunits for DNA sequencing, we linked two M1-MspA monomers, whose constriction zones were modified to enable DNA translocation. Lipid bilayer experiments demonstrated that this construct also formed functional channels. Voltage gating of MspA pores made from M1 monomers and M1-M1 dimers was identical indicating similar structural and dynamic channel properties. Glucose uptake in M. smegmatis cells lacking porins was restored by expressing the dimeric mspA M1 gene indicating correct folding and localization of M1-M1 pores in their native membrane. Single-stranded DNA hairpins produced identical ionic current blockades in pores made from monomers and subunit dimers demonstrating that M1-M1 pores are suitable for DNA sequencing. This study provides the proof of principle that production of single-chain MspA pores in M. smegmatis is feasible and paves the way for generating MspA pores with altered stoichiometries. Subunit dimers enable better control of the chemical and physical properties of the constriction zone of MspA. This approach will be valuable both in understanding transport across the outer membrane in mycobacteria and in tailoring MspA for nanopore

  7. Simple approach to thieno[3,2-d]pyrimidines as new scaffolds of antimicrobial activities

    Directory of Open Access Journals (Sweden)

    Hafez Hend N.

    2016-09-01

    Full Text Available 6ʹ-(4-Chlorophenyl-spiro[cyclohexane-1,2ʹ-thieno[3,2-d][1,3] oxazin]-4ʹ(1ʹH-one (1 was synthesized and used as a starting material for the synthesis of a novel series of spiro compounds having biologically active sulfonamide 2a-e and 3ʹ-(4-acetylphenyl-6ʹ- (4-chlorophenyl-1ʹH-spiro[cyclohexane-1,2ʹ-thieno[3,2-d] pyrimidine-4ʹ(3ʹH-one (3. Compound 2a was used as a key intermediate for the synthesis of sulfonyl carbothioamide derivatives 4a-c. Also, compound 3 was used as an intermediate for the synthesis of 3ʹH-spiro[cyclohexane-1,2ʹ-thieno[3,2-d]pyrimidin]-3ʹ-yl] phenyl}-2-imino-4-(substituted phenyl and/or thienyl-1,2-dihydropyridine- 3-carbonitrile derivatives 5a-e, 3ʹH-spiro[cyclohexane- 1,2ʹ- thieno[3,2-d]pyrimidin]-3ʹ-yl]phenyl}-2-oxo-4-(substituted phenyl and/or thienyl-1,2-dihydropyridine-3-carbonitrile derivatives 6a-e, and 4-[(2Z-3-substituted-arylprop-2-enoyl] phenyl-1ʹH-spiro[cyclohexane-1,2ʹ-thieno[3,2-d]pyrimidine derivatives 7a-e. Cyclocondensation of 7a-e with hydrazine hydrate produced 6ʹ-(4-chlorophenyl-3ʹ-[4-(5-substituted aryl-4,5-dihydro- 1H-pyrazol-3-ylphenyl]-1ʹH-spiro[cyclohexane-1,2ʹ-thieno- [3,2-d]pyrimidin]-4ʹ(3ʹH-ones 8a-e but with hydroxylamine hydrochloride afforded the corresponding isoxazoline derivatives 9a-e. Also, cyclocondensation by thiourea afforded 2-thioxo-1,2- dihydropyrimidin-4-yl-phenyl-spiro-{cyclohexanethieno[3,2-d] pyrimidin}-4-one derivatives 10a-e. The new compounds were investigated for antimicrobial activity. Compounds 2c, 8b,c, 9b and 10b were the most potent ones against both Gram-negative and Gram-positive bacteria. Compound 8c exhibited higher antifungal activity towards the examined fungi with MIC of 1-2 μmol mL-1 compared to ketoconazole (MIC 2-3 μmol mL-1 .

  8. Synthesis, and Fluorescence Properties of Coumarin and Benzocoumarin Derivatives Conjugated Pyrimidine Scaffolds for Biological Imaging Applications.

    Science.gov (United States)

    Al-Masoudi, Najim A; Al-Salihi, Niran J; Marich, Yossra A; Markus, Timo

    2015-11-01

    Series of coumarin and 5,6-benzomcomarin substituted pyrimidine derivatives 11-15 and 22-25 were synthesized, aiming to develop new imaging fluorescent agents. Analogously, treatment of 4-chloropyrimidine analog 16 with coumarin 3-carbohyrazide 5 under MWI condition followed by boiling with NH4OAc in HOAc furnished coumarin-1,2,4-triazolo-pyrimidine analog 18. The fluorescence property was investigated spectrophotometrically in MeOH with Rhodamine 6G as standard dye. All the compounds showed emission in the region between 331 and 495 nm. The quantum yield of all the compounds were found to be weak, except methyl benzocoumarin 3-carboxylate 22 which showed (ΦF = 0.98) in comparison to Rhodamine 6G as standard (ΦF = 0.95).

  9. The effect of purine and pyrimidine analogues and virazole on adenovirus replication.

    Science.gov (United States)

    Scheffler, P; Haghchenas, D; Wigand, R

    1975-04-01

    The multiplication of adenovirus 19 in HeLa cells was inhibited by various purine and pyrimidine analogues and by virazole. The formation of infectious virus and of capsid proteins (haemagglutin, group-specific complement-fixing antigen) was inhibited to the same degree, while the viral cytopathic effect (CPE) was not inhibited. The reversibility of the inhibition after removal of the substances was more complete for purine than for pyrimidine analogues. The inhibition was counteracted by simulataneous addition of the corresponding nucleosides. Adenosine was more effected than guanosine against purine analogues; both were partially effective against virazole, but none of them against arabinofuranosyladenine. The time-dependence of inhibition, the ensuing eclipse period after removal of the inhibitors, and the successive application of two inhibitors led to the conclusion that most of them affect the viral multiplication mainly by inhibition of DNA synthesis. Azacytidine inhibits the synthesis of structural proteins as well.

  10. Direct Isolation of Purines and Pyrimidines from Nucleic Acids Using Sublimation

    Science.gov (United States)

    Glavin, Daniel P.; Schubert, Michael; Bada, Jeffrey L.

    2003-01-01

    A sublimation technique was developed to isolate purines and pyrimidines directly from lambda-deoxyribonucleic acid (lambda-DNA) and Escherichia coli cells. The sublimation of adenine, cytosine, guanine, and thymine from lambda-DNA was tested under reduced pressure (approx. 0.5 Torr) at temperatures of >150 C. With the exception of guanine, approximately 60 -75% of each base was sublimed directly from the lambda-DNA and recovered on a coldfinger of the sublimation apparatus after heating to 450 C. Several nucleobases including adenine, cytosine, thymine, and uracil were also recovered from E. coli bacteria after heating the cells to the same temperature, although some thermal decomposition of the bases also occurred. These results demonstrate the feasibility of using sublimation to isolate purines and pyrimidines from native E. coli DNA and RNA without any chemical treatment of the cells.

  11. cis-Aquadichlorido[pyrimidin-2(1H-one-κN3]copper(II

    Directory of Open Access Journals (Sweden)

    A. Guy Orpen

    2008-07-01

    Full Text Available In the title compound, [CuCl2(C4H4N2O(H2O], the CuII cation is coordinated by two chloride anions, one pyrimidin-2-one N atom and one water molecule, giving a slightly distorted square-planar geometry. In the crystal structure, the pyrimidin-2-one rings stack along the b axis, with an interplanar distance of 3.306 Å, as do the copper coordination planes (interplanar spacing = 2.998 Å. The coordination around the Jahn–Teller-distorted CuII ion is completed by long Cu...O [3.014 (5 Å] and Cu...Cl [3.0194 (15 Å] interactions with adjacent molecules involved in this stacking. Several N—H...Cl, O—H...Cl and O—H...O intermolecular hydrogen bonds form a polar three-dimensional network.

  12. 3-({5-Bromo-4-[pyrrolidin-1-yl]pyrimidin-2-yl}aminophenol

    Directory of Open Access Journals (Sweden)

    Alan M. Jones

    2015-05-01

    Full Text Available Re-investigation of the 1H-NMR spectrum reported for 15-bromo-4-oxa-2,9-diaza-1(2,4-pyrimidine-3(1,3-benzenacyclononaphane (2 prepared via a Mitsunobu- mediated macroether cyclisation led to a proposed structural isomer (3. The title compound (3 was prepared via a two-step protocol and assigned using 1H, 13C-NMR and LC-MS.

  13. A Facile Microwave-Assisted Synthesis of Some Fused Pyrimidine Derivatives

    Directory of Open Access Journals (Sweden)

    S. A. Al-Issa

    2014-06-01

    Full Text Available The highly accelerated synthesis of thienopyrimidinones, theino- pyrimidines,thioxotheinopyrimidinones and a thienotriazolopyrimidinone derivatives under microwave irradiation is reported. Compared to conventional conditions, microwaves method offered several advantage likes short time, good yields, simple procedure, mild conditions and easy workup. The structure of synthesized compounds have been characterized on the basis of their elemental analysis and spectral data, and screened for their antimicrobial activity.

  14. Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis.

    Science.gov (United States)

    Rabinovich, Shiran; Adler, Lital; Yizhak, Keren; Sarver, Alona; Silberman, Alon; Agron, Shani; Stettner, Noa; Sun, Qin; Brandis, Alexander; Helbling, Daniel; Korman, Stanley; Itzkovitz, Shalev; Dimmock, David; Ulitsky, Igor; Nagamani, Sandesh C S; Ruppin, Eytan; Erez, Ayelet

    2015-11-19

    Cancer cells hijack and remodel existing metabolic pathways for their benefit. Argininosuccinate synthase (ASS1) is a urea cycle enzyme that is essential in the conversion of nitrogen from ammonia and aspartate to urea. A decrease in nitrogen flux through ASS1 in the liver causes the urea cycle disorder citrullinaemia. In contrast to the well-studied consequences of loss of ASS1 activity on ureagenesis, the purpose of its somatic silencing in multiple cancers is largely unknown. Here we show that decreased activity of ASS1 in cancers supports proliferation by facilitating pyrimidine synthesis via CAD (carbamoyl-phosphate synthase 2, aspartate transcarbamylase, and dihydroorotase complex) activation. Our studies were initiated by delineating the consequences of loss of ASS1 activity in humans with two types of citrullinaemia. We find that in citrullinaemia type I (CTLN I), which is caused by deficiency of ASS1, there is increased pyrimidine synthesis and proliferation compared with citrullinaemia type II (CTLN II), in which there is decreased substrate availability for ASS1 caused by deficiency of the aspartate transporter citrin. Building on these results, we demonstrate that ASS1 deficiency in cancer increases cytosolic aspartate levels, which increases CAD activation by upregulating its substrate availability and by increasing its phosphorylation by S6K1 through the mammalian target of rapamycin (mTOR) pathway. Decreasing CAD activity by blocking citrin, the mTOR signalling, or pyrimidine synthesis decreases proliferation and thus may serve as a therapeutic strategy in multiple cancers where ASS1 is downregulated. Our results demonstrate that ASS1 downregulation is a novel mechanism supporting cancerous proliferation, and they provide a metabolic link between the urea cycle enzymes and pyrimidine synthesis.

  15. Dichloridobis[2-methyl-sulfanyl-4-(pyridin-2-yl)pyrimidine-κN,N]cobalt(II).

    Science.gov (United States)

    Yang, Wen-Na

    2011-09-01

    The asymmetric unit of the title compound, [CoCl(2)(C(10)H(9)N(3)S)(2)], contains one half-mol-ecule with the Co(II) atom situtated on a twofold rotational axis. The Co(II) atom, in an octa-hedral enviroment, is coordinated by four N atoms from two 2-methyl-sulfanyl-4-(pyridin-2-yl)pyrimidine ligands and two Cl atoms.

  16. The photochemistry of pyrimidine in realistic astrophysical ices and the production of nucleobases

    Energy Technology Data Exchange (ETDEWEB)

    Nuevo, Michel; Materese, Christopher K.; Sandford, Scott A., E-mail: michel.nuevo-1@nasa.gov [NASA Ames Research Center, MS 245-6, Moffett Field, CA 94035 (United States)

    2014-10-01

    Nucleobases, together with deoxyribose/ribose and phosphoric acid, are the building blocks of DNA and RNA for all known life. The presence of nucleobase-like compounds in carbonaceous chondrites delivered to the Earth raises the question of an extraterrestrial origin for the molecules that triggered life on our planet. Whether these molecules are formed in interstellar/protostellar environments, in small parent bodies in the solar system, or both, is currently unclear. Recent experiments show that the UV irradiation of pyrimidine (C{sub 4}H{sub 4}N{sub 2}) in H{sub 2}O-rich ice mixtures that contain NH{sub 3}, CH{sub 3}OH, or CH{sub 4} leads to the formation of the pyrimidine-based nucleobases uracil, cytosine, and thymine. In this work, we discuss the low-temperature UV irradiation of pyrimidine in realistic astrophysical ice mixtures containing H{sub 2}O, CH{sub 3}OH, and NH{sub 3}, with or without CH{sub 4}, to search for the production of nucleobases and other prebiotic compounds. These experiments show the presence of uracil, urea, glycerol, hexamethylenetetramine, small amino acids, and small carboxylic acids in all samples. Cytosine was only found in one sample produced from ices irradiated with a higher UV dose, while thymine was not found in any sample, even after irradiation with a higher UV dose. Results are discussed to evaluate the role of the photochemistry of pyrimidine in the inventory of organic molecules detected in meteorites and their astrophysical/astrobiological implications.

  17. Metal enhanced fluorescence of Ag-nanoshell dimer

    Science.gov (United States)

    Liaw, Jiunn-Woei; Chen, Huang-Chih; Chen, Bae-Renn; Kuo, Mao-Kuen

    2014-04-01

    The plasmon modes of Ag-nanoshell dimer on metal enhanced fluorescence (MEF) are studied theoretically. The amplified excitation rate of a dimer (two identical Ag nanoshells) illuminated by a plane wave for exciting a molecule located at the gap center is calculated. Subsequently, the apparent quantum yield of the emission of the excited molecule affected by the dimer is investigated. The multiple multipole method is used for the both simulations. Finally, the enhancement factor of the dimer on the overall photoluminescence of the molecule in terms of the two parameters is evaluated. Our results show that Ag-nanoshell dimer is a dual-band photoluminescence enhancer for MEF at the bonding dipole and quadrupole modes. The former is broadband, and the latter narrowband. Both bands depend on the gap size. Moreover, the average enhancement factor of Ag-nanoshell dimer for MEF with a Stokes shift is discussed.

  18. Cytochrome P450 as dimerization catalyst in diketopiperazine alkaloid biosynthesis.

    Science.gov (United States)

    Saruwatari, Takayoshi; Yagishita, Fumitoshi; Mino, Takashi; Noguchi, Hiroshi; Hotta, Kinya; Watanabe, Kenji

    2014-03-21

    As dimeric natural products frequently exhibit useful biological activities, identifying and understanding their mechanisms of dimerization is of great interest. One such compound is (−)-ditryptophenaline, isolated from Aspergillus flavus, which inhibits substance P receptor for potential analgesic and anti-inflammatory activity. Through targeted gene knockout in A. flavus and heterologous yeast gene expression, we determined for the first time the gene cluster and pathway for the biosynthesis of a dimeric diketopiperazine alkaloid. We also determined that a single cytochrome P450, DtpC, is responsible not only for pyrroloindole ring formation but also for concurrent dimerization of N-methylphenylalanyltryptophanyl diketopiperazine monomers into a homodimeric product. Furthermore, DtpC exhibits relaxed substrate specificity, allowing the formation of two new dimeric compounds from a non-native monomeric precursor, brevianamide F. A radical-mediated mechanism of dimerization is proposed.

  19. Fluorescent property of 3-hydroxymethyl imidazo[1,2-a]pyridine and pyrimidine derivatives

    Directory of Open Access Journals (Sweden)

    Velázquez-Olvera Stephania

    2012-08-01

    Full Text Available Abstract Background Imidazo[1,2-a]pyridines and pyrimidines are important organic fluorophores which have been investigated as biomarkers and photochemical sensors. The effect on the luminescent property by substituents in the heterocycle and phenyl rings, have been studied as well. In this investigation, series of 3-hydroxymethyl imidazo[1,2-a]pyridines and pyrimidines were synthesized and evaluated in relation to fluorescence emission, based upon the hypothesis that the hydroxymethyl group may act as an enhancer of fluorescence intensity. Results Compounds of both series emitted light in organic solvents dilutions as well as in acidic and alkaline media. Quantitative fluorescence spectroscopy determined that both fused heterocycles fluoresced more intensely than the parent unsubstituted imidazo[1,2-a]azine fluorophore. In particular, 3-hydroxymethyl imidazo[1,2-a]pyridines fluoresced more intensely than 3-hydroxymethyl imidazo[1,2-a]pyrimidines, the latter emitting blue light at longer wavelengths, whereas the former emitted purple light. Conclusion It was concluded that in most cases the hydroxymethyl moiety did act as an enhancer of the fluorescence intensity, however, a comparison made with the fluorescence emitted by 2-aryl imidazo[1,2-a]azines revealed that in some cases the hydroxymethyl substituent decreased the fluorescence intensity.

  20. Absolute cross sections for electronic excitation of pyrimidine by electron impact

    Energy Technology Data Exchange (ETDEWEB)

    Regeta, Khrystyna; Allan, Michael [Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg (Switzerland); Mašín, Zdeněk [Max-Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, Max-Born-Straße 2A, 12489 Berlin (Germany); Gorfinkiel, Jimena D. [Department of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA (United Kingdom)

    2016-01-14

    We measured differential cross sections for electron-impact electronic excitation of pyrimidine, both as a function of electron energy up to 18 eV, and of scattering angle up to 180°. The emphasis of the present work is on recording detailed excitation functions revealing resonances in the excitation process. The differential cross sections were summed to obtain integral cross sections. These are compared to results of R-matrix calculations, which successfully reproduce both the magnitude of the cross section and the major resonant features. Comparison of the experiment to the calculated contributions of different symmetries to the integral cross section permitted assignment of several features to specific core-excited resonances. Comparison of the resonant structure of pyrimidine with that of benzene revealed pronounced similarities and thus a dominant role of π–π{sup ∗} excited states and resonances. Electron energy loss spectra were measured as a preparation for the cross section measurements and vibrational structure was observed for some of the triplet states. A detailed analysis of the electronic excited states of pyrimidine is also presented.

  1. Isolation of Purines and Pyrimidines from the Murchison Meteorite Using Sublimation

    Science.gov (United States)

    Glavin, D. P.; Bada, J. L.

    2004-01-01

    The origin of life on Earth, and possibly on other planets such as Mars, would have required the presence of liquid water and a continuous supply of prebiotic organic compounds. The exogenous delivery of organic matter by asteroids, comets, and carbonaceous meteorites could have contributed to the early Earth s prebiotic inventory by seeding the planet with biologically important organic compounds. A wide variety of prebiotic organic compounds have previously been detected in the Murchison CM type carbonaceous chondrite including amino acids, purines and pyrimidines. These compounds dominate terrestrial biochemistry and are integral components of proteins, DNA and RNA. Several purines including adenine, guanine, hypoxanthine, and xanthine, as well as the pyrimidine uracil, have previously been detected in water or formic acid extracts of Murchison using ion-exclusion chromatography and ultraviolet spectroscopy. However, even after purification of these extracts, the accurate identification and quantification of nucleobases is difficult due to interfering UV absorbing compounds. In order to reduce these effects, we have developed an extraction technique using sublimation to isolate purines and pyrimidines from other non-volatile organic compounds in Murchison acid extracts.

  2. Intermediate energy cross sections for electron-impact vibrational-excitation of pyrimidine

    Energy Technology Data Exchange (ETDEWEB)

    Jones, D. B. [School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001 (Australia); Ellis-Gibbings, L.; García, G. [Instituto de Física Fundamental, CSIC, Serrano 113-bis, 28006 Madrid (Spain); Nixon, K. L. [Departamento de Física, Universidade Federal de Juiz de Fora, 36036-330 Juiz de Fora, Minas Gerais (Brazil); School of Biology, Chemistry and Forensic Science, University of Wolverhampton, Wolverhampton WV1 1LY (United Kingdom); Lopes, M. C. A. [Departamento de Física, Universidade Federal de Juiz de Fora, 36036-330 Juiz de Fora, Minas Gerais (Brazil); Brunger, M. J., E-mail: Michael.Brunger@flinders.edu.au [School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001 (Australia); Institute of Mathematical Sciences, University of Malaya, 50603 Kuala Lumpur (Malaysia)

    2015-09-07

    We report differential cross sections (DCSs) and integral cross sections (ICSs) for electron-impact vibrational-excitation of pyrimidine, at incident electron energies in the range 15–50 eV. The scattered electron angular range for the DCS measurements was 15°–90°. The measurements at the DCS-level are the first to be reported for vibrational-excitation in pyrimidine via electron impact, while for the ICS we extend the results from the only previous condensed-phase study [P. L. Levesque, M. Michaud, and L. Sanche, J. Chem. Phys. 122, 094701 (2005)], for electron energies ⩽12 eV, to higher energies. Interestingly, the trend in the magnitude of the lower energy condensed-phase ICSs is much smaller when compared to the corresponding gas phase results. As there is no evidence for the existence of any shape-resonances, in the available pyrimidine total cross sections [Baek et al., Phys. Rev. A 88, 032702 (2013); Fuss et al., ibid. 88, 042702 (2013)], between 10 and 20 eV, this mismatch in absolute magnitude between the condensed-phase and gas-phase ICSs might be indicative for collective-behaviour effects in the condensed-phase results.

  3. Purine and pyrimidine metabolism: Convergent evidence on chronic antidepressant treatment response in mice and humans

    Science.gov (United States)

    Park, Dong Ik; Dournes, Carine; Sillaber, Inge; Uhr, Manfred; Asara, John M.; Gassen, Nils C.; Rein, Theo; Ising, Marcus; Webhofer, Christian; Filiou, Michaela D.; Müller, Marianne B.; Turck, Christoph W.

    2016-01-01

    Selective Serotonin Reuptake Inhibitors (SSRIs) are commonly used drugs for the treatment of psychiatric diseases including major depressive disorder (MDD). For unknown reasons a substantial number of patients do not show any improvement during or after SSRI treatment. We treated DBA/2J mice for 28 days with paroxetine and assessed their behavioral response with the forced swim test (FST). Paroxetine-treated long-time floating (PLF) and paroxetine-treated short-time floating (PSF) groups were stratified as proxies for drug non-responder and responder mice, respectively. Proteomics and metabolomics profiles of PLF and PSF groups were acquired for the hippocampus and plasma to identify molecular pathways and biosignatures that stratify paroxetine-treated mouse sub-groups. The critical role of purine and pyrimidine metabolisms for chronic paroxetine treatment response in the mouse was further corroborated by pathway protein expression differences in both mice and patients that underwent chronic antidepressant treatment. The integrated -omics data indicate purine and pyrimidine metabolism pathway activity differences between PLF and PSF mice. Furthermore, the pathway protein levels in peripheral specimens strongly correlated with the antidepressant treatment response in patients. Our results suggest that chronic SSRI treatment differentially affects purine and pyrimidine metabolisms, which may explain the heterogeneous antidepressant treatment response and represents a potential biosignature. PMID:27731396

  4. Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

    Science.gov (United States)

    Phan, Andy; Mailey, Katherine; Sakai, Jessica; Gu, Xiaobo; Schroeder, Susan J

    2017-02-17

    Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased towards small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with more than 6 nucleotides that occur frequently in viral RNA. This paper presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Protonated cytosine and uracil base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with more than 6 nucleotides are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2x2 have been measured (Mathews 2004). These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites.

  5. SYNTHESIS AND BIOLOGICAL ACTIVITY OF IMIDAZOLE DERIVED CHALCONES AND IT’S PYRIMIDINES

    Directory of Open Access Journals (Sweden)

    Pavan Kumar Padarthi

    2013-06-01

    Full Text Available Microbial contribution increasing rapidly due to invasion by the pathogenic organisms like bacteria, fungi and virus in the present disease burden of human health. To treat these diseases many potent and broad spectrum antibiotics were discovered e.g., ampicillin, amoxicillin, carbenicillin, ofloxacin and tetracycline etc., Even though antibiotics are life saving drugs in therapeutics but they are potentially harmful. These harmful effects include allergic and anaphylactic reaction, development of resistance, destruction of normal non-pathogenic bacterial flora and selective toxicity like aplastic anemia, kidney damage. As the microbial resistance make anti-microbial therapy very complex, there is a definite need of novel anti-microbials or drugs for combination therapy with standard antibiotics. Our aim was to synthesize and explore the anti-microbial activity of chalcones and its derived pyrimidines against various pathological micro organisms. Novel imidazole derived chalcones were synthesized and characterization was carried out by analyzing melting point, IR, 1H NMR data. The synthesized chalcones and pyrimidines are tested for their antimicrobial activity against various bacteria as well as fungi. Further synthesis of novel heterocyclic chalcones, structural elucidation, spectral analysis, biological activity of synthesized chalcones and its derived pyrimidines gives a hope for enhanced biological action using QSAR Studies.

  6. Rim2, a pyrimidine nucleotide exchanger, is needed for iron utilization in mitochondria

    Science.gov (United States)

    Yoon, Heeyong; Zhang, Yan; Pain, Jayashree; Lyver, Elise R.; Lesuisse, Emmanuel; Pain, Debkumar; Dancis, Andrew

    2016-01-01

    Mitochondria transport and utilize iron for the synthesis of haem and Fe–S clusters. Although many proteins are known to be involved in these processes, additional proteins are likely to participate. To test this hypothesis, in the present study we used a genetic screen looking for yeast mutants that are synthetically lethal with the mitochondrial iron carriers Mrs3 and Mrs4. Several genes were identified, including an isolate mutated for Yfh1, the yeast frataxin homologue. All such triple mutants were complemented by increased expression of Rim2, another mitochondrial carrier protein. Rim2 overexpression was able to enhance haem and Fe–S cluster synthesis in wild-type or Δmrs3/Δmrs4 backgrounds. Conversely Rim2 depletion impaired haem and Fe–S cluster synthesis in wild-type or Δmrs3/Δmrs4 backgrounds, indicating a unique requirement for this mitochondrial transporter for these processes. Rim2 was previously shown to mediate pyrimidine exchange in and out of vesicles. In the present study we found that isolated mitochondria lacking Rim2 exhibited concordant iron defects and pyrimidine transport defects, although the connection between these two functions is not explained. When organellar membranes were ruptured to bypass iron transport, haem synthesis from added iron and porphyrin was still markedly deficient in Rim2-depleted mitochondrial lysate. The results indicate that Rim2 is a pyrimidine exchanger with an additional unique function in promoting mitochondrial iron utilization. PMID:21777202

  7. Insights into the pyrimidine biosynthetic pathway of human malaria parasite Plasmodium falciparum as chemotherapeutic target.

    Science.gov (United States)

    Krungkrai, Sudaratana R; Krungkrai, Jerapan

    2016-06-01

    Malaria is a major cause of morbidity and mortality in humans. Artemisinins remain as the first-line treatment for Plasmodium falciparum (P. falciparum) malaria although drug resistance has already emerged and spread in Southeast Asia. Thus, to fight this disease, there is an urgent need to develop new antimalarial drugs for malaria chemotherapy. Unlike human host cells, P. falciparum cannot salvage preformed pyrimidine bases or nucleosides from the extracellular environment and relies solely on nucleotides synthesized through the de novo biosynthetic pathway. This review presents significant progress on understanding the de novo pyrimidine pathway and the functional enzymes in the human parasite P. falciparum. Current knowledge in genomics and metabolomics are described, particularly focusing on the parasite purine and pyrimidine nucleotide metabolism. These include gene annotation, characterization and molecular mechanism of the enzymes that are different from the human host pathway. Recent elucidation of the three-dimensional crystal structures and the catalytic reactions of three enzymes: dihydroorotate dehydrogenase, orotate phosphoribosyltransferase, and orotidine 5'-monophosphate decarboxylase, as well as their inhibitors are reviewed in the context of their therapeutic potential against malaria.

  8. Thermodynamic properties for the sodium dimer

    Science.gov (United States)

    Song, Xiao-Qin; Wang, Chao-Wen; Jia, Chun-Sheng

    2017-04-01

    We present a closed-form expression of the classical vibrational partition function for the improved Rosen-Morse potential energy model. We give explicit expressions for the vibrational mean energy, vibrational specific heat, vibrational free energy, and vibrational entropy for diatomic molecule systems. The properties of these thermodynamic functions for the Na2 dimer are discussed in detail. We find that the improved Rosen-Morse potential model is superior to the harmonic oscillator in calculating the heat capacity for the Na2 molecules.

  9. Thermodynamics of acetylene van der Waals dimerization

    Science.gov (United States)

    Colussi, A. J.; Sander, S. P.; Friedl, R. R.

    1991-01-01

    Integrated band intensities of the 620/cm absorption in (C2H2)2 are measured by FTIR spectroscopy at constant acetylene pressure between 198 and 273 K. These data, in conjunction with ab initio results for (C2H2)2, are used for the statistical evaluation of the equilibrium constant Kp(T) for acetylene-cluster dimerization. The present results are used to clarify the role of molecular clusters in chemical systems at or near equilibrium, in particular in Titan's stratosphere.

  10. The properties of dimers confined between two charged plates.

    Science.gov (United States)

    Hatlo, Marius M; Bohinc, Klemen; Lue, Leo

    2010-03-21

    We consider two like-charged planar surfaces immersed in solution of oppositely charged dimer counterions with a bond length l. To analyze this system, we extend and employ a self-consistent field theory that has been shown to be accurate from the weak to the intermediate through to the strong coupling regimes. In the limit of very short dimers, the results converge to the results for pointlike divalent ions. Near the surfaces, the dimers lie parallel to the charged plates. In the intermediate coupling regime, the dimers are aligned perpendicularly to the surface when they are a distance l from a surface. In the weak coupling regime, the interactions are only repulsive. At slightly higher couplings, there is a minimum in the variation of the free energy with distance at approximately the bond length of the dimers, which arises from bridging conformations of the dimers. In the intermediate coupling regime, an additional minimum in the free energy is observed at much smaller distances, which is due to the correlations between the dimers. For large dimer bond lengths, this minimum is metastable with respect to the previous minimum. However, as the bond length decreases, this minimum becomes the stable, while the minimum associated with the dimer bond length becomes metastable and eventually disappears. For shorter dimer bond length the attractive interaction is the result of correlations between counterions and charges on the surfaces. We find that dimers can mediate attractive interaction between like-charged surfaces in the intermediate coupling regime. The analysis of orientations confirms the bridging mechanism for sufficiently long dimers, whereas at high electrostatic couplings charge correlations contribute to the attraction.

  11. Rotational spectra of propargyl alcohol dimer: A dimer bound with three different types of hydrogen bonds

    Energy Technology Data Exchange (ETDEWEB)

    Mani, Devendra; Arunan, E., E-mail: arunan@ipc.iisc.ernet.in [Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012 (India)

    2014-10-28

    Pure rotational spectra of the propargyl alcohol dimer and its three deuterium isotopologues have been observed in the 4 to 13 GHz range using a pulsed-nozzle Fourier transform microwave spectrometer. For the parent dimer, a total of 51 transitions could be observed and fitted within experimental uncertainty. For two mono-substituted and one bi-substituted deuterium isotopologues, a total of 14, 17, and 19 transitions were observed, respectively. The observed rotational constants for the parent dimer [A = 2321.8335(4) MHz, B = 1150.4774(2) MHz, and C = 1124.8898(2) MHz] are close to those of the most stable structure predicted by ab initio calculations. Spectra of the three deuterated isotopologues and Kraitchman analysis positively confirm this structure. Geometrical parameters and “Atoms in Molecules” analysis on the observed structure reveal that the two propargyl alcohol units in the dimer are bound by three different types of hydrogen bonds: O–H⋯O, O–H⋯π, and C–H⋯π. To the best of our knowledge, propargyl alcohol seems to be the smallest molecule forming a homodimer with three different points of contact.

  12. Synthesis of Symmetrical Biaryls via Rhodium Catalyzed Dimerization of Arylmercurials and Mechanism of the Dimerization

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A series of symmetrical biaryls was synthesized from arylmercuric chlorides and biarylmercurials in the presence of [ClRh(CO)2]2 in hexamethylphosphoramide(HMPA). The mechanism of the [ClRh(CO)2]2 catalyzed dimerization of biarylmercurials was studied, and shown to be mainly intermolecular reaction.

  13. Assembly of Drosophila centromeric nucleosomes requires CID dimerization.

    Science.gov (United States)

    Zhang, Weiguo; Colmenares, Serafin U; Karpen, Gary H

    2012-01-27

    Centromeres are essential chromosomal regions required for kinetochore assembly and chromosome segregation. The composition and organization of centromeric nucleosomes containing the essential histone H3 variant CENP-A (CID in Drosophila) is a fundamental, unresolved issue. Using immunoprecipitation of CID mononucleosomes and cysteine crosslinking, we demonstrate that centromeric nucleosomes contain CID dimers in vivo. Furthermore, CID dimerization and centromeric targeting require a residue implicated in formation of the four-helix bundle, which mediates intranucleosomal H3 dimerization and nucleosome integrity. Taken together, our findings suggest that CID nucleosomes are octameric in vivo and that CID dimerization is essential for correct centromere assembly.

  14. Disordered clusters of Bak dimers rupture mitochondria during apoptosis

    Science.gov (United States)

    Uren, Rachel T; O’Hely, Martin; Iyer, Sweta; Bartolo, Ray; Shi, Melissa X; Brouwer, Jason M; Alsop, Amber E; Dewson, Grant; Kluck, Ruth M

    2017-01-01

    During apoptosis, Bak and Bax undergo major conformational change and form symmetric dimers that coalesce to perforate the mitochondrial outer membrane via an unknown mechanism. We have employed cysteine labelling and linkage analysis to the full length of Bak in mitochondria. This comprehensive survey showed that in each Bak dimer the N-termini are fully solvent-exposed and mobile, the core is highly structured, and the C-termini are flexible but restrained by their contact with the membrane. Dimer-dimer interactions were more labile than the BH3:groove interaction within dimers, suggesting there is no extensive protein interface between dimers. In addition, linkage in the mobile Bak N-terminus (V61C) specifically quantified association between dimers, allowing mathematical simulations of dimer arrangement. Together, our data show that Bak dimers form disordered clusters to generate lipidic pores. These findings provide a molecular explanation for the observed structural heterogeneity of the apoptotic pore. DOI: http://dx.doi.org/10.7554/eLife.19944.001 PMID:28182867

  15. Pathogenic Cysteine Removal Mutations in FGFR Extracellular Domains Stabilize Receptor Dimers and Perturb the TM Dimer Structure.

    Science.gov (United States)

    Sarabipour, Sarvenaz; Hristova, Kalina

    2016-10-09

    Missense mutations that introduce or remove cysteine residues in receptor tyrosine kinases are believed to cause pathologies by stabilizing the active receptor tyrosine kinase dimers. However, the magnitude of this stabilizing effect has not been measured for full-length receptors. Here, we characterize the dimer stabilities of three full-length fibroblast growth factor receptor (FGFR) mutants harboring pathogenic cysteine substitutions: the C178S FGFR1 mutant, the C342R FGFR2 mutant, and the C228R FGFR3 mutant. We find that the three mutations stabilize the FGFR dimers. We further see that the mutations alter the configuration of the FGFR transmembrane dimers. Thus, both aberrant dimerization and perturbed dimer structure likely contribute to the pathological phenotypes arising due to these mutations.

  16. Dimeric Labdane Diterpenes: Synthesis and Antiproliferative Effects

    Directory of Open Access Journals (Sweden)

    Guillermo Schmeda-Hirschmann

    2013-05-01

    Full Text Available Several diterpenes with the labdane skeleton show biological activity, including antiproliferative effects. Most of the research work on bioactive labdanes has been carried out on naturally occurring diterpenes and semisynthetic derivatives, but much less is known on the effects of diterpene dimers. The aim of the present work was to synthesize dimeric diterpenes from the labdane imbricatolic acid using esters, ethers and the triazole ring as linkers. Some 18 new derivatives were prepared and the compounds were evaluated for antiproliferative activity on human normal fibroblasts (MRC-5 and the following human tumor cell lines: AGS, SK-MES-1, J82 and HL-60. The diethers 8–10, differing in the number of CH2 units in the linker, presented better antiproliferative activity with a maximum effect for the derivative 9. The best antiproliferative effect against HL-60 cells was found for compounds 3 and 17, with IC50 values of 22.3 and 23.2 μM, lower than that found for the reference compound etoposide (2.23 μM. The compounds 9, 17 and 11 were the most active derivatives towards AGS cells with IC50 values of 17.8, 23.4 and 26.1 μM. A free carboxylic acid function seems relevant for the effect as several of the compounds showed less antiproliferative effect after methylation.

  17. Water dimer absorption of visible light

    Directory of Open Access Journals (Sweden)

    J. Hargrove

    2007-07-01

    Full Text Available Laboratory measurements of water vapor absorption using cavity ring-down spectroscopy revealed a broad absorption at 405 nm with a quadratic dependence on water monomer concentration, a similar absorption with a linear component at 532 nm, and only linear absorption at 570 nm in the vicinity of water monomer peaks. D2O absorption is weaker and linear at 405 nm. Van't Hoff plots constructed at 405.26 nm suggest that for dimerization, Keq=0.056±0.02 atm−1, ΔH°301 K=−16.6±2 kJ mol−1 and ΔS°301 K=−80±10 J mol−1 K−1. This transition peaks at 409.5 nm, could be attributed to the 8th overtone of water dimer and the 532 nm absorption to the 6th overtone. It is possible that some lower overtones previously searched for are less enhanced. These absorptions could increase water vapor feed back calculations leading to higher global temperature projections with currently projected greenhouse gas levels or greater cooling from greenhouse gas reductions.

  18. 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.

  19. p53 mutant human glioma cells are sensitive to UV-C-induced apoptosis due to impaired cyclobutane pyrimidine dimer removal.

    Science.gov (United States)

    Batista, Luis F Z; Roos, Wynand P; Kaina, Bernd; Menck, Carlos F M

    2009-02-01

    The p53 protein is a key regulator of cell responses to DNA damage, and it has been shown that it sensitizes glioma cells to the alkylating agent temozolomide by up-regulating the extrinsic apoptotic pathway, whereas it increases the resistance to chloroethylating agents, such as ACNU and BCNU, probably by enhancing the efficiency of DNA repair. However, because these agents induce a wide variety of distinct DNA lesions, the direct importance of DNA repair is hard to access. Here, it is shown that the induction of photoproducts by UV light (UV-C) significantly induces apoptosis in a p53-mutated glioma background. This is caused by a reduced level of photoproduct repair, resulting in the persistence of DNA lesions in p53-mutated glioma cells. UV-C-induced apoptosis in p53 mutant glioma cells is preceded by strong transcription and replication inhibition due to blockage by unrepaired photolesions. Moreover, the results indicate that UV-C-induced apoptosis of p53 mutant glioma cells is executed through the intrinsic apoptotic pathway, with Bcl-2 degradation and sustained Bax and Bak up-regulation. Collectively, the data indicate that unrepaired DNA lesions induce apoptosis in p53 mutant gliomas despite the resistance of these gliomas to temozolomide, suggesting that efficiency of treatment of p53 mutant gliomas might be higher with agents that induce the formation of DNA lesions whose global genomic repair is dependent on p53.

  20. Establishment and characterization of melanoma cell line from a xeroderma pigmentosum patient: activation of N-ras at a potential pyrimidine dimer site.

    NARCIS (Netherlands)

    W. Keijzer; M.P. Mulder; J.C.M. Langeveld; E.M.E. Smit (Elisabeth); J.L. Bos; D. Bootsma (Dirk); J.H.J. Hoeijmakers (Jan)

    1989-01-01

    textabstractPatients suffering from the genetic disorder xeroderma pigmentosum (XP) display an extreme sensitivity of their skin to sun (UV) exposure and predisposition to skin cancer due to deficiencies in the excision DNA repair pathway. Here we describe the establishment and characterization of t

  1. Synthesis and Antimicrobial Activity of Some New Pyrazole, Fused Pyrazolo[3,4-d]-pyrimidine and Pyrazolo[4,3-e][1,2,4]- triazolo[1,5-c]pyrimidine Derivatives

    Directory of Open Access Journals (Sweden)

    Omar A. Miqdad

    2008-07-01

    Full Text Available Hydrazonyl bromides 2a,b reacted with active methylene compounds (dibenzoylmethane, acetylacetone, ethyl acetoacetate, phenacyl cyanide, acetoacetanilide, ethyl cyanoacetate, cyanoacetamide and malononitrile to afford the corresponding 1,3,4,5- tetrasubstituted pyrazole derivatives 5-12a,b. Reaction of 12a,b with formamide, formic acid and triethyl orthoformate give the pyrazolo[3,4-d]pyrimidine, pyrazolo[3,4- d]pyrimidin-4(3Hone and 5-ethoxymethylene-aminopyrazole-4-carbo-nitrile derivatives 13-15a,b, respectively. Compounds 15a,b reacted with benzhydrazide and hydrazine hydrate to afford pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidine and [4-iminopyrazolo- [3,4-d]pyrimidin-5-yl]amine derivatives 16a,b and 17a,b. Reactions of compounds 17a,b with triethyl orthoformate and carbon disulfide give the corresponding pyrazolo[4,3-e]- [1,2,4]triazolo[1,5-c]pyrimidine derivatives 18a,b and 19a,b, respectively.

  2. HPLC analysis for the clinical-biochemical diagnosis of inborn errors of metabolism of purines and pyrimidines.

    Science.gov (United States)

    Lazzarino, Giuseppe; Amorini, Angela Maria; Di Pietro, Valentina; Tavazzi, Barbara

    2011-01-01

    The determination of purines and pyrimidines in biofluids is useful for the clinical-biochemical characterization of acute and chronic pathological states that induce transient or permanent alterations of metabolism. In particular, the diagnosis of several inborn errors of metabolism (IEMs) is accomplished by the analysis of circulating and excreted purines and pyrimidines. It is certainly advantageous to simultaneously determine the full purine and pyrimidine profile, as well as to quantify other compounds of relevance (e.g., organic acids, amino acids, sugars) in various metabolic hereditary diseases, in order to screen for a large number of IEMs using a reliable and sensitive analytical method characterized by mild to moderate costs. Toward this end, we have developed an ion-pairing HPLC method with diode array detection for the synchronous separation of several purines and pyrimidines. This method also allows the quantification of additional compounds such as N-acetylated amino acids and dicarboxylic acids, the concentrations of which are profoundly altered in different IEMs. The application of the method in the analysis of biological samples from patients with suspected purine and pyrimidine disorders is presented to illustrate its applicability for the clinical-biochemical diagnosis of IEM.

  3. Critical importance of the de novo pyrimidine biosynthesis pathway for Trypanosoma cruzi growth in the mammalian host cell cytoplasm

    Energy Technology Data Exchange (ETDEWEB)

    Hashimoto, Muneaki, E-mail: muneaki@juntendo.ac.jp [Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421 (Japan); Morales, Jorge; Fukai, Yoshihisa; Suzuki, Shigeo; Takamiya, Shinzaburo; Tsubouchi, Akiko; Inoue, Syou [Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421 (Japan); Inoue, Masayuki [Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Kita, Kiyoshi [Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Harada, Shigeharu [Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585 (Japan); Tanaka, Akiko [Systems and Structural Biology Center, RIKEN, Tsurumi, Yokohama 230-0045 (Japan); Aoki, Takashi [Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421 (Japan); Nara, Takeshi, E-mail: tnara@juntendo.ac.jp [Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421 (Japan)

    2012-01-20

    Highlights: Black-Right-Pointing-Pointer We established Trypanosoma cruzi lacking the gene for carbamoyl phosphate synthetase II. Black-Right-Pointing-Pointer Disruption of the cpsII gene significantly reduced the growth of epimastigotes. Black-Right-Pointing-Pointer In particular, the CPSII-null mutant severely retarded intracellular growth. Black-Right-Pointing-Pointer The de novo pyrimidine pathway is critical for the parasite growth in the host cell. -- Abstract: The intracellular parasitic protist Trypanosoma cruzi is the causative agent of Chagas disease in Latin America. In general, pyrimidine nucleotides are supplied by both de novo biosynthesis and salvage pathways. While epimastigotes-an insect form-possess both activities, amastigotes-an intracellular replicating form of T. cruzi-are unable to mediate the uptake of pyrimidine. However, the requirement of de novo pyrimidine biosynthesis for parasite growth and survival has not yet been elucidated. Carbamoyl-phosphate synthetase II (CPSII) is the first and rate-limiting enzyme of the de novo biosynthetic pathway, and increased CPSII activity is associated with the rapid proliferation of tumor cells. In the present study, we showed that disruption of the T. cruzicpsII gene significantly reduced parasite growth. In particular, the growth of amastigotes lacking the cpsII gene was severely suppressed. Thus, the de novo pyrimidine pathway is important for proliferation of T. cruzi in the host cell cytoplasm and represents a promising target for chemotherapy against Chagas disease.

  4. Poly purine.pyrimidine sequences upstream of the beta-galactosidase gene affect gene expression in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Brahmachari Samir K

    2001-10-01

    Full Text Available Abstract Background Poly purine.pyrimidine sequences have the potential to adopt intramolecular triplex structures and are overrepresented upstream of genes in eukaryotes. These sequences may regulate gene expression by modulating the interaction of transcription factors with DNA sequences upstream of genes. Results A poly purine.pyrimidine sequence with the potential to adopt an intramolecular triplex DNA structure was designed. The sequence was inserted within a nucleosome positioned upstream of the β-galactosidase gene in yeast, Saccharomyces cerevisiae, between the cycl promoter and gal 10Upstream Activating Sequences (UASg. Upon derepression with galactose, β-galactosidase gene expression is reduced 12-fold in cells carrying single copy poly purine.pyrimidine sequences. This reduction in expression is correlated with reduced transcription. Furthermore, we show that plasmids carrying a poly purine.pyrimidine sequence are not specifically lost from yeast cells. Conclusion We propose that a poly purine.pyrimidine sequence upstream of a gene affects transcription. Plasmids carrying this sequence are not specifically lost from cells and thus no additional effort is needed for the replication of these sequences in eukaryotic cells.

  5. Two new Pb coordination polymers derived from pyrimidine-2-thiolate: Synthesis, methyl substitution-induced effect and properties

    Science.gov (United States)

    Song, Jiang-Feng; Li, Si-Zhe; Zhou, Rui-Sha; Hu, Tuo-Ping; Shao, Jia; Zhang, Xiao

    2016-07-01

    Two new coordination compounds, {Pb(pymt)2}∞ (1) and {Pb(mpymt)2}∞ (2) (pymt = pyrimidine-2-thiolate and mpymt = 4-methyl-pyrimidine-2-thione) have been synthesized under solvothermal conditions and characterized by elemental analyses, IR spectroscopy, thermogravimetric analysis, powder X-ray diffraction and single-crystal X-ray diffraction. In compounds 1 and 2, pymt- and mpymt- adopt the same coordination modes (μ-1 κN, S and μ2-1 κN, S: 2 κS, N) to interacted with Pb2+, however, different topology structures for compounds 1 and 2 are obtained. Compound 1 displays a one-dimensional (1D) ribbon with square cavity constructed from two double concentric chains of [Pb-S]∞ and [Pb-Pyrimidine] ∞ sharing Pb1 ions. Compound 2 shows 1D polymeric single chain constructed by [Pb-S]∞ and [Pb-methyl-pyrimidine]∞ chains. The results revealed that the methyl groups don't influence the coordination modes of pyrimidine-2-thiolate but directed the structural variations. Moreover, the fluorescent properties of compounds 1 and 2 were investigated.

  6. 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...... differential equation....

  7. Synthesis of novel organo-phosphorus C60 dimers

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Carbon bridged organophosphorus C60 dimers were obtained by the reaction of aminome- thylenebisphosphonate anion with C60 and fully characterized by 1HNMR, 31PNMR, 13CNMR, FT- MALDI-MS, FT-IR, UV-Vis, DEPT and HMBC, and the dimeric compounds undergo hydrolysis by using TMSI.

  8. Local field enhancement: comparing self-similar and dimer nanoantennas

    CERN Document Server

    Pellegrini, Giovanni; Finazzi, Marco; Biagioni, Paolo

    2016-01-01

    We study the local field enhancement properties of self-similar nanolenses and compare the obtained results with the performance of standard dimer nanoantennas. We report that, despite the additional structural complexity, self-similar nanolenses are unable to provide significant improvements over the field enhancement performance of standard plasmonic dimers.

  9. Synthesis,Characterization,and Electrochemical Property of Nanometer Porphyrin Dimer

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A nanometer porphyrin dimer was synthesized with fumaryl chloride as a bridge-linked reagent. The characterization was carried out with elemental analyses, 1H NMR, UV-Vis, and IR spectrometries, and then the electrochemical properties of the porphyrins were studied. The authors found that there was moderate electronic communication between the two porphyrin rings in the nanometer porphyrin dimer.

  10. Loop groups, Clusters, Dimers and Integrable systems

    CERN Document Server

    Fock, V V

    2014-01-01

    We describe a class of integrable systems on Poisson submanifolds of the affine Poisson-Lie groups $\\widehat{PGL}(N)$, which can be enumerated by cyclically irreducible elements the co-extended affine Weyl groups $(\\widehat{W}\\times \\widehat{W})^\\sharp$. Their phase spaces admit cluster coordinates, whereas the integrals of motion are cluster functions. We show, that this class of integrable systems coincides with the constructed by Goncharov and Kenyon out of dimer models on a two-dimensional torus and classified by the Newton polygons. We construct the correspondence between the Weyl group elements and polygons, demonstrating that each particular integrable model admits infinitely many realisations on the Poisson-Lie groups. We also discuss the particular examples, including the relativistic Toda chains and the Schwartz-Ovsienko-Tabachnikov pentagram map.

  11. Pseudo-two-dimensional random dimer lattices

    Energy Technology Data Exchange (ETDEWEB)

    Naether, U., E-mail: naether@unizar.es [Instituto de Ciencia de Materiales de Aragón and Departamento de Física de la Materia Condensada, CSIC – Universidad de Zaragoza, 50009 Zaragoza (Spain); Mejía-Cortés, C.; Vicencio, R.A. [Departamento de Física and MSI – Nucleus for Advanced Optics, Center for Optics and Photonics (CEFOP), Facultad de Ciencias, Universidad de Chile, Santiago (Chile)

    2015-06-05

    We study the long-time wave transport in correlated and uncorrelated disordered 2D arrays. When a separation of dimensions is applied to the model, we find that the previously predicted 1D random dimer phenomenology also appears in so-called pseudo-2D arrays. Therefore, a threshold behavior is observed in terms of the effective size for eigenmodes, as well as in long-time dynamics. A minimum system size is required to observe this threshold, which is very important when considering a possible experimental realization. For the long-time evolution, we find that for correlated lattices a super-diffusive long-range transport is observed. For completely uncorrelated disorder 2D transport becomes sub-diffusive within the localization length and for random binary pseudo-2D arrays localization is observed.

  12. Dimerization and oligomerization of the chaperone calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, Charlotte S; Ryder, L Rebekka; Steinø, Anne;

    2003-01-01

    protein. Using PAGE, urea gradient gel electrophoresis, capillary electrophoresis and MS, we show that dimerization through the SH group can be induced by lowering the pH to 5-6, heating, or under conditions that favour partial unfolding such as urea concentrations above 2.6 m or SDS concentrations above...... 0.025%. Moreover, we show that calreticulin also has the ability to self-oligomerize through noncovalent interactions at urea concentrations above 2.6 m at pH below 4.6 or above pH 10, at temperatures above 40 degrees C, or in the presence of high concentrations of organic solvents (25%), conditions...... urea or 1% SDS, and heat-induced oligomerization could be inhibited by 8 m urea or 1% SDS when present during heating. Comparison of the binding properties of monomeric and oligomeric calreticulin in solid-phase assays showed increased binding to peptides and denatured proteins when calreticulin...

  13. Edge Magnon Excitation in Spin Dimer Systems

    Science.gov (United States)

    Sakaguchi, Ryo; Matsumoto, Masashige

    2016-10-01

    Magnetic excitation in a spin dimer system on a bilayer honeycomb lattice is investigated in the presence of a zigzag edge, where disordered and ordered phases can be controlled by a quantum phase transition. In analogy with the case of graphene with a zigzag edge, a flat edge magnon mode appears in the disordered phase. In an ordered phase, a finite magnetic moment generates a mean-field potential to the magnon. Since the potential is nonuniform on the edge and bulk sites, it affects the excitation, and the dispersion of the edge mode deviates from the flat shape. We investigate how the edge magnon mode evolves when the phase changes through the quantum phase transition and discuss the similarities to ordered spin systems on a monolayer honeycomb lattice.

  14. Molecular Dynamics Simulation of Amyloid Beta Dimer Formation

    CERN Document Server

    Urbanc, B; Ding, F; Sammond, D; Khare, S; Buldyrev, S V; Stanley, H E; Dokholyan, N V

    2004-01-01

    Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce a molecular dynamics approach to study Abeta dimer formation: (1) we use discrete molecular dynamics simulations of a coarse-grained model to identify a variety of dimer conformations, and (2) we employ all-atom molecular mechanics simulations to estimate the thermodynamic stability of all dimer conformations. Our simulations of a coarse-grained Abeta peptide model predicts ten different planar beta-strand dimer conformations. We then estimate the free energies of all dimer conformations in all-atom molecular mechanics simulations with explicit water. We compare the free energies of Abeta(1-42) and Abeta(1-40...

  15. 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 electromagnetic response of an arbitrary dimer based on the Green functions approach. The theory confirms that a great variety of polarization properties, such as birefringence, chirality and elliptical dichroism, can be achieved in a metal layer with such slot-dimer patterning (i.e. in a metasurface). Optical...... properties of the metasurface can be extensively tuned by varying the geometry (shape and dimensions) of the dimer, for example, by adjusting the sizes and mutual placement of the slots (e.g. inter-slot distance and alignment angle). Three basic shapes of dimers are analyzed: II-shaped (parallel slots), V...

  16. Three types of couplings between asymmetric plasmonic dimers.

    Science.gov (United States)

    Chao, Yen-Chun; Tseng, Hsuan-Chi; Chang, Kao-Der; Chang, Chih-Wei

    2012-01-30

    We report extensive numerical studies on plasmonic dimers of different configurations and find that their coupling effects can be categorized into three types of phenomena. First, like ordinary mechanical systems, the plasmonic dimers can exhibit positive couplings that show anti-crossing behavior. Second, they can also be arranged to exhibit negative couplings that display opposite trends in resonant frequency shifts. Third, when there are surface currents in proximity to each other, the resonance frequencies of the dimers exhibit unusual redshifts that do not have any analogies in conventional systems. Our work suggests that in addition to the well-known electric and magnetic dipolar interactions, contributions from the inductance of displacement currents in the near field cannot be ignored. Overall, asymmetric plasmonic dimers exhibit better sensitivities than the symmetric counterparts and our extensive studies also enable us to identify the plasmonic dimer with the highest sensing capabilities.

  17. Heteroaromatization with 4-Hydroxycoumarin Part II: Synthesis of Some New Pyrano[2,3-d]pyrimidines, [1,2,4]triazolo[1,5-c]pyrimidines and Pyrimido[1,6-b]-[1,2,4]triazine Derivatives

    Directory of Open Access Journals (Sweden)

    A. H. Bedair

    2001-05-01

    Full Text Available A variety of novel [1,2,4]triazolo[1,5-c]pyrimidine-13-ones (4a-f and (5b-d could be obtained via reaction of 9-amino-7-(4’-chlorophenyl-8,9-dihydro-8-imino-6H,7H-[1]benzopyrano[3`,4`:5,6]pyrano[2,3-d]pyrimidine-6-one (3 with a variety of reagents. Pyrano[2,3-d]pyrimidine-6-ones 5a, 8a-c and pyrimido[1,6-b][1,2,4]-triazine-3,14-dione (6 were also prepared. The antimicrobial activity of some of the synthesized compounds was tested.

  18. Sensitivity of silver(I) complexes of a pyrimidine-hydrazone ligand to solvent, counteranion, and metal-to-ligand ratio changes.

    Science.gov (United States)

    Hutchinson, Daniel J; Cameron, Scott A; Hanton, Lyall R; Moratti, Stephen C

    2012-05-07

    Metal complexation studies were performed with AgSO(3)CF(3) and AgBF(4) and the ditopic pyrimidine-hydrazone ligand 6-(hydroxymethyl)pyridine-2-carboxaldehyde (2-methylpyrimidine-4,6-diyl)bis(1-methylhydrazone) (1) in both CH(3)CN and CH(3)NO(2) in a variety of metal-to-ligand ratios. The resulting complexes were studied in solution by NMR spectroscopy and in the solid state by X-ray crystallography. Reacting either AgSO(3)CF(3) or AgBF(4) with 1 in either CH(3)CN or CH(3)NO(2) in a 1:1 metal-to-ligand ratio produced a double helicate in solution. This double helicate could be converted into a linear complex by increasing the metal-to-ligand ratio; however, the degree of conversion depended on the solvent and counteranion used. Attempts to crystallize the linear AgSO(3)CF(3) complex resulted in crystals with the dimeric structure [Ag(2)1(CH(3)CN)(2)](2)(SO(3)CF(3))(4) (2), while attempts to crystallize the AgSO(3)CF(3) double helicate from CH(3)CN resulted in crystals of another dimeric complex, [Ag(2)1(SO(3)CF(3))(CH(3)CN)(2)](2)(SO(3)CF(3))(2)·H(2)O (3). The AgSO(3)CF(3) double helicate was successfully crystallized from a mixture of CH(3)CN and CH(3)NO(2) and had the structure [Ag(2)1(2)](SO(3)CF(3))(2)·3CH(3)NO(2) (4). The linear AgBF(4) complex could not be isolated from the double helicate in solution; however, crystals grown from a solution containing both the AgBF(4) double helicate and linear complexes in CH(3)CN had the structure [Ag(2)1(CH(3)CN)(2)](BF(4))(2) (5). The AgBF(4) double helicate could only be crystallized from CH(3)NO(2) and had the structure [Ag(2)1(2)](BF(4))(2)·2CH(3)NO(2) (6).

  19. Studies on Synthesis of Some Novel Heterocyclic Chalcone, Pyrazoline, Pyrimidine - 2 - One, Pyrimidine - 2 - Thione, para-Acetanilide Sulphonyl and Benzoyl Derivatives and their Antimicrobial Activity

    Directory of Open Access Journals (Sweden)

    Rakesh N. Mistry

    2005-01-01

    Full Text Available 1, 2 - Dichloro benzene on chlorosulphonation by chlorosulphonic acid gives 1, 2 - [dichloro] - benzene sulphonyl chloride which on condensation with p –amino acetophenone gives 1-[acetyl] - 1’ , 2’ - [dichloro] - dibenz sulphonamide derivative. This derivative undergo condensation with 2,4- dichloro benzaldehyde gives 1- [3” - (sub. phenyl - 2” - propene - 1” - one] - 1’ , 2’ - [dichloro] - dibenz sulphonamide derivative which on reaction with 99% hydrazine hydrate and glacial acetic acid gives 1-[acetyl]-3- [1’ , 2’ - (dichloro - dibenz sulphonamide] -5 - [2” , 4” - dichloro phenyl] - 2 - pyrazoline derivative. This derivative reacts with various substituted aldehydes to give corresponding substituted chalcone derivatives [1(a-j]. Now, these chalcone derivatives [1(a-j] on condensation with urea gives corresponding substituted pyrimidine - 2 - one derivatives [2(a-j] and on condensation with thio-urea gives corresponding substituted pyrimidine- 2 -thione derivatives [3(a-j]. Further, these chalcone derivatives [1(a-j] on reaction with 99% hydrazine hydrate gives 1 - [1’ - (H - 5’ - (sub. phenyl - 2’ - pyrazoline]- 3 - [1” , 2” - (dichloro - dibenz sulphonamide] - 5 - [2’’’ , 4’’’ - dichloro phenyl]-2- pyrazoline derivatives [4(a-j] as an intermediate compounds, which on condensation with p-acetanilide sulphonyl chloride gives corresponding substituted p - acetanilide sulphonyl derivatives [5(a-j] and on condensation with benzoyl chloride gives corresponding substituted benzoyl derivatives [6(a-j]. Structure elucidation of synthesised compounds has been made on the basis of elemental analysis, I.R. spectral studies and 1H N.M.R. spectral studies. The antimicrobial activity of the synthesised compounds has been studied against the cultures “Staphylococcus aureus”, “Escherichia coli” and “Candela albicans”.

  20. An unusual correlation between ppGpp pool size and rate of ribosome synthesis during partial pyrimidine starvation of Escherichia coli

    DEFF Research Database (Denmark)

    Vogel, Ulla; Pedersen, Steen; Jensen, Kaj Frank

    1991-01-01

    Escherichia coli was exposed to partial pyrimidine starvation by feeding a pyrBI strain orotate as the only pyrimidine source. Subsequently, differential rates of synthesis of rRNA and of a few ribosome-associated proteins as well as the pool sizes of nucleoside triphosphates and ppGpp were...

  1. 1-(2-Ethoxyethyl)-1H-pyrazolo[4,3-d]pyrimidines as potent phosphodiesterase 5 (PDE5) inhibitors.

    Science.gov (United States)

    Tollefson, Michael B; Acker, Brad A; Jacobsen, E J; Hughes, Robert O; Walker, John K; Fox, David N A; Palmer, Michael J; Freeman, Sandra K; Yu, Ying; Bond, Brian R

    2010-05-15

    1H-Pyrazolo[4,3-d]pyrimidines are a class of potent and selective second generation phosphodiesterase 5 (PDE5) inhibitors. This work explores the potency, selectivity and efficacy of 1-(2-ethoxyethyl)-1H-pyrazolo[4,5-d]pyrimidines as PDE5 inhibitors resulting in the advancement of a clinical candidate.

  2. Synthesis and Antimicrobial Activity of some Tetrahydro Quinolone Diones and Pyrano[2,3-d]pyrimidine Derivatives

    Science.gov (United States)

    Shahi, Masoume; Foroughifar, Naser; Mobinikhaledi, Akbar

    2015-01-01

    There has been special interest in the chemistry of quinolone and pyrimidine derivatives due to their diverse biological activities such as anticonvulsant, anti-malarial agents, antibacterial, antiviral, cytostatic, antithelemintic, antigenotoxic, anti-cancer agents. These compounds are also used as targeting delayed-type hypersensivity and anti-convulsant agents. As a part of our research works in the synthesis of pyrimidine derivatives containing biological activities, a series of novel pyrano[2,3-d]pyrimidine derivatives 2 and tetrahydro quinolone dione derivatives 3 were synthesized via reaction of tetrahydrobenzo[b]pyrano derivatives 1 with different reagents in suitable yields. The characterization of these synthesized compounds was established by IR, 1H NMR and 13C NMR spectroscopic data. Furthermore, all compounds were subsequently evaluated for their in-vitro antibacterial activity against three bacteria: Staphylococcus aureus (ATTC-25923), Escherichia Coli (ATTC-25922) and Bacillus anthracic (ATTC-25924). PMID:26330864

  3. A study of the valence shell photoionisation dynamics of pyrimidine and pyrazine

    Energy Technology Data Exchange (ETDEWEB)

    Holland, D.M.P., E-mail: david.holland@stfc.ac.uk [Daresbury Laboratory, Daresbury, Warrington, Cheshire WA4 4AD (United Kingdom); Potts, A.W. [Department of Physics, King' s College, Strand, London WC2R 2LS (United Kingdom); Karlsson, L. [Department of Physics, Uppsala University, Box 530, SE-751 21 Uppsala (Sweden); Stener, M.; Decleva, P. [Dipartimento di Scienze Chimiche, Universita di Trieste, Via L. Giorgieri, I-34127 Trieste (Italy); Consorzio Interuniversitario Nazionale per la Scienze e Tecnologia dei Materiali, INSTM, Unita' di Trieste, Via L. Giorgieri, I-34127 Trieste (Italy); CNR-IOM, Area Science Park - Basovizza, Strada Statale 14 km 163,5, I-34149 Trieste (Italy)

    2011-11-18

    Graphical abstract: The complete valence shell photoelectron spectra of pyrimidine and pyrazine have been recorded with synchrotron radiation and interpreted with the aid of vertical ionisation energies and relative spectral intensities calculated using time-dependent density functional theory. Highlights: Black-Right-Pointing-Pointer Valence shell photoelectron spectra of pyrimidine and pyrazine have been recorded. Black-Right-Pointing-Pointer Many-body effects are important. Black-Right-Pointing-Pointer Photoionisation dynamics are affected by shape resonances. Black-Right-Pointing-Pointer Theoretical predictions for single-hole ionic states are satisfactory. - Abstract: The complete valence shell photoelectron spectra of pyrimidine and pyrazine have been recorded with synchrotron radiation and the observed structure has been interpreted with the aid of vertical ionisation energies and relative spectral intensities calculated using time-dependent density functional theory. The theoretical predictions for the single-hole ionic states due to outer valence shell ionisation agree satisfactorily with the experimental results. Ionisation from the inner valence orbitals is strongly influenced by many-body effects and the intensity associated with a particular orbital is spread amongst numerous satellites. Photoelectron angular distributions and partial cross sections have been determined both experimentally and theoretically, and demonstrate that shape resonances affect the valence shell photoionisation dynamics. In addition to shape resonances occurring a few eV above the ionisation threshold, the calculations indicate that many of the orbitals are influenced by shape resonant processes at much higher energies. Some of these higher energy resonances have been confirmed through a comparison between the relevant theoretical and experimental photoelectron asymmetry parameters. The spectral behaviour of asymmetry parameters associated with {pi}-orbitals has been shown to

  4. Irradiation of pyrimidine in pure H2O ice with high-energy ultraviolet photons.

    Science.gov (United States)

    Nuevo, Michel; Chen, Yu-Jung; Hu, Wei-Jie; Qiu, Jun-Ming; Wu, Shang-Ruei; Fung, Hok-Sum; Chu, Ching-Chi; Yih, Tai-Sone; Ip, Wing-Huen; Wu, C-Y Robert

    2014-02-01

    The detection of nucleobases, the informational subunits of DNA and RNA, in several meteorites suggests that these compounds of biological interest were formed via astrophysical, abiotic processes. This hypothesis is in agreement with recent laboratory studies of irradiation of pyrimidine in H2O-rich ices with vacuum UV photons emitted by an H2-discharge lamp in the 6.9-11.3 eV (110-180 nm) range at low temperature, shown to lead to the abiotic formation of several compounds including the nucleobases uracil, cytosine, and thymine. In this work, we irradiated H2O:pyrimidine ice mixtures under astrophysically relevant conditions (14 K, ≤10(-9) torr) with high-energy UV photons provided by a synchrotron source in three different ranges: the 0(th) order light (4.1-49.6 eV, 25-300 nm), the He i line (21.2 eV, 58.4 nm), and the He ii line (40.8 eV, 30.4 nm). The photodestruction of pyrimidine was monitored with IR spectroscopy, and the samples recovered at room temperature were analyzed with liquid and gas chromatographies. Uracil and its precursor 4(3H)-pyrimidone were found in all samples, with absolute and relative abundances varying significantly from one sample to another. These results support a scenario in which compounds of biological interest can be formed and survive in environments subjected to high-energy UV radiation fields.

  5. Synthesis, solid-state fluorescence properties, and computational analysis of novel 2-aminobenzo[4,5]thieno[3,2-d]pyrimidine 5,5-dioxides

    Directory of Open Access Journals (Sweden)

    Kenichirou Yokota

    2012-02-01

    Full Text Available New fluorescent compounds, benzo[4,5]thieno[3,2-d]pyrimidine 5,5-dioxides (3a–g, 2-amino-4-methylsulfanylbenzo[4,5]thieno[3,2-d]pyrimidine (6, and 2-amino-4-methylsulfanyl-7-methoxybenzo[4,5]furo[3,2-d]pyrimidine (7, were synthesized in good yields from heterocyclic ketene dithioacetals (1a–c and guanidine carbonate (2a or (S-methylisothiourea sulfate (2b in pyridine under reflux. Among the fused pyrimidine derivatives, compound 3c, which has an amino group at the 2-position and a benzylamino group at the 4-position of the pyrimidine ring, showed the strongest solid-state fluorescence. The absorption and emission properties of the compounds were quantitatively reproduced by a series of ab initio quantum-chemical calculations.

  6. Measurement of small scalar and dipolar couplings in purine and pyrimidine bases.

    Science.gov (United States)

    Zídek, L; Wu, H; Feigon, J; Sklenár, V

    2001-10-01

    A suite of spin-state-selective excitation (S3E) NMR experiments for the measurements of small one-bond (13C-13C, 15N-13C) and two-bond (1H-13C, 1H-15N) coupling constants in 13C,15N labeled purine and pyrimidine bases is presented. The incorporation of band-selective shaped pulses, elimination of the cross talk between alpha and beta sub-spectra, and accuracy and precision of the proposed approach are discussed. Merits of using S3E rather than alpha/beta-half-filter are demonstrated using results obtained on isotopically labeled DNA oligonucleotides.

  7. Antagonists of the human A(2A) receptor. Part 6: Further optimization of pyrimidine-4-carboxamides.

    Science.gov (United States)

    Gillespie, Roger J; Bamford, Samantha J; Clay, Alex; Gaur, Suneel; Haymes, Tim; Jackson, Philip S; Jordan, Allan M; Klenke, Burkhard; Leonardi, Stefania; Liu, Jeanette; Mansell, Howard L; Ng, Sean; Saadi, Mona; Simmonite, Heather; Stratton, Gemma C; Todd, Richard S; Williamson, Douglas S; Yule, Ian A

    2009-09-15

    Antagonists of the human A(2A) receptor have been reported to have potential therapeutic benefit in the alleviation of the symptoms associated with neurodegenerative movement disorders such as Parkinson's disease. As part of our efforts to discover potent and selective antagonists of this receptor, we herein describe the detailed optimization and structure-activity relationships of a series of pyrimidine-4-carboxamides. These optimized derivatives display desirable physiochemical and pharmacokinetic profiles, which have led to promising oral activity in clinically relevant models of Parkinson's disease.

  8. Methylpalladium complexes with pyrimidine-functionalized N-heterocyclic carbene ligands

    Science.gov (United States)

    Meyer, Dirk

    2016-01-01

    Summary A series of methylpalladium(II) complexes with pyrimidine-NHC ligands carrying different aryl- and alkyl substituents R ([((pym)^(NHC-R))PdII(CH3)X] with X = Cl, CF3COO, CH3) has been prepared by transmetalation reactions from the corresponding silver complexes and chloro(methyl)(cyclooctadiene)palladium(II). The dimethyl(1-(2-pyrimidyl)-3-(2,6-diisopropylphenyl)imidazolin-2-ylidene)palladium(II) complex was synthesized via the free carbene route. All complexes were fully characterized by standard methods and in three cases also by a solid state structure. PMID:27559406

  9. Synthesis, in vitro antimicrobial and cytotoxic activities of novel pyrimidine-benzimidazol combinations.

    Science.gov (United States)

    Chen, Peng-Ju; Yang, Ang; Gu, Yi-Fei; Zhang, Xiao-Song; Shao, Kun-Peng; Xue, Deng-Qi; He, Peng; Jiang, Teng-Fei; Zhang, Qiu-Rong; Liu, Hong-Min

    2014-06-15

    A series of novel 4-substituted-2-{[(1H-benzo[d]imidazol-2-yl)methyl] thio}-6-methylpyrimidine derivatives were designed, synthesized and evaluated for their cytotoxic activities against four human cancer cell lines and inhibitory activities against five type culture strains in vitro. Some of synthetic pyrimidine-benzimidazol combinations showed good inhibitory activities against Stenotrophomonas maltophilia, especially compounds 7b and 7c. Compounds 7a and 7d exhibited enhanced activities against MGC-803 in vitro, when compared to 5-Fu.

  10. Polymerization in Liquid Crystal Medium: Preparation of Polythiophene Derivatives Bearing a Bulky Pyrimidine Substituent

    Directory of Open Access Journals (Sweden)

    Hiromasa Goto

    2010-10-01

    Full Text Available We carried out polycondensation of monomers bearing a bulky pyrimidine substituent in a liquid crystal solvent. The resultant polymers formed nematic liquid crystals. The polymers prepared in liquid crystals had higher coplanarity than the polymers prepared in toluene. This can be due to the fact that the ordered medium of the liquid crystal produces an aggregated structure with well-developed π-stacking between the main chains. The present results demonstrated that polymerization of bulky monomers is possible in liquid crystal solvents.

  11. [Quantum-chemical investigation of the elementary molecular mechanisms of pyrimidine-purine transversions].

    Science.gov (United States)

    Brovarets', O O; Govorun D M

    2010-01-01

    Purine-purine mispairs of DNA (thus involving template base in anti-conformation along the glycosidic bond and base of the incoming nucleotide - in syn-conformation) leading to pyrimidine-purine "transversions"-type point mutations were revealed and characterized at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory in vacuum approach adequately modeling hydrophobic environment of the active centre of high-fidelity replicative DNA-polymerases.

  12. Efficient and Selective Construction of Pyrrolo[3,2-d]pyrimidine Derivatives

    Energy Technology Data Exchange (ETDEWEB)

    He, Ping; Wu, Jing; Hu, Yanggen; Li, Zaifang; Hou, Qiufei; Wang, Yanling; Zhao, Kun; Zhang, Erli [Hubei Univ. of Arts and Science, Xiangyang (China)

    2014-02-15

    An efficient and selective method for the synthesis of ethyl 2-amino/aryloxy-3-aryl-4-oxo-5-phenyl-4,5-dihydro-3H-pyrrolo[3,2-d] pyrimidine-7-carboxylate derivatives has been developed. The main process involved the reaction of diethyl 1-phenyl-3-((triphenylphosphoranylidene)amino)-1H-pyrrole-2,4-dicarboxylate and aromatic isocyanates, followed by addition of amines/phenols in the presence of catalytic amount of sodium ethoxide or solid potassium carbonate.

  13. An Efficient Microwave-assisted Synthesis of Pyrido[2,3-d]pyrimidine Derivatives

    Institute of Scientific and Technical Information of China (English)

    TU Shujiang; WU Shanshan; HAN Zhengguo; HAO Wenjuan

    2009-01-01

    A series of new pyrido[2,3-d]pyrimidine derivatives were synthesized by multi-component reactions of equi-molar amount of aromatic aldehydes with barbituric acids (barbituric acid or 1,3-dimethylbarbituric acid) and 5-amino-2-methylbenzo[d]thiazol in mixed solvent of glacial acetic acid and ethylene glycol without catalyst under microwave irradiation. This one-pot method has the advantage of good yields (90%-93%), simple workup proce-dure and short reaction time (5 min).

  14. Acceleration of 5-methylcytosine deamination in cyclobutane dimers by G and its implications for UV-induced C-to-T mutation hotspots.

    Science.gov (United States)

    Cannistraro, Vincent J; Taylor, John-Stephen

    2009-10-01

    Sunlight-induced C-->T mutation hotspots occur most frequently at methylated CpG sites in tumor suppressor genes and are thought to arise from translesion synthesis past deaminated cyclobutane pyrimidine dimers (CPDs). While it is known that methylation enhances CPD formation in sunlight, little is known about the effect of methylation and sequence context on the deamination of 5-methylcytosine ((m)C) and its contribution to mutagenesis at these hotspots. Using an enzymatic method, we have determined the yields and deamination rates of C and (m)C in CPDs and find that the frequency of UVB-induced CPDs correlates with the oxidation potential of the flanking bases. We also found that the deamination of T(m)C and (m)CT CPDs is about 25-fold faster when flanked by G's than by A's, C's or T's in duplex DNA and appears to involve catalysis by the O6 group of guanine. In contrast, the first deamination of either C or (m)C in AC(m)CG with a flanking G was much slower (t(1/2) >250 h) and rate limiting, while the second deamination was much faster. The observation that C(m)CG dimers deaminate very slowly but at the same time correlate with C-->T mutation hotspots suggests that their repair must be slow enough to allow sufficient time for deamination. There are, however, a greater number of single C-->T mutations than CC-->TT mutations at C(m)CG sites even though the second deamination is very fast, which could reflect faster repair of doubly deaminated dimers.

  15. A convenient four-component one-pot strategy toward the synthesis of pyrazolo[3,4-d]pyrimidines

    Directory of Open Access Journals (Sweden)

    Mingxing Liu

    2015-11-01

    Full Text Available An efficient one-pot synthesis of pyrazolo[3,4-d]pyrimidine derivatives by the four-component condensation of hydrazines, methylenemalononitriles, aldehydes and alcohols has been developed via two different reaction pathways. The structures of target products were characterized by IR spectroscopy, NMR (1H and 13C spectroscopy and HRMS (ESI spectrometry. The crystal structure of 4-ethoxy-6-(2-nitrophenyl-1-phenyl-1H-pyrazolo[3,4-d]pyrimidine was determined by single crystal X-ray diffraction.

  16. Threshold electron attachment and electron impact ionization involving oxygen dimers

    Science.gov (United States)

    Kreil, J.; Ruf, M.-W.; Hotop, H.; Ettischer, I.; Buck, U.

    1998-12-01

    Using two different crossed-beams machines we have carried out the first quantitative study of threshold electron attachment and electron impact-induced ionization and fragmentation involving oxygen dimers (O 2) 2. In the electron attachment experiment we study electron transfer from state-selected Ar **(20d) Rydberg atoms to O 2 molecules and dimers in a skimmed supersonic beam at variable nozzle temperatures ( T0) and stagnation pressures ( p0). The relative dimer density is determined through measurements of Penning ionization by metastable Ne *(3s 3P2,0) atoms and used to estimate the absolute cross-section for O 2- formation in collisions of Ar **(20d) Rydberg atoms with O 2 dimers to be nearly 10 -17 m 2, almost four orders of magnitude larger than that for O 2- formation in collisions of Ar **(20d) Rydberg atoms with O 2 monomers. The fragmentation of the oxygen cluster beam is quantitatively characterized by the transverse helium beam scattering method which allows us to spatially separate different clusters. It is shown that in 70 eV electron impact of (O 2) 2 only 3.6(4)% of the dimers are detected as dimer ions (O 2) 2+. In additional experiments involving SF 6 clusters we show that SF 6 dimers fragment nearly completely upon 70 eV electron impact, yielding SF 5+ ions (probability for (SF 6)·SF 5+ production at most 0.3%).

  17. 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.

  18. Stochastic optimization-based study of dimerization kinetics

    Indian Academy of Sciences (India)

    Srijeeta Talukder; Shrabani Sen; Ralf Metzler; Suman K Banik; Pinaki Chaudhury

    2013-11-01

    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 techniques (genetic algorithm, simulated annealing and parallel tempering) to obtain the rate constants involved in each reaction step. We find good convergence of the numerical scheme to the rate constants of the process. We also perform a sensitivity test on the reaction kinetic parameters to see the relative effects of the parameters for the associated profile of the monomer/dimer distribution.

  19. 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....

  20. Circular dimers of lambda DNA in infected, nonlysogenic Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Freifelder, D.; Baran, N.; Folkmanis, A.; Freifelder, D.L.R.

    1977-09-01

    Covalently closed circular dimerss of phage lambda DNA have been found in Escherichia coli infected with lambda. These dimers can be formed by either the lambda Red or Int systems, by a nonrecombinational replicative mechanism requiring the activity of the lambda O and P genes or by joining of the cohesive ends. Dimers mediated by the E. coli Rec system have not been observed. Those formed by the Int system often result from recombination between different DNA molecules; however, the Red-mediated dimer may be a result of replicative extension of a single DNA molecule. Trimers have also been observed but studied only briefly.

  1. Time resolved structural dynamics of butadiyne-linked porphyrin dimers.

    Science.gov (United States)

    Camargo, Franco V A; Hall, Christopher R; Anderson, Harry L; Meech, Stephen R; Heisler, Ismael A

    2016-03-01

    In this work, the timescales and mechanisms associated with the structural dynamics of butadiyne-linked porphyrin dimers are investigated through time resolved narrowband pump/broadband probe transient absorption spectroscopy. Our results confirm previous findings that the broadening is partly due to a distribution of structures with different (dihedral) angular conformations. Comparison of measurements with excitations on the red and blue sides of the Q-band unravel the ground and excited state conformational re-equilibration timescales. Further comparison to a planarized dimer, through the addition of a ligand, provides conclusive evidence for the twisting motion performed by the porphyrin dimer in solution.

  2. Time resolved structural dynamics of butadiyne-linked porphyrin dimers

    Directory of Open Access Journals (Sweden)

    Franco V. A. Camargo

    2016-03-01

    Full Text Available In this work, the timescales and mechanisms associated with the structural dynamics of butadiyne-linked porphyrin dimers are investigated through time resolved narrowband pump/broadband probe transient absorption spectroscopy. Our results confirm previous findings that the broadening is partly due to a distribution of structures with different (dihedral angular conformations. Comparison of measurements with excitations on the red and blue sides of the Q-band unravel the ground and excited state conformational re-equilibration timescales. Further comparison to a planarized dimer, through the addition of a ligand, provides conclusive evidence for the twisting motion performed by the porphyrin dimer in solution.

  3. Multicritical tensor models and hard dimers on spherical random lattices

    CERN Document Server

    Bonzom, Valentin

    2012-01-01

    Random tensor models which display multicritical behaviors in a remarkably simple fashion are presented. They come with entropy exponents \\gamma = (m-1)/m, similarly to multicritical random branched polymers. Moreover, they are interpreted as models of hard dimers on a set of random lattices for the sphere in dimension three and higher. Dimers with their exclusion rules are generated by the different interactions between tensors, whose coupling constants are dimer activities. As an illustration, we describe one multicritical point, which is interpreted as a transition between the dilute phase and a crystallized phase, though with negative activities.

  4. How to use D-dimer in acute cardiovascular care

    DEFF Research Database (Denmark)

    Giannitsis, Evangelos; Mair, Johannes; Christersson, Christina

    2015-01-01

    D-dimer testing is important to aid in the exclusion of venous thromboembolic events (VTEs), including deep venous thrombosis and pulmonary embolism, and it may be used to evaluate suspected aortic dissection. D-dimer is produced upon activation of the coagulation system with the generation and s...... testing. For the exclusion of pulmonary embolism/deep vein thrombosis, age-adjusted cut-offs are recommend. Clinicians must be aware of the validated use of their hospital's D-dimer assay to avoid inappropriate use of this biomarker in routine care....

  5. Third-Order Optical Nonlinearity in Novel Porphyrin Dimers

    Institute of Scientific and Technical Information of China (English)

    PEI Song-Hao; ZHAO Da-Peng; ZHANG Wei; ZHENG Wen-Qi; WANG Xing-Qiao; PENG Wei-Xian; SHI Guang; SONG Ying-Lin

    2008-01-01

    @@ We investigate the third-order optical nonlinearities in four novel porphyrin dimers (directs A to I)) and a monomeric porphyrin H2 CPTPP measured by using the single-beam z-scan technique with a pulsed Q-switched Nd:YAG nanosecond laser at 532nm.All the samples show strong excited state absorption (ESA) and high value of X(3) in the ns domain at this wavelength.We perform a comparison between dimer A and its monomer H2 CPTPP in their third-order optical nonlinearity, and discuss the relationships between the values of X(3) and the different bridging groups for all the dimers.

  6. 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.

  7. Stabilities and Spectroscopy of Hydrogen Bonding Complexes Formed by 2,4-Bis(acrylamido)pyrimidines

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ye; LI Ting; TENG Qi-Wen

    2008-01-01

    Hydrogen bonds play important roles to living organisms containing pyrimidine-based derivatives.The electronic structures of the hydrogen bonding complexes formed by 2,4-bis(acrylamido)pyrimidine (2,4-BAAP) derivatives with 1-substituted uracil were studied using Austin Model 1 (AMl) and density function theory (DFT) methods.The UV and NMR spectra of the complexes were calculated with the INDO/CIS (configuration interaction for singlet in intermediate neglect of differential overlap) and B3LYP/6-31G(d)methods.It was shown that the complexes could be formed via the triple hydrogen bonding between two monomers owing to the negative binding energies.The binding energies of the complexes were weakened in the presence of substituents,but this weakening effect depended on the simultaneous influence of the electronic and steric effects.The binding energies of the complexes were also decreased owing to the formation of the isomeric complexes in the presence of piperidyl on 2,4-BAAP.The energy gaps of the complexes were lessened in the presence of electron-donating groups.Holes and electrons were easily injected to the complexes due to the extension of the conjugation chain.The first UV absorptions of the complexes relative to those of the parent compound were red-shifted because of the narrow energy gaps.The chemical shifts of the carbon atoms on the C=O bonds in the complexes were changed downfield.

  8. Formation of Nucleobases from the UV Photo-Irradiation of Pyrimidine in Astrophysical Ice Analogs

    Science.gov (United States)

    Milam, S. N.; Nuevo, M.; Sandford, S. A.; Elsila, J. E.; Dworkin, J. P.

    2010-01-01

    Astrochemistry laboratory simulations have shown that complex organic molecules including compounds of astrobiological interest can be formed under interstellarl/circumstellar conditions from the vacuum UV irradiation of astrophysical ice analogs containing H2O, CO, CO2, CH3OH, NH13, etc. Of all prebiotic compounds, the formation of amino acids under such experimental conditions has been the most extensively studied. Although the presence of amino acids in the interstellar medium (ISM) has yet to be confirmed, they have been detected in meteorites, indicating that biomolecules and/or their precursors can be formed under extraterrestrial, abiotic conditions. Nucleobases, the building blocks of DNA and RNA, as well as other 1V-heterocycles, have also been detected in meteorites, but like amino acids, they have yet to be observed in the ISM. In this work, we present an experimental study of the formation of pyrimidine-based compounds from the UV photo-irradiation of pyrimidine in ice mixtures containing H2O, NH3, and/or CH3OH at low temperature and pressure.

  9. Purine and pyrimidine nucleosides preserve human astrocytoma cell adenylate energy charge under ischemic conditions.

    Science.gov (United States)

    Balestri, Francesco; Giannecchini, Michela; Sgarrella, Francesco; Carta, Maria Caterina; Tozzi, Maria Grazia; Camici, Marcella

    2007-02-01

    The brain depends on both glycolysis and mitochondrial oxidative phosphorylation for maintenance of ATP pools. Astrocytes play an integral role in brain functions providing trophic supports and energy substrates for neurons. In this paper, we report that human astrocytoma cells (ADF) undergoing ischemic conditions may use both purine and pyrimidine nucleosides as energy source to slow down cellular damage. The cells are subjected to metabolic stress conditions by exclusion of glucose and incubation with oligomycin (an inhibitor of oxidative phosphorylation). This treatment brings about a depletion of the ATP pool, with a concomitant increase in the AMP levels, which results in a significant decrease of the adenylate energy charge. The presence of purine nucleosides in the culture medium preserves the adenylate energy charge, and improves cell viability. Besides purine nucleosides, also pyrimidine nucleosides, such as uridine and, to a lesser extent, cytidine, are able to preserve the ATP pool. The determination of lactate in the incubation medium indicates that nucleosides can preserve the ATP pool through anaerobic glycolysis, thus pointing to a relevant role of the phosphorolytic cleavage of the N-glycosidic bond of nucleosides which generates, without energy expense, the phosphorylated pentose, which through the pentose phosphate pathway and glycolysis can be converted to energetic intermediates also in the absence of oxygen. In fact, ADF cells possess both purine nucleoside phosphorylase and uridine phosphorylase activities.

  10. OCLI-023, a Novel Pyrimidine Compound, Suppresses Osteoclastogenesis In Vitro and Alveolar Bone Resorption In Vivo

    Science.gov (United States)

    Kim, Ju Ang; Lee, Doohyun; Kim, Nam Doo; Shin, Hong-In; Bae, Yong Chul; Park, Eui Kyun

    2017-01-01

    An abnormal increase in osteoclast differentiation and activation results in various bone-resorptive diseases, including periodontitis, rheumatoid arthritis, and osteoporosis. Chemical compounds containing pyrimidine ring have been shown to regulate a variety of biological processes. Therefore, in order to identify an antiresorptive agent, we synthesized a series of pyrimidine ring-containing chemical compounds, and found that OCLI-023 suppressed the differentiation and activation of osteoclasts in vitro. OCLI-023 directly inhibited receptor activator of nuclear factor-κB ligand (RANKL)-induced differentiation of bone marrow macrophages into osteoclasts, without a cytotoxic response. OCLI-023 also downregulated the RANKL-induced mRNA expression of osteoclast markers as well as inhibited the formation of actin rings and resorption pits. OCLI-023 attenuated the RANKL-induced activation of c-Jun N-terminal kinase and nuclear factor kappa-light-chain-enhancer of activated B cell signaling pathways. In a mouse model of periodontitis, ligature induced an increase of distance between cementoenamel junction (CEJ) and alveolar bone crest (ABC) in the second molar, and OCLI-023 significantly reduced it. Histological analysis showed ligature-induced increase of osteoclast numbers was also significantly reduced by OCLI-023. These data demonstrated the inhibitory effect of OCLI-023 on osteoclast differentiation and activity of osteoclasts in vitro, as well as on ligature-induced bone loss in vivo, and OCLI-023 can be proposed as a novel anti-resorptive compound. PMID:28085946

  11. Smectic Phase Formed by DNA Dimers

    Science.gov (United States)

    Salamonczyk, Miroslaw; Gleeson, James; Jakli, Antal; Sprunt, Samuel; Dhont, Jan; Stiakakis, Emmanuel

    The rapidly expanding bio market is driving the development and characterization of new multifunctional materials. In particular, nucleic acids are under intense study for gene therapy, drug delivery and other bio-safe applications [1,2,3]. DNA is well-known to form a cholesteric nematic liquid crystal in its native form; however, much recent research has focused on self-assembly and mesomorphic behavior in concentrated solutions of short DNA helices [4]. Our work focuses on DNA dimers, consisting of 48 base-pair double-stranded helices connected by a 5 to 20 base flexible single strand, and suspended in a natural buffer. Depending on temperature, concentration and length of the flexible spacer, polarizing optical microscopy and small angle x-ray scattering reveal cholesteric nematic and, remarkably, smectic liquid crystalline phases. A model for smectic phase formation in this system will be presented. 1] J.-L. Lim et al., Int. J. of. Pharm. 490 (2015) 2652] D.-H. Kim et al., Nature Biotech. 23 (2005) 2223] K. Liu et al., Chem. Eur. J. 21 (2015) 48984] M. Nakata et al., Science 318 (2007) 1276 NSF DMR 1307674.

  12. Vibrations of the carbon dioxide dimer

    Science.gov (United States)

    Chen, Hua; Light, J. C.

    2000-03-01

    Fully coupled four-dimensional quantum-mechanical calculations are presented for intermolecular vibrational states of rigid carbon dioxide dimer for J=0. The Hamiltonian operator is given in collision coordinates. The Hamiltonian matrix elements are evaluated using symmetrized products of spherical harmonics for angles and a potential optimized discrete variable representation (PO-DVR) for the intermolecular distance. The lowest ten or so states of each symmetry are reported for the potential energy surface (PES) given by Bukowski et al. [J. Chem. Phys. 110, 3785 (1999)]. Due to symmetries, there is no interconversion tunneling splitting for the ground state. Our calculations show that there is no tunneling shift of the ground state within our computation precision (0.01 cm-1). Analysis of the wave functions shows that only the ground states of each symmetry are nearly harmonic. The van der Waals frequencies and symmetry adapted force constants are found and compared to available experimental values. Strong coupling between the stretching coordinates and the bending coordinates are found for vibrationally excited states. The interconversion tunneling shifts are discussed for the vibrationally excited states.

  13. Synthesis and evaluation of a classical 2,4-diamino-5-substituted-furo[2,3-d]pyrimidine and a 2-amino-4-oxo-6-substituted-pyrrolo[2,3-d]pyrimidine as antifolates☆

    Science.gov (United States)

    Gangjee, Aleem; Yang, Jie; McGuire, John J.; Kisliuk, Roy L.

    2013-01-01

    Two classical antifolates, a 2,4-diamino-5-substituted furo[2,3-d]pyrimidine and a 2-amino-4-oxo-6-substituted pyrrolo[2,3-d]pyrimidine, were synthesized as potential inhibitors of dihydrofolate reductase (DHFR) and thymidylate synthase (TS). The syntheses were accomplished by condensation of 2,6-diamino-3(H)-4-oxo-pyrimidine with α-chloro-ketone 21 to afford two key intermediates 23 and 24, followed by hydrolysis, coupling with l-glutamate diethyl ester and saponification of the diethyl ester to afford the classical antifolates 13 and 14. Compounds 13 and 14 with a single carbon atom bridge are both substrates for folylpoly-γ-glutamate synthetase (FPGS), the enzyme responsible for forming critical poly-γ-glutamate antifolate metabolites with increased potency and/or increased cell retention. Compound 14 is a highly efficient FPGS substrate demonstrating that 2,4-diamino-5-substituted furo[2,3-d]pyrimidines are important lead structures for the design of antifolates with FPGS substrate activity. It retains inhibitory potency for DHFR and TS compared to the two atom bridged analog 5. Compound 13 is a poor inhibitor of purified DHFR and TS, and both 13 and 14 are poor inhibitors of the growth of CCRF-CEM human leukemia cells in culture, indicating that single carbon bridged compounds in these series though conducive to FPGS substrate activity were not potent inhibitors. PMID:16990006

  14. Family C 7TM receptor dimerization and activation

    DEFF Research Database (Denmark)

    Bonde, Marie Mi; Sheikh, Søren P; Hansen, Jakob Lerche

    2006-01-01

    The family C seven transmembrane (7TM) receptors constitutes a small and especially well characterized subfamily of the large 7TM receptor superfamily. Approximately 50% of current prescription drugs target 7TM receptors, this biologically important family represents the largest class of drug......-targets today. It is well established that family C 7TM receptors form homo- or hetero-dimers on the cell surface of living cells. The large extra-cellular domains (ECD) have been crystallized as a dimer in the presence and absence of agonist. Upon agonist binding, the dimeric ECD undergoes large conformational...... 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....

  15. Metallothionein dimers studied by nano-spray mass spectrometry.

    Science.gov (United States)

    Hathout, Yetrib; Reynolds, Kristy J; Szilagyi, Zoltan; Fenselau, Catherine

    2002-01-15

    Both transient and stable dimers of metallothionein have been characterized, based on earlier studies using NMR, circular dichroism and size-exclusion chromatography. Here additional characterization is provided by nanospray mass spectrometry. Rapid redistribution of metal ions between monomeric Cd7- and Zn7-metallothionein 2a is monitored by nanospray. An experiment in which theses two forms of the monomeric protein are separated by a dialysis membrane, which will pass metal ions but not proteins, confirms that a transient dimer must form for metal ions to be redistributed. On the other hand, size-exclusion chromatography of reconstituted Zn7- or Cd7-metallothionein revealed the presence of monomeric and dimeric species. These dimers do not equilibrate readily to form monomers and they are shown to be covalent.

  16. 21 CFR 176.120 - Alkyl ketene dimers.

    Science.gov (United States)

    2010-04-01

    ... derived from the fatty acids of animal or vegetable fats and oils. (b) The alkyl ketene dimers are used as... HUMAN CONSUMPTION (CONTINUED) INDIRECT FOOD ADDITIVES: PAPER AND PAPERBOARD COMPONENTS Substances...

  17. [Antioxidant and antibacterial activities of dimeric phenol compounds].

    Science.gov (United States)

    Ogata, Masahiro

    2008-08-01

    We studied the antioxidant and antibacterial activities of monomeric and dimeric phenol compounds. Dimeric compounds had higher antioxidant activities than monomeric compounds. Electron spin resonance spin-trapping experiments showed that phenol compounds with an allyl substituent on their aromatic rings directly scavenged superoxide, and that only eugenol trapped hydroxyl radicals. We developed a generation system of the hydroxyl radical without using any metals by adding L-DOPA and DMPO to PBS or MiliQ water in vitro. We found that eugenol trapped hydroxyl radicals directly and is metabolized to a dimer. On the other hand, dipropofol, a dimer of propofol, has strong antibacterial activity against Gram-positive bacteria. However, it lacks solubility in water and this property is assumed to limit its efficacy. We tried to improve the solubility and found a new solubilization method of dipropofol in water with the addition of a monosaccharide or ascorbic acid.

  18. Gnetuhainin S, a New Resveratrol Dimer from Gnetum hainanense

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Gnetuhainin S, a new resveratrol dimer, was isolated from the lianas of Gnetum hainanense C. Y. Cheng. Its structure and relative configuration were established on the basis of spectroscopic evidence.

  19. UV spectra of benzene isotopomers and dimers in helium nanodroplets

    Science.gov (United States)

    Schmied, Roman; ćarçabal, Pierre; Dokter, Adriaan M.; Lonij, Vincent P. A.; Lehmann, Kevin K.; Scoles, Giacinto

    2004-08-01

    We report spectra of various benzene isotopomers and their dimers in helium nanodroplets in the region of the first Herzberg-Teller allowed vibronic transition 601 1B2u←1A1g (the A00 transition) at ˜260 nm. Excitation spectra have been recorded using both beam depletion detection and laser-induced fluorescence. Unlike for many larger aromatic molecules, the monomer spectra consist of a single "zero-phonon" line, blueshifted by ˜30 cm-1 from the gas phase position. Rotational band simulations show that the moments of inertia of C6H6 in the nanodroplets are at least six-times larger than in the gas phase. The dimer spectra present the same vibronic fine structure (though modestly compressed) as previously observed in the gas phase. The fluorescence lifetime and quantum yield of the dimer are found to be equal to those of the monomer, implying substantial inhibition of excimer formation in the dimer in helium.

  20. DLTS study of the oxygen dimer formation kinetics in silicon

    Science.gov (United States)

    Yarykin, Nikolai; Weber, Jörg

    2009-12-01

    The introduction rates of radiation defects, in particular the X- and M-centers for which the oxygen dimer is a precursor, are investigated as a function of duration of the pre-irradiation heat treatment at 480∘ C in Czochralski-grown silicon both of n- and p-types. The characteristic annealing time to grow the X-center concentration in the n-type crystal is found to be about 1 h in accordance with the model which implies no significant barrier for the dimer formation. The M-center concentration in the p-type crystal is found to be nearly independent of duration of the pre-irradiation annealing after a few minutes transient period. This behavior is ascribed to the stabilization of dimer concentration due to an effective dimer trapping in these samples.

  1. DLTS study of the oxygen dimer formation kinetics in silicon

    Energy Technology Data Exchange (ETDEWEB)

    Yarykin, Nikolai, E-mail: nay@iptm.r [Institute of Microelectronics Technology RAS, 142432 Chernogolovka, Moscow Region (Russian Federation); Weber, Joerg [Technische Universitaet Dresden, 01062 Dresden (Germany)

    2009-12-15

    The introduction rates of radiation defects, in particular the X- and M-centers for which the oxygen dimer is a precursor, are investigated as a function of duration of the pre-irradiation heat treatment at 480 deg. C in Czochralski-grown silicon both of n- and p-types. The characteristic annealing time to grow the X-center concentration in the n-type crystal is found to be about 1 h in accordance with the model which implies no significant barrier for the dimer formation. The M-center concentration in the p-type crystal is found to be nearly independent of duration of the pre-irradiation annealing after a few minutes transient period. This behavior is ascribed to the stabilization of dimer concentration due to an effective dimer trapping in these samples.

  2. Dimer representations of the Temperley-Lieb algebra

    CERN Document Server

    Morin-Duchesne, Alexi; Ruelle, Philippe

    2014-01-01

    A new spin-chain representation of the Temperley-Lieb algebra $TL_n(\\beta=0)$ is introduced and related to the dimer model. Unlike the usual XXZ spin-chain representations of dimension $2^n$, this dimer representation is of dimension $2^{n-1}$. A detailed analysis of its structure is presented and found to yield indecomposable zigzag modules not appearing in traditional spin-chain scenarios.

  3. Theoretical Study on the Intermolecular Interactions of Tetrazole Dimers

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Tetrazole monomers (Ⅰ,Ⅱ) and all of their possible stable dimers (1, 2, 3, 4, 5, 6, 7and 8) were fully optimized by DFT method at the B3LYP/6-311++G** level. Among the eight dimers, there were two 1H-tetrazole dimers, three 2H-tetrazole dimers and three hetero dimers of 1H-tetrazole and 2H-tetrazole. Vibrational frequencies were calculated to ascertain that each structure was stable (no imaginary frequencies). The basis set superposition errors (BSSE) are 2.78,2.28, 2.97, 2.75, 2.74, 2.18, 1.23 and 3.10 kJ/mol, and the zero point energy (ZPE) corrections for the interaction energies are 4.88, 4.18, 3.87, 3.65, 3.54, 3.22, 2.87 and 4.34 kJ/mol for 1, 2, 3, 4, 5, 6,7 and 8, respectively. After BSSE and ZPE corrections, the greatest corrected intermolecular interaction energy ofthe dimers is -43.71 kJ/mol. The charge redistribution mainly occurs on the very small. Natural bond orbital (NBO) analysis was performed to reveal the origin of the interaction. Based on the statistical thermodynamic method, the standard thermodynamic functions, heat capacities (C0p), entropies (S0T) and thermal corrections to enthalpy (H0T), and the changes of thermodynamic properties from monomer to dimer in the temperature range of 200.00 K to 700 K have been obtained. 1H-tetrazole monomer can spontaneously tum into two stable dimers at 298.15 K.

  4. 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....

  5. Quantum Phase Transitions and Dimerized Phases in Frustrated Spin Ladder

    Institute of Scientific and Technical Information of China (English)

    WEN Rui; LIU Guang-Hua; TIAN Guang-Shan

    2011-01-01

    In this paper, we study the phase diagram of a frustrated spin ladder model by applying the bosonization technique and the density-matrix renormalization-group (DMRG) algorithm. Effect of the intra-chain next-nearestneighbor (NNN) super-exchange interaction is investigated in detail and the order parameters are calculated to detect the emergence of the dimerized phases. We find that the intra-chain NNN interaction plays a key role in inducing dimerized phases.

  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. Elucidating the mechanism of cytochrome P450-mediated pyrimidine ring conversion to pyrazole metabolites with the BACE1 inhibitor GNE-892 in rats.

    Science.gov (United States)

    Takahashi, Ryan; Ma, Shuguang; Deese, Alan; Yue, Qin; Kim-Kang, Heasook; Yi, Yijun; Siu, Michael; Hunt, Kevin W; Kallan, Nicholas C; Hop, Cornelis E C A; Liu, Xingrong; Khojasteh, S Cyrus

    2014-05-01

    We investigated an uncommon biotransformation of pyrimidine during the metabolism of GNE-892 ((R)-2-amino-1,3',3'-trimethyl-7'-(pyrimidin-5-yl)-3',4'-dihydro-2'H-spiro[imidazole-4,1'-naphthalen]-5(1H)-one), a β-secretase 1 inhibitor. Three novel metabolites, formed by conversion of pyrimidine to pyrazole, were observed in the (14)C-radiolabeled mass balance study in rats. Their structures were characterized by high-resolution mass spectrometry and nuclear magnetic resonance. Although these metabolites accounted for pyrazole-containing metabolites were formed in vitro with rat hepatocytes and liver microsomes, which supported that they were formed during hepatic metabolism. Further, their generation was inhibited by 1-aminobenzotriazole, indicating involvement of cytochrome P450s. Studies with rat recombinant enzymes identified that CYP2D2 generated the N-hydroxypyrazole metabolite from GNE-892. This biotransformation proceeded through multiple steps from the likely precursor, pyrimidine N-oxide. On the basis of these data, we propose a mechanism in which the pyrimidine is activated via N-oxidation, followed by a second oxidative process that opens the pyrimidine ring to form a formamide intermediate. After hydrolysis of the formamide, a carbon is lost as formic acid, together with ring closure to form the pyrazole ring. This article highlights a mechanistic approach for determining the biotransformation of the pyrimidine to a pyrazole for GNE-892.

  8. [Effect of hydroxylated pyrimidine derivatives on activities of thiamine-dependent enzymes and some parameters of lipid metabolism in mice].

    Science.gov (United States)

    Oparin, D A; Gorenshteĭn, B I; Karaedova, L M; Naruta, E E; Zabrodskaia, S V; Rudiak, T V; Akat'ev, V E; Larin, F S

    1997-01-01

    It has been found that hydroxylated pyrimidine derivatives actively participate in metabolic proceeds related to functioning of vitamin B1-dependent enzymes (transketolase, 2-oxo acid dehydrogenase). Hydroxypyrimidines also induce a significant increase in the levels of total lipids and cholesterol in the mice liver, not changing the phospholipid content.

  9. Consortium analysis of gene and gene–folate interactions in purine and pyrimidine metabolism pathways with ovarian carcinoma risk

    DEFF Research Database (Denmark)

    Kelemen, Linda E; Terry, Kathryn L; Goodman, Marc T

    2014-01-01

    SCOPE: We reevaluated previously reported associations between variants in pathways of one-carbon (1-C) (folate) transfer genes and ovarian carcinoma (OC) risk, and in related pathways of purine and pyrimidine metabolism, and assessed interactions with folate intake. METHODS AND RESULTS: Odds rat...

  10. Synthesis, structural, conformational and DFT studies of N-3 and O-4 alkylated regioisomers of 5-(hydroxypropyl)pyrimidine

    Science.gov (United States)

    Salihović, Mirsada; Osmanović, Amar; Špirtović-Halilović, Selma; Roca, Sunčica; Meščić, Andrijana; Vujisić, Ljubodrag; Trifunović, Snežana; Završnik, Davorka; Sofić, Emin

    2015-07-01

    Because of the great pharmacological potential of the pyrimidine motif, novel C-5 substituted N-3 acyclic and O-4 acyclic pyrimidine derivatives were prepared as an interesting class of compounds for biological evaluation. Introduction of the 2,3-dihydroxypropyl (DHP) and penciclovir (PCV)-like side chains to 2-methoxypyrimidin-4-one (2) afforded a mixture of N- and O-acyclic pyrimidine nucleosides in the ratio of 54: 29 (3:4) and 57:21 (5:6) with N-3 isomer being dominant. Distinction between N- and O-alkylated pyrimidine moiety was deduced from extensive experimental FT-IR, HPLC-MS and 1D (1H, 13C) and 2D (COSY, HMQC and HMBC) NMR analyses. The N-, O-regioisomers were also examined by computational method at density functional theory (DFT) RB3LYP/6-31G(d), 6-31G∗∗ and 6-31+G∗ levels. DFT global chemical reactivity descriptors (total energy, chemical hardness, electronic chemical potential and electrophilicity) were calculated for the isomers and used to predict and describe their relative stability and reactivity. The chemical reactivity indices were related to the C2sbnd N3sbnd C4 bond angle. Theoretical predictions can be used to compare chemical reactivity and stability with future biological evaluation and behaviour of these compounds.

  11. A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site.

    Science.gov (United States)

    Tanpure, Arun A; Srivatsan, Seergazhi G

    2011-11-04

    Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events.

  12. Prodrugs of purine and pyrimidine analogues for the intestinal di/tri-peptide transporter PepT1

    DEFF Research Database (Denmark)

    Thomsen, Anne Engelbrecht; Friedrichsen, Gerda Marie; Sørensen, Arne Hagsten

    2003-01-01

    A general drug delivery approach for increasing oral bioavailability of purine and pyrimidine analogues such as acyclovir may be to link these compounds reversibly to stabilized dipeptide pro-moieties with affinity for the human intestinal di/tri-peptide transporter, hPepT1. In the present study...

  13. The role of pyrimidine and water as underlying molecular constituents for describing radiation damage in living tissue: A comparative study

    Energy Technology Data Exchange (ETDEWEB)

    Fuss, M. C.; Ellis-Gibbings, L. [Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid (Spain); Jones, D. B. [School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001 (Australia); Brunger, M. J. [School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001 (Australia); Institute of Mathematical Sciences, University of Malaya, 50603 Kuala Lumpur (Malaysia); Blanco, F. [Departamento de Física Atómica, Molecular y Nuclear, Universidad Complutense de Madrid, Avenida Complutense, 28040 Madrid (Spain); Muñoz, A. [Centro de Investigaciones Energéticas Medioambientales y Tecnológicas, Avenida Complutense 22, 28040 Madrid (Spain); Limão-Vieira, P. [School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001 (Australia); Laboratório de Colisões Atómicas e Moleculares, CEFITEC, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); García, G., E-mail: g.garcia@csic.es [Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid (Spain); Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW 2522 (Australia)

    2015-06-07

    Water is often used as the medium for characterizing the effects of radiation on living tissue. However, in this study, charged-particle track simulations are employed to quantify the induced physicochemical and potential biological implications when a primary ionising particle with energy 10 keV strikes a medium made up entirely of water or pyrimidine. Note that pyrimidine was chosen as the DNA/RNA bases cytosine, thymine, and uracil can be considered pyrimidine derivatives. This study aims to assess the influence of the choice of medium on the charged-particle transport, and identify how appropriate it is to use water as the default medium to describe the effects of ionising radiation on living tissue. Based on the respective electron interaction cross sections, we provide a model, which allows the study of radiation effects not only in terms of energy deposition (absorbed dose and stopping power) but also in terms of the number of induced molecular processes. Results of these parameters for water and pyrimidine are presented and compared.

  14. DEFORMATION OF COPOLYMER MICELLES INDUCED BY AMPHIPHILIC DIMER PARTICLES

    Institute of Scientific and Technical Information of China (English)

    Xiao-chun Qin; Chun-lai Ren

    2012-01-01

    Combining self-consistent-field theory and density-functional theory,we systematically study the deformation of copolymer micelles induced by the presence of amphiphilic dimer particles.Due to the amphiphilic nature,dimer particles tend to accumulate onto the interface of the copolymer micelle.With increasing concentration of the symmetric dimer particles,which are made of two identical spherical particles,the micelle deforms from the initial sphere to ellipse,dumbbell,and finally separates into two micelles.Furthermore,asymmetric dimer particles,composed by two particles with different sizes,are considered to investigate the influence of geometry of dimer particles on the deformation of the micelle.It is found that the micelle inclines to deform into dumbbell due to the additional curvature originating in the gathering of asymmetric dimer particles onto the interface of the micelle.The present study on the deformation of micelles is useful to understand the possible shape variation in the course of cell division/fusion.

  15. Tetramerization reinforces the dimer interface of MnSOD.

    Directory of Open Access Journals (Sweden)

    Yuewei Sheng

    Full Text Available Two yeast manganese superoxide dismutases (MnSOD, one from Saccharomyces cerevisiae mitochondria (ScMnSOD and the other from Candida albicans cytosol (CaMnSODc, have most biochemical and biophysical properties in common, yet ScMnSOD is a tetramer and CaMnSODc is a dimer or "loose tetramer" in solution. Although CaMnSODc was found to crystallize as a tetramer, there is no indication from the solution properties that the functionality of CaMnSODc in vivo depends upon the formation of the tetrameric structure. To elucidate further the functional significance of MnSOD quaternary structure, wild-type and mutant forms of ScMnSOD (K182R, A183P mutant and CaMnSODc (K184R, L185P mutant with the substitutions at dimer interfaces were analyzed with respect to their oligomeric states and resistance to pH, heat, and denaturant. Dimeric CaMnSODc was found to be significantly more subject to thermal or denaturant-induced unfolding than tetrameric ScMnSOD. The residue substitutions at dimer interfaces caused dimeric CaMnSODc but not tetrameric ScMnSOD to dissociate into monomers. We conclude that the tetrameric assembly strongly reinforces the dimer interface, which is critical for MnSOD activity.

  16. Dimeric interactions and complex formation using direct coevolutionary couplings.

    Science.gov (United States)

    dos Santos, Ricardo N; Morcos, Faruck; Jana, Biman; Andricopulo, Adriano D; Onuchic, José N

    2015-09-04

    We develop a procedure to characterize the association of protein structures into homodimers using coevolutionary couplings extracted from Direct Coupling Analysis (DCA) in combination with Structure Based Models (SBM). Identification of dimerization contacts using DCA is more challenging than intradomain contacts since direct couplings are mixed with monomeric contacts. Therefore a systematic way to extract dimerization signals has been elusive. We provide evidence that the prediction of homodimeric complexes is possible with high accuracy for all the cases we studied which have rich sequence information. For the most accurate conformations of the structurally diverse dimeric complexes studied the mean and interfacial RMSDs are 1.95Å and 1.44Å, respectively. This methodology is also able to identify distinct dimerization conformations as for the case of the family of response regulators, which dimerize upon activation. The identification of dimeric complexes can provide interesting molecular insights in the construction of large oligomeric complexes and be useful in the study of aggregation related diseases like Alzheimer's or Parkinson's.

  17. Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

    Science.gov (United States)

    De Jong, Djurre H; Schäfer, Lars V; De Vries, Alex H; Marrink, Siewert J; Berendsen, Herman J C; Grubmüller, Helmut

    2011-07-15

    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 covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.

  18. Structural modifications leading to changes in supramolecular aggregation of thiazolo[3, 2-]pyrimidines: Insights into their conformational features

    Indian Academy of Sciences (India)

    H Nagarajaiah; Noor Shahina Begum

    2014-09-01

    The compounds, 7-methyl-3,5-diphenyl-5-thiazolo[3,2-a]pyrimidine-6-carboxylic acid ethyl ester (1), 3-amino-2-cyano-7-methyl-5-phenyl-5-thiazolo[3,2-]pyrimidine-6-carboxylic acid methyl ester (2), 2-dimethylaminomethylene-7-methyl-3-oxo-5-phenyl-2,3-dihydro-5-thiazolo[3,2-]pyrimidine-6-carboxylic acid ethyl ester (3), 2-(3-cyano-benzylidene)-5-(4-hydroxy-phenyl)-7-methyl-3-oxo-2,3-dihydro-5-thiazolo[3,2-]pyrimidine-6-carboxylic acid methyl ester; with ,-dimethyl-formamide (4) and 3-ethoxycarbonylmethyl-5-(4-hydroxy-3-methoxy-phenyl)-7-methyl-5-thiazolo[3,2-]pyrimidine-6-carboxylic acid methyl ester (5) have been synthesized and their structures evaluated crystallographically. Compound 1 crystallizes in the space group $\\bar{ı}$ with Z=8, with four molecules in the asymmetric unit. Compound 2 also crystallizes in the space group $\\bar{ı}$ with Z=4 wherein asymmetric unit accommodates two molecules. Compound 3 belongs to 21/ with Z=4, compound 4 crystallizes in bc21 with Z= 4 and compound 5 belongs to $\\bar{ı}$ with Z=2. In all the above compounds, the aryl ring positioned at C5 of thiazolopyrimidine ring is almost perpendicular. In the case of compounds with substituted phenyl ring, aryl group-up conformation predominates. However, for compounds with unsubstituted phenyl ring, aryl group-down conformation is adopted. By varying the substituents at positions C2, C3, C6 and on the aryl at C5 in the main molecular scaffold of (1-5), we have observed significant differences in the intermolecular interaction patterns. The packing features of the compounds are controlled by C-H…O, C-H…N, N-H…N O-H…N, C-H$\\ldots$ and $\\ldots$ weak interactions.

  19. Supramolecular systems based on novel mono- and dicationic pyrimidinic amphiphiles and oligonucleotides: a self-organization and complexation study.

    Science.gov (United States)

    Zakharova, Lucia; Voronin, Mikhail; Semenov, Vyacheslav; Gabdrakhmanov, Dinar; Syakaev, Victor; Gogolev, Yuri; Giniyatullin, Rashit; Lukashenko, Svetlana; Reznik, Vladimir; Latypov, Shamil; Konovalov, Alexander; Zuev, Yuri

    2012-02-01

    Novel mono- and dicationic pyrimidinic surfactants are synthesized and their aggregation behavior is studied by methods of tensiometry and nuclear magnetic resonance (NMR) self-diffusion. To estimate their potentiality as gene delivery agents, the complexation with oligonucleotides (ONus) is explored by dynamic light scattering (DLS) and zeta-potential titration methods and ethidium bromide exclusion experiments. Bola-type pyrimidinic amphiphile (BPM) demonstrates rather a weak affinity to ONus. Although it induces mixed associations with ONus, only slight charge compensation changes occur at a large excess of bola, with no recharging reached. Similarly, the ethydium bromide exclusion study reveals a slow increase in the binding capacity toward an ONu with an increment in BPM concentration. The monocationic pyrimidinic surfactant (MPM) and its gemini analogue (GPM-1) are ranked as intermediates in both their aggregative activity and complexing properties toward ONus. They both form mixed associates with ONus well below the critical micelle concentrations (cmcs) of 2 and 15 mM respectively. However, GPM-1 has a much lower isoelectric point at the molar ratio surfactant/ONu r~1 compared to r~3 for MPM. This probably indicates a larger electrostatic contribution to the ONu complexation in the case of GPM-1. The most hydrophobic pyrimidinic surfactant (GPM-2), bearing three alkyl tails, demonstrates enhanced aggregative activity and binding capacity toward ONus as compared to former pyrimidinic surfactants. Due to effective aggregative (low cmc of 0.04 mM) plus binding properties (fraction of bound ONu β=0.76 at r=2.5), GPM-2 may be ranked as a promising agent for wider biological applications. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Products and mechanism of acene dimerization. A computational study.

    Science.gov (United States)

    Zade, Sanjio S; Zamoshchik, Natalia; Reddy, A Ravikumar; Fridman-Marueli, Galit; Sheberla, Dennis; Bendikov, Michael

    2011-07-20

    The high reactivity of acenes can reduce their potential applications in the field of molecular electronics. Although pentacene is an important material for use in organic field-effect transistors because of its high charge mobility, its reactivity is a major disadvantage hindering the development of pentacene applications. In this study, several reaction pathways for the thermal dimerization of acenes were considered computationally. The formation of acene dimers via a central benzene ring and the formation of acene-based polymers were found to be the preferred pathways, depending on the length of the monomer. Interestingly, starting from hexacene, acene dimers are thermodynamically disfavored products, and the reaction pathway is predicted to proceed instead via a double cycloaddition reaction (polymerization) to yield acene-based polymers. A concerted asynchronous reaction mechanism was found for benzene and naphthalene dimerization, while a stepwise biradical mechanism was predicted for the dimerization of anthracene, pentacene, and heptacene. The biradical mechanism for dimerization of anthracene and pentacene proceeds via syn or anti transition states and biradical minima through stepwise biradical pathways, while dimerization of heptacene proceeds via asynchronous ring closure of the complex formed by two heptacene molecules. The activation barriers for thermal dimerization decrease rapidly with increasing acene chain length and are calculated (at M06-2X/6-31G(d)+ZPVE) to be 77.9, 57.1, 33.3, -0.3, and -12.1 kcal/mol vs two isolated acene molecules for benzene, naphthalene, anthracene, pentacene, and heptacene, respectively. If activation energy is calculated vs the initially formed complex of two acene molecules, then the calculated barriers are 80.5, 63.2, 43.7, 16.7, and 12.3 kcal/mol. Dimerization is exothermic from anthracene onward, but it is endothermic at the terminal rings, even for heptacene. Phenyl substitution at the most reactive meso

  1. 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.

  2. Intermolecular disulfide bond influences unphosphorylated STAT3 dimerization and function.

    Science.gov (United States)

    Butturini, Elena; Gotte, Giovanni; Dell'Orco, Daniele; Chiavegato, Giulia; Marino, Valerio; Canetti, Diana; Cozzolino, Flora; Monti, Maria; Pucci, Piero; Mariotto, Sofia

    2016-10-01

    Signal transducer and activator of transcription 3 (STAT3) is a transcription factor activated by the phosphorylation of tyrosine 705 in response to many cytokines and growth factors. Recently, the roles for unphosphorylated STAT3 (U-STAT3) have been described in response to cytokine stimulation, in cancers, and in the maintenance of heterochromatin stability. It has been reported that U-STAT3 dimerizes, shuttles between the cytoplasm and nucleus, and binds to DNA, thereby driving genes transcription. Although many reports describe the active role of U-STAT3 in oncogenesis in addition to phosphorylated STAT3, the U-STAT3 functional pathway remains elusive.In this report, we describe the molecular mechanism of U-STAT3 dimerization, and we identify the presence of two intermolecular disulfide bridges between Cys367 and Cys542 and Cys418 and Cys426, respectively. Recently, we reported that the same cysteines contribute to the redox regulation of STAT3 signaling pathway both in vitro and in vivo The presence of these disulfides is here demonstrated to largely contribute to the structure and the stability of U-STAT3 dimer as the dimeric form rapidly dissociates upon reduction in the S-S bonds. In particular, the Cys367-Cys542 disulfide bridge is shown to be critical for U-STAT3 DNA-binding activity. Mutation of the two Cys residues completely abolishes the DNA-binding capability of U-STAT3. Spectroscopic investigations confirm that the noncovalent interactions are sufficient for proper folding and dimer formation, but that the interchain disulfide bonds are crucial to preserve the functional dimer. Finally, we propose a reaction scheme of U-STAT3 dimerization with a first common step followed by stabilization through the formation of interchain disulfide bonds. © 2016 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  3. Threshold electron attachment and electron impact ionization involving oxygen dimers

    Energy Technology Data Exchange (ETDEWEB)

    Kreil, J.; Ruf, M.-W.; Hotop, H. [Fachbereich Physik, Universitaet Kaiserslautern, D-67653 Kaiserslautern (Germany); Ettischer, I.; Buck, U. [Max-Planck-Institut fuer Stroemungsforschung, Bunsenstrasse 10, D-37073 Goettingen (Germany)

    1998-12-15

    Using two different crossed-beams machines we have carried out the first quantitative study of threshold electron attachment and electron impact-induced ionization and fragmentation involving oxygen dimers (O{sub 2}){sub 2}. In the electron attachment experiment we study electron transfer from state-selected Ar{sup **}(20d) Rydberg atoms to O{sub 2} molecules and dimers in a skimmed supersonic beam at variable nozzle temperatures (T{sub 0}) and stagnation pressures (p{sub 0}). The relative dimer density is determined through measurements of Penning ionization by metastable Ne{sup *}(3s {sup 3}P{sub 2,0}) atoms and used to estimate the absolute cross-section for O{sub 2}{sup -} formation in collisions of Ar{sup **}(20d) Rydberg atoms with O{sub 2} dimers to be nearly 10{sup -17} m{sup 2}, almost four orders of magnitude larger than that for O{sub 2}{sup -} formation in collisions of Ar{sup **}(20d) Rydberg atoms with O{sub 2} monomers. The fragmentation of the oxygen cluster beam is quantitatively characterized by the transverse helium beam scattering method which allows us to spatially separate different clusters. It is shown that in 70 eV electron impact of (O{sub 2}){sub 2} only 3.6(4)% of the dimers are detected as dimer ions (O{sub 2}){sub 2}{sup +}. In additional experiments involving SF{sub 6} clusters we show that SF{sub 6} dimers fragment nearly completely upon 70 eV electron impact, yielding SF{sub 5}{sup +} ions (probability for (SF{sub 6}){center_dot}SF{sub 5}{sup +} production at most 0.3%). (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

  4. Integrability and conformal data of the dimer model

    Science.gov (United States)

    Morin-Duchesne, Alexi; Rasmussen, Jørgen; Ruelle, Philippe

    2016-04-01

    The central charge of the dimer model on the square lattice is still being debated in the literature. In this paper, we provide evidence supporting the consistency of a c=-2 description. Using Lieb’s transfer matrix and its description in terms of the Temperley-Lieb algebra {{TL}}n at β =0, we provide a new solution of the dimer model in terms of the model of critical dense polymers on a tilted lattice and offer an understanding of the lattice integrability of the dimer model. The dimer transfer matrix is analyzed in the scaling limit, and the result for {L}0-\\frac{c}{24} is expressed in terms of fermions. Higher Virasoro modes are likewise constructed as limits of elements of {{TL}}n and are found to yield a c=-2 realization of the Virasoro algebra, familiar from fermionic bc ghost systems. In this realization, the dimer Fock spaces are shown to decompose, as Virasoro modules, into direct sums of Feigin-Fuchs modules, themselves exhibiting reducible yet indecomposable structures. In the scaling limit, the eigenvalues of the lattice integrals of motion are found to agree exactly with those of the c=-2 conformal integrals of motion. Consistent with the expression for {L}0-\\frac{c}{24} obtained from the transfer matrix, we also construct higher Virasoro modes with c = 1 and find that the dimer Fock space is completely reducible under their action. However, the transfer matrix is found not to be a generating function for the c = 1 integrals of motion. Although this indicates that Lieb’s transfer matrix description is incompatible with the c = 1 interpretation, it does not rule out the existence of an alternative, c = 1 compatible, transfer matrix description of the dimer model.

  5. Monitoring of receptor dimerization using plasmonic coupling of gold nanoparticles.

    Science.gov (United States)

    Crow, Matthew J; Seekell, Kevin; Ostrander, Julie H; Wax, Adam

    2011-11-22

    The dimerization of receptors on the cell membrane is an important step in the activation of cell signaling pathways. Several methods exist for observing receptor dimerization, including coimmunoprecipitation, chemical cross-linking, and fluorescence resonance energy transfer (FRET). These techniques are limited in that only FRET is appropriate for live cells, but even that method suffers from photobleaching and bleed-through effects. In this study, we implement an alternative method for the targeting of HER-2 homodimer formation based on the plasmonic coupling of gold nanoparticles functionalized with HER-2 Ab. In the presented studies, SK-BR-3 cells, known to overexpress HER-2, are labeled with these nanoparticles and receptor colocalization is observed using plasmonic coupling. HER-2 targeted nanoparticles bound to these cells exhibit a peak resonance that is significantly red-shifted relative to those bound to similar receptors on A549 cells, which have significantly lower levels of HER-2 expression. This significant red shift indicates plasmonic coupling is occurring and points to a new avenue for assessing dimerization by monitoring their colocalization. To determine that dimerization is occurring, the refractive index of the nanoenvironment of the labels is assessed using a theoretical analysis based on the Mie coated sphere model. The results indicate scattering by single, isolated nanoparticles for the low HER-2 expressing A549 cell line, but the scattering observed for the HER-2 overexpressing SK-BR-3 cell line may only be explained by plasmonic-coupling of proximal nanoparticle pairs. To validate the conformation of nanoparticles bound to HER-2 receptors undergoing dimerization, discrete dipole approximation (DDA) models are used to assess spectra of scattering by coupled nanoparticles. Comparison of the experimental results with theoretical models indicates that NP dimers are formed for the labeling of SK-BR-3 cells, suggesting that receptor

  6. Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Monomucleotides

    Science.gov (United States)

    Kanavarioti, Anastassia

    1997-08-01

    Phosphoimidazolide activated ribomononucleotides (*pN) are useful substrates for the non-enzymatic synthesis of polynucleotides. However, dilute neutral aqueous solutions of *pN typically yield small amounts of dimers and traces of polymers; most of *pN hydrolyzes to yield nucleoside 5'-monophosphate. Here we report the self-condensation of nucleoside 5'-phosphate 2-methylimidazolide (2-MeImpN with N = cytidine, uridine or guanosine) in the presence of Mg2+ in concentrated solutions, such as might have been found in an evaporating lagoon on prebiotic Earth. The product distribution indicates that oligomerization is favored at the expense of hydrolysis. At 1.0 M, 2-MeImpU and 2-MeImpC produce about 65% of oligomers including 4% of the 3',5'-linked dimer. Examination of the product distribution of the three isomeric dimers in a self-condensation allows identification of reaction pathways that lead to dimer formation. Condensations in a concentrated mixture of all three nucleotides (U,C,G mixtures) is made possible by the enhanced solubility of 2-MeImpG in such mixtures. Although percent yield of internucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MeImpU, 16% for 2-MeImpC and 25% of the total pyrophosphate in the U,C,G mixtures. The efficiency by which oligomers are produced in these concentrated solutions makes the evaporating lagoon scenario a potentially interesting medium for the prebiotic synthesis of dimers and short RNAs.

  7. Synthesis and biological evaluation of novel pyrimidine-benzimidazol hybrids as potential anticancer agents.

    Science.gov (United States)

    Shao, Kun-Peng; Zhang, Xu-Yao; Chen, Peng-Ju; Xue, Deng-Qi; He, Peng; Ma, Li-Ying; Zheng, Jia-Xin; Zhang, Qiu-Rong; Liu, Hong-Min

    2014-08-15

    A series of pyrimidine-benzimidazol hybrids was synthesized and evaluated for anticancer activity on four human cancer cell lines including MCF-7, MGC-803, EC-9706 and SMMC-7721. Some of the synthesized compounds exhibited moderate to potent activity against MGC-803 and MCF-7. Among them, compounds 5a-b and 6a-b showed most effective activity. Compounds 5b and 6b were more cytotoxic than 5-fluorouracil against all tested four human cancer cell lines, with IC50 values ranging from 2.03 to 10.55 μM and 1.06 to 12.89 μM, respectively. Flow cytometry analysis demonstrated that treatment of MGC-803 with 6b led to cell cycle arrest at G2/M phase accompanied by an increase in apoptotic cell death.

  8. Design, synthesis and antifungal activities of novel strobilurin derivatives containing pyrimidine moieties

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xiang; Geo, Yongxin; Liu, Huijun; Guo, Baoyuan; Wang, Huili [Research Center for Eco-Environmental Sciences/Chinese Academy of Sciences, Beijing (China)

    2012-04-15

    Strobilurins are one of the most important classes of agricultural fungicides. To discover new strobilurin derivatives with high activity against resistant pathogens, a series of novel β-methoxy acrylate analogues were designed and synthesized by integrating substituted pyrimidine with a strobilurin pharmacophore. The compounds were confirmed and characterized by infrared, {sup 1}H nuclear magnetic resonance, elemental analysis and mass spectroscopy. The bioassays indicated that most of the compounds (1a-1h) exhibited potent antifungal activities against Colletotrichum orbicular, Botrytis cinerea Pers and Protoporphyria caps ici Leon ian at the concentration of 50 μg/mL. Exhilaratingly, compound 1d (R=3-trifluoromethylphenyl) showed better antifungal activity against all the tested fungi than the commercial stilbenetriol fungicide azoxystrobin.

  9. Synthesis, characterization and antimicrobial screening of hybrid molecules containing quinoline, pyrimidine and morpholine analogues

    Indian Academy of Sciences (India)

    N C Desai; K M Rajpara; V V Joshi; H V Vaghani; H M Satodiya

    2013-03-01

    In an attempt to find new bio-active molecules, a series of compounds -(4-(2-chloroquinolin-3-yl)-6-(aryl)pyrimidin-2-yl)-2-morpholinoacetamides (5a-l) were synthesized by multistep reactions. Compounds were characterized by IR, NMR and mass spectra. Antimicrobial screening of title compounds (5a-l) was carried out against Gram-positive bacteria (Staphylococcus aureus, Streptococcus pyogenes), Gramnegative bacteria (Escherichia coli, Pseudomonas aeruginosa) and fungi (Candida albicans, Aspergillus niger, Aspergillus clavatus) using serial broth dilution method. On the basis of statistical analysis, it is observed that these compounds gave significant co-relation. Newly synthesized compounds 5e, 5f, 5g, 5i and 5l showed significant potency against different microbial strains.

  10. Syntheses and anti-microbial evaluation of new quinoline scaffold derived pyrimidine derivatives

    Directory of Open Access Journals (Sweden)

    Shikha S. Dave

    2016-09-01

    Full Text Available A series of diversely substituted chalcones derived from a quinoline scaffold, e.g. (E-3-(2-chloroquinolin-3-yl-1-(2-hydroxyphenyl prop-2-en-1-one and its pyrimidine analogues e.g. 2-[2-amino-6-(2-chloroquinolin-3-yl-5,6-dihydropyrimidin-4-yl]phenols have been prepared by condensation of 2-chloro-3-formyl quinoline with differently substituted 2-hydroxy acetophenones and further treatment with guanidine carbonate. All the newly synthesized compounds have been evaluated for their in vitro growth inhibitory activity against Escherichia coli, Pseudomonas vulgaris, Bacillus subtilis, Staphylococcus aureus, Staphylococcus typhi, Candida albicans, Aspergillus niger and Pseudomonas chrysogenum.

  11. Synthesis of novel indolyl-pyrimidine antiinflammatory, antioxidant and antibacterial agents

    Directory of Open Access Journals (Sweden)

    Panda S

    2008-01-01

    Full Text Available A number of chalcones were synthesized by reacting indole-3-aldehyde, prepared by Vilsemeir Haack reaction with 4-substituted acetophenone in NaOH solution in ethanol. These chalcones were immediately reacted with urea, thiourea and guanidine hydrochloride in presence of concentrated hydrochloric acid as reagent to obtain the corresponding hydroxy, thio and amino pyrimidines. The synthesized heterocyclics were characterized on the basis of physical, chemical tests and spectroscopic data and were tested for the acute antiinflammatory activity, antioxidant, antibacterial activity using carragenan-induced rat paw oedema method, DPPH (diphenylpicrylhydrazyl radical scavenging method and cup plate method using Muller-Hinton agar media respectively. Evaluation of the compounds revealed remarkable antiinflammatory activity reflected by their ability to reduce the carragenan-induced inflammation in rats, appreciable antioxidant activity and also antibacterial activity was observed.

  12. Effect of the third π ∗ resonance on the angular distributions for electron-pyrimidine scattering

    Science.gov (United States)

    Mašín, Zdeněk; Gorfinkiel, Jimena D.

    2016-07-01

    We present a detailed analysis of the effect of the well known third π∗ resonance on the angular behaviour of the elastic cross section in electron scattering from pyrimidine. This resonance, occurring approximately at 4.7 eV, is of mixed shape and core-excited character. Experimental and theoretical results show the presence of a peak/dip behaviour in this energy range, that is absent for other resonances. Our investigations show that the cause of the peak/dip is an interference of background p-wave to p-wave scattering amplitudes with the amplitudes for resonant scattering. The equivalent resonance in pyrazine shows the same behaviour and the effect is therefore likely to appear in other benzene-like molecules. Contribution to the Topical Issue "Advances in Positron and Electron Scattering", edited by Paulo Limao-Vieira, Gustavo Garcia, E. Krishnakumar, James Sullivan, Hajime Tanuma and Zoran Petrovic.

  13. Synthesis of Polynuclear Heterocyclic Compounds Derived from Thieno[2,3-d]pyrimidine Derivatives

    Directory of Open Access Journals (Sweden)

    N. A. Hassan

    2000-06-01

    Full Text Available Reaction of 2-hydrazino-3-methyl-3,4-dihydrothieno[2,3-d]pyrimidin-4-one derivatives 2a,b with aliphatic acids afforded the thienotriazolopyrimidinone derivatives 3a-d, with nitrous acid yielded tetrazolothienopyrimidinone derivatives 4a,b and with carbon disulphide furnished 3-mercaptothienotriazolopyrimidinone derivatives 5a,b. Also, 2a,b reacted with aldehydes to afford the arylhydrazones 6a-f which cyclized into thienotriazolopyrimidinone derivatives 7a-f. Furthermore, 2a,b condensed with ethyl acetoacetate and ethyl cyanoacetate to afford 2-(1-pyrazolyl derivatives 9a,b and 10a,b, respectively. On the other hand, 2-hydrazino derivatives 2a,b condensed with a-halo-ketones to yield thienpyrimidotriazinone derivatives 11a,b and with β-diketones, to form 2-(1-pyrazolyl derivatives 12a-f.

  14. An efficient one-pot synthesis, characterization and antibacterial activity of novel chromeno-pyrimidine derivatives

    Science.gov (United States)

    Suresh, Lingala; Kumar, P. Sagar Vijay; Chandramouli, G. V. P.

    2017-04-01

    A simple and efficient one-pot three component, green protocol was established for the synthesis of chromenopyrano[2,3-d]pyrimidine derivatives starting from 3-amino-pyrano[2,3-c]chromene-2-carbonitrile, N,N-dimethylformamide dimethylacetal and aromatic amines in the presence of 1-butyl-3-methylimidazolium hydrogen sulphate[Bmim]HSO4 ionic liquid. The present procedure offers a domino reaction strategy, cleaner conversion, short reaction times and high yields. Among the screened derivatives, the compounds 4g and 4h were identified as lead molecules which established promising antimicrobial towards Gram-positive bacterial strains such as Staphylococcus aureus MTCC 96, Staphylococcus aureus MLS16 MTCC 2940 and Bacillus subtilis MTCC 121.

  15. Novel pyrazole-5-carboxamide and pyrazole-pyrimidine derivatives: synthesis and anticancer activity.

    Science.gov (United States)

    Shi, Jing Bo; Tang, Wen Jian; Qi, Xing Bao; Li, Rong; Liu, Xin Hua

    2015-01-27

    A series of novel pyrazole-5-carboxamide and pyrazole-pyrimidine derivatives were designed and synthesized. All compounds have been screened for their antiproliferative activity against MGC-803, SGC-7901 and Bcap-37 cell lines in vitro. The results revealed that compounds 8a, 8c and 8e exhibited strong inhibitory activity against MGC-803 cell line. The flow cytometric analysis result showed that compound 8e could inhibit MGC-803 proliferation. Some title compounds were tested against telomerase, and compound 8e showed the most potent inhibitory activity with IC50 value at 1.02 ± 0.08 μM. The docking simulation of compound 8e was performed to get the probable binding model, among them, LYS 189, LYS 372, LYS 249 and ASP 254 may be the key residues for the telomerase activity.

  16. Design, synthesis and vasorelaxant evaluation of novel coumarin-pyrimidine hybrids.

    Science.gov (United States)

    Amin, Kamilia M; Awadalla, Fadi M; Eissa, Amal A M; Abou-Seri, Sahar M; Hassan, Ghaneya S

    2011-10-15

    The main objective of the present work depends on the hybridization of coumarin moiety as a vasorelaxant scaffold and pyrimidine ring with known potential cardiovascular activity in order to prepare some new potent antihypertensive candidates. Hence, two groups of pyrimidinyl coumarin derivatives were synthesized and evaluated for their vasorelaxing activity. These compounds were prepared via two routes; either preparation of the guanidinocoumarin 4 followed by a cocktail of cyclization reactions to yield a different array of 6-(substituted pyrimidin-2-yl)aminocoumarins 5-17, or through cyclization of the precursor chalcones 22a-g with guanidine hydrochloride to generate the corresponding final compounds, 8-(6-aryl-2-aminopyrimidin-4-yl)-7-methoxycoumarins 23a-g. The effect of these compounds and the coumarin intermediates 3, 4, 21 and 22a-g on nor-epinephrine induced contracture in thoracic rat aortic rings was investigated using prazocin as reference drug. Several derivatives showed promising activities either equal or even better than that of prazocin (IC(50) 0.487 mM). The most prospective compounds; the pyrimidinylamino coumarin derivatives 8, 17 (IC(50) 0.411, IC(50) 0.421 mM) and the chalcones 22b, 22e (IC(50) 0.371, 0.374 mM) that displayed the highest activity can be a base for lead optimization and simple but efficient design of new compounds. 2D-QSAR analysis was applied to find a correlation between the experimental vasorelaxant activities of the newly synthesized coumarin derivatives and their different physicochemical parameters. The result of this study showed that the increase in aqueous solubility while retaining good hydrophobic character of the overall molecule is the key for maintaining high relaxation activity.

  17. Synthesis of some pyrazolines and pyrimidines derived from polymethoxy chalcones as anticancer and antimicrobial agents.

    Science.gov (United States)

    Rostom, Sherif A F; Badr, Mona H; Abd El Razik, Heba A; Ashour, Hayam M A; Abdel Wahab, Abeer E

    2011-09-01

    The synthesis of a series of certain polymethoxy chalcones and some derived pyrazole, pyrimidine, and thiazolopyrimidine ring structures is reported. Eleven compounds 4, 6, 9, 11, 14-17, 22, 24, and 25 were selected by the National Cancer Institute (NCI) to be screened for their in-vitro anticancer activity, whereas all the synthesized compounds were evaluated for their in-vitro antimicrobial activity. Compounds 4, 6, and 11 were found to possess a significant broad spectrum antitumor potential against most of the tested subpanel tumor cell lines. The pyrazolines 4 and 6 displayed remarkable growth inhibitory activities (GI(50) MG-MID values of 2.10 and 1.38 µM, respectively), together with moderate cytostatic effects (TGI MG-MID values of 47.9 and 42.7 µM, respectively). Meanwhile, the pyrimidin-2-one 11 showed a noticeable overall tumor growth inhibitory activity, together with high cytostatic and cytotoxic efficacies (GI(50) , TGI and LC(50) MG-MID values of 3.39, 17.4, and 61.7 µM, respectively). On the other hand, compounds 3, 4, 13, 15, 19, 20, and 23 were found to be the most active antimicrobial members in this investigation with a broad spectrum of activity. Compound 23 was four times superior to ampicillin against Pseudomonas aeruginosa. The best antifungal activity was demonstrated by compounds 4, 5, and 11 which possessed almost half the activity of clotrimazole against Candida albicans. Collectively, the obtained biological results suggest that compound 4 could be considered as a possible dual antimicrobial-anticancer agent.

  18. Synthesis and Applications of Non-spherical Dimer Colloids

    Science.gov (United States)

    Yoon, Kisun

    Colloids are promising building blocks in material synthesis because of their controllability of size and surface properties. The synthesis of chemically and/or geometrically anisotropic colloidal particles has received attentions with the expectation of building blocks for complex structures. However, the synthesis of anisotropic colloidal particles is by far more difficult than the synthesis of spherical colloidal particles. Lack of monodispersity and productivity of many anisotropic particles often limits their applications as a building block for complex structures. Thus, it is highly desirable to develop methods which can produce a large amount of monodisperse non-spherical particles with controllable asymmetric surface properties. This dissertation details the work for developing such a method. The major result of this dissertation is a synthetic method to produce monodisperse non-spherical colloids with anisotropic surface property in a large quantity. The anisotropic colloid, which we call it as Dimer particle, has two fused lobes like a dumbbell and each lobe's size can be independently controlled. We present a novel method to synthesize sub-micron size Dimer particles. This method can produce a large amount of submicron-sized Dimer particles with good monodispersity and well-controlled shape. Submicron-sized Dimer particles have been highly desired since they can be used as a building block for self assembly using Brownian motion, colloidal surfactant for Pickering emulsion, and photonic materials. To fully take advantage of the anisotropy of the particles, we develop a facile method to tailor the surface property of each lobe independently by asymmetrically coating the particles with gold nanoparticles. This method doesn't need the arrangement of particles onto any type of interfaces. Asymmetric coating of gold nanoparticles can be carried out simply by mixing Dimer particles with gold nanoparticles. The formation mechanism of the submicron-sized Dimer

  19. Computational analysis for antimicrobial active pyrano[2,3-d]pyrimidine derivatives on the basis of theoretical and experimental ground

    Directory of Open Access Journals (Sweden)

    Ajmal R. Bhat

    2016-06-01

    Full Text Available Annulated pyrano[2,3-d]pyrimidine derivatives were synthesized with methoxy, hydroxyl, nitrile and bromine substituents in its skeleton and correlated by electronic effect of substituents on the magnitude of antimicrobial activity. The different electron donating and electron withdrawing substituents of the pyrano[2,3-d]pyrimidine derivatives exerted positive influence on its antimicrobial activity against some Gram positive and Gram negative bacteria such as, Bacillus cereus, Staphylococcus aureus, Klebsiella pneumonia, Pseudomonas aureus and Escherichia coli, respectively. Antibacterial screening revealed that the presence of heteroaryl, cyano and amino groups on pyrano[2,3-d]pyrimidine skeleton increases its penetrating power on bacterial cell wall and becomes more biologically active. All the pyrano[2,3-d]pyrimidine derivatives were characterized by IR, 1H NMR, 13C NMR and mass spectra.

  20. Synthesis, characterization and biological activity of new cyclization products of 3-(4-substituted benzylidene)-2-pyrido[1,2-]pyrimidine 2,4-(3)-diones

    Indian Academy of Sciences (India)

    Abha Bishnoi; Suruchi Singh; Anil K Tiwari; Krishna Srivastava; Ram Raghuvir; Chandrakant M Tripathi

    2013-03-01

    A method is presented for the synthesis of 4-(substituted phenyl)-3-(3-substituted phenyl)4-spiro[isoxazole-5,3'-pyrido[1,2-]pyrimidine]-2',4'-dione (3), 3-(4-substituted phenyl)-3-isoxazole[3, 4-]pyrido[1,2-]pyrimidin-4-(3a)-one (4) and 3-(4-substituted phenyl) 3,3a-dihydropyrazolo[3,4-]pyrido[1,2-]pyrimidin-4-(2)-one (5) which consists of the conversion of 2-pyrido[1,2-]pyrimidine-2,4(3)-dione (1) to chalcones (2) and their 1,3-dipolar cycloaddition with appropriate aldoximes to give spiro compounds and heterocyclization using amines to yield isoxazolines and pyrazolines. All the compounds were screened for their antimicrobial and antitubercular activity.

  1. Synthesis of New Bis-Alkylated Phosphono Alkenyl Acyclonucleosides : (Z) and (E)-Diethyl-2-(3-alkyl pyrimidin-1-yl)ethylen-1-yl Phosphonate

    OpenAIRE

    Imbach, J L; J. L. Barascut; Lazrek, H B; Taourirte, M.; Rochdi, A.

    2000-01-01

    The E- and Z- phosphonoalkenyl acyclonucleosides of uracil and thymine were synthesized under Michael addition conditions. Introduction of an alkyl, alkenyl or alkynyl group at the N-3 position of the pyrimidine moiety was accomplished using potassium carbonate in DMF.

  2. Mechanism of ubiquitylation by dimeric RING ligase RNF4

    Science.gov (United States)

    Plechanovová, Anna; Jaffray, Ellis G.; McMahon, Stephen A.; Johnson, Kenneth A.; Navrátilová, Iva; Naismith, James H.; Hay, Ronald T.

    2012-01-01

    Mammalian RNF4 is a dimeric RING ubiquitin E3 ligase that ubiquitylates poly-SUMOylated proteins. We found that RNF4 bound ubiquitin-charged UbcH5a tightly but free UbcH5a weakly. To provide insight into the mechanism of RING-mediated ubiquitylation we docked the UbcH5~ubiquitin thioester onto the RNF4 RING structure. This revealed that with E2 bound to one monomer of RNF4, the thioester-linked ubiquitin could reach across the dimer to engage the other monomer. In this model the “Ile44 hydrophobic patch” of ubiquitin is predicted to engage a conserved tyrosine located at the dimer interface of the RING and mutation of these residues blocked ubiquitylation activity. Thus, dimeric RING ligases are not simply inert scaffolds that bring substrate and E2-loaded ubiquitin into close proximity. Instead, they facilitate ubiquitin transfer by preferentially binding the E2~ubiquitin thioester across the dimer and activating the thioester bond for catalysis. PMID:21857666

  3. 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.

  4. Integrability and conformal data of the dimer model

    CERN Document Server

    Morin-Duchesne, Alexi; Ruelle, Philippe

    2015-01-01

    The central charge of the dimer model on the square lattice is still being debated in the literature. In this paper, we provide evidence supporting the consistency of a $c=-2$ description. Using Lieb's transfer matrix and its description in terms of the Temperley-Lieb algebra $TL_n$ at $\\beta = 0$, we provide a new solution of the dimer model in terms of the model of critical dense polymers on a tilted lattice and offer an understanding of the lattice integrability of the dimer model. The dimer transfer matrix is analysed in the scaling limit and the result for $L_0-\\frac c{24}$ is expressed in terms of fermions. Higher Virasoro modes are likewise constructed as limits of elements of $TL_n$ and are found to yield a $c=-2$ realisation of the Virasoro algebra, familiar from fermionic $bc$ ghost systems. In this realisation, the dimer Fock spaces are shown to decompose, as Virasoro modules, into direct sums of Feigin-Fuchs modules, themselves exhibiting reducible yet indecomposable structures. In the scaling lim...

  5. Recognition of HIV TAR RNA by triazole linked neomycin dimers.

    Science.gov (United States)

    Kumar, Sunil; Arya, Dev P

    2011-08-15

    A series of neomycin dimers have been synthesized using 'click chemistry' with varying linker functionality and length to target the TAR RNA region of HIV virus. TAR (trans activation response) RNA region, a 59 base pair stem loop structure located at 5'-end of all nascent HIV-1 transcripts interacts with a key regulatory protein, Tat, and necessitates the replication of HIV-1 virus. Neomycin, an aminosugar, has been shown to exhibit more than one binding site with HIV TAR RNA. Multiple TAR binding sites of neomycin prompted us to design and synthesize a small library of neomycin dimers using click chemistry. The binding between neomycin dimers and HIV TAR RNA was characterized using spectroscopic techniques including FID (Fluorescent Intercalator Displacement) titration and UV-thermal denaturation. UV thermal denaturation studies demonstrate that neomycin dimer binding increase the melting temperature (T(m)) of the HIV TAR RNA up to 10°C. Ethidium bromide displacement titrations revealed nanomolar IC(50) between neomycin dimers and HIV TAR RNA, whereas with neomycin, a much higher IC(50) in the micromolar range is observed.

  6. Regulation of primate lentiviral RNA dimerization by structural entrapment

    Directory of Open Access Journals (Sweden)

    Lodmell J Stephen

    2008-07-01

    Full Text Available Abstract Background Genomic RNA dimerization is an important process in the formation of an infectious lentiviral particle. One of the signals involved is the stem-loop 1 (SL1 element located in the leader region of lentiviral genomic RNAs which also plays a role in encapsidation and reverse transcription. Recent studies revealed that HIV types 1 and 2 leader RNAs adopt different conformations that influence the presentation of RNA signals such as SL1. To determine whether common mechanisms of SL1 regulation exist among divergent lentiviral leader RNAs, here we compare the dimerization properties of SIVmac239, HIV-1, and HIV-2 leader RNA fragments using homologous constructs and experimental conditions. Prior studies from several groups have employed a variety of constructs and experimental conditions. Results Although some idiosyncratic differences in the dimerization details were observed, we find unifying principles in the regulation strategies of the three viral RNAs through long- and short-range base pairing interactions. Presentation and efficacy of dimerization through SL1 depends strongly upon the formation or dissolution of the lower stem of SL1 called stem B. SL1 usage may also be down-regulated by long-range interactions involving sequences between SL1 and the first codons of the gag gene. Conclusion Despite their sequence differences, all three lentiviral RNAs tested in this study showed a local regulation of dimerization through the stabilization of SL1.

  7. Dimer-tetramer transition controls RUNX1/ETO leukemogenic activity.

    Science.gov (United States)

    Wichmann, Christian; Becker, Yvonne; Chen-Wichmann, Linping; Vogel, Vitali; Vojtkova, Anna; Herglotz, Julia; Moore, Sandra; Koch, Joachim; Lausen, Jörn; Mäntele, Werner; Gohlke, Holger; Grez, Manuel

    2010-07-29

    RUNX1/ETO, the fusion protein resulting from the chromosomal translocation t(8;21), is one of the most frequent translocation products in acute myeloid leukemia. Several in vitro and in vivo studies have shown that the homo-tetramerization domain of ETO, the nervy homology region 2 (NHR2), is essential for RUNX1/ETO oncogenic activity. We analyzed the energetic contribution of individual amino acids within the NHR2 to RUNX1/ETO dimer-tetramer transition and found a clustered area of 5 distinct amino acids with strong contribution to the stability of tetramers. Substitution of these amino acids abolishes tetramer formation without affecting dimer formation. Similar to RUNX1/ETO monomers, dimers failed to bind efficiently to DNA and to alter expression of RUNX1-dependent genes. RUNX1/ETO dimers do not block myeloid differentiation, are unable to enhance the self-renewal capacity of hematopoietic progenitors, and fail to induce leukemia in a murine transplantation model. Our data reveal the existence of an essential structural motif (hot spot) at the NHR2 dimer-tetramer interface, suitable for a molecular intervention in t(8;21) leukemias.

  8. Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Chuanying; Beck, Brian W.; Krause, Kurt; Weksberg, Tiffany E.; Pettitt, Bernard M.

    2007-02-15

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.

  9. PET imaging of HSV1-tk mutants with acquired specificity toward pyrimidine- and acycloguanosine-based radiotracers

    Energy Technology Data Exchange (ETDEWEB)

    Likar, Yury; Dobrenkov, Konstantin; Olszewska, Malgorzata; Shenker, Larissa; Hricak, Hedvig; Ponomarev, Vladimir [Memorial Sloan-Kettering Cancer Center, Molecular Imaging Laboratory, Department of Radiology, New York, NY (United States); Cai, Shangde [Memorial Sloan-Kettering Cancer Center, Radiochemistry/Cyclotron Core Facility, New York, NY (United States)

    2009-08-15

    The aim of this study was to create an alternative mutant of the herpes simplex virus type 1 thymidine kinase (HSV1-tk) reporter gene with reduced phosphorylation capacity for acycloguanosine derivatives, but not pyrimidine-based compounds that will allow for successful PET imaging. A new mutant of HSV1-tk reporter gene, suitable for PET imaging using pyrimidine-based radiotracers, was developed. The HSV1-tk mutant contains an arginine-to-glutamine substitution at position 176 (HSV1-R176Qtk) of the nucleoside binding region of the enzyme. The mutant-gene product showed favorable enzymatic characteristics toward pyrimidine-based nucleosides, while exhibiting reduced activity with acycloguanosine derivatives. In order to enhance HSV1-R176Qtk reporter activity with pyrimidine-based radiotracers, we introduced the R176Q substitution into the more active HSV1-sr39tk mutant. U87 human glioma cells transduced with the HSV1-R176Qsr39tk double mutant reporter gene showed high {sup 3}H-FEAU pyrimidine nucleoside and low {sup 3}H-penciclovir acycloguanosine analog uptake in vitro. PET imaging also demonstrated high {sup 18}F-FEAU and low {sup 18}F-FHBG accumulation in HSV1-R176Qsr39tk+ xenografts. The feasibility of imaging two independent nucleoside-specific HSV1-tk mutants in the same animal with PET was demonstrated. Two opposite xenografts expressing the HSV1-R176Qsr39tk reporter gene and the previously described acycloguanosine-specific mutant of HSV1-tk, HSV1-A167Ysr39tk reporter gene, were imaged using a short-lived pyrimidine-based {sup 18}F-FEAU and an acycloguanosine-based {sup 18}F-FHBG radiotracer, respectively, administered on 2 consecutive days. We conclude that in combination with acycloguanosine-specific HSV1-A167Ysr39tk reporter gene, a HSV1-tk mutant containing the R176Q substitution could be used for PET imaging of two different cell populations or concurrent molecular biological processes in the same living subject. (orig.)

  10. Design, Synthesis and Biological Evaluation of Novel Pyrimido[4,5-d]pyrimidine CDK2 Inhibitors as Anti-Tumor Agents

    Science.gov (United States)

    El-Moghazy, Samir M.; Ibrahim, Diaa A.; Abdelgawad, Nagwa M.; Farag, Nahla A. H.; El-Khouly, Ahmad S.

    2011-01-01

    A series of 2,5,7-trisubstituted pyrimido[4,5-d]pyrimidine cyclin-dependent kinase (CDK2) inhibitors is designed and synthesized. 6-Amino-2-thiouracil is reacted with an aldehyde and thiourea to prepare the pyrimido[4,5-d]-pyrimidines. Alkylation and amination of the latter ones give different amino derivatives. These compounds show potent and selective CDK inhibitory activities and inhibit in vitro cellular proliferation in cultured human tumor cells. PMID:21886895

  11. Photodissociation pathways and lifetimes of protonated peptides and their dimers

    DEFF Research Database (Denmark)

    Gopalan, Aravind; Klærke, Benedikte; Rajput, Jyoti

    2012-01-01

    Photodissociation lifetimes and fragment channels of gas-phase, protonated YAn (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ∼200 ns while the protonated dimers show...... 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...... of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both...

  12. Self-deactivation of water vapor - Role of the dimer

    Science.gov (United States)

    Zuckerwar, A. J.

    1984-01-01

    A phenomenological multiple-relaxation theory of the deactivation rate constant for the nu-2 (1 - 0) bending mode of water vapor is presented which incorporates the role not only of the excited monomer but also of the bound molecular complex, in particular the dimer. The deactivation takes place by means of three parallel processes: (1) collisional deexcitation of the excited monomer, (2) a two-step reaction involving association and spontaneous redissociation of an H2O collision complex, and (3) spontaneous dissociation of the stably bound H2O dimer. Oxygen, but not nitrogen or argon, serves as an effective chaperon for the formation of the activated complex. This observation explains the impurity dependence of the self-deactivation rate constant of water vapor. Analysis of an ultrasonic absorption peak based on the third process yields values for the standard entropy and enthalpy of dissociation of the stably bound H2O dimer.

  13. 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.

  14. Dimer Models from Mirror Symmetry and Quivering Amoebae

    CERN Document Server

    Feng, B; Kennaway, K D; Vafa, C; Feng, Bo; He, Yang-Hui; Kennaway, Kristian D.; Vafa, Cumrun

    2005-01-01

    Dimer models are 2-dimensional combinatorial systems that have been shown to encode the gauge groups, matter content and tree-level superpotential of the world-volume quiver gauge theories obtained by placing D3-branes at the tip of a singular toric Calabi-Yau cone. In particular the dimer graph is dual to the quiver graph. However, the string theoretic explanation of this was unclear. In this paper we use mirror symmetry to shed light on this: the dimer models live on a T^2 subspace of the T^3 fiber that is involved in mirror symmetry and is wrapped by D6-branes. These D6-branes are mirror to the D3-branes at the singular point, and geometrically encode the same quiver theory on their world-volume.

  15. Inequivalent models of irreversible dimer filling: ``Transition state'' dependence

    Science.gov (United States)

    Nord, R. S.; Evans, J. W.

    1990-12-01

    Irreversible adsorption of diatomics on crystalline surfaces is sometimes modeled as random dimer filling of adjacent pairs of sites on a lattice. We note that this process can be implemented in two distinct ways: (i) randomly pick adjacent pairs of sites, jj', and fill jj' only if both are empty (horizontal transition state); or (ii) randomly pick a single site, j, and if j and at least one neighbor are empty, then fill j and a randomly chosen empty neighbor (vertical transition state). Here it is instructive to consider processes which also include competitive random monomer filling of single sites. We find that although saturation (partial) coverages differ little between the models for pure dimer filling, there is a significant difference for comparable monomer and dimer filling rates. We present exact results for saturation coverage behavior for a linear lattice, and estimates for a square lattice. Ramifications for simple models of CO oxidation on surfaces are indicated.

  16. Intrinsic Kinetic Modeling of Thermal Dimerization of C5 Fraction

    Institute of Scientific and Technical Information of China (English)

    Guo Liang; Wang Tiefeng; Li Dongfeng; Wang Jinfu

    2016-01-01

    This work aims to investigate the intrinsic kinetics of thermal dimerization of C5 fraction in the reactive distilla-tion process. Experiments are conducted in an 1000-mL stainless steel autoclave under some selected design conditions. By means of the weighted least squares method, the intrinsic kinetics of thermal dimerization of C5 fraction is established, and the corresponding pre-exponential factor as well as the activation energy are determined. For example, the pre-exponential factor A is equal to 4.39×105 and the activation energy Ea is equal to 6.58×104 J/mol for the cyclopentadiene dimerization re-action. The comparison between the experimental and calculated results shows that the kinetics model derived in this work is accurate and reliable, which can be used in the design of reactive distillation columns.

  17. Ultrafast Dissociation of Metastable CO2 + in a Dimer

    Science.gov (United States)

    Ding, Xiaoyan; Haertelt, M.; Schlauderer, S.; Schuurman, M. S.; Naumov, A. Yu.; Villeneuve, D. M.; McKellar, A. R. W.; Corkum, P. B.; Staudte, A.

    2017-04-01

    We triply ionize the van der Waals bound carbon monoxide dimer with intense ultrashort pulses and study the breakup channel (CO )23 +→C++O++CO+ . The fragments are recorded in a cold target recoil ion momentum spectrometer. We observe a fast CO2 + dissociation channel in the dimer, which does not exist for the monomer. We found that a nearby charge breaks the symmetry of a X3Π state of CO2 + and induces an avoided crossing that allows a fast dissociation. Calculation on the full dimer complex shows the coupling of different charge states, as predicted from excimer theory, gives rise to electronic state components not present in the monomer, thereby enabling fast dissociation with higher kinetic energy release. These results demonstrate that the electronic structure of molecular cluster complexes can give rise to dynamics that is qualitatively different from that observed in the component monomers.

  18. 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.

  19. Photodissociation pathways and lifetimes of protonated peptides and their dimers

    DEFF Research Database (Denmark)

    Gopalan, Aravind; Klærke, Benedikte; Rajput, Jyoti

    2012-01-01

    channel in the dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical......Photodissociation lifetimes and fragment channels of gas-phase, protonated YAn (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ∼200 ns while the protonated dimers show...... of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both...

  20. Micellisation and immunoreactivities of dimeric beta-caseins.

    Science.gov (United States)

    Yousefi, Reza; Gaudin, Jean-Charles; Chobert, Jean-Marc; Pourpak, Zahra; Moin, Mostafa; Moosavi-Movahedi, Ali Akbar; Haertle, Thomas

    2009-12-01

    Bovine beta-casein (beta-CN) is a highly amphiphilic micellising phospho-protein showing chaperone-like activity in vitro. Recently, existence of multiple sequential epitopes on beta-CN polypeptide chain in both hydrophilic-polar (psi) and hydrophobic-apolar domains (phi) has been evidenced. In order to clarify specific contribution of polar and apolar domains in micellisation process and in shaping immunoreactivity of beta-CN, its dimeric/bi-amphiphilic "quasi palindromic" forms covalently connected by a disulfide bond linking either N-terminal (C4 beta-CND) or C-terminal domain (C208 beta-CND) were produced and studied. Depending on the C- or N-terminal position of inserted cysteine, each dimeric beta-CN contains one polar/apolar region at the centre and two external hydrophobic/hydrophilic ends. Consequently, such casein dimers have radically different polarities/hydrophobicities on their outside surfaces. Dynamic light scattering (DLS) measurements indicate that these dimeric casein molecules form micelles of different sizes depending on arrangement of polar fragments of the beta-CN mutants in their constrained dimers. Non-aggregated dimers have different hydrodynamic diameters that could be explained by their different geometries. Measurements of fluorescence showed more hydrophobic environment of Trp residues of C208 beta-CND, while in similar experimental conditions Trp residues of C4 beta-CND and native beta-CN were more exposed to the polar medium. Both fluorescence and DLS studies showed greater propensity for micellisation of the dimeric beta-CNs, suggesting that the factors inducing the formation of micelles are stronger in the bi-amphiphilic dimers. 1-anilino-naphthalene-8-sulfonate (ANS) binding studies showed different binding of ANS by these dimers as well as different exposition of ANS binding (hydrophobic) regions in the micellar states. The differences in fluorescence resonance energy transfer (FRET) profiles of C4 beta-CND and C208 beta-CND can

  1. REVISITING THE PUTATIVE TCR Cα DIMERIZATION MODEL THROUGH STRUCTURAL ANALYSIS

    Directory of Open Access Journals (Sweden)

    Jia-huai eWang

    2013-01-01

    Full Text Available Despite major advances in T cell receptor (TCR biology and structure, how peptide-MHC complex (pMHC ligands trigger αβ TCR activation remains unresolved. Two views exist. One model postulates that monomeric TCR-pMHC ligation events are sufficient while a second proposes that TCR-TCR dimerization in cis via Cα domain interaction plus pMHC binding is critical. We scrutinized 22 known TCR/pMHC complex crystal structures, and did not find any predicted molecular Cα-Cα contacts in these crystals that would allow for physiological TCR dimerization. Moreover, the presence of conserved glycan adducts on the outer face of the Cα domain preclude the hypothesized TCR dimerization through the Cα domain. Observed functional consequences of Cα mutations are likely indirect, with TCR microclusters at the immunological synapse driven by TCR transmembrane/cytoplasmic interactions via signaling molecules, scaffold proteins and/or cytoskeletal elements.

  2. Microwave Spectrum of the Isopropanol-Water Dimer

    Science.gov (United States)

    Mead, Griffin; Finneran, Ian A.; Carroll, Brandon; Blake, Geoffrey

    2016-06-01

    Microwave spectroscopy provides a unique opportunity to study model non-covalent interactions. Of particular interest is the hydrogen bonding of water, whose various molecular properties are influenced by both strong and weak intermolecular forces. More specifically, measuring the hydrogen bonded structures of water-alcohol dimers investigates both strong (OH ··· OH) and weak (CH ··· OH) hydrogen bond interactions. Recently, we have measured the pure rotational spectrum of the isopropanol-water dimer using chirped-pulse Fourier transform microwave spectroscopy (CP-FTMW) between 8-18 GHz. Here, we present the spectrum of this dimer and elaborate on the structure's strong and weak hydrogen bonding.

  3. Dimeric α-Cobratoxin X-ray Structure

    Science.gov (United States)

    Osipov, Alexey V.; Rucktooa, Prakash; Kasheverov, Igor E.; Filkin, Sergey Yu.; Starkov, Vladislav G.; Andreeva, Tatyana V.; Sixma, Titia K.; Bertrand, Daniel; Utkin, Yuri N.; Tsetlin, Victor I.

    2012-01-01

    In Naja kaouthia cobra venom, we have earlier discovered a covalent dimeric form of α-cobratoxin (αCT-αCT) with two intermolecular disulfides, but we could not determine their positions. Here, we report the αCT-αCT crystal structure at 1.94 Å where intermolecular disulfides are identified between Cys3 in one protomer and Cys20 of the second, and vice versa. All remaining intramolecular disulfides, including the additional bridge between Cys26 and Cys30 in the central loops II, have the same positions as in monomeric α-cobratoxin. The three-finger fold is essentially preserved in each protomer, but the arrangement of the αCT-αCT dimer differs from those of noncovalent crystallographic dimers of three-finger toxins (TFT) or from the κ-bungarotoxin solution structure. Selective reduction of Cys26-Cys30 in one protomer does not affect the activity against the α7 nicotinic acetylcholine receptor (nAChR), whereas its reduction in both protomers almost prevents α7 nAChR recognition. On the contrary, reduction of one or both Cys26-Cys30 disulfides in αCT-αCT considerably potentiates inhibition of the α3β2 nAChR by the toxin. The heteromeric dimer of α-cobratoxin and cytotoxin has an activity similar to that of αCT-αCT against the α7 nAChR and is more active against α3β2 nAChRs. Our results demonstrate that at least one Cys26-Cys30 disulfide in covalent TFT dimers, similar to the monomeric TFTs, is essential for their recognition by α7 nAChR, although it is less important for interaction of covalent TFT dimers with the α3β2 nAChR. PMID:22223648

  4. Simulations of coherent nonlinear optical response of molecular vibronic dimers

    CERN Document Server

    Perlík, Václav

    2016-01-01

    We have implemented vibronic dynamics for simulations of the third order coherent response of electronic dimers. In the present communication we provide the full and detailed description of the dynamical model, recently used for simulations of chlorophyll-carotenoid dyads, terylene dimers, or hypericin. We allow for explicit vibronic level structure, by including selected vibrational modes into a "system". Bath dynamics include the Landau-Teller vibrational relaxation, electronic dephasing, and nonlinear vibronic (to bath) coupling. Simulations combine effects of transport and dephasing between vibronic levels. Transport is described by master equation within secular approximation, phase is accumulated in cumulants and its calculation follows the transport pathways during waiting time period.

  5. Dimerization of argon and the properties of its small clusters

    Science.gov (United States)

    Titov, S. V.; Serov, S. A.; Ostrovskii, G. M.

    2016-12-01

    Statistical thermodynamic means are used to study the bound state of a small cluster AN (2 ≤ N ≤ 5) of Lennard-Jones particles in a spherical cavity. The statistical sum is calculated by the Monte Carlo method. For the dimer, integration is reduced to quadratures. The integration region contains only phase space points corresponding to the bound cluster state. Dimerization constant 2A = A2 is calculated via the probability of finding a molecule in the bound state using the example of argon.

  6. Synthesis and polarized photoluminescence of novel phosphorescent cyclometalated platinum dimer

    Institute of Scientific and Technical Information of China (English)

    Shi Ping Jiang; Kai Jun Luo; Ying Han Wang; Xin Wang; Ying Jiang; Yan Yan Wei

    2011-01-01

    A novel phosphorescent cyclometalated platinum dimer with bis-[2-(p-dodecyloxyphenyl) pyridyl]-hexane-l,6-diol as ligand and 1,3-( 1-n-hexyl,3-n-heptadecyl) diketone as ancillary ligand was synthesized. The chemical structure and liquid crystal property of the dimer were characterized by 1H NMR, ESI-MS, polarizing optical microscopy (POM) and differential scanning calorimetry (DSC). The aligned film of title compound on the rubbed polyimide film is intensely emissive at room temperature with emission maximum at 516 nm. The luminescence dichroic ratio (I∥/ IL) at 516 nm is 3.1.

  7. Bis{μ-2-[(pyrimidin-2-yl)amino-meth-yl]phenolato}-κ(2) N (1):O;κ(2) O:N (1)-bis-({2-[(pyrimidin-2-yl-κN)amino-meth-yl]phenol}silver(I)) dihydrate.

    Science.gov (United States)

    Gao, Shan; Ng, Seik Weng

    2012-12-01

    The Ag(I) atom in the title centrosymmetric dinuclear compound, [Ag2(C11H10N3O)2(C11H11N3O)2]·2H2O, shows a T-shaped coordination arising from bonding to the N atom of a neutral 2-[(pyrimidin-2-yl)amino-meth-yl]phenol ligand, the N atom of the 2-[(pyrimidin-2-yl)amino-meth-yl]phenolate anion [N-Ag-N = 171.8 (1)°] and the terminal O atom of the other anion [Ag-O = 2.606 (3) Å]. A pair of 2-[(pyrimidin-2-yl)amino-meth-yl]phenolate anions link the two Ag(I) atoms to form the dinuclear compound. In the crystal, adjacent dinuclear mol-ecules are linked to the lattice water mol-ecules, generating an O-H⋯O- and N-H⋯O-connected three-dimensional network. In the crystal, the hy-droxy H atom is disordered over two positions in a 1:1 ratio; one half-occupancy H atom is connected to one hy-droxy group, whereas the other half-occupancy H atom is connected to another hy-droxy group.

  8. Preparation and optimization of pyrazolo[1,5-a]pyrimidines as new potent PDE4 inhibitors.

    Science.gov (United States)

    Le Roux, Jacques; Leriche, Caroline; Chamiot-Clerc, Philippe; Feutrill, John; Halley, Frank; Papin, David; Derimay, Nathalie; Mugler, Christelle; Grépin, Claudine; Schio, Laurent

    2016-01-15

    A new series of pyrazolo[1,5-a]pyrimidines exemplified by compound 1, has been identified with moderate activity (IC50=165nM), following GSK256066 rescaffolding. Compound 1 optimization at positions 2, 3, 6 and 7 gave compound 10 with high in vitro activity (IC50=0.7nM). Modeling studies based on the PDB structure 3GWT with compound 5 showed the expected overlay with the carboxamide, the aryl moiety and the sulfone. Cyclisation of the primary amide to the 5 position of the pyrazolo[1,5-a]pyrimidines scaffold afforded compounds 15 and 16 with 200-fold enhancement in activity and cellular potency. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Probing mechanism of α-formylketene dithioacetal towards the facile formation of functionalized pyrimidines: A structural approach

    Science.gov (United States)

    Joy, Monu; Adeniyi, Adebayo A.; Mathews, Annie; Mathew, Bijo; Prasanth, S.; Soliman, Mohmoud E. S.; Malayan, Jalaja J.; Anabha, E. R.

    2017-01-01

    α-Formylketene dithioacetal is an active precursor for the synthesis of a variety of organic compounds including pyrimidines and its functionalized materials. The present study deals with the structural versatility of a solid representative compound from the family of α-formylketene dithioacetal to the formation of functionalized pyrimidines derivatives through experimental as well as theoretical methods. 2-(3,4-dimethoxybenzoyl)-3,3-bis(methylsulfanyl)prop-2-enal, the representative compound was synthesized with a reported protocol and characterized through spectral methods. The complete three dimensional solid state structural studies were carried out utilizing single crystal X-ray crystallographic technique along with theoretical methods like classical and accelerated molecular dynamics simulation. Various quantum chemical parameters were also discussed to reveals the complete molecular geometry and reactivity of designated compound.

  10. TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids

    DEFF Research Database (Denmark)

    Fahleson, Tobias; Kauczor, Joanna; Norman, Patrick

    2015-01-01

    We present a computational study of the magnetic circular dichroism (MCD) spectra in the 200–300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil, thymine, and cytosine, using the B3LYP and CAM–B3LYP functionals. Solvent...... effects are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In general, the computed spectra are found to be in good agreement with the experimental ones, apart from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines...... and the B term shape of the spectra of pyrimidine bases are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific, but they do not in general alter...

  11. Cytotoxicity of three new triazolo-pyrimidine derivatives against the plant trypanosomatid: Phytomonas sp. isolated from Euphorbia characias

    Directory of Open Access Journals (Sweden)

    Rosa Magán

    2004-10-01

    Full Text Available There is no effective chemotherapy against diseases caused by Phytomonas sp., a plant trypanosomatid responsible for economic losses in major crops. We tested three triazolo-pyrimidine complexes [two with Pt(II, and another with Ru(III] against promastigotes of Phytomonas sp. isolated from Euphorbia characias. The incorporation of radiolabelled precursors, ultrastructural alterations and changes in the pattern of metabolite excretion were examined. Different degrees of toxicity were found for each complex: the platinun compound showed an inhibition effect on nucleic acid synthesis, provoking alterations on the levels of mitochondria, nucleus and glycosomes. These results, together with others reported previously in our laboratory about the activity of pyrimidine derivatives, reflect the potential of these compounds as agents in the treatment of Phytomonas sp.

  12. Structure-based discovery of novel 4,5,6-trisubstituted pyrimidines as potent covalent Bruton's tyrosine kinase inhibitors.

    Science.gov (United States)

    Zou, Yi; Xiao, Jianhu; Tu, Zhengchao; Zhang, Yingyi; Yao, Kun; Luo, Minghao; Ding, Ke; Zhang, Yihua; Lai, Yisheng

    2016-07-01

    A series of novel 4,5,6-trisubstituted pyrimidines were designed as potent covalent Bruton's tyrosine kinase (BTK) inhibitors based on the structure of ibrutinib by using a ring-opening strategy. Among these derivatives, compound I1 exhibited the most potent inhibitory activity with an IC50 value of 0.07μM. The preliminary structure-activity relationship was discussed and the primary amino group at the C-4 position of pyrimidine was crucial for maintaining BTK activity. Furthermore, molecular dynamics simulations and binding free energy calculations were performed for three inhibitor-BTK complexes to determine the probable binding model, which provided a comprehensive guide for further structural modification and optimization. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Synthesis, Characterization and Biological Evaluation of Some Novel 2-Pyrazoline Analogues with Amino Pyrimidine Moiety as Potential Antimicrobial Agents

    Directory of Open Access Journals (Sweden)

    Y. A. Hatwar

    2016-05-01

    Full Text Available In pursuit to synthesize the molecules with enhanced biological activities, efforts have been made to accommodate 2-pyrazoline and amino pyrimidine moieties in a single molecular framework. In the present study some novel 2-pyrazoline analogues with amino pyrimidine moiety IV(a-k have been synthesized by refluxing N-substituted chalcone 2-pyrazoline (III with guanidinium carbonate. The chemical structures of the compounds were proved by elemental analysis, IR, 1H NMR, 13C NMR and mass spectrometric data. The synthesized compounds were screened for their anti-bacterial and anti-fungal activities against four bacterial and two fungal strains comparable to the reference standard ciprofloxacin and flucanozole respectively. Some of the compounds showed promising activity and proved that pyrazolines are found to be interesting lead molecules for further synthesis as antimicrobial agents.

  14. Crystal structure of 1-methyl-4-methylsulfanyl-1H-pyrazolo[3,4-d]pyrimidine

    Directory of Open Access Journals (Sweden)

    Mohammed El Fal

    2014-12-01

    Full Text Available In the title compound, C7H8N4S, the non-H atoms of the pyrazolo[3,4-d]pyrimidine ring system and the methylsulfanyl group lie on a crystallographic mirror plane. In the crystal, molecules are linked via a number of π–π interactions [centroid–centroid distances vary from 3.452 (7 to 3.6062 (8 Å], forming a three-dimensional structure.

  15. Facile Syntheses of New Pyrazolo[1,5-a] pyrimidines Derivatives via Reactions of Enaminones with Aminopyrazole

    Institute of Scientific and Technical Information of China (English)

    LI Ming; WANG Shu-wen; WEN Li-rong; KE Zi-qin

    2005-01-01

    Ethyl 7-aryl-2-benzylthiopyrazolo [ 1,5-a ] pyrimidine-3-carboxylates (3a-3f) were conveniently synthesized through the reactions of enaminones with 5-amino-3-benzylthio-4-ethoxycarbonyl-1H-pyrazole in good yields and high regioselectivity. The structures of the new compounds were fully characterized by spectroscopic measurments, elemental analysis and X-ray diffraction analysis. A plausible reaction mechanism for the formation of the title compounds was also presented.

  16. Design, synthesis and antiproliferative activity of novel 2,7-disubstituted triazolo[1,5-a]pyrimidines

    Institute of Scientific and Technical Information of China (English)

    Xin Zhai; Nan Jiang; Ke Liang Zhang; Feng Bao; Ping Gong

    2009-01-01

    In our efforts to identify novel potent anticancer agents, we synthesized a series of 2,7-disubstituted triazolo[1,5-a]pyrimidines (6-16). Their antiproliferative activity against Bel-7402, HT- 1080 and WI-38 cell lines was tested by MTT assay in vitro. Four of the compounds (9-11 and 16) displayed promising antiproliferative activity superior to gefitinib, especially compound 9. A preliminary SAR study of these derivatives was performed.

  17. Potentiometric investigation of acid-base equilibria of two newv pyrimidine derivatives in various methanol–water media

    Directory of Open Access Journals (Sweden)

    HASAN KILIÇ

    2006-01-01

    Full Text Available The acid-base properties of 1-amino-5-benzoyl-4-phenyl-1H-pyrimidine-2-one (L1 and 1-amino-5-benzoyl-4-phenyl-1H-pyrimidine-2-thione (L2 were investigated potentiometrically at an ionic strength of 0.10M(LiCl in 19.8, 33.6 and 55.9 % (v/v methanol–water mixtures at 25.0 ± 0.1 ºC. The apparent dissociation constants (psKa were calculated for the di-protonated form (L1H2+2 and L2H2+2 of pyrimidine bases, using a software package TITFIT, which were then extrapolated to pure water to derive the dissociation constants in aqueous solution (pKa. The aqueous pKa constants were found to be: L1, pKa1 = 3.76 and pKa2 = 6.95; L2, pKa1 = 3.57 and pKa1 = 6.90. At pH 2.00, the dominant species in solution were the protonated form of the amino group substituted at the 1-position, while at a pH around 5.00, they were the protonated form of the pyrimidine ring nitrogen at the 3-position. An effect of intramolecular hydrogen bonding on the psKa values was observed with L1 but not L2. The effects ofmolecular structure and solvent medium on the psKa values are also discussed.

  18. Novel N-(pyrimidin-4-ylthiazol-2-amine derivatives as dual-action hypoglycemic agents that activate GK and PPARγ

    Directory of Open Access Journals (Sweden)

    Hui-peng Song

    2011-10-01

    Full Text Available A series of novel N-(pyrimidin-4-ylthiazol-2-amine derivatives have been synthesized and evaluated as glucokinase (GK activators. Ethyl 2-(6-(4-(2-hydroxyethylpiperazin-1-yl-2-methylpyrimidin-4-yl-aminothiazole-5-carboxylate was found to be a potent dual-acting hypoglycemic agent activating both GK and PPARγ. When given orally to normal mice, the compound demonstrated significant efficacy in decreasing the glucose level after oral glucose loading.

  19. Biophysical characterization of the dimer and tetramer interface interactions of the human cytosolic malic enzyme.

    Directory of Open Access Journals (Sweden)

    Sujithkumar Murugan

    Full Text Available The cytosolic NADP(+-dependent malic enzyme (c-NADP-ME has a dimer-dimer quaternary structure in which the dimer interface associates more tightly than the tetramer interface. In this study, the urea-induced unfolding process of the c-NADP-ME interface mutants was monitored using fluorescence and circular dichroism spectroscopy, analytical ultracentrifugation and enzyme activities. Here, we demonstrate the differential protein stability between dimer and tetramer interface interactions of human c-NADP-ME. Our data clearly demonstrate that the protein stability of c-NADP-ME is affected predominantly by disruptions at the dimer interface rather than at the tetramer interface. First, during thermal stability experiments, the melting temperatures of the wild-type and tetramer interface mutants are 8-10°C higher than those of the dimer interface mutants. Second, during urea denaturation experiments, the thermodynamic parameters of the wild-type and tetramer interface mutants are almost identical. However, for the dimer interface mutants, the first transition of the urea unfolding curves shift towards a lower urea concentration, and the unfolding intermediate exist at a lower urea concentration. Third, for tetrameric WT c-NADP-ME, the enzyme is first dissociated from a tetramer to dimers before the 2 M urea treatment, and the dimers then dissociated into monomers before the 2.5 M urea treatment. With a dimeric tetramer interface mutant (H142A/D568A, the dimer completely dissociated into monomers after a 2.5 M urea treatment, while for a dimeric dimer interface mutant (H51A/D90A, the dimer completely dissociated into monomers after a 1.5 M urea treatment, indicating that the interactions of c-NADP-ME at the dimer interface are truly stronger than at the tetramer interface. Thus, this study provides a reasonable explanation for why malic enzymes need to assemble as a dimer of dimers.

  20. A facile environment-friendly one-pot two-step regioselective synthetic strategy for 3,7-diarylpyrazolo[1,5-a]pyrimidines related to zaleplon and 3,6-diarylpyrazolo[1,5-a]pyrimidine-7-amines assisted by KHSO[Formula: see text] in aqueous media.

    Science.gov (United States)

    Devi, Asem Satyapati; Kaping, Shunan; Vishwakarma, Jai Narain

    2015-11-01

    3-Aminopyrazoles required for the synthesis of pyrazolo[1,5-a]pyrimidines were obtained by the reaction of enaminonitriles with hydrazine hydrate. The resulting aminopyrazoles are reacted with formylated acetophenones under reflux at [Formula: see text] assisted by KHSO[Formula: see text] in aqueous media to form regioselectively 3,7-diarylpyrazolo[1,5-a]pyrimidines and 3,6-diarylpyrazolo[1,5-a]pyrimidine-7-amines. X-ray crystallography of selected compounds 5b and 7i further confirmed the regioselective formation of these products.

  1. Consortium analysis of gene and gene-folate interactions in purine and pyrimidine metabolism pathways with ovarian carcinoma risk

    Science.gov (United States)

    Kelemen, Linda E.; Terry, Kathryn L.; Goodman, Marc T.; Webb, Penelope M.; Bandera, Elisa V.; McGuire, Valerie; Rossing, Mary Anne; Wang, Qinggang; Dicks, Ed; Tyrer, Jonathan P.; Song, Honglin; Kupryjanczyk, Jolanta; Dansonka-Mieszkowska, Agnieszka; Plisiecka-Halasa, Joanna; Timorek, Agnieszka; Menon, Usha; Gentry-Maharaj, Aleksandra; Gayther, Simon A.; Ramus, Susan J.; Narod, Steven A.; Risch, Harvey A.; McLaughlin, John R.; Siddiqui, Nadeem; Glasspool, Rosalind; Paul, James; Carty, Karen; Gronwald, Jacek; Lubiński, Jan; Jakubowska, Anna; Cybulski, Cezary; Kiemeney, Lambertus A.; Massuger, Leon F. A. G.; van Altena, Anne M.; Aben, Katja K. H.; Olson, Sara H.; Orlow, Irene; Cramer, Daniel W.; Levine, Douglas A.; Bisogna, Maria; Giles, Graham G.; Southey, Melissa C.; Bruinsma, Fiona; Kjær, Susanne Krüger; Høgdall, Estrid; Jensen, Allan; Høgdall, Claus K.; Lundvall, Lene; Engelholm, Svend-Aage; Heitz, Florian; du Bois, Andreas; Harter, Philipp; Schwaab, Ira; Butzow, Ralf; Nevanlinna, Heli; Pelttari, Liisa M.; Leminen, Arto; Thompson, Pamela J.; Lurie, Galina; Wilkens, Lynne R.; Lambrechts, Diether; Van Nieuwenhuysen, Els; Lambrechts, Sandrina; Vergote, Ignace; Beesley, Jonathan; Fasching, Peter A.; Beckmann, Matthias W.; Hein, Alexander; Ekici, Arif B.; Doherty, Jennifer A.; Wu, Anna H.; Pearce, Celeste L.; Pike, Malcolm C.; Stram, Daniel; Chang-Claude, Jenny; Rudolph, Anja; Dörk, Thilo; Dürst, Matthias; Hillemanns, Peter; Runnebaum, Ingo B.; Bogdanova, Natalia; Antonenkova, Natalia; Odunsi, Kunle; Edwards, Robert P.; Kelley, Joseph L.; Modugno, Francesmary; Ness, Roberta B.; Karlan, Beth Y.; Walsh, Christine; Lester, Jenny; Orsulic, Sandra; Fridley, Brooke L.; Vierkant, Robert A.; Cunningham, Julie M.; Wu, Xifeng; Lu, Karen; Liang, Dong; Hildebrandt, Michelle A.T.; Weber, Rachel Palmieri; Iversen, Edwin S.; Tworoger, Shelley S.; Poole, Elizabeth M.; Salvesen, Helga B.; Krakstad, Camilla; Bjorge, Line; Tangen, Ingvild L.; Pejovic, Tanja; Bean, Yukie; Kellar, Melissa; Wentzensen, Nicolas; Brinton, Louise A.; Lissowska, Jolanta; Garcia-Closas, Montserrat; Campbell, Ian G.; Eccles, Diana; Whittemore, Alice S.; Sieh, Weiva; Rothstein, Joseph H.; Anton-Culver, Hoda; Ziogas, Argyrios; Phelan, Catherine M.; Moysich, Kirsten B.; Goode, Ellen L.; Schildkraut, Joellen M.; Berchuck, Andrew; Pharoah, Paul D.P.; Sellers, Thomas A.; Brooks-Wilson, Angela; Cook, Linda S.; Le, Nhu D.

    2014-01-01

    Scope We re-evaluated previously reported associations between variants in pathways of one-carbon (folate) transfer genes and ovarian carcinoma (OC) risk, and in related pathways of purine and pyrimidine metabolism, and assessed interactions with folate intake. Methods and Results Odds ratios (OR) for 446 genetic variants were estimated among 13,410 OC cases and 22,635 controls and among 2,281 cases and 3,444 controls with folate information. Following multiple testing correction, the most significant main effect associations were for DPYD variants rs11587873 (OR=0.92, P=6x10−5) and rs828054 (OR=1.06, P=1x10−4). Thirteen variants in the pyrimidine metabolism genes, DPYD, DPYS, PPAT and TYMS, also interacted significantly with folate in a multi-variant analysis (corrected P=9.9x10−6) but collectively explained only 0.2% of OC risk. Although no other associations were significant after multiple testing correction, variants in SHMT1 in one-carbon transfer, previously reported with OC, suggested lower risk at higher folate (Pinteraction=0.03-0.006). Conclusions Variation in pyrimidine metabolism genes, particularly DPYD, which was previously reported to be associated with OC, may influence risk; however, stratification by folate intake is unlikely to modify disease risk appreciably in these women. SHMT1 SNP-byfolate interactions are plausible but require further validation. Polymorphisms in selected genes in purine metabolism were not associated with OC. PMID:25066213

  2. [Distribution of pyrimidine blocks in the DNA of Brevibacterium linens, Arthrobacter globiformis, Nocardia corallina and Nocardia rubra].

    Science.gov (United States)

    Eroshina, N V; Golovlev, E L; Geĭdarov, T G; Bur'ianov, Ia I

    1975-01-01

    The nucleotide composition and the frequency of pyrimidine blocks were studied in DNA of the following bacteria: Brevibacterium linens (Weignamm, 1910) Breed, 1953; Arthrobacter globiformis (Conn, 1928) Conn et Dimmick, 1947; Nocardia corallina (Bergey et al., 1923) Waksman et Henrici, 1948; Nocardia rubra (Krassilnikov, 1949) Waksman et Henrici, 1948. These organisms are classed by some microbiologists as mycobacteria (the Mycobacteriaceae family) while other authors regard them as representatives of three families belonging to two orders. About 60 percent of all pyrimidines in DNA of these bacteria are found in the sequences pur-pyr-pur and pur-pyr-pyr-pur, the number of dipyrimidines being higher than the amount of monopyrimidine nucleotides. The content of dipyrimidine nucleotides in DNA of Nocardia corallina and Nocardia rubra is higher (16.8 mole %) than the content of dipyrimidine blocks in DNA of Brevibacterium linens and Arthrobacter globiformis, in which the quantity of dipyrimidines is almost the same (13.9 and 14.4 mole %). A new characteristic, the selected mean value, is suggested to evaluate differences in the distribution of pyrimidines in DNA.

  3. Microwave-Assisted Synthesis and Antimicrobial Evaluation of Novel Spiroisoquinoline and Spiropyrido[4,3-d]pyrimidine Derivatives

    Directory of Open Access Journals (Sweden)

    Rasha M. Faty

    2015-01-01

    Full Text Available Bromination of N-substituted homophthalimides and tetrahydropyrido[4,3-d]- pyrimidine-5,7-diones produces 4,4-dibromohomophthalimide and 8,8-dibromo-tetrahydropyrido[4,3-d]pyrimidine-5,7-dione derivatives, respectively, that can be used as precursors for spiro derivatives. The dibromo derivatives react with different binucleophilic reagents to produce several spiroisoquinoline and spirotetrahydropyrido[4,3-d]- pyrimidine-5,7-dione derivatives, respectively. Reaction of the dibromo derivatives with malononitrile produces dicyanomethylene derivatives which react with different binucleophiles to produce new spiro derivatives. All new compounds are prepared by using the usual chemical conditions and microwave assisted conditions. The latter conditions improved the reaction yields, reduced reaction times and ameliorated the effects on the surrounding environment as the reactions are carried out in closed systems. Structures of the newly synthesized compounds are proved using spectroscopic methods such as IR, MS, 1H-NMR and 13C-NMR and elemental analyses. Some of the newly synthesized compounds were tested for their antimicrobial activities, whereby four of them showed moderate activities and the rest showed low or no activities towards the investigated species.

  4. Plasma D-dimer concentration in patients with systemic sclerosis

    Directory of Open Access Journals (Sweden)

    Montagnana Martina

    2006-01-01

    Full Text Available Abstract Background Systemic sclerosis (SSc is an autoimmune disorder of the connective tissue characterized by widespread vascular lesions and fibrosis. Little is known so far on the activation of the hemostatic and fibrinolytic systems in SSc, and most preliminary evidences are discordant. Methods To verify whether SSc patients might display a prothrombotic condition, plasma D-dimer was assessed in 28 consecutive SSc patients and in 33 control subjects, matched for age, sex and environmental habit. Results and discussion When compared to healthy controls, geometric mean and 95% confidence interval (IC95% of plasma D-dimer were significantly increased in SSc patients (362 ng/mL, IC 95%: 361–363 ng/mL vs 229 ng/mL, IC95%: 228–231 ng/mL, p = 0.005. After stratifying SSc patients according to disease subset, no significant differences were observed between those with limited cutaneous pattern and controls, whereas patients with diffuse cutaneous pattern displayed substantially increased values. No correlation was found between plasma D-dimer concentration and age, sex, autoantibody pattern, serum creatinine, erythrosedimentation rate, nailfold videocapillaroscopic pattern and pulmonary involvement. Conclusion We demonstrated that SSc patients with diffuse subset are characterized by increased plasma D-dimer values, reflecting a potential activation of both the hemostatic and fibrinolytic cascades, which might finally predispose these patients to thrombotic complications.

  5. Two-Dimensional Electronic Spectroscopy of a Model Dimer System

    Directory of Open Access Journals (Sweden)

    Prokhorenko V.I.

    2013-03-01

    Full Text Available Two-dimensional spectra of a dimer were measured to determine the timescale for electronic decoherence at room temperature. Anti-correlated beats in the crosspeaks were observed only during the period corresponding to the measured homogeneous lifetime.

  6. Weakly Stabilized Primary Borenium Cations and their Dicationic Dimers

    Science.gov (United States)

    Prokofjevs, Aleksandrs; Kampf, Jeff W.; Solovyev, Andrey; Curran, Dennis P.; Vedejs, Edwin

    2013-01-01

    Hydride abstraction from monocationic hydride bridged salts [H(H2B–L)2]+ [B(C6F5)4]− (L = Lewis base) generates an observable primary borenium cation for L = iPr2NEt, but with L = Me3N, Me2NPr, or several N-heterocyclic carbenes, highly reactive dicationic dimers are formed. PMID:24087933

  7. Dimeric Complexes of Tryptophan with M2+ Metal Ions

    NARCIS (Netherlands)

    Dunbar, R. C.; Steill, J. D.; Polfer, N. C.; Oomens, J.

    2009-01-01

    IRMPD spectroscopy using the FELIX free electron laser and a Fourier transform ICR mass spectrometer was used to characterize the structures of electrosprayed dimer complexes M(2+)Trp(2) of tryptophan with a series of eight doubly charged metal ions, including alkaline earths Ca, Sr, and Ba, and tra

  8. FOUR NEW STILBENE DIMERS FROM THE LIANAS OF GNETUM HAINANENSE

    Institute of Scientific and Technical Information of China (English)

    YING-HONG WANG; KAI-SHENG HUANG; MAO LIN

    2001-01-01

    Four new stilbene dimers, gnetuhainins P (1), Q (2), K (3) and L (4), were isolated from the lianas of Gnetum hainanense C. Y. Cheng. Their structures and relative configurations were determined on the basis of spectroscopic evidence, especially 2D NMR techniques.

  9. Dispersion Interactions and the Stability of Amine Dimers

    Science.gov (United States)

    Guttmann, Robin

    2017-01-01

    Abstract Weak, intermolecular interactions in amine dimers were studied by using the combination of a dispersionless density functional and a function that describes the dispersion contribution to the interaction energy. The validity of this method was shown by comparison of structural and energetic properties with data obtained with a conventional density functional and the coupled cluster method. The stability of amine dimers was shown to depend on the size, the shape, and the relative orientation of the alkyl substituents, and it was shown that the stabilization energy for large substituents is dominated by dispersion interactions. In contrast to traditional chemical explanations that attribute stability and condensed matter properties solely to hydrogen bonding and, thus, to the properties of the atoms forming the hydrogen bridge, we show that without dispersion interactions not even the stability and structure of the ammonia dimer can be correctly described. The stability of amine dimers depends crucially on the interaction between the non‐polar alkyl groups, which is dominated by dispersion interactions. This interaction is also responsible for the energetic part of the free energy interaction used to describe hydrophobic interactions in liquid alkanes. The entropic part has its origin in the high degeneracy of the interaction energy for complexes of alkane molecules, which exist in a great variety of conformers, having their origin in internal rotations of the alkane chains. PMID:28794953

  10. A Novel Dimeric Eremophilane from Ligularia virgaurea spp. Oligocephala

    Institute of Scientific and Technical Information of China (English)

    Quan Xiang WU; Xia LIU; Yan Ping SHI

    2005-01-01

    A novel dimeric eremophilane, ligulolide B, was isolated from the alcoholic extract of the whole plant of Ligularia virgaurea spp. oligocephala. The structure was elucidated by various spectroscopic methods including intensive 2D NMR techniques (1H-1H COSY, gHMQC,gHMBC and 1H-1H NOESY) and HR-ESI-MS.

  11. Centrosymmetric dimer of quinuclidine betaine and squaric acid complex

    Science.gov (United States)

    Dega-Szafran, Z.; Katrusiak, A.; Szafran, M.

    2012-12-01

    The complex of squaric acid (3,4-dihydroxy-3-cyclobuten-1,2-dion, H2SQ) with quinuclidine betaine (1-carboxymethyl-1-azabicyclo[2.2.2]octane inner salt, QNB), 1, has been characterized by single-crystal X-ray analysis, FTIR and NMR spectroscopies and by DFT calculations. In the crystal of 1, monoclinic space group P21/n, one proton from H2SQ is transferred to QNB. QNBH+ and HSQ- are linked together by a Osbnd H⋯O hydrogen bond of 2.553(2) Å. Two such QNBH+·HSQ- complexes form a centrosymmetric dimer bridged by two Osbnd H⋯O bonds of 2.536(2) Å. The FTIR spectrum is consistent with the X-ray results. The structures of monomer QNBH+·HSQ- (1a) and dimer [QNB·H2SQ]2 (2) have been optimized at the B3LYP/6-311++G(d,p) level of theory. Isolated dimer 2 optimized back to a molecular aggregate of H2SQ and QNB. The calculated frequencies for the optimized structure of dimer 2 have been used to explain the frequencies of the experimental FTIR spectrum. The interpretation of 1H and 13C NMR spectra has been based on the calculated GIAO/B3LYP/6-311++G(d,p) magnetic isotropic shielding constants for monomer 1a.

  12. Entanglement Transfer in a Four-Qubit Dimerized Heisenberg System

    Institute of Scientific and Technical Information of China (English)

    SHAO Bin; HUANG Min; WANG Zhao-ming; ZOU Jian

    2008-01-01

    Entanglement transfer is investigated in a dimerized Heisenberg system.Coneurrence as the measure of entanglement is calculated by the time-evolved state starting from an initially entangled state of spin pair.It is shown that perfect entanglement transfer can be realized at 80me special time and suitable interacting.

  13. Dimers of Azurin as model systems for electron transfer

    NARCIS (Netherlands)

    Jongh, Thyra Estrid de

    2006-01-01

    This thesis describes the investigation of crosslinked complexes of the blue copper protein azurin by means of spectroscopic techniques such as Uv-Vis and NMR as well as by X-ray crystallography. These non-physiological dimers serve as model systems for interprotein electron transfer (ET) and allow

  14. Gnapholide: a new guaiac-dimer from Pulicaria gnaphalodes (Asteraceae).

    Science.gov (United States)

    Ali, Muhammad Shaiq; Jahangir, Muhammad; Uzair, Syed Shah; Erian, Ayman Wahba; Tareen, Rasool Bakhsh

    2002-06-01

    The ethyl acetate soluble part of the chloroform extract of Pulicaria gnaphalodes belonging to the family Asteraceae afforded a new sesquiterpene-dimer of guaiane class named as gnapholide and anabsinthin of the same skeleton. The structures of both the compounds were elucidated with the aid of spectroscopic techniques including 2D NMR.

  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. A novel dimeric procyanidin glucoside from Polygonum aviculare

    Institute of Scientific and Technical Information of China (English)

    Hai Jian Cong; Shu Wei Zhang; Chong Zhang; Yu Jie Huang; Li Jiang Xuan

    2012-01-01

    A novel dimeric procyanidin glucoside,catechin 3-O-acetate-(4α→8)-catechin 3-O-acetate-3′-O-β-D-glucopyranoside (1),along with five flavonoids and one lignan were isolated from the aerial parts of Polygonum aviculare.Their structures were elucidated by spectroscopic analyses including 1D,2D NMR,MS and CD methods.

  17. 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.

  18. Entanglement in spin-1/2 dimerized Heisenberg systems

    CERN Document Server

    Sun, Z; Hu, A Z; Li, Y Q; Sun, Zhe; Wang, XiaoGuang; Hu, AnZi; Li, You-Quan

    2005-01-01

    We study entanglement in dimerized Heisenberg systems. In particular, we give exact results of ground-state pairwise entanglement for the four-qubit model by identifying a Z_2 symmetry. Although the entanglements cannot identify the critical point of the system, the mean entanglement of nearest-neighbor qubits really does, namely, it reaches a maximum at the critical point.

  19. Entanglement in Spin-1/2 Dimerized Heisenberg Systems

    Institute of Scientific and Technical Information of China (English)

    SUN Zhe; WANG Xiao-Guang; HU An-Zi; LI You-Quan

    2005-01-01

    We study entanglement in dimerized Heisenberg systems. In particular, we give exact results of groundstate pairwise entanglement for the four-qubit model by identifying a Z2 symmetry. Although the entanglements cannot identify the critical point of the system, the mean entanglement of the nearest-neighbor qubits really does, namely, it reaches a maximum at the critical point.

  20. 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 c

  1. Construction of covalently coupled, concatameric dimers of 7TM receptors

    DEFF Research Database (Denmark)

    Terpager, Marie; Scholl, D Jason; Kubale, Valentina;

    2009-01-01

    -Ala repeats flanked by flexible spacers and positively charged residues to ensure correct inside-out orientation plus an extracellular HA-tag to construct covalently coupled dimers of 7TM receptors. Such 15 TM concatameric homo- and heterodimers of the beta(2)-adrenergic and the NK(1) receptors, which...

  2. Ising anyons in frustration-free Majorana-dimer models

    Science.gov (United States)

    Ware, Brayden; Son, Jun Ho; Cheng, Meng; Mishmash, Ryan V.; Alicea, Jason; Bauer, Bela

    2016-09-01

    Dimer models have long been a fruitful playground for understanding topological physics. Here, we introduce a class, termed Majorana-dimer models, wherein bosonic dimers are decorated with pairs of Majorana modes. We find that the simplest examples of such systems realize an intriguing, intrinsically fermionic phase of matter that can be viewed as the product of a chiral Ising theory, which hosts deconfined non-Abelian quasiparticles, and a topological px-i py superconductor. While the bulk anyons are described by a single copy of the Ising theory, the edge remains fully gapped. Consequently, this phase can arise in exactly solvable, frustration-free models. We describe two parent Hamiltonians: one generalizes the well-known dimer model on the triangular lattice, while the other is most naturally understood as a model of decorated fluctuating loops on a honeycomb lattice. Using modular transformations, we show that the ground-state manifold of the latter model unambiguously exhibits all properties of the Ising×(px-i py) theory. We also discuss generalizations with more than one Majorana mode per site, which realize phases related to Kitaev's 16-fold way in a similar fashion.

  3. Measurement of oxidative damage at pyrimidine bases in gamma-irradiated DNA.

    Science.gov (United States)

    Douki, T; Delatour, T; Paganon, F; Cadet, J

    1996-01-01

    Oxidized nucleobases represent one of the main classes of damage induced in DNA by ionizing radiation. Emphasis was placed in this work on the measurement of four oxidized pyrimidine bases, including 5-(hydroxymethyl)uracil (5-HMUra), 5-formyluracil (5-ForUra), 5-hydroxycytosine (5-OHCyt), and 5-hydroxyuracil (5-OHUra), in isolated DNA upon exposure to gamma radiation in aerated aqueous solution. For this purpose, both high performance liquid chromatography associated with electrochemical detection (HPLC-EC) and gas chromatography coupled to mass spectrometry (GC-MS) were used. Conditions of hydrolysis of the N-glycosidic bond were carefully checked in order to achieve a quantitative release of the lesions. We showed that 60% formic acid treatment leads to the decomposition of the four lesions studied. On the other hand, hydrolysis based on the use of either 88% formic acid or 70% hydrogen fluoride in pyridine (HF/Pyr) allowed the quantitative release of the modified bases, with the exception of 5-HMUra when the latter reagent was utilized. A dose course study of the radiation-induced formation of 5-HMUra and 5-ForUra in DNA by using the GC-MS assay showed that the latter lesion was produced in a 2.1-fold higher yield than the former one. HF/Pyr and 88% formic acid hydrolysis provided similar results for 5-ForUra, indicating the reliability of both techniques for the measurement of this lesion. For 5-OHUra and 5-OHCyt, the level of modification determined by GC-MS analysis was higher after 88% formic acid treatment than upon HF/Pyr hydrolysis. When DNA was enzymatically digested and analyzed by HPLC-EC for 5-OHdCyd and 5-OHdUrd, the results were very close to those obtained by GC-MS following HF/Pyr treatment. It was concluded that additional amounts of both 5-OHUra and 5-OHCyt are produced during the 88% formic acid treatment from radiation-induced 5,6-saturated pyrimidine precursors. It is likely that cytosine and uracil diols are involved in this reaction. The

  4. Efficacy of a pyrimidine derivative to control spot disease on Solanum melongena caused by Alternaria alternata

    Directory of Open Access Journals (Sweden)

    Nemat M. Hassan

    2013-07-01

    Full Text Available The pyrimidine derivative (4,6-dimethyl-N-phenyldiethyl pyrimidine, DPDP was tested as a foliar spray fungicide at 50 mg l−1 for protection of eggplant (Solanum melongena from spot disease caused by Alternaria alternata. Varied concentrations of DPDP (10–50 mg l−1 differentially inhibited mycelial growth, conidial count and conidial germination of A. alternata growth in vitro; the magnitude of inhibition increased with increasing concentration. In vivo, an experiment was conducted in pots using a complete block randomized design and repeated twice with three replications and four treatments (control, A. alternata alone, DPDP alone and combination of DPDP and A. alternata for 5 weeks (1 plant in pot × 3 pots per set (3 replications per treatment × 4 sets (4 treatments × 5 weeks × 2 experimental repetitions = 120 pots. In this experiment, 10-day-old eggplant seedlings were transplanted in pots and then inoculated with A. alternata, DPDP or their combination 1 week later. Leaves of the A. alternata-infected eggplant suffered from chlorosis, necrosis and brown spots during the subsequent 5 weeks. Disease intensity was obvious in infected leaves but withdrawn by DPDP. There were relationships between incidence and severity, greater in plant leaves infected A. alternata alone and diminished with the presence of DPDP. Moreover, the infection resulted in reductions in growth, decreases in contents of anthocyanins, chlorophylls, carotenoids and thiols as well as inhibitions in activities of superoxide dismutase (SOD, glutathione peroxidase (GPX and glutathione-S-transferase (GST. Nonetheless, the application of DPDP at 50 mg led to a recovery of the infected eggplant; the infection-induced deleterious effects were mostly reversed by DPDP. However, treatment with DPDP alone seemed with no significant impacts. Due to its safe use to host and the inhibition for the pathogen, DPDP could be suggested as an efficient fungicide for

  5. 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.

  6. Structural proof of a dimeric positive modulator bridging two identical AMPA receptor-binding sites

    DEFF Research Database (Denmark)

    Kaae, Birgitte Høiriis; Harpsøe, Kasper; Kastrup, Jette Sandholm Jensen;

    2007-01-01

    Dimeric positive allosteric modulators of ionotropic glutamate receptors were designed, synthesized, and characterized pharmacologically in electrophysiological experiments. The designed compounds are dimers of arylpropylsulfonamides and have been constructed without a linker. The monomeric...

  7. 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

  8. Radiation-enhanced optical antenna based on nonperiodic metallic nanoparticle dimer chain

    Science.gov (United States)

    Chen, Xiaolin; Yu, Wenhai; Yue, Wencheng; Yao, Peijun; Liu, Wen

    2015-07-01

    With the aid of multi-sphere dyadic Green's function, we present a design of optical nanoantenna which is composed of a nonperiodic nanoparticle dimer chain. By breaking the periodicity of the dimer chain, the radiative emission of the dimer chain is significantly enhanced because the strong coupling which limits radiation enhancement is inhibited when the separations between dimers are reduced. Our work clearly shows the crucial role of nonperiodicity in the design of the Yagi-Uda nanoantenna.

  9. Stereo- and regio-selectivity in the photosensitized dimerization of 1, 3-dimethylthymine in solution

    Institute of Scientific and Technical Information of China (English)

    HEI Xiaoming; SONG Qinhua; TANG Wenjian; WANG Hongbo; GUO Qingxiang; YU Shuqin

    2005-01-01

    The effects of reaction pathway and temperature on stereo- and regio-selectivity of photocycloaddition of 1, 3-dimethylthymine (DMT) which gives four cyclobutane type dimers in solution using acetone as the photosensitizer, are investigated by measuring the product distribution. It is demonstrated that the ground-state aggregation between DMT molecules mainly leads to (h-t)dimers, and the diffusion-controlled triplet dimerization is favorable to the formation of (h-h) dimers.

  10. 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...

  11. Synthesis of β,β'-Porphyrin Dimer Linked by Vinylene

    Institute of Scientific and Technical Information of China (English)

    Jiang, Xuliang; Li, Panli; Wang, Yucheng; Shen, Qi; Tao, Jingchao; Shi, Weimin

    2012-01-01

    Synthesis of a novel β,β'-tetraalkylporphyrin dimer linked by vinylene was discribed, in which the dimer was readily prepared from a porphyrin-derived Wittig reagent and a mono-formylated porphyrin via Wittig reaction. No π-conjugation between the two porphyrin rings was obserbed, and the dimer was in trans form.

  12. A Large Conformational Change of a Bridged β-Cyclodextrin Dimer in Aqueous Solution

    Institute of Scientific and Technical Information of China (English)

    Xiao Qi ZHENG; Yong Hui WANG; Qing Xiang GUO; Li YANG; You Cheng LIU

    2003-01-01

    A novel bridged β-CD dimer in which two β-cyclodextrins were linked by a naphthalene at positions 2 and 7 has been synthesized. 1H and 13CNMR measurements showed that a large change in the conformation of the dimer occurred in aqueous solution. The dimer interacted with methyl and ethyl orange to form stable inclusion complexes via "induced fit" mechanism.

  13. 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...

  14. Sublattice signatures of transitions in a $\\mathcal{PT}$-symmetric dimer lattice

    CERN Document Server

    Harter, Andrew K

    2016-01-01

    Lattice models with non-hermitian, parity and time-reversal ($\\mathcal{PT}$) symmetric Hamiltonians, realized most readily in coupled optical systems, have been intensely studied in the past few years. A $\\mathcal{PT}$-symmetric dimer lattice consists of dimers with intra-dimer coupling $\

  15. Pyrimidines and the X-ray response of Tribolium confusum Duval.

    Science.gov (United States)

    Hogan, G R

    1968-11-01

    Radiosensitizing effects of incorporation into DNA of the halogenated pyrimidines 5-bromouracil or 5-iodouracil, or their nucleosides (BUdR and IUdR), have been demonstrated in a variety of cell types. The results indicate that these antimetabolites influence lethality in x-irradiated adult Tribolium. At relatively low concentrations in the medium, BUdR and IUdR exhibit toxicity 3 to 5 weeks after transfer of beetles to analog-containing medium. Toxicity of IUdR on nonirradiated adults is less pronounced than that of BUdR and is slower to develop. Analog-treated Tribolium exposed to 7 kR, which is sublethal for adults in normal medium, die much earlier than those treated with analog alone or with lethal doses of x-rays alone. Transfer of beetles to normal medium after 3 weeks or less in the presence of analog virtually eliminates lethality attributable to the analog. X-irradiation at the time of transfer, however, leads to high mortality, and the amount of mortality appears to be a function of the duration of analog treatment. Insects grown in medium containing uracil or thymine exhibit the same survival as those reared in unsupplemented medium. Two weeks after 7 kR of irradiation a sharp decline in survival is seen in both uracil- and thymine-treated groups.

  16. 5-(2-amimo-4-styryl pyrimidine-4-yl-4-methoxybenzofuran-6-ol

    Directory of Open Access Journals (Sweden)

    Atteyat A Labib

    2013-05-01

    Full Text Available This study describes the organic synthesis of 5-(2-amimo-4-styryl pyrimidine-4-yl-4-methoxy benzofuran-6-ol (SPBF as an example of a benzofuran derivative used as a new series of amyloid imaging agents. These benzofuran derivatives may be useful amyloid imaging agents for detecting B-amyloid plagues in the brain of Alzheimer’s disease. The precursor is 1-[6-hydroxy-4-methoxybenzofuran-5-yl]-phenyl butadiene ketone, which react with guanidine hydrochloride. The purification process was done via crystallization using solvent ethanol. The overall yield was 75% and the structure of the synthesized compound was confirmed by correct analytical and spectral data. Also, The synthesized compound was labeled with radioactive iodine -125 via electrophilic substitution reaction, in the presence of iodogen as an oxidizing agent, the labeling process was carried out at 95oC for 20min. The radiochemical yield was determined by using a thin layer chromatography and the yield was equal to 80%. Preliminary an in-vivo study examined normal mice after intravenous injection through the tail vein and the data showed the labeling compound was quickly cleared from most body organs. The radioiodinated compound showed high brain uptake.The results of this study suggest that radioiodinated (SPBF may be useful as a brain imaging agents.

  17. Purine and pyrimidine composition in 5S rRNA and its mutational significance

    Directory of Open Access Journals (Sweden)

    Subacius Sandra Maria Rodrigues

    1998-01-01

    Full Text Available Variations observed in 5S rRNA base compositions are almost entirely due to fixation of point mutations. As a consequence, 5S rRNA size has remained relatively constant during evolution and, therefore, dependencies among the four bases can be predicted. In order to characterize the nature and to determine the degree of such dependencies, correlation analysis followed by principal component factorial analysis was conducted on a large sample of 5S rRNA sequences. The results show that the purine and pyrimidine contents tend to remain constant, so that A + G = Kpur and C + U = Kpyr. The composition of the four bases expressed now by Kpur/Kpyr relationships is also constant (Ks. These relationships imply that the behavior of the mutations in the variable sites of the molecule follows rules imposed by the chemical nature of the bases involved. Consequently, transition mutations would be more favored than substitutions in transversion sites and also than insertion-deletion (rare in 5S rRNAs, since transitions would not significantly alter the values of the Ks-index.

  18. High-resolution photoelectron spectra of the pyrimidine-type nucleobases.

    Science.gov (United States)

    Fulfer, K D; Hardy, D; Aguilar, A A; Poliakoff, E D

    2015-06-14

    High-resolution photoelectron spectra of the gas phase pyrimidine-type nucleobases, thymine, uracil, and cytosine, were collected using synchrotron radiation over the photon energy range 17 ≤ hν ≤ 150 eV. These data provide the highest resolution photoelectron spectra of thymine, uracil, and cytosine published to date. By comparing integrated regions of the energy dependent photoelectron spectra of thymine, the ionization potentials of the first four ionic states of thymine were estimated to be 8.8, 9.8, 10.3, and 10.8 eV. The thymine data also show evidence for low energy shape resonances in three of the outermost valence electronic states. Comparing the uracil spectrum with the thymine spectrum, the four outermost valence electronic states of uracil likely begin at binding energies 9.3, 9.9, 10.5, and 11.0 eV. High-resolution spectra indicate only one tautomeric form of cytosine contributes significantly to the spectrum with the four outermost valence electronic states beginning at binding energies 8.9, 9.9, 10.4, and 10.85 eV.

  19. High-resolution photoelectron spectra of the pyrimidine-type nucleobases

    Energy Technology Data Exchange (ETDEWEB)

    Fulfer, K. D.; Hardy, D.; Poliakoff, E. D., E-mail: epoliak@lsu.edu [Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Aguilar, A. A. [Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2015-06-14

    High-resolution photoelectron spectra of the gas phase pyrimidine-type nucleobases, thymine, uracil, and cytosine, were collected using synchrotron radiation over the photon energy range 17 ≤ hν ≤ 150 eV. These data provide the highest resolution photoelectron spectra of thymine, uracil, and cytosine published to date. By comparing integrated regions of the energy dependent photoelectron spectra of thymine, the ionization potentials of the first four ionic states of thymine were estimated to be 8.8, 9.8, 10.3, and 10.8 eV. The thymine data also show evidence for low energy shape resonances in three of the outermost valence electronic states. Comparing the uracil spectrum with the thymine spectrum, the four outermost valence electronic states of uracil likely begin at binding energies 9.3, 9.9, 10.5, and 11.0 eV. High-resolution spectra indicate only one tautomeric form of cytosine contributes significantly to the spectrum with the four outermost valence electronic states beginning at binding energies 8.9, 9.9, 10.4, and 10.85 eV.

  20. Synthesis and biological evaluation of oxindole linked indolyl-pyrimidine derivatives as potential cytotoxic agents.

    Science.gov (United States)

    Prajapti, Santosh Kumar; Nagarsenkar, Atulya; Guggilapu, Sravanthi Devi; Gupta, Keshav Kumar; Allakonda, Lingesh; Jeengar, Manish Kumar; Naidu, V G M; Babu, Bathini Nagendra

    2016-07-01

    In our endeavor towards the development of effective cytotoxic agents, a series of oxindole linked indolyl-pyrimidine derivatives were synthesized and characterized by IR, (1)H NMR, (13)C NMR and Mass spectral analysis. All the newly synthesized target compounds were assessed against PA-1 (ovarian), U-87MG (glioblastoma), LnCaP (prostate), and MCF-7 (Breast) cancer cell lines for their cytotoxic potential, with majority of them showing inhibitory activity at low micro-molar concentrations. Significantly, compound 8e was found to be most potent amongst all the tested compounds with an IC50 value of (2.43±0.29μM) on PA-1 cells. The influence of the most active cytotoxic compound 8e on the cell cycle distribution was assessed on the PA-1 cell line, exhibiting a cell cycle arrest at the G2/M phase. Moreover, acridine orange/ethidium bromide staining and annexin V binding assay confirmed that compound 8e can induce cell apoptosis in PA-1 cells. These preliminary results persuade further investigation on the synthesized compounds aiming to the development of potential cytotoxic agents.

  1. Investigating the role of vibrational excitation in simulating charged-particle tracks in liquid pyrimidine

    Science.gov (United States)

    Brunger, Michael J.; Ratnavelu, Kuru; Buckman, Stephen J.; Jones, Darryl B.; Muñoz, Antonio; Blanco, Francisco; García, Gustavo

    2016-03-01

    We report on our results of a study into the sensitivity of charged-particle (electron) track simulations in liquid pyrimidine, to the vibrational cross sections and vibrational energy loss distribution function employed in those simulations. We achieve this by repeating the earlier investigation of Fuss et al. [J. Appl. Phys. 117, 214701 (2015)], but now incorporating more accurate data for the vibrational integral cross sections and the energy loss distribution function that have recently become available. We find that while changes in absorbed dose or particle range are quite minor, due to the energy transferred via vibrational excitations being low in comparison to that for other processes such as ionisation, at the very end of the tracks, where non-ionizing interactions dominate, the significantly large numbers of vibrational excitation processes increases the electrons' ability to induce other effects (e.g. sample heating, bond breaking and radical formation) that might cause damage. Contribution to the Topical Issue "Advances in Positron and Electron Scattering", edited by Paulo Limao-Vieira, Gustavo Garcia, E. Krishnakumar, James Sullivan, Hajime Tanuma and Zoran Petrovic.

  2. Divergent Functions Through Alternative Splicing: The Drosophila CRMP Gene in Pyrimidine Metabolism, Brain, and Behavior

    Science.gov (United States)

    Morris, Deanna H.; Dubnau, Josh; Park, Jae H.; Rawls, John M.

    2012-01-01

    DHP and CRMP proteins comprise a family of structurally similar proteins that perform divergent functions, DHP in pyrimidine catabolism in most organisms and CRMP in neuronal dynamics in animals. In vertebrates, one DHP and five CRMP proteins are products of six genes; however, Drosophila melanogaster has a single CRMP gene that encodes one DHP and one CRMP protein through tissue-specific, alternative splicing of a pair of paralogous exons. The proteins derived from the fly gene are identical over 90% of their lengths, suggesting that unique, novel functions of these proteins derive from the segment corresponding to the paralogous exons. Functional homologies of the Drosophila and mammalian CRMP proteins are revealed by several types of evidence. Loss-of-function CRMP mutation modifies both Ras and Rac misexpression phenotypes during fly eye development in a manner that is consistent with the roles of CRMP in Ras and Rac signaling pathways in mammalian neurons. In both mice and flies, CRMP mutation impairs learning and memory. CRMP mutant flies are defective in circadian activity rhythm. Thus, DHP and CRMP proteins are derived by different processes in flies (tissue-specific, alternative splicing of paralogous exons of a single gene) and vertebrates (tissue-specific expression of different genes), indicating that diverse genetic mechanisms have mediated the evolution of this protein family in animals. PMID:22649077

  3. CONSTRUCTION OF 3D MODEL FOR CYCLOBUTANE PYRIMIDINE (CPD PHOTOLYASE FROM CHLORELLA PYRENOIDOSA

    Directory of Open Access Journals (Sweden)

    Vinod Rishi

    2010-08-01

    Full Text Available Chlorella pyrenoidosa is a freshwater green alga and belongs to class Chlorophyceae, order Chlorellales and family Chlorellaceae. CPD photolyase is an enzyme found in Chlrella pyrnoidosa and responsible for repairing of DNA damages caused by UV radiations. The cyclobutane pyrimidine dimmer (CPDs and 6-4 pyrimidone photoproducts (6-4 PPs are major form of DNA damages and these damages are caused by various physical and chemical agents occurs in the environment such as UV and ionizing radiations, chemical mutagens fungal and bacterial toxins, and free radicals or alkalizing agents produced by metabolism. Mostly DNA damages induced by UV radiations, about 75% cyclobutane pyrimidinedimers (CPDs and rest 6-4 photoproducts (6-4PPs.If these are not repaired then both dimmers may be block transcription and DNA replication. CPD photolyase binds to the DNA and prevent the production of CPDs and 6-4 PPs. The three dimensional structure of CPD photolyase of Chlorella pyrenoidosa is not available for the further investigation , so it is required to generate a computational model by using Modeler 9v3 program. The quality of modeled structure is verified through various online (ProSA as well as offline (Procheck, Swiss PDB viewer tools. This protein may be useful in prevention of skin cancer.

  4. Photochemical Hydrogen Abstraction and Electron Transfer Reactions of Tetrachlorobenzoquinone with Pyrimidine Nucleobases

    Institute of Scientific and Technical Information of China (English)

    Kun-hui Liu; Li-dan Wu; Xiao-ran Zou; Wen Yang; Qian Du; Hong-mei Su

    2011-01-01

    Pentachlorophenol,a widespread environmental pollutant that is possibly carcinogenic to humans,is metabolically oxidized to tetrachloroquinone (TCBQ) which can result in DNA damage.We have investigated the photochemical reaction dynamics of TCBQ with two pyrimidine type nucleobases (thymine and uracil) upon UVA (355 nm) excitation using the technique of nanosecond time-resolved laser flash photolysis.It has been found that 355 nm excitation populates TCBQ molecules to their triplet state 3TCBQ*,which are highly reactive towards thymine or uracil and undergo two parallel reactions,the hydrogen abstraction and electron transfer,leading to the observed photoproducts of TCBQH.and TCBQ.- in transient absorption spectra.The concomitantly produced nucleobase radicals and radical cations are expected to induce a series of oxidative or strand cleavage damage to DNA afterwards.By characterizing the photochemical hydrogen abstraction and electron transfer reactions,our results provide potentially important molecular reaction mechanisms for understanding the carcinogenic effects of pentachlorophenol and its metabolites TCBQ.

  5. Isomeric signatures in the fragmentation of pyridazine and pyrimidine induced by fast ion impact

    Energy Technology Data Exchange (ETDEWEB)

    Wolff, Wania, E-mail: wania@if.ufrj.br; Luna, Hugo; Montenegro, Eduardo C. [Instituto de Física, Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro, RJ (Brazil)

    2015-07-28

    We present fast proton impact induced fragmentations of pyrimidine and pyridazine as an experimental resource to investigate isomeric signatures. Major isomeric imprints are identified for few fragment ions and differences of more than an order of magnitude for the cross sections of fragments of the same mass were measured. The observation of the molecular structure of these isomers gives no apparent indication for the reasons for such substantial differences. It is verified that the simple displacement of the position of one nitrogen atom strongly inhibits or favors the production of some ionic fragment species. The dependency of the fragmentation cross sections on the proton impact energy, investigated by means of time of flight mass spectroscopy and of a model calculation based in first order perturbation theory, allows us to disentangle the complex collision dynamics of the ionic fragments. The proton-induced fragmentation discriminates rather directly the association between a molecular orbital ionization and the fragment-ions creation and abundance, as well as how the redistribution of the energy imparted to the molecules takes place, triggering not only single but also double vacancy and leads to specific fragmentation pathways.

  6. Double Variational Binding—(SMILES Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz

    2015-08-01

    Full Text Available Variational quantitative binding–conformational analysis for a series of anti-HIV pyrimidine-based ligands is advanced at the individual molecular level. This was achieved by employing ligand-receptor docking algorithms for each molecule in the 1,3-disubstituted uracil derivative series that was studied. Such computational algorithms were employed for analyzing both genuine molecular cases and their simplified molecular input line entry system (SMILES transformations, which were created via the controlled breaking of chemical bonds, so as to generate the longest SMILES molecular chain (LoSMoC and Branching SMILES (BraS conformations. The study identified the most active anti-HIV molecules, and analyzed their special and relevant bonding fragments (chemical alerts, and the recorded energetic and geometric docking results (i.e., binding and affinity energies, and the surface area and volume of bonding, respectively. Clear computational evidence was also produced concerning the ligand-receptor pocket binding efficacies of the LoSMoc and BraS conformation types, thus confirming their earlier presence (as suggested by variational quantitative structure-activity relationship, variational-QSAR as active intermediates for the molecule-to-cell transduction process.

  7. Double Variational Binding—(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands

    Science.gov (United States)

    Putz, Mihai V.; Dudaș, Nicoleta A.; Isvoran, Adriana

    2015-01-01

    Variational quantitative binding–conformational analysis for a series of anti-HIV pyrimidine-based ligands is advanced at the individual molecular level. This was achieved by employing ligand-receptor docking algorithms for each molecule in the 1,3-disubstituted uracil derivative series that was studied. Such computational algorithms were employed for analyzing both genuine molecular cases and their simplified molecular input line entry system (SMILES) transformations, which were created via the controlled breaking of chemical bonds, so as to generate the longest SMILES molecular chain (LoSMoC) and Branching SMILES (BraS) conformations. The study identified the most active anti-HIV molecules, and analyzed their special and relevant bonding fragments (chemical alerts), and the recorded energetic and geometric docking results (i.e., binding and affinity energies, and the surface area and volume of bonding, respectively). Clear computational evidence was also produced concerning the ligand-receptor pocket binding efficacies of the LoSMoc and BraS conformation types, thus confirming their earlier presence (as suggested by variational quantitative structure-activity relationship, variational-QSAR) as active intermediates for the molecule-to-cell transduction process. PMID:26295229

  8. Pyrimidine-based compounds modulate CXCR2-mediated signaling and receptor turnover.

    Science.gov (United States)

    Ha, Helen; Neamati, Nouri

    2014-07-07

    Chemokine receptor CXCR2 is expressed on various immune cells and is essential for neutrophil recruitment and angiogenesis at sites of acute and chronic inflammation caused by tissue injury or infection. Because of its role in inflammation, it has been implicated in a number of immune-mediated inflammatory diseases such as psoriasis, arthritis, COPD, cystic fibrosis, asthma, and various types of cancer. CXCR2 and its ligands are up-regulated in cancer cells as well as the tumor microenvironment, promoting tumor growth, angiogenesis, and invasiveness. Although pharmaceutical companies have pursued the development of CXCR2-specific small-molecule inhibitors as anti-inflammatory agents within the last decades, there are currently no clinically approved CXCR2 inhibitors. Using a high-throughput, cell-based assay specific for CXCR2, we screened an in-house library of structurally diverse compounds and identified a class of pyrimidine-based compounds that alter CXCR2-mediated second messenger signaling. Our lead compound, CX797, inhibited IL8-mediated cAMP signaling and receptor degradation while specifically up-regulating IL8-mediated β-arrestin-2 recruitment. CX797 also inhibited IL8-mediated cell migration. Mechanistic comparison of CX797 and a previously reported CXCR2 inhibitor, SB265610, show these two classes of compounds have a distinct mechanism of action on CXCR2.

  9. Synthesis of 2-substituted 9-oxa-guanines {5-aminooxazolo[5,4-d]pyrimidin-7(6H-ones} and 9-oxa-2-thio-xanthines {5-mercaptooxazolo[5,4-d]pyrimidin-7(6H-ones}

    Directory of Open Access Journals (Sweden)

    2008-07-01

    Full Text Available Oxazolo[5,4-d]pyrimidines can be considered as 9-oxa-purine analogs of naturally occurring nucleic acid bases. Interest in this ring system has increased due to recent reports of biologically active derivatives. In particular, 5-aminooxazolo[5,4-d]pyrimidine-7(6H-ones (9-oxa-guanines have been shown to inhibit ricin. The preparation of a series of 2-substituted 5-aminooxazolo[5,4-d]pyrimidin-7(6H-ones and related 5-thio-oxazolo[5,4-d]pyrimidines is described, including analogs suitable for further elaboration employing “click” chemistry utilizing copper-catalyzed Huisgen 1,3-dipolar cycloadditions. Two of the compounds prepared were found to inhibit ricin with IC50 ca. 1–3 mM.

  10. Synthesis of New Pyrazolo[1,5-a]pyrimidine, Triazolo[4,3-a]pyrimidine Derivatives, and Thieno[2,3-b]pyridine Derivatives from Sodium 3-(5-Methyl-1-phenyl-1H-pyrazol-4-yl-3-oxoprop-1-en-1-olate

    Directory of Open Access Journals (Sweden)

    Abdou O. Abdelhamid

    2013-01-01

    Full Text Available Condensation of sodium 3-oxo-3-(1-phenyl-1H-pyrazol-4-ylprop-1-en-1-olate (2 with several heterocyclic amines, cyanoacetamide, cyanothioacetamide, and 2-cyanoacetohydrazide gives pyrazolo[1,5-a]pyrimidines (5a–d, pyrido[2′,3′:3,4]pyrazolo[1,5-a]pyrimidine (9, benzo[4,5]imidazo[1,2-a]pyrimidine (10, [1,2,4]triazolo[1,5-a]pyrimidine (11, and pyridine derivatives (12–14. Also, thieno[2,3-b]pyridines (15–18 were synthesized via pyridinethione (13 with α-halo ketones and α-halo ester. Structures of the newly synthesized compounds were elucidated by elemental analysis, spectral data, alternative synthetic routes, and chemical transformation whenever possible.

  11. 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.

  12. In vitro anti-Giardia lamblia activity of 2-aryl-3-hydroxymethyl imidazo[1,2-a]pyridines and -pyrimidines, individually and in combination with albendazole.

    Science.gov (United States)

    Velázquez-Olvera, Stephanía; Salgado-Zamora, Héctor; Jiménez-Cardoso, Enedina; Campos-Aldrete, Maria-Elena; Pérez-González, Cuauhtémoc; Ben Hadda, Taibi

    2016-03-01

    Giardiasis is a major diarrheal disease found throughout the world, the causative agent being the flagellate protozoan Giardia intestinalis. Infection is more common in children than in adults. The appearance of drug resistance has complicated the treatment of several parasitic diseases, including giardiasis. Thus, the aim of this investigation was to make an in vitro evaluation of the antigiardia response of synthetic derivatives 2-aryl-3-hydroxymethylimidazo[1,2-a]pyridines 1 and -pyrimidines 2 against trophozoites of Giardia lamblia WB, in comparison with the reference drug, albendazole. Additionally, the synergistic action of albendazole in combination with each of the most active 2-aryl-3-hydroxymethyl imidazo[1,2-a]pyridines and pyrimidines was also assessed. Based on the IC50 values obtained, the best anti-Giardia activity was provided by the 3-hydroxymethyl-4-fluorophenylimidazo[1,2-a]pyrimidine derivative 2c and the corresponding imidazo[1,2-a]pyrimidine with the p-tolyl substituent 2d, followed by 2a and 2b. These four compounds showed effectiveness at a concentration similar to that of albendazole. Regarding synergism, the IC50 of the combination of albendazole with 2a, 2b or 2c gave the best anti-Giardia action, showing greater efficacy than albendazole alone. Hence, G. lamblia WB showed high susceptibility to some 2-aryl-3-hydroxymethyl imidazo[1,2-a] pyrimidines, which acted synergistically when used in combination with albendazole.

  13. RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines.

    Science.gov (United States)

    Shimada, Tomohiro; Hirao, Kiyo; Kori, Ayako; Yamamoto, Kaneyoshi; Ishihama, Akira

    2007-11-01

    Using the genomic SELEX, a total of six Escherichia coli DNA fragments have been identified, which formed complexes with transcription factor RutR. The RutR regulon was found to include a large number of genes encoding components for not only degradation of pyrimidines but also transport of glutamate, synthesis of glutamine, synthesis of pyrimidine nucleotides and arginine, and degradation of purines. DNase I footprinting indicated that RutR recognizes a palindromic sequence of TTGACCAnnTGGTCAA. The RutR box in P1 promoter of carAB encoding carbamoyl phosphate synthetase, a key enzyme of pyrimidine synthesis, overlaps with the PepA (CarP) repressor binding site, implying competition between RutR and PepA. Adding either uracil or thymine abolished RutR binding in vitro to the carAB P1 promoter. Accordingly, in the rutR-deletion mutant or in the presence of uracil, the activation in vivo of carAB P1 promoter was markedly reduced. Northern blot analysis of the RutR target genes indicated that RutR represses the Gad system genes involved in glutamate-dependent acid resistance and allantoin degradation. Altogether we propose that RutR is the pyrimidine sensor and the master regulator for a large set of the genes involved in the synthesis and degradation of pyrimidines.

  14. Solution structure of the dimeric cytoplasmic domain of syndecan-4

    DEFF Research Database (Denmark)

    Shin, J; Lee, W; Lee, D

    2001-01-01

    The syndecans, transmembrane proteoglycans which are involved in the organization of cytoskeleton and/or actin microfilaments, have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions. Since previous studies indicate that the function of the syndecan-4...... 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...

  15. Acylphenols and dimeric acylphenols from Myristica maxima Warb.

    Science.gov (United States)

    Othman, Muhamad Aqmal; Sivasothy, Yasodha; Looi, Chung Yeng; Ablat, Abdulwali; Mohamad, Jamaludin; Litaudon, Marc; Awang, Khalijah

    2016-06-01

    Giganteone E (1), a new dimeric acylphenol was isolated as a minor constituent from the bark of Myristica maxima Warb. The structure of 1 was established on the basis of 1D and 2D NMR techniques and LCMS-IT-TOF analysis. Malabaricones A-C (2-4), giganteones A and C (5 and 6), maingayones A and B (7 and 8), maingayic acid B (9) and β-sitosteryl oleate (10) were also characterized in this plant for the first time. Compound 10 was identified for the first time in the Myristicaceae. Compounds 2 and 5 were active against human prostate cancer cell-lines, thus making this the first report on the prostate cancer inhibiting potential of acylphenols and dimeric acylphenols. Compounds 1, 4, 5, 7 and 8 exhibited potent DPPH free radical scavenging activity. This is the first report on their free radical scavenging capacity.

  16. Antioxidant Properties of Aminoethylcysteine Ketimine Decarboxylated Dimer: A Review

    Directory of Open Access Journals (Sweden)

    Rosa Marina Matarese

    2011-05-01

    Full Text Available Aminoethylcysteine ketimine decarboxylated dimer is a natural sulfur-containing compound detected in human plasma and urine, in mammalian brain and in many common edible vegetables. Over the past decade many studies have been undertaken to identify its metabolic role. Attention has been focused on its antioxidant properties and on its reactivity against oxygen and nitrogen reactive species. These properties have been studied in different model systems starting from plasma lipoproteins to specific cellular lines. All these studies report that aminoethylcysteine ketimine decarboxylated dimer is able to interact both with reactive oxygen and nitrogen species (hydrogen peroxide, superoxide anion, hydroxyl radical, peroxynitrite and its derivatives. Its antioxidant activity is similar to that of Vitamin E while higher than other hydrophilic antioxidants, such as trolox and N-acetylcysteine.

  17. 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...

  18. Probing quantum discord in a Heisenberg dimer compound.

    Science.gov (United States)

    Chakraborty, Tanmoy; Singh, Harkirat; Singh, Sourabh; Gopal, Radha Krishna; Mitra, Chiranjib

    2013-10-23

    A quantitative estimation of quantum discord is performed for a Heisenberg spin 1/2 dimer compound (NH4CuPO4, H2O) by means of experimental magnetic and thermal measurements. Magnetic susceptibility and specific heat data were collected for NH4CuPO4, H2O and analyzed within the framework of the Heisenberg isolated dimer model. Internal energy as a function of temperature is obtained by integrating the specific heat versus temperature data. Subsequently, quantum discord, total correlations and spin-spin correlation function are quantified from susceptibility and internal energy and plotted as a function of temperature. Violation of Bell's inequality is also tested for NH4CuPO4, H2O via both experimental susceptibility and specific heat data signifying the presence of entanglement.

  19. GLYCOLALDEHYDE FORMATION VIA THE DIMERIZATION OF THE FORMYL RADICAL

    Energy Technology Data Exchange (ETDEWEB)

    Woods, Paul M.; Viti, Serena [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom); Slater, Ben; Raza, Zamaan; Brown, Wendy A.; Burke, Daren J., E-mail: p.woods@qub.ac.uk [Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ (United Kingdom)

    2013-11-10

    Glycolaldehyde, the simplest monosaccharide sugar, has recently been detected in low- and high-mass star-forming cores. Following our previous investigation into glycolaldehyde formation, we now consider a further mechanism for the formation of glycolaldehyde that involves the dimerization of the formyl radical, HCO. Quantum mechanical investigation of the HCO dimerization process upon an ice surface is predicted to be barrierless and therefore fast. In an astrophysical context, we show that this mechanism can be very efficient in star-forming cores. It is limited by the availability of the formyl radical, but models suggest that only very small amounts of CO are required to be converted to HCO to meet the observational constraints.

  20. Glycolaldehyde Formation via the Dimerization of the Formyl Radical

    Science.gov (United States)

    Woods, Paul M.; Slater, Ben; Raza, Zamaan; Viti, Serena; Brown, Wendy A.; Burke, Daren J.

    2013-11-01

    Glycolaldehyde, the simplest monosaccharide sugar, has recently been detected in low- and high-mass star-forming cores. Following our previous investigation into glycolaldehyde formation, we now consider a further mechanism for the formation of glycolaldehyde that involves the dimerization of the formyl radical, HCO. Quantum mechanical investigation of the HCO dimerization process upon an ice surface is predicted to be barrierless and therefore fast. In an astrophysical context, we show that this mechanism can be very efficient in star-forming cores. It is limited by the availability of the formyl radical, but models suggest that only very small amounts of CO are required to be converted to HCO to meet the observational constraints.

  1. Dimerization effect of sucrose octasulfate on rat FGF1

    DEFF Research Database (Denmark)

    Kulahin, Nikolaj; Kiselyov, Vladislav; Kochoyan, Artur

    2008-01-01

    Fibroblast growth factors (FGFs) constitute a family of at least 23 structurally related heparin-binding proteins that are involved in regulation of cell growth, survival, differentiation and migration. Sucrose octasulfate (SOS), a chemical analogue of heparin, has been demonstrated to activate FGF...... 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......, Lys118, Arg122 and Lys128. An arginine at position 116 is a consensus residue in mammalian FGF molecules; however, it is a serine in rat FGF1. This difference may be important for SOS-mediated FGF1 dimerization in rat....

  2. Solitons in a chain of PT-invariant dimers

    CERN Document Server

    Suchkov, Sergey V; Dmitriev, Sergey V; Kivshar, Yuri S

    2011-01-01

    Dynamics of a chain of interacting parity-time invariant nonlinear dimers is investigated. A dimer is built as a pair of coupled elements with equal gain and loss. A relation between stationary soliton solutions of the model and solitons of the discrete nonlinear Schrodinger (DNLS) equation is demonstrated. Approximate solutions for solitons whose width is large in comparison to the lattice spacing are derived, using a continuum counterpart of the discrete equations. These solitons are mobile, featuring nearly elastic collisions. Stationary solutions for narrow solitons, which are immobile due to the pinning by the effective Peierls-Nabarro potential, are constructed numerically, starting from the anti-continuum limit. The solitons with the amplitude exceeding a certain critical value suffer an instability leading to blowup, which is a specific feature of the nonlinear PT-symmetric chain, making it dynamically different from DNLS lattices. A qualitative explanation of this feature is proposed. The instability...

  3. Inhibition of HIV-1 Reverse Transcriptase Dimerization by Small Molecules.

    Science.gov (United States)

    Tintori, Cristina; Corona, Angela; Esposito, Francesca; Brai, Annalaura; Grandi, Nicole; Ceresola, Elisa Rita; Clementi, Massimo; Canducci, Filippo; Tramontano, Enzo; Botta, Maurizio

    2016-04-15

    Because HIV-1 reverse transcriptase is an enzyme whose catalytic activity depends on its heterodimeric structure, this system could be a target for inhibitors that perturb the interactions between the protein subunits, p51 and p66. We previously demonstrated that the small molecule MAS0 reduced the association of the two RT subunits and simultaneously inhibited both the polymerase and ribonuclease H activities. In this study, some analogues of MAS0 were rationally selected by docking studies and evaluated in vitro for their ability to disrupt dimeric assembly. Two inhibitors were identified with improved activity compared to MAS0. This study lays the basis for the rational design of more potent inhibitors of RT dimerization.

  4. Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization

    Science.gov (United States)

    Fahrenkamp, Dirk; Li, Jinyu; Ernst, Sabrina; Schmitz-van de Leur, Hildegard; Chatain, Nicolas; Küster, Andrea; Koschmieder, Steffen; Lüscher, Bernhard; Rossetti, Giulia; Müller-Newen, Gerhard

    2016-10-01

    STAT5 is an essential transcription factor in hematopoiesis, which is activated through tyrosine phosphorylation in response to cytokine stimulation. Constitutive activation of STAT5 is a hallmark of myeloid and lymphoblastic leukemia. Using homology modeling and molecular dynamics simulations, a model of the STAT5 phosphotyrosine-SH2 domain interface was generated providing first structural information on the activated STAT5 dimer including a sequence, for which no structural information is available for any of the STAT proteins. We identified a novel intramolecular interaction mediated through F706, adjacent to the phosphotyrosine motif, and a unique hydrophobic interface on the surface of the SH2 domain. Analysis of corresponding STAT5 mutants revealed that this interaction is dispensable for Epo receptor-mediated phosphorylation of STAT5 but essential for dimer formation and subsequent nuclear accumulation. Moreover, the herein presented model clarifies molecular mechanisms of recently discovered leukemic STAT5 mutants and will help to guide future drug development.

  5. UV resonance Raman analysis of trishomocubane and diamondoid dimers

    Energy Technology Data Exchange (ETDEWEB)

    Meinke, Reinhard, E-mail: rene@physik.tu-berlin.de; Thomsen, Christian; Maultzsch, Janina [Institut für Festkörperphysik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin (Germany); Richter, Robert; Merli, Andrea [Institut für Optik und Atomare Physik, Technische Universität Berlin, Hardenbergstr. 36, D-10623 Berlin (Germany); Fokin, Andrey A. [Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen (Germany); Department of Organic Chemistry, Kiev Polytechnic Institute, pr. Pobedy 37, 03056 Kiev (Ukraine); Koso, Tetyana V.; Schreiner, Peter R. [Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen (Germany); Rodionov, Vladimir N. [Department of Organic Chemistry, Kiev Polytechnic Institute, pr. Pobedy 37, 03056 Kiev (Ukraine)

    2014-01-21

    We present resonance Raman measurements of crystalline trishomocubane and diamantane dimers containing a C=C double bond. Raman spectra were recorded with excitation energies between 2.33 eV and 5.42 eV. The strongest enhancement is observed for the C=C stretch vibration and a bending mode involving the two carbon atoms of the C=C bond, corresponding to the B{sub 2g} wagging mode of ethylene. This is associated with the localization of the π-HOMO and LUMO and the elongation of the C=C bond length and a pyramidalization of the two sp{sup 2}-hybridized carbon atoms at the optical excitation. The observed Raman resonance energies of the trishomocubane and diamantane dimers are significantly lower than the HOMO-LUMO gaps of the corresponding unmodified diamondoids.

  6. Role of the Chlorophyll Dimer in Bacterial Photosynthesis

    Science.gov (United States)

    Warshel, Arieh

    1980-06-01

    The role of a special dimer (D) of bacterio-chlorophyll molecules in bacterial photosynthesis was examined by calculations of the rates of electron transfer reactions in a system of the dimer and a bacteriopheophytin (BPh) molecule. It was found that the dependence of the potential surfaces of D on the distance between the monomers allows a fast light-induced electron transfer from D to BPh but only a slow back reaction (reduction of D+ by BPh-). The same potential surfaces allow efficient reduction of D+ by cytochrome c. Possible advantages of greatly different values of the electronic matrix elements for the forward and back reactions are pointed out. It is suggested that the electrostatic interaction between D+ and an ionized group of the protein might play an important role in the photosynthetic reaction.

  7. Dimers on surface graphs and spin structures. II

    DEFF Research Database (Denmark)

    Cimasoni, David; Reshetikhin, Nicolai

    2009-01-01

    In a previous paper [3], we showed how certain orientations of the edges of a graph Γ embedded in a closed oriented surface Σ can be understood as discrete spin structures on Σ. We then used this correspondence to give a geometric proof of the Pfaffian formula for the partition function of the di......In a previous paper [3], we showed how certain orientations of the edges of a graph Γ embedded in a closed oriented surface Σ can be understood as discrete spin structures on Σ. We then used this correspondence to give a geometric proof of the Pfaffian formula for the partition function...... of the dimer model on Γ. In the present article, we generalize these results to the case of compact oriented surfaces with boundary. We also show how the operations of cutting and gluing act on discrete spin structures and how they change the partition function. These operations allow to reformulate the dimer...

  8. Mechanism of Processive Movement of Monomeric and Dimeric Kinesin Molecules

    Directory of Open Access Journals (Sweden)

    Ping Xie

    2010-01-01

    Full Text Available Kinesin molecules are motor proteins capable of moving along microtubule by hydrolyzing ATP. They generally have several forms of construct. This review focuses on two of the most studied forms: monomers such as KIF1A (kinesin-3 family and dimers such as conventional kinesin (kinesin-1 family, both of which can move processively towards the microtubule plus end. There now exist numerous models that try to explain how the kinesin molecules convert the chemical energy of ATP hydrolysis into the mechanical energy to “power” their proceesive movement along microtubule. Here, we attempt to present a comprehensive review of these models. We further propose a new hybrid model for the dimeric kinesin by combining the existing models and provide a framework for future studies in this subject.

  9. Dimerization-assisted energy transport in light-harvesting complexes.

    Science.gov (United States)

    Yang, S; Xu, D Z; Song, Z; Sun, C P

    2010-06-21

    We study the role of the dimer structure of light-harvesting complex II (LH2) in excitation transfer from the LH2 [without a reaction center (RC)] to the LH1 (surrounding the RC) or from the LH2 to another LH2. The excited and unexcited states of a bacteriochlorophyll (BChl) are modeled by a quasispin. In the framework of quantum open system theory, we represent the excitation transfer as the total leakage of the LH2 system and then calculate the transfer efficiency and average transfer time. For different initial states with various quantum superposition properties, we study how the dimerization of the B850 BChl ring can enhance the transfer efficiency and shorten the average transfer time.

  10. Dimerization-assisted energy transport in light-harvesting complexes

    CERN Document Server

    Yang, S; Song, Z; Sun, C P

    2010-01-01

    We study the role of the dimer structure of light-harvesting complex II (LH2) in excitation transfer from the LH2 (without a reaction center (RC)) to the LH1 (surrounding the RC), or from the LH2 to another LH2. The excited and un-excited states of a bacteriochlorophyll (BChl) are modeled by quasi-spin. In the framework of quantum open system theory, we represent the excitation transfer as the total leakage of the LH2 system, and then calculate the transfer efficiency and average transfer time at a low enough temperature. For different initial states with various quantum superposition properties, we study how the dimerization of the B850 BChl ring can enhance the transfer efficiency and shorten the average transfer time.

  11. Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation

    Science.gov (United States)

    Liao, Chenyi; Zhang, Zhi; Kale, Justin; Andrews, David W.; Lin, Jialing; Li, Jianing

    2016-07-01

    Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model — using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation.

  12. 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.

  13. 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.

  14. 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.

  15. Wave packet dynamics of potassium dimers attached to helium nanodroplets

    OpenAIRE

    Claas, P.; Droppelmann, G.; Schulz, C. P.; Mudrich, M.; Stienkemeier, F.

    2006-01-01

    The dynamics of vibrational wave packets excited in K$_2$ dimers attached to superfluid helium nanodroplets is investigated by means of femtosecond pump-probe spectroscopy. The employed resonant three-photon-ionization scheme is studied in a wide wavelength range and different pathways leading to K$^+_2$-formation are identified. While the wave packet dynamics of the electronic ground state is not influenced by the helium environment, perturbations of the electronically excited states are obs...

  16. A New Hydroxychavicol Dimer from the Roots of Piper betle

    OpenAIRE

    Huei-Yu Tu; Horng-Liang Lay; Chun-Chien Chien; Chwan-Fwu Lin; Tsong-Long Hwang

    2013-01-01

    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.

  17. 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.

  18. A new hydroxychavicol dimer from the roots of Piper betle.

    Science.gov (United States)

    Lin, Chwan-Fwu; Hwang, Tsong-Long; Chien, Chun-Chien; Tu, Huei-Yu; Lay, Horng-Liang

    2013-02-26

    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.

  19. Naturally occurring pentaoxygenated, hexaoxygenated and dimeric xanthones: a literature survey

    Directory of Open Access Journals (Sweden)

    V. Peres

    1997-08-01

    Full Text Available This review gives information on the chemical study of 71 pentaoxygenated, 11 hexaoxygenated and 9 dimeric and more complex xanthones naturally occurring in 7 families, 29 genus and 62 species of higher plants, and 11 described as fern and fungal metabolites. The value of these groups of substances in the connection with the pharmacological activity and the therapeutic use of some species is shown. The structural formulas of 23 isolated compounds and their distribution in the species studied are given.

  20. Excited State Pathways Leading to Formation of Adenine Dimers.

    Science.gov (United States)

    Banyasz, Akos; Martinez-Fernandez, Lara; Ketola, Tiia-Maaria; Muñoz-Losa, Aurora; Esposito, Luciana; Markovitsi, Dimitra; Improta, Roberto

    2016-06-02

    The reaction intermediate in the path leading to UV-induced formation of adenine dimers A═A and AA* is identified for the first time quantum mechanically, using PCM/TD-DFT calculations on (dA)2 (dA: 2'deoxyadenosine). In parallel, its fingerprint is detected in the absorption spectra recorded on the millisecond time-scale for the single strand (dA)20 (dA: 2'deoxyadenosine).

  1. A DFT study of substituent effects in corannulene dimers.

    Science.gov (United States)

    Josa, Daniela; Rodríguez Otero, Jesús; Cabaleiro Lago, Enrique M

    2011-12-21

    Corannulene dimers made up of corannulene monomers with different curvature and substituents were studied using M06-2X, B97D and ωB97XD functionals and 6-31+G* basis set. Corannulene molecules were substituted with five alternating Br, Cl, CH(3), C(2)H or CN units. Geometric results showed that substituents gave rise to small changes in the curvature of corannulene bowls. So, there was not a clear relationship between the curvature of bowls and the changes on interaction energy generated by addition of substituents in the bowl. Electron withdrawing substituents gave rise to a more positive molecular electrostatic potential (MEP) of the bowl, which was able to get a strong interaction with the negative MEP at the surface of a fullerene. Substitution with CN caused the largest effect, giving rise to the most positive MEP and to a large interaction energy of -24.64 kcal mol(-1), at the ωB97XD/6-31+G* level. Dispersive effects must be taken into account to explain the catching ability of the different substituted corannulenes. For unsubstituted dimers, calculations with DFT-D methods employing ωB97XD and B97D functionals led to similar results to those previously reported at the SCS-MP2/cc-pVTZ level for corannulene dimers (A. Sygula and S. Saebø, Int. J. Quant. Chem., 2009, 109, 65). In particular, the ωB97XD functional led to a difference of only 0.35 kcal mol(-1), regarding MP2 interaction energy for corannulene dimers. On the other hand, the M06-2X functional showed a general considerable underestimation of interaction energies. This functional worked quite well to study trends, but not to obtain absolute interaction energies.

  2. Dimer Models, Free Fermions and Super Quantum Mechanics

    CERN Document Server

    Dijkgraaf, R; Reffert, S

    2007-01-01

    This note relates topics in statistical mechanics, graph theory and combinatorics, lattice quantum field theory, super quantum mechanics and string theory. We give a precise relation between the dimer model on a graph embedded on a torus and the massless free Majorana fermion living on the same lattice. A loop expansion of the fermion determinant is performed, where the loops turn out to be compositions of two perfect matchings. These loop states are sorted into co-chain groups using categorification techniques similar to the ones used for categorifying knot polynomials. The Euler characteristic of the resulting co-chain complex recovers the Newton polynomial of the dimer model. We re-interpret this system as supersymmetric quantum mechanics, where configurations with vanishing net winding number form the ground states. Finally, we make use of the quiver gauge theory - dimer model correspondence to obtain an interpretation of the loops in terms of the physics of D-branes probing a toric Calabi-Yau singularity...

  3. 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.

  4. Assembly and separation of semiconductor quantum dot dimers and trimers.

    Science.gov (United States)

    Xu, Xiangxing; Stöttinger, Sven; Battagliarin, Glauco; Hinze, Gerald; Mugnaioli, Enrico; Li, Chen; Müllen, Klaus; Basché, Thomas

    2011-11-16

    Repeated precipitation of colloidal semiconductor quantum dots (QD) from a good solvent by adding a poor solvent leads to an increasing number of QD oligomers after redispersion in the good solvent. By using density gradient ultracentrifugation we have been able to separate QD monomer, dimer, and trimer fractions from higher oligomers in such solutions. In the corresponding fractions QD dimers and trimers have been enriched up to 90% and 64%, respectively. Besides directly coupled oligomers, QD dimers and trimers were also assembled by linkage with a rigid terrylene diimide dye (TDI) and separated again by ultracentrifugation. High-resolution transmission electron micrographs show that the interparticle distances are clearly larger than those for directly coupled dots proving that the QDs indeed are cross-linked by the dye. Moreover, energy transfer from the QDs to the TDI "bridge" has been observed. Individual oligomers (directly coupled or dye-linked) can be readily deposited on a substrate and studied simultaneously by scanning force and optical microscopy. Our simple and effective scheme is applicable to a wide range of ligand stabilized colloidal nanoparticles and opens the way to a detailed study of electronic coupling in, e.g., QD molecules.

  5. Nonlinearity and trapping in excitation transfer Dimers and Trimers.

    CERN Document Server

    Barvik, I; Schanz, H; Barvik, Ivan; Esser, Bernd; Schanz, Holger

    1995-01-01

    We study the interplay between nonlinearity in exciton transport and trapping due to a sink site for the dimer and the trimer with chain configuration by a numerical integration of the discrete nonlinear Schroedinger equation. Our results for the dimer show, that the formation of a self trapped state due to the nonlinear coupling increases the life time of the exciton substantially. Self trapping can be enhanced by the sink for short times, but for long times it disappears. In the trimer consisting of a subdimer extended by a sink site exists a transition between states localized on the two sites of the subdimer before for larger nonlinear coupling self trapping on one site of the subdimer is observed. For large trapping rates the fear of death effect leads to an increasing life time of the excitation on both, the dimer and the trimer. The sink site is then effectively decoupled. We explain this effect using an asymptotic theory for strong trapping and demonstrate it by direct numerical computation.

  6. Benchmark calculations for elastic fermion-dimer scattering

    CERN Document Server

    Bour, Shahin; Lee, Dean; Meißner, Ulf-G

    2012-01-01

    We present continuum and lattice calculations for elastic scattering between a fermion and a bound dimer in the shallow binding limit. For the continuum calculation we use the Skorniakov-Ter-Martirosian (STM) integral equation to determine the scattering length and effective range parameter to high precision. For the lattice calculation we use the finite-volume method of L\\"uscher. We take into account topological finite-volume corrections to the dimer binding energy which depend on the momentum of the dimer. After subtracting these effects, we find from the lattice calculation kappa a_fd = 1.174(9) and kappa r_fd = -0.029(13). These results agree well with the continuum values kappa a_fd = 1.17907(1) and kappa r_fd = -0.0383(3) obtained from the STM equation. We discuss applications to cold atomic Fermi gases, deuteron-neutron scattering in the spin-quartet channel, and lattice calculations of scattering for nuclei and hadronic molecules at finite volume.

  7. Quantum Monte Carlo calculations of the dimerization energy of borane.

    Science.gov (United States)

    Fracchia, Francesco; Bressanini, Dario; Morosi, Gabriele

    2011-09-07

    Accurate thermodynamic data are required to improve the performance of chemical hydrides that are potential hydrogen storage materials. Boron compounds are among the most interesting candidates. However, different experimental measurements of the borane dimerization energy resulted in a rather wide range (-34.3 to -39.1) ± 2 kcal/mol. Diffusion Monte Carlo (DMC) simulations usually recover more than 95% of the correlation energy, so energy differences rely less on error cancellation than other methods. DMC energies of BH(3), B(2)H(6), BH(3)CO, CO, and BH(2)(+) allowed us to predict the borane dimerization energy, both via the direct process and indirect processes such as the dissociation of BH(3)CO. Our D(e) = -43.12(8) kcal/mol, corrected for the zero point energy evaluated by considering the anharmonic contributions, results in a borane dimerization energy of -36.59(8) kcal/mol. The process via the dissociation of BH(3)CO gives -34.5(2) kcal/mol. Overall, our values suggest a slightly less D(e) than the most recent W4 estimate D(e) = -44.47 kcal/mol [A. Karton and J. M. L. Martin, J. Phys. Chem. A 111, 5936 (2007)]. Our results show that reliable thermochemical data for boranes can be predicted by fixed node (FN)-DMC calculations.

  8. Solvent control: dinuclear versus tetranuclear complexes of a bis-tetradentate pyrimidine-based ligand.

    Science.gov (United States)

    Gobeze, Worku A; Milway, Victoria A; Moubaraki, Boujemaa; Murray, Keith S; Brooker, Sally

    2012-08-28

    A new bis-tetradentate acyclic amine ligand L(Et) has been synthesized from 4,6-bis(aminomethyl)-2-phenylpyrimidine and 2-vinylpyridine. Dinuclear complexes, Mn(II)(2)L(Et)(MeCN)(H(2)O)(3)(ClO(4))(4) (1), Fe(II)(2)L(Et)(H(2)O)(4)(BF(4))(4) (2), Co(II)(2)L(Et)(H(2)O)(3)(MeCN)(2)(BF(4))(4) (3), Ni(II)(2)L(Et)(H(2)O)(4)(BF(4))(4) (4), Ni(II)(2)L(Et)(H(2)O)(4)(ClO(4))(4)·8H(2)O (4'), Cu(II)(2)L(Et)(BF(4))(4)·MeCN (5), Zn(II)(2)L(Et)(BF(4))(2)(BF(4))(2)·½MeCN (6), were obtained from 1 : 2 reactions of L(Et) and the appropriate metal salts in MeCN, whereas in MeOH tetranuclear complexes, Mn(II)(4)(L(Et))(2)(OH)(4)(ClO(4))(4) (7), Fe(II)(4)(L(Et))(2)(F)(4)(BF(4))(4)·5/2H(2)O (8), Co(II)(4)(L(Et))(2)(F)(4)(BF(4))(4)·3H(2)O (9), Ni(II)(4)(L(Et))(2)(F)(4)(BF(4))(4)·4H(2)O (10), Cu(II)(4)(L(Et))(2)(F)(4)(BF(4))(4)·3H(2)O (11) and Zn(II)(4)(L(Et))(2)(F)(4)(BF(4))(4) (12), result. Six complexes have been structurally characterized: in all cases each L(Et) is bis-tetradentate and provides a pyrimidine bridge between two metal centres. As originally anticipated, complexes 1, 4' and 6 are dinuclear, while 9, 10 and 12 are revealed to be tetranuclear, with two M(2)(L(Et))(4+) moieties bridged by two pairs of fluoride anions. Weak to moderate antiferromagnetic coupling between the metal centres is a feature of complexes 2, 3, 4, 8, 9 and 10. The dinuclear complexes 1-6 undergo multiple, mostly irreversible, redox processes. However, the pyrimidine-based dicopper(II) complex 5 undergoes a two electron quasi-reversible reduction, Cu(II)(2)→ Cu(I)(2), and this occurs at a more positive potential [E(m) = +0.11 V (E(pc) = -0.03 and E(pa) = +0.26 V) vs. 0.01 M AgNO(3)/Ag] than for either of the dicopper(II) complexes of the analogous pyrazine-based ligands.

  9. (3,5-Dimethylpyrazol-1-yl-[4-(1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4-ylaminophenyl]methanone

    Directory of Open Access Journals (Sweden)

    Rania B. Bakr

    2016-11-01

    Full Text Available In an attempt to enhance cytotoxic activity of pyrazolo[3,4-d]pyrimidine core, we synthesized (3,5-dimethylpyrazol-1-yl-[4-(1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4-ylaminophenyl]methanone (4 by reacting 4-(1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4-ylaminobenzohydrazide (3 with acetylacetone. Antiproliferative activity of this compound was screened against breast (MCF-7, colon (HCT-116, and liver (HEPG-2 cancer cell lines. The tested compound exhibited cytotoxic activity with IC50 = 5.00–32.52 μM. Moreover, inhibitory activity of this compound was evaluated against the epidermal growth factor receptor (EGFR, the fibroblast growth factor receptor (FGFR, the insulin receptor (IR, and the vascular endothelial growth factor receptor (VEGFR. This target compound showed potent inhibitory activity, especially against FGFR with IC50 = 5.18 μM.

  10. Poly[(μ(2)-2-amino-pyrimidine-κ(2)N(1):N(3))di-μ(2)-chlorido-mercury(II)].

    Science.gov (United States)

    Eshtiagh-Hosseini, Hossein; Yousefi, Zakieh; Janiak, Agnieszka

    2012-04-01

    The title compound, [HgCl(2)(C(4)H(5)N(3))](n), features a two-dimensional network parallel to (001) that is based on an Hg(II) atom octahedrally coordinated by four μ(2)-Cl atoms and two μ(2)-2-amino-pyrimidine (apym) ligands in trans positions, yielding a distorted HgCl(4)N(2) octa-hedron. The coordination network can be described as an uninodal 4-connected net with the sql topology. The Hg(II) ion lies on a site of -1 symmetry and the apym ligand lies on sites of m symmetry with the mirror plane perpendicular to the pyrimidine plane and passing through the NH(2) group N atom. This polymeric structure is stabilized by N-H⋯Cl hydrogen bonds and columnar π-π stacking of pyrimidine rings, with a centroid-centroid distance of 3.832 (2) Å.

  11. Discovery of pyrazolo[1,5-a]pyrimidine-based CHK1 inhibitors: A template-based approach-Part 2

    Energy Technology Data Exchange (ETDEWEB)

    Labroli, Marc; Paruch, Kamil; Dwyer, Michael P.; Alvarez, Carmen; Keertikar, Kartik; Poker, Cory; Rossman, Randall; Duca, Jose S.; Fischmann, Thierry O.; Madison, Vincent; Parry, David; Davis, Nicole; Seghezzi, Wolfgang; Wiswell, Derek; Guzi, Timothy J. [Merck

    2013-11-20

    Previous efforts by our group have established pyrazolo[1,5-a]pyrimidine as a viable core for the development of potent and selective CDK inhibitors. As part of an effort to utilize the pyrazolo[1,5-a]pyrimidine core as a template for the design and synthesis of potent and selective kinase inhibitors, we focused on a key regulator in the cell cycle progression, CHK1. Continued SAR development of the pyrazolo[1,5-a]pyrimidine core at the C5 and C6 positions, in conjunction with previously disclosed SAR at the C3 and C7 positions, led to the discovery of potent and selective CHK1 inhibitors.

  12. Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix.

    Science.gov (United States)

    Brown, Jessica A; Kinzig, Charles G; DeGregorio, Suzanne J; Steitz, Joan A

    2016-05-01

    Triple-stranded RNA was first deduced to form in vitro more than 50 years ago and has since been implicated in RNA catalysis, stability, and small molecule binding. Despite the emerging biological significance of RNA triple helices, it remains unclear how their nucleotide composition contributes to their thermodynamic stability and cellular function. To investigate these properties, we used in vitro RNA electrophoretic mobility shift assays (EMSAs) and in vivo intronless β-globin reporter assays to measure the relative contribution of 20 RNA base triples (N•A-U, N•G-C, N•C-G, N•U-A, and N•G-U) to triple-helical stability. These triples replaced a single internal U•A-U within the known structure of the triple-helical RNA stability element of human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), which contains 10 major-groove base triples. In addition to the canonical C•G-C triple, the noncanonical base triples U•G-C, U•G-U, C•C-G, and U•C-G exhibited at least 30% stability relative to the wild-type U•A-U base triple in both assays. Of these triples, only U•A-U, C•G-C, and U•G-C, when tested as four successive triples, formed stabilizing structures that allowed accumulation of the intronless β-globin reporter. Overall, we find that Hoogsteen-position pyrimidines support triple helix stability and function and that thermodynamic stability, based on EMSA results, is necessary but not sufficient for stabilization activity of the MALAT1 triple helix in cells. These results suggest that additional RNA triple helices containing noncanonical triples likely exist in nature.

  13. Spectroscopic analysis on the binding interaction of biologically active pyrimidine derivative with bovine serum albumin

    Directory of Open Access Journals (Sweden)

    Vishwas D. Suryawanshi

    2016-02-01

    Full Text Available A biologically active antibacterial reagent, 2–amino-6-hydroxy–4–(4-N, N-dimethylaminophenyl-pyrimidine-5-carbonitrile (AHDMAPPC, was synthesized. It was employed to investigate the binding interaction with the bovine serum albumin (BSA in detail using different spectroscopic methods. It exhibited antibacterial activity against Escherichia coli and Staphylococcus aureus which are common food poisoning bacteria. The experimental results showed that the fluorescence quenching of model carrier protein BSA by AHDMAPPC was due to static quenching. The site binding constants and number of binding sites (n≈1 were determined at three different temperatures based on fluorescence quenching results. The thermodynamic parameters, enthalpy change (ΔH, free energy (ΔG and entropy change (ΔS for the reaction were calculated to be 15.15 kJ/mol, –36.11 kJ/mol and 51.26 J/mol K according to van't Hoff equation, respectively. The results indicated that the reaction was an endothermic and spontaneous process, and hydrophobic interactions played a major role in the binding between drug and BSA. The distance between donor and acceptor is 2.79 nm according to Förster's theory. The alterations of the BSA secondary structure in the presence of AHDMAPPC were confirmed by UV–visible, synchronous fluorescence, circular dichroism (CD and three-dimensional fluorescence spectra. All these results indicated that AHDMAPPC can bind to BSA and be effectively transported and eliminated in the body. It can be a useful guideline for further drug design.

  14. 2, 4-Diamino-6- hydroxy pyrimidine inhibits NSAIDs induced nitrosyl-complex EPR signals and ulcer in rat jejunum

    Science.gov (United States)

    Somasundaram, S; Simpson, R; Rafi, S; Shergill, JK; Bjarnason, I; Wrigglesworth, J

    2002-01-01

    Background It has been suggested that one aspect of non-steroidal anti-inflammatory drugs induced intestinal damage is due to either uncoupling of mitochondrial oxidative phosphorylation or inhibition of electron transport. We investigated the latter possibility using electron paramagnetic resonance spectroscopy. Results Electron paramagnetic studies of NSAIDS on sub-mitochondrial particles revealed that indomethacin, but not with nabumetone, bound to a site near to Complex I and ubiquinone to generate a radical species. Normal rats exhibited prominent [3Fe-4S]ox signals (g ~ 2.01) at 20 K. One hour after indomethacin there was a prominent, intense and broad absorption pattern at (g ~2.07) suggesting, appearance of radical species overlapping [3Fe-4S]ox and was unaffected by pretreatment with 2,4 diamino -6-hydroxy pyrimidine. At 24 hrs, when macroscopic ulcers were seen, there was a new signal due to a nitric oxide radical (NO•). In contrast, nabumetone and 2,4 diamino-6-hydroxy pyrimidine pre-treated animals receiving indomethacin exhibited electron paramagnetic resonance spectra identical to those of controls at 24 hrs and neither was associated with small intestinal ulcers. Indomethacin and 2,4 diamino hydroxy pyrimidine pre-treated rats, but not nabumetone, had increased intestinal permeability. Conclusion The results suggest that the in vivo effects of indomethacin modulate the mitochondrial respiratory chain directly at 1 h and 24 h through formation of nitric oxide. NO• appears to play an important role in the late pathogenic stages of NSAID enteropathy and may be the site for targeted treatment to reduce their toxicity. PMID:11960558

  15. 2, 4-Diamino-6- hydroxy pyrimidine inhibits NSAIDs induced nitrosyl-complex EPR signals and ulcer in rat jejunum

    Directory of Open Access Journals (Sweden)

    Bjarnason I

    2002-04-01

    Full Text Available Abstract Background It has been suggested that one aspect of non-steroidal anti-inflammatory drugs induced intestinal damage is due to either uncoupling of mitochondrial oxidative phosphorylation or inhibition of electron transport. We investigated the latter possibility using electron paramagnetic resonance spectroscopy. Results Electron paramagnetic studies of NSAIDS on sub-mitochondrial particles revealed that indomethacin, but not with nabumetone, bound to a site near to Complex I and ubiquinone to generate a radical species. Normal rats exhibited prominent [3Fe-4S]ox signals (g ~ 2.01 at 20 K. One hour after indomethacin there was a prominent, intense and broad absorption pattern at (g ~2.07 suggesting, appearance of radical species overlapping [3Fe-4S]ox and was unaffected by pretreatment with 2,4 diamino -6-hydroxy pyrimidine. At 24 hrs, when macroscopic ulcers were seen, there was a new signal due to a nitric oxide radical (NO•. In contrast, nabumetone and 2,4 diamino-6-hydroxy pyrimidine pre-treated animals receiving indomethacin exhibited electron paramagnetic resonance spectra identical to those of controls at 24 hrs and neither was associated with small intestinal ulcers. Indomethacin and 2,4 diamino hydroxy pyrimidine pre-treated rats, but not nabumetone, had increased intestinal permeability. Conclusion The results suggest that the in vivo effects of indomethacin modulate the mitochondrial respiratory chain directly at 1 h and 24 h through formation of nitric oxide. NO• appears to play an important role in the late pathogenic stages of NSAID enteropathy and may be the site for targeted treatment to reduce their toxicity.

  16. Poly(alizarin red)/Graphene modified glassy carbon electrode for simultaneous determination of purine and pyrimidine

    Energy Technology Data Exchange (ETDEWEB)

    Ba Xi; Luo Liqiang [Department of Chemistry, Shanghai University, Shanghai 200444 (China); Ding Yaping, E-mail: wdingyp@sina.com [Department of Chemistry, Shanghai University, Shanghai 200444 (China); Zhang Zhen [Department of Chemistry, Shanghai University, Shanghai 200444 (China); Chu Yuliang [Instrumental Analysis and Research Center, Shanghai University, Shanghai 200444 (China); Wang Bijun; Ouyang Xiaoqian [Department of Chemistry, Shanghai University, Shanghai 200444 (China)

    2012-11-08

    Graphical abstract: DPVs of PAR/Graphene/GCE (a) and the bare GCE (c) in 0.1 M PBS containing 50.0 {mu}M G, 50.0 {mu}M A, 100.0 {mu}M T and 100.0 {mu}M C, (b) PAR/Graphene/GCE in 0.1 M PBS. Highlights: Black-Right-Pointing-Pointer The sensor exhibited well-separated peaks and low detection limit. Black-Right-Pointing-Pointer The sensor possesses high sensitivity and wide linear range. Black-Right-Pointing-Pointer The sensor was used for simultaneous detection of G, A, T and C successfully. Black-Right-Pointing-Pointer The sensor was applied in a fish sperm DNA sample with satisfactory results. Black-Right-Pointing-Pointer The proposed sensor has good stability and reproducibility. - Abstract: In this work, a poly(alizarin red)/Graphene composite film modified glassy carbon electrode (PAR/Graphene/GCE) was prepared for simultaneous determination of four DNA bases (guanine, adenine, thymine and cytosine) without any pretreatment. The morphology and interface property of PAR/Graphene films were examined by scanning electron microscopy and electrochemical impedance spectroscopy. The PAR/Graphene/GCE exhibited excellent electrocatalytic activity toward purine (guanine and adenine) and pyrimidine (thymine and cytosine) in 0.1 M phosphate buffer solution (pH 7.4). Under optimum conditions, differential pulse voltammetry was used to detect the oxidation of purine and pyrimidine. The results showed that PAR/Graphene/GCE exhibited well-separated peaks, low detection limit, high sensitivity and wide linear range for simultaneous detection of purine and pyrimidine. The proposed sensor also has good stability and reproducibility. Furthermore, the modified electrode was applied for the detection of DNA bases in a fish sperm DNA sample with satisfactory results.

  17. Infrared study of some 2-substituted-6-hydroxy-4-pyrimidine carboxylic acids. Correlation with MO-calculations

    Directory of Open Access Journals (Sweden)

    IVAN O. JURANIC

    2000-06-01

    Full Text Available The IR spectra of a series of 2-substituted-6-hydroxy-4-pyrimidine carboxylic acids (substituent = OH, SH, CH3, CH3S and NH2 were studied from the aspect of the influence of the subsitutent on the polarizability of some bonds, keto-enol tautomerism and hydrogen bond formation. The spectra were taken using solids due to the low solubility of the acids. Theoretical calculations were done using the MNDO-AM1 semiempirical molecular-orbital method. The stabilities of various tautomers were calculated simulating the dielectric continuum using the COSMO facility of the MOPAC program package. Theoretical calculations were made for all the possible tautomers of the 2-substituted-6-hydroxy-4-pyrimidine carboxylic acids. For the most stable isomers, the vibrational spectra were calculated. For the majority of the compounds the most stable isomer was identified having the structure 2-Y-6-oxo-4-carboxy-3H-pyrimidine. Besides this structure, for the 2-amino-, and 2-methyl- derivatives the zwitterionic forms have very similar stability. The 2-hydroxy compound is most stable as the 2,6-dioxo-1H, 3H isomer. The calculated vibrations for the compounds with a single stable structure correlate very well with the experimental frequencies. For the 2-methyl- and 2-amino- compounds the correlation is considerably less satisfactory. The most probable reason for this deviation is the existence of two or more tautomets in equilibrium. The correlation of the measured frequencies and the pKa values of the acids, indicate that the same tautomers exist in the solid state and in the solution.

  18. An Efficient Synthesis of bi-Aryl Pyrimidine Heterocycles: Potential New Drug Candidates to Treat Alzheimer's Disease.

    Science.gov (United States)

    Rehman, Tanzeel Ur; Khan, Islam Ullah; Ashraf, Muhammad; Tarazi, Hamadeh; Riaz, Sadaf; Yar, Muhammad

    2017-02-21

    A series of 13 novel pyrimidine-based sulfonamides 6a-m were synthesized in short periods of time under microwave conditions in good to excellent yield (54-86%). The chemical structures of these heterocycles consist of a central pyrimidine ring having a phenyl group and pyrimidine groups with sulfonamide motifs. The enzyme inhibitory potential of these compounds was investigated against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) because these enzymes play a crucial role in the treatment of Alzheimer's disease. As compared to the reference compound eserine (IC50  = 0.04 ± 0.0001 μM for AChE and IC50  = 0.85 ± 0.0001 μM for BChE), the IC50 values of the synthesized compounds ranged from 3.73 ± 0.61 μM to 57.36 ± 0.22 μM for AChE and 4.81 ± 0.16 μM to 111.61 ± 0.53 μM for BChE. Among these tested compounds, 6j having a -CH3 group was found to be the most potent one against both enzymes (AChE, IC50  = 3.73 ± 0.61 μM; BChE, IC50  = 4.81 ± 0.16 μM). Quantitative structure-activity relationship (QSAR) and molecular docking studies of the synthesized compounds were also performed.

  19. Spectral and photophysical studies of inclusion complexes of 2-amino-4,6-dimethyl pyrimidine with beta-cyclodextrin.

    Science.gov (United States)

    El-Kemary, M A; El-Gezawy, H S; El-Baradie, H Y; Issa, R M

    2002-02-01

    The interaction of 2-amino-4,6-dimethyl pyrimidine (ADMP) with beta-cyclodextrin (beta-CD) has been studied by means of UV absorption, steady state and time resolved fluorescence techniques. Spectral characteristics, bandwidths and photophysical parameters indicating that ADMP experience two different environments in aqueous solutions: bulk water and 1:1 (ADMP:beta-CD) inclusion complexation. The size restriction of the upper rim of beta-CD partially include ADMP and prevent the possibility of formation of 1:2 complex. The effective polarity of the cyclodextrin cavity experienced by the induced ADMP is equivalent with the polarity of an 80:20 methanol-water mixture.

  20. Cleaner and convenient preparation of 3-(4,6-dimethoxy-pyrimidin-2-yloxy)-2-methyl-phenol.

    Science.gov (United States)

    Wen, Yue-Zhong; Fang, Zhao-Hua; Liu, Wei-Ping

    2004-08-01

    Environmental concerns have highlighted the need of cleaner technologies. A cleaner, convenient and selective technology has been developed for the preparation of 3-(4,6-dimethoxy-pyrimidin-2-yloxy)-2-methyl-phenol (DPMP) from 2-methyl-benzene-1,3-diol in water as solvent. The isolated yield of DPMP is up to 86% in good selectivity. The product structure was characterized by conventional methods, 1H-NMR and MS. This technology belongs to the modern concept of environmentally friendly low wastes or non-wastes technology (LWNWT).