WorldWideScience

Sample records for chloroethyinitrosourea-derived ethano cytosine

  1. Chloroethyinitrosourea-derived ethano cytosine and adenine adducts are substrates for escherichia coli glycosylases excising analogous etheno adducts

    Energy Technology Data Exchange (ETDEWEB)

    Guliaev, Anton B.; Singer, B.; Hang, Bo

    2004-05-05

    Exocyclic ethano DNA adducts are saturated etheno ring derivatives formed mainly by therapeutic chloroethylnitrosoureas (CNUs), which are also mutagenic and carcinogenic. In this work, we report that two of the ethano adducts, 3,N{sup 4}-ethanocytosine (EC) and 1,N{sup 6}-ethanoadenine (EA), are novel substrates for the Escherichia coli mismatch-specific uracil-DNA glycosylase (Mug) and 3-methyladenine DNA glycosylase II (AlkA), respectively. It has been shown previously that Mug excises 3,N{sup 4}-ethenocytosine ({var_epsilon}C) and AlkA releases 1,N{sup 6}-ethenoadenine ({var_epsilon}A). Using synthetic oligonucleotides containing a single ethano or etheno adduct, we found that both glycosylases had a {approx}20-fold lower excision activity toward EC or EA than that toward their structurally analogous {var_epsilon}C or {var_epsilon}A adduct. Both enzymes were capable of excising the ethano base paired with any of the four natural bases, but with varying efficiencies. The Mug activity toward EC could be stimulated by E. coli endonuclease IV and, more efficiently, by exonuclease III. Molecular dynamics (MD) simulations showed similar structural features of the etheno and ethano derivatives when present in DNA duplexes. However, also as shown by MD, the stacking interaction between the EC base and Phe 30 in the Mug active site is reduced as compared to the {var_epsilon}C base, which could account for the lower EC activity observed in this study.

  2. Inheritance of Cytosine Methylation.

    Science.gov (United States)

    Tillo, Desiree; Mukherjee, Sanjit; Vinson, Charles

    2016-11-01

    There are numerous examples of parental transgenerational inheritance that is epigenetic. The informational molecules include RNA, chromatin modifications, and cytosine methylation. With advances in DNA sequencing technologies, the molecular and epigenetic mechanisms mediating these effects are now starting to be uncovered. This mini-review will highlight some of the examples of epigenetic inheritance, the establishment of cytosine methylation in sperm, and recent genomic studies linking sperm cytosine methylation to epigenetic effects on offspring. A recent paper examining changes in diet and sperm cytosine methylation from pools of eight animals each, found differences between a normal diet, a high fat diet, and a low protein diet. However, epivariation between individuals within a group was greater than the differences between groups obscuring any potential methylation changes linked to diet. Learning more about epivariation may help unravel the mechanisms that regulate cytosine methylation. In addition, other experimental and genetic systems may also produce more dramatic changes in the sperm methylome, making it easier to unravel potential transgenerational phenomena. J. Cell. Physiol. 231: 2346-2352, 2016. © 2016 Wiley Periodicals, Inc. PMID:26910768

  3. Modification of Cilembu sweet potato starch with ethanoic acid

    Science.gov (United States)

    Mahmudatussa’adah, A.; Rahmawati, Y.; Sudewi

    2016-04-01

    Cilembu sweet potato harvest was abundant, its use was still limited. Starch was required by various industries. Starch is generally beige, and requires a long time for the drying process. The purpose of this research was to produce a modified starch with ethanoic acid. The method used in this study was the experimental method. The results showed acid modified starch yield was 18%, with the color characteristics of L*: 96.38 ± 0.82; a*: -0.70±0.02 b*: 2.70±0.03 C: 2.79±0.02. Native starch yield was 16%, with the color characteristics of L*: 93.55 ± 0.91; a*: -0.86±0.06 b*: 2.93±0.04 C: 3.05±0.03. The conclusion of this study was modified starch of Cilembu sweet potato using ethanoic acid have higher yield and more white bright than native starch.

  4. Cadmium(2) complexes of cytosine

    International Nuclear Information System (INIS)

    Complexes of cadmium(2) with cytosine obtained from aqueous or physiological solutions at room temperature are reported. The complexes were characterized by spectroscopic, conductometric, 1H-NMR, and 13C-NMR measurements and also by thermogravimetry. (Authors)

  5. Electrokinetic remediation of cobalt contaminated soil using ethanoic buffer

    International Nuclear Information System (INIS)

    After kaolin clay was artificially contaminated with Co2+ ion, the remediation characteristics were analyzed by the electrokinetic method. Ethanoic buffer was injected in the soil column and CH3COOH was continuously inputted to the cathode reservoir to restrain the pH increase. Since the pH of the cathode side of the soil column was 4.0 initially and increased to only 6.5 after remediation for 43.6 hours, precipitate, Co(OH)2, was not formed in the column. The effluent rate increased with the passage of time and Co2+ removal in the column at the initial time were mainly controlled by ion migration. 13.1% of the total amount of Co2+ in the soil column was removed in 10 hours, 46.8% of the total Co2+ in 20.8 hours, 71.7% of the total Co2+ in 30.1 hours, and 94.6% of the total Co2+ in 43.6 hours. Meanwhile, residual concentrations in the column calculated by the developed model were similar to those by experiment

  6. Raman Spectroscopic Study of the Vapour Phase of 1-Methylimidazolium Ethanoate, a Protic Ionic Liquid

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Canongia Lopes, Jose N.; Ferreira, Rui; Rebelo, Luis P. N.; Seddon, Kenneth R.; Tomaszowska, Alina A.

    2010-01-01

    The gas phase over the ionic liquid 1-methylimidazolium ethanoate, [Hmim][O2CCH3], was studied by means of Raman spectroscopy. Raman spectra are presented, the species in the gas phase are identified, and their bands are assigned. The results are interpreted using ab initio quantum mechanical cal...... calculations that also predict vibrational spectra. The obtained data reinforce a previous interpretation, based on FT-ICR mass spectrometric data, that the vapor phase over [Hmim][O2CCH3] consists predominantly of two neutral molecules, monomeric ethanoic acid and 1-methylimidazole....

  7. Discovery of novel dihydro-9,10-ethano-anthracene carboxamides as glucocorticoid receptor modulators.

    Science.gov (United States)

    Yang, Bingwei V; Vaccaro, Wayne; Doweyko, Arthur M; Doweyko, Lidia M; Huynh, Tram; Tortolani, David; Nadler, Steven G; McKay, Lorraine; Somerville, John; Holloway, Deborah A; Habte, Sium; Weinstein, David S; Barrish, Joel C

    2009-04-15

    A series of dihydro-9,10-ethano-anthracene-11-carboxamides as novel glucocorticoid receptor modulators is reported. SAR exploration identified compounds from this series displaying a promising dissociation profile in discriminating between transrepression and transactivation activities. 17a is a partial agonist of GR-mediated transactivation which elicits potent and efficacious transrepression in reporter gene assays. A hypothetical binding mode is provided which accounts for the induction of functional activity by a bridgehead methyl group. PMID:19321341

  8. Probing High School Students' Cognitive Structures and Key Areas of Learning Difficulties on Ethanoic Acid Using the Flow Map Method

    Science.gov (United States)

    Zhou, Qing; Wang, Tingting; Zheng, Qi

    2015-01-01

    The purpose of this study was primarily to explore high school students' cognitive structures and to identify their learning difficulties on ethanoic acid through the flow map method. The subjects of this study were 30 grade 1 students from Dong Yuan Road Senior High School in Xi'an, China. The interviews were conducted a week after the students…

  9. Characterization of the Escherichia coli codBA operon encoding cytosine permease and cytosine deaminase

    DEFF Research Database (Denmark)

    Danielsen, S; Kilstrup, M; Barilla, K;

    1992-01-01

    The nucleotide sequence of a 3.1 kb segment carrying the cytosine deaminase gene (codA) from Escherichia coli was determined. The sequence revealed the presence of two open reading frames, the first (codB) specifying a highly hydrophobic polypeptide and the second specifying cytosine deaminase. A...

  10. Analysis of DNA Cytosine Methylation on Cotton under Salt Stress

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    DNA methylation,especially methylation of cytosine in eukaryotic organisms,has been implicated in gene regulation,genomic imprinting,the timing of DNA replication,and determination of chromatin structure.It was reported that 6.5% of the whole cytosine residues in the nuclear DNA in higher

  11. Information Thermodynamics of Cytosine DNA Methylation.

    Science.gov (United States)

    Sanchez, Robersy; Mackenzie, Sally A

    2016-01-01

    Cytosine DNA methylation (CDM) is a stable epigenetic modification to the genome and a widespread regulatory process in living organisms that involves multicomponent molecular machines. Genome-wide cytosine methylation patterning participates in the epigenetic reprogramming of a cell, suggesting that the biological information contained within methylation positions may be amenable to decoding. Adaptation to a new cellular or organismal environment also implies the potential for genome-wide redistribution of CDM changes that will ensure the stability of DNA molecules. This raises the question of whether or not we would be able to sort out the regulatory methylation signals from the CDM background ("noise") induced by thermal fluctuations. Here, we propose a novel statistical and information thermodynamic description of the CDM changes to address the last question. The physical basis of our statistical mechanical model was evaluated in two respects: 1) the adherence to Landauer's principle, according to which molecular machines must dissipate a minimum energy ε = kBT ln2 at each logic operation, where kB is the Boltzmann constant, and T is the absolute temperature and 2) whether or not the binary stretch of methylation marks on the DNA molecule comprise a language of sorts, properly constrained by thermodynamic principles. The study was performed for genome-wide methylation data from 152 ecotypes and 40 trans-generational variations of Arabidopsis thaliana and 93 human tissues. The DNA persistence length, a basic mechanical property altered by CDM, was estimated with values from 39 to 66.9 nm. Classical methylome analysis can be retrieved by applying information thermodynamic modelling, which is able to discriminate signal from noise. Our finding suggests that the CDM signal comprises a language scheme properly constrained by molecular thermodynamic principles, which is part of an epigenomic communication system that obeys the same thermodynamic rules as do current

  12. Analysis of DNA Cytosine Methylation on Cotton under Salt Stress

    Institute of Scientific and Technical Information of China (English)

    ZHAO Yun-le; YE Wu-wei; WANG Jun-juan; FAN Bao-xiang

    2008-01-01

    @@ DNA methylation,especially methylation of cytosine in eukaryotic organisms,has been implicated in gene regulation,genomic imprinting,the timing of DNA replication,and determination of chromatin structure.It was reported that 6.5% of the whole cytosine residues in the nuclear DNA in higher plants were methylated.The methylation of cytosine in plant nuclear DNA occurs usually in both CpG and CpNG sequences,and the methylation state can be maintained through the cycles of DNA replication and is likely to play an integral role in regulating gene expression.

  13. Human repair endonuclease incises DNA at cytosine photoproducts

    International Nuclear Information System (INIS)

    The nature of DNA damage by uvB and uvC irradiation was investigated using a defined sequence of human DNA. A UV-irradiated, 3'-end-labeled, 92 base pair sequence from the human alphoid segment was incubated with a purified human lymphoblast endonuclease that incises DNA at non-dimer photoproducts. Analysis by polyacrylamide gel electrophoresis identified all sites of endonucleolytic incision as cytosines. These were found in regions of the DNA sequence lacking adjacent pyrimidines and therefore are neither cyclobutane pyrimidine dimers nor 6-4'-pyrimidines. Incision at cytosine photoproducts was not detected at loci corresponding to alkali-labile sites in either control or irradiated substrates. This demonstrates that the bands detected after the enzymic reactions were not the result of DNA strand breaks, base loss sites or ring-opened cytosines. The optimal wavelengths for formation of cytosine photoproducts are 270-295 nm, similar to those associated with maximal tumor yields in animal ultraviolet carcinogenesis studies. Irradiation by monochromatic 254 nm light resulted in reduced cytosine photoproduct formation. This human UV endonuclease has an apparently identical substrate specificity to E. coli endonuclease III. Both the human and bacterial enzymes incise cytosine moieties in UV irradiated DNA and modified thymines in oxidized DNA

  14. Correlation and prediction of mixing thermodynamic properties of ester-containing systems: Ester + alkane and ester + ester binary systems and the ternary dodecane + ethyl pentanoate + ethyl ethanoate

    International Nuclear Information System (INIS)

    Highlights: ► Excess enthalpies and volumes were measured for ester–ester–alkane. ► Mixing behaviour for ester–ester, ester–alkane and ester–ester–alkane are analyzed. ► Correlations with a new polynomial model reproduce well the mixing properties. ► UNIFAC predictions for hE result acceptable excluding the ester–ester mixtures. - Abstract: Excess thermodynamic properties VmE and HmE, have been measured for the ternary mixture dodecane + ethyl pentanoate + ethyl ethanoate and for the corresponding binaries dodecane + ethyl pentanoate, dodecane + ethyl ethanoate, ethyl pentanoate + ethyl ethanoate at 298.15 K. All mixtures show endothermic and expansive effects. Experimental results are correlated with a suitable equation whose final form for the excess ternary quantity ME contains the particular contributions of the three binaries (i–j) and a last term corresponding to the ternary, all of them obtained considering fourth-order interactions. The fit goodness for all mixtures is good and comparable to others equations taken from the literature. In this work the dissolution model for the binaries and ternary is analyzed with a special attention to ester–ester binaries whose behaviour is discussed. The application of the UNIFAC group contribution model to estimate the HmE yields acceptable results for the binaries (with the exception of ester–ester) and for the ternary mixture.

  15. Combined QM(DFT)/MM molecular dynamics simulations of the deamination of cytosine by yeast cytosine deaminase (yCD).

    Science.gov (United States)

    Zhang, Xin; Zhao, Yuan; Yan, Honggao; Cao, Zexing; Mo, Yirong

    2016-05-15

    Extensive combined quantum mechanical (B3LYP/6-31G*) and molecular mechanical (QM/MM) molecular dynamics simulations have been performed to elucidate the hydrolytic deamination mechanism of cytosine to uracil catalyzed by the yeast cytosine deaminase (yCD). Though cytosine has no direct binding to the zinc center, it reacts with the water molecule coordinated to zinc, and the adjacent conserved Glu64 serves as a general acid/base to shuttle protons from water to cytosine. The overall reaction consists of several proton-transfer processes and nucleophilic attacks. A tetrahedral intermediate adduct of cytosine and water binding to zinc is identified and similar to the crystal structure of yCD with the inhibitor 2-pyrimidinone. The rate-determining step with the barrier of 18.0 kcal/mol in the whole catalytic cycle occurs in the process of uracil departure where the proton transfer from water to Glu64 and nucleophilic attack of the resulting hydroxide anion to C2 of the uracil ring occurs synchronously. © 2016 Wiley Periodicals, Inc. PMID:26813441

  16. Communication: UV photoionization of cytosine catalyzed by Ag+

    OpenAIRE

    Martin, Taccone; Féraud, Geraldine; Berdakin, Matías; Dedonder-Lardeux, Claude; Jouvet, Christophe; A. Pino, Gustavo

    2015-01-01

    The photo-induced damages of DNA in interaction with metal cations, which are found in various environments, still remain to be characterized. In this paper, we show how the complexation of a DNA base (cytosine (Cyt)) with a metal cation (Ag+) changes its electronic properties. By means of UV photofragment spectroscopy of cold ions, it was found that the photoexcitation of the CytAg+ complex at lowenergy (315-282) nm efficiently leads to ionized cytosine (Cyt+) as the single product. This occ...

  17. Conformational switching of ethano-bridged Cu,H2-bis-porphyrin induced by aromatic amines

    Directory of Open Access Journals (Sweden)

    Simona Bettini

    2015-11-01

    Full Text Available Cu,H2-bis-porphyrin (Cu,H2-Por2, in which copper porphyrin and free-base porphyrin are linked together by an ethano-bridge, was dissolved in chloroform and spread at the air/liquid subphase interface of a Langmuir trough. The bis-porphyrin derivative, floating film was characterized by reflection spectroscopy and the surface pressure of the floating film was studied as a function of the mean area per molecule. When aromatic amines are dissolved in the subphase, an evident interaction between the bis-porphyrin host and the aromatic amine guest is observed. A clear-cut variation of the profile of surface pressure vs area per molecule curve is observed. Reflection spectroscopy highlights that the aromatic amines dissolved in the subphase are able to induce the syn-to-anti conformational switching in the bis-porphyrin derivative. The Langmuir–Schaefer technique has been used to transfer the floating bis-porphyrin film (when using pure water as a subphase to a surface plasmon resonance (SPR substrate and the resulting device was able to detect the presence of aniline at concentrations as low as 1 nM in aqueous solution. The high selectivity of the SPR sensing device has been verified by checking the spectral response of the active layer towards other analytes dissolved in the aqueous solutions.

  18. Photophysical properties of pyrrolocytosine, a cytosine fluorescent base analogue.

    Science.gov (United States)

    Nguyen, Quynh L; Spata, Vincent A; Matsika, Spiridoula

    2016-07-27

    The photophysical behavior of pyrrolocytosine (PC), a fluorescent base analogue of cytosine, has been investigated using theoretical approaches. The similarities between the PC and cytosine structures allow PC to maintain the pseudo-Watson-Crick base-pairing arrangement with guanine. Cytosine, similar to the other natural nucleobases, is practically non-fluorescent, because of ultrafast radiationless decay occurring through conical intersections. PC displays a much higher fluorescence quantum yield than cytosine, making it an effective fluorescent marker to study the structure, function, and dynamics of DNA/RNA complexes. Similar to 2-aminopurine, a constitutional isomer of adenine that base-pairs with thymine, PC's fluorescence is quenched when it is incorporated into a dinucleotide or a trinucleotide. In this work we examine the photophysical properties of isolated PC, microhydrated PC, as well as, complexes where PC is either base-stacked or hydrogen-bonded with guanine. Our results indicate that hydration affects the radiationless decay pathways in PC by destabilizing conical intersections. The calculations of dimers and trimers show that the radiative decay is affected by π stacking, while the presence of charge transfer states between PC and guanine may contribute to radiationless decay. PMID:27251599

  19. Theoretical investigation of the interaction of cytosine and its tautomers with alkali metals

    International Nuclear Information System (INIS)

    Quantum-chemical calculations have been applied in order to explore the interaction of alkali metals (M=Li-Cs) with cytosine and its tautomers. The optimized geometries, harmonic vibrational frequencies, and the energies of cytosine, metallated cytosine, and its tautomers have been calculated. The calculations show that metallated cytosine is more stable than non metallated one. The stability of metallated cytosine decreases with the growth of atomic number of alkali metals. Estimated charge on the metals demonstrates that there is some covalency in the metal-ligand interaction, especially in the Li+ system

  20. Generation of Absolute Controlled Crystal Chirality by the Removal of Crystal Water from Achiral Crystal of Nucleobase Cytosine

    OpenAIRE

    Kawasaki, Tsuneomi; Hakoda, Yuko; Mineki, Hiroko; Suzuki, Kenta; Soai, Kenso

    2010-01-01

    The enantioselective formation of chiral crystal of achiral nucleobase cytosine was achieved mediated by the crystal direction selective dehydration of crystal water in the achiral crystal of cytosine monohydrate (P21/c). Heat transfer from the enantiotopic face of the single crystal of cytosine monohydrate afforded the enantiomorphous crystal of anhydrous cytosine.

  1. Communication: UV photoionization of cytosine catalyzed by Ag+

    International Nuclear Information System (INIS)

    The photo-induced damages of DNA in interaction with metal cations, which are found in various environments, still remain to be characterized. In this paper, we show how the complexation of a DNA base (cytosine (Cyt)) with a metal cation (Ag+) changes its electronic properties. By means of UV photofragment spectroscopy of cold ions, it was found that the photoexcitation of the CytAg+ complex at low energy (315-282) nm efficiently leads to ionized cytosine (Cyt+) as the single product. This occurs through a charge transfer state in which an electron from the p orbital of Cyt is promoted to Ag+, as confirmed by ab initio calculations at the TD-DFT/B3LYP and RI-ADC(2) theory level using the SV(P) basis set. The low ionization energy of Cyt in the presence of Ag+ could have important implications as point mutation of DNA upon sunlight exposition

  2. AID/APOBEC cytosine deaminase induces genome-wide kataegis

    Directory of Open Access Journals (Sweden)

    Lada Artem G

    2012-12-01

    Full Text Available Abstract Clusters of localized hypermutation in human breast cancer genomes, named “kataegis” (from the Greek for thunderstorm, are hypothesized to result from multiple cytosine deaminations catalyzed by AID/APOBEC proteins. However, a direct link between APOBECs and kataegis is still lacking. We have sequenced the genomes of yeast mutants induced in diploids by expression of the gene for PmCDA1, a hypermutagenic deaminase from sea lamprey. Analysis of the distribution of 5,138 induced mutations revealed localized clusters very similar to those found in tumors. Our data provide evidence that unleashed cytosine deaminase activity is an evolutionary conserved, prominent source of genome-wide kataegis events. Reviewers This article was reviewed by: Professor Sandor Pongor, Professor Shamil R. Sunyaev, and Dr Vladimir Kuznetsov.

  3. Communication: UV photoionization of cytosine catalyzed by Ag+

    Science.gov (United States)

    Taccone, Martín I.; Féraud, Geraldine; Berdakin, Matías; Dedonder-Lardeux, Claude; Jouvet, Christophe; Pino, Gustavo A.

    2015-07-01

    The photo-induced damages of DNA in interaction with metal cations, which are found in various environments, still remain to be characterized. In this paper, we show how the complexation of a DNA base (cytosine (Cyt)) with a metal cation (Ag+) changes its electronic properties. By means of UV photofragment spectroscopy of cold ions, it was found that the photoexcitation of the CytAg+ complex at low energy (315-282) nm efficiently leads to ionized cytosine (Cyt+) as the single product. This occurs through a charge transfer state in which an electron from the p orbital of Cyt is promoted to Ag+, as confirmed by ab initio calculations at the TD-DFT/B3LYP and RI-ADC(2) theory level using the SV(P) basis set. The low ionization energy of Cyt in the presence of Ag+ could have important implications as point mutation of DNA upon sunlight exposition.

  4. Communication: UV photoionization of cytosine catalyzed by Ag(+).

    Science.gov (United States)

    Taccone, Martín I; Féraud, Geraldine; Berdakin, Matías; Dedonder-Lardeux, Claude; Jouvet, Christophe; Pino, Gustavo A

    2015-07-28

    The photo-induced damages of DNA in interaction with metal cations, which are found in various environments, still remain to be characterized. In this paper, we show how the complexation of a DNA base (cytosine (Cyt)) with a metal cation (Ag(+)) changes its electronic properties. By means of UV photofragment spectroscopy of cold ions, it was found that the photoexcitation of the CytAg(+) complex at low energy (315-282) nm efficiently leads to ionized cytosine (Cyt(+)) as the single product. This occurs through a charge transfer state in which an electron from the p orbital of Cyt is promoted to Ag(+), as confirmed by ab initio calculations at the TD-DFT/B3LYP and RI-ADC(2) theory level using the SV(P) basis set. The low ionization energy of Cyt in the presence of Ag(+) could have important implications as point mutation of DNA upon sunlight exposition. PMID:26233098

  5. Effects of cytosine methylation on transcription factor binding sites

    KAUST Repository

    Medvedeva, Yulia A

    2014-03-26

    Background: DNA methylation in promoters is closely linked to downstream gene repression. However, whether DNA methylation is a cause or a consequence of gene repression remains an open question. If it is a cause, then DNA methylation may affect the affinity of transcription factors (TFs) for their binding sites (TFBSs). If it is a consequence, then gene repression caused by chromatin modification may be stabilized by DNA methylation. Until now, these two possibilities have been supported only by non-systematic evidence and they have not been tested on a wide range of TFs. An average promoter methylation is usually used in studies, whereas recent results suggested that methylation of individual cytosines can also be important.Results: We found that the methylation profiles of 16.6% of cytosines and the expression profiles of neighboring transcriptional start sites (TSSs) were significantly negatively correlated. We called the CpGs corresponding to such cytosines " traffic lights" We observed a strong selection against CpG " traffic lights" within TFBSs. The negative selection was stronger for transcriptional repressors as compared with transcriptional activators or multifunctional TFs as well as for core TFBS positions as compared with flanking TFBS positions.Conclusions: Our results indicate that direct and selective methylation of certain TFBS that prevents TF binding is restricted to special cases and cannot be considered as a general regulatory mechanism of transcription. 2013 Medvedeva et al.; licensee BioMed Central Ltd.

  6. Cytosine photoproduct-DNA glycosylase in Escherichia coli and cultured human cells

    International Nuclear Information System (INIS)

    Ultraviolet irradiation of DNA produces a variety of pyrimidine base damages. The activities of Escherichia coli endonuclease III and a human lymphoblast endonuclease that incises ultraviolet-irradiated DNA at modified cytosine moieties were compared. Both the bacterial and human enzymes release this cytosine photoproduct as a free base. These glycosylase activities are linear with times of reaction, quantities of enzyme, and irradiation dosages of the substrates. Both enzyme activities are similarly inhibited by the addition of monovalent and divalent cations. Analysis by DNA sequencing identified loci of endonucleolytic incision as cytosines. These are neither cyclobutane pyrimidine dimers, 6-(1,2-dihydro-2-oxo-4-pyrimidinyl)-5-methyl-2,4(1H,3H)-pyrimidinediones, nor apyrimidinic sites. This cytosine photoproduct is separable from unmodified cytosine by high-performance liquid chromatography. This separation should facilitate identification of this modified cytosine and elucidation of its biological significance

  7. The pharmacokinetics of subcutaneous cytosine arabinoside in patients with acute myelogenous leukaemia.

    OpenAIRE

    Slevin, M L; Piall, E M; Aherne, G.W.; Johnston, A.; Sweatman, M C; Lister, T. A.

    1981-01-01

    1 The pharmacokinetics of subcutaneous cytosine arabinoside were compared with bolus intravenous injection and intravenous infusion in five patients with acute myelogenous leukaemia. 2 Subcutaneous cytosine arabinoside was rapidly absorbed and then declined biexponentially with initial and terminal half-lives similar to intravenous bolus injection. 3 Cytosine arabinoside levels declined rapidly after intravenous bolus and subcutaneous bolus injection, and fell below steady state infusion leve...

  8. Cytosinium–hydrogen maleate–cytosine (1/1/1)

    OpenAIRE

    Benali-Cherif, Nourredine; Falek, Wahiba; Direm, Amani

    2009-01-01

    The title organic salt, C4H6N3O+·C4H3O4 −·C4H5N3O, was synthesized from cytosine base and maleic acid. An intra­molecular O—H⋯O hydrogen bond occurs in the hydrogen maleate anion. The crystal packing is stabilized by inter­molecular N—H⋯O, N—H⋯N and C—H⋯O hydrogen bonds, giving rise to a nearly planar two-dimensional network parallel to (101).

  9. Communication: UV photoionization of cytosine catalyzed by Ag{sup +}

    Energy Technology Data Exchange (ETDEWEB)

    Taccone, Martín I.; Berdakin, Matías; Pino, Gustavo A., E-mail: gpino@fcq.unc.edu.ar [INFIQC (CONICET – Universidad Nacional de Córdoba), Dpto. de Fisicoquímica, Facultad de Ciencias Químicas, Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba (Argentina); Féraud, Geraldine; Dedonder-Lardeux, Claude; Jouvet, Christophe [Physique des Interactions Ioniques et Moléculaires (PIIM): UMR- 7345, CNRS, Aix Marseille Université, 13397 Marseille (France)

    2015-07-28

    The photo-induced damages of DNA in interaction with metal cations, which are found in various environments, still remain to be characterized. In this paper, we show how the complexation of a DNA base (cytosine (Cyt)) with a metal cation (Ag{sup +}) changes its electronic properties. By means of UV photofragment spectroscopy of cold ions, it was found that the photoexcitation of the CytAg{sup +} complex at low energy (315-282) nm efficiently leads to ionized cytosine (Cyt{sup +}) as the single product. This occurs through a charge transfer state in which an electron from the p orbital of Cyt is promoted to Ag{sup +}, as confirmed by ab initio calculations at the TD-DFT/B3LYP and RI-ADC(2) theory level using the SV(P) basis set. The low ionization energy of Cyt in the presence of Ag{sup +} could have important implications as point mutation of DNA upon sunlight exposition.

  10. Effects of cytosine methylation on DNA charge transport

    Science.gov (United States)

    Hihath, Joshua; Guo, Shaoyin; Zhang, Peiming; Tao, Nongjian

    2012-04-01

    The methylation of cytosine bases in DNA commonly takes place in the human genome and its abnormality can be used as a biomarker in the diagnosis of genetic diseases. In this paper we explore the effects of cytosine methylation on the conductance of DNA. Although the methyl group is a small chemical modification, and has a van der Waals radius of only 2 Å, its presence significantly changes the duplex stability, and as such may also affect the conductance properties of DNA. To determine if charge transport through the DNA stack is sensitive to this important biological modification we perform multiple conductance measurements on a methylated DNA molecule with an alternating G:C sequence and its non-methylated counterpart. From these studies we find a measurable difference in the conductance between the two types of molecules, and demonstrate that this difference is statistically significant. The conductance values of these molecules are also compared with a similar sequence that has been previously studied to help elucidate the charge transport mechanisms involved in direct DNA conductance measurements.

  11. Triplex-mediated analysis of cytosine methylation at CpA sites in DNA

    OpenAIRE

    Johannsen, Marie W.; Gerrard, Simon R.; Melvin, Tracy; Brown, Tom

    2014-01-01

    Modified triplex-forming oligonucleotides distinguish 5-methyl cytosine from unmethylated cytosine in DNA duplexes by differences in triplex melting temperatures. The discrimination is sequence-specific; dramatic differences in stabilisation are seen for CpA methylation, whereas CpG methylation is not detected. This direct detection of DNA methylation constitutes a new approach for epigenetic analysis.

  12. Enzymic excision of ultraviolet-induced cytosine hydrates from left-handed DNA

    International Nuclear Information System (INIS)

    Ultraviolet irradiation of DNA produces a variety of pyrimidine modifications. These include cytosine hydrate (5,6-dihydro-6-hydroxycytosine), released as a free base by E. coli endonuclease III. The enzymic excision of cytosine hydrate by this purified enzyme was investigated by assaying release of labeled photoproduct from DNA into the ethanol-soluble fraction. Ultraviolet-irradiated poly(dG-dC):poly(dG-dC), radio-labeled in cytosines, was used as substrate. Shifts between the right-handed B-conformation and the left-handed Z-conformation were effected by heating the polymer in the presence of either Ni[II] or Co[II]. Conformational states were determined by ultraviolet circular dichroism. Rates of enzymic cytosine hydrate release did not differ between the different substrate conformations, B-DNA and Z-DNA. Irradiation of left-handed poly(dG-dC):poly(dG-dC) resulted in cytosine hydrate formation. Therefore, neither formation nor enzymic excision of ultraviolet-induced cytosine hydrates are substantially affected by the DNA conformational state. Cytosine hydrates are most likely to occur in alternating purine:pyrimidine sequences. Such segments can adopt the Z-conformation as a result of reactions with chemical carcinogens, the presence of metal ions, or negative superhelicity. These results indicate repair of cytosine hydrates to be likely, regardless of the DNA conformational state

  13. Cytosine methylation of sperm DNA in horse semen after cryopreservation.

    Science.gov (United States)

    Aurich, Christine; Schreiner, Bettina; Ille, Natascha; Alvarenga, Marco; Scarlet, Dragos

    2016-09-15

    Semen processing may contribute to epigenetic changes in spermatozoa. We have therefore addressed changes in sperm DNA cytosine methylation induced by cryopreservation of stallion semen. The relative amount of 5-methylcytosine relative to the genomic cytosine content of sperm DNA was analyzed by ELISA. In experiment 1, raw semen (n = 6 stallions, one ejaculate each) was shock-frozen. Postthaw semen motility and membrane integrity were completely absent, whereas DNA methylation was similar in raw (0.4 ± 0.2%) and shock-frozen (0.3 ± 0.1%) semen (not significant). In experiment 2, three ejaculates per stallion (n = 6) were included. Semen quality and DNA methylation was assessed before addition of the freezing extender and after freezing-thawing with either Ghent (G) or BotuCrio (BC) extender. Semen motility, morphology, and membrane integrity were significantly reduced by cryopreservation but not influenced by the extender (e.g., total motility: G 69.5 ± 2.0, BC 68.4 ± 2.2%; P < 0.001 vs. centrifugation). Cryopreservation significantly (P < 0.01) increased the level of DNA methylation (before freezing 0.6 ± 0.1%, postthaw G 6.4 ± 3.7, BC 4.4 ± 1.5%; P < 0.01), but no differences between the freezing extenders were seen. The level of DNA methylation was not correlated to semen motility, morphology, or membrane integrity. The results demonstrate that semen processing for cryopreservation increases the DNA methylation level in stallion semen. We conclude that assessment of sperm DNA methylation allows for evaluation of an additional parameter characterizing semen quality. The lower fertility rates of mares after insemination with frozen-thawed semen may at least in part be explained by cytosine methylation of sperm-DNA induced by the cryopreservation procedure. PMID:27242182

  14. Bonded Excimer in Stacked Cytosines: A Semiclassical Simulation Study

    Directory of Open Access Journals (Sweden)

    Weifeng Wu

    2015-01-01

    Full Text Available The formation of a covalent bond between two stacked cytosines, one of which is excited by an ultrafast laser pulse, was studied by semiclassical dynamics simulations. The results show that a bonded excimer is created, which sharply lowers the energy gap between the LUMO and HOMO and consequently facilitates the deactivation of the electronically excited molecule. This is different from the case of two stacked adenines, where the formation of a covalent bond alters the nonadiabatic deactivation mechanism in two opposite ways. It lowers the energy gap and consequently leads to the coupling between the HOMO and LUMO levels, thus enhancing the deactivation of the electronically excited molecule. On the other hand, it leads to restriction of the deformation vibration of the pyrimidine in the excited molecule, because of a steric effect, and this delays the deactivation process of the excited adenine molecule with return to the electronic ground state.

  15. Syntheses of [5-2H]-uracil, [5-2H]-cytosine, [6-2H]-uracil and [6-2H]-cytosine

    International Nuclear Information System (INIS)

    Syntheses of [5-2H]-, [6-2H]-uracil and [5-2H]-, [6-2H]-cytosine were investigated. The catalytic reaction of uracil or cytosine with 2H2 gas in alkaline media gave rise to [6-2H]-compounds almost exclusively. On the other hand, the reaction of 5-bromouracil or 5-bromocytosine with 2H2 gas gave rise to a mixture of [5-2H]-, [6-2H]- and [5-2H, 6-2H]-compounds depending on the experimental conditions. By controlling the temperature, the pressure of 2H2 gas and the amount of catalyst, [5-2H]-uracil and [5-2H]-cytosine were obtained. The isotopic distribution in each product was measured by 1H NMR spectroscopy combined with an HPLC method. (author)

  16. Safety of intrathecal administration of cytosine arabinoside and methotrexate in dogs and cats.

    Science.gov (United States)

    Genoni, S; Palus, V; Eminaga, S; Cherubini, G B

    2016-09-01

    The objective of the study was to retrospectively evaluate the short-term safety of intrathecal administration of cytosine arabinoside alone or in combination with methotrexate in dogs and cats. One hundred and twelve dogs and eight cats admitted between September 2008 and December 2013, diagnosed with suspected inflammatory (meningoencephalomyelitis of unknown aetiology) or neoplastic disease affecting brain or spinal cord and treated with an intrathecal administration of cytosine arabinoside alone or in combination with methotrexate were included in the study. Recorded information regarding possible adverse events during administration while recovering from anaesthesia and during hospitalization period were evaluated. The results showed that one patient developed generalized tonic-clonic seizure activity after administration of cytosine arabinoside and methotrexate during recovery from anaesthesia, however responded to intravenous administration of diazepam. On the base of our results we can conclude that intrathecal administration of cytosine arabinoside alone or in combination with methotrexate is a safe procedure in dogs and cats. PMID:25041580

  17. Effect of Different Substituents on the Amino-Oxo/Amino-Hydroxy Cytosine Tautomeric System

    Directory of Open Access Journals (Sweden)

    Hamzeh S.M. Al-Omari

    2008-01-01

    Full Text Available Amino-oxo cytosine and amino-hydroxy cytosine tautomeric system was studied by employing MNDO semi-empirical method of calculations. The amino-hydroxy structure was found to be energetically favorable over amino-oxo form of cytosine as indicated by the calculated heat of formation and Gibbs free energy. The substitution of F, OH, CN, NH2, BH2 and CH3 at carbon 6-position was studied. All the substituents are found to affect the geometrical parameters of the substituted structures. The equilibria between the substituted amino-oxo and amino-hydroxy cytosines were studied by the Gibbs free energy change and by isodesmic reactions. The calculations were performed at 25C. It is found that all substituents push the equilibria in the forward direction compared to the unsubstituted tautomeric pairs except in the case of BH2 substituent where the equilibrium becomes slightly less favourable in the forward direction.

  18. Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants

    Indian Academy of Sciences (India)

    Sushil Kumar; Renu Kumari; Vishakha Sharma; Vinay Sharma

    2013-12-01

    Heritable information in plants consists of genomic information in DNA sequence and epigenetic information superimposed on DNA sequence. The latter is in the form of cytosine methylation at CG, CHG and CHH elements (where H = A, T or C) and a variety of histone modifications in nucleosomes. The epialleles arising from cytosine methylation marks on the nuclear genomic loci have better heritability than the epiallelic variation due to chromatin marks. Phenotypic variation is increased manifold by epiallele comprised methylomes. Plants (angiosperms) have highly conserved genetic mechanisms to establish, maintain or erase cytosine methylation from epialleles. The methylation marks in plants fluctuate according to the cell/tissue/organ in the vegetative and reproductive phases of plant life cycle. They also change according to environment. Epialleles arise by gain or loss of cytosine methylation marks on genes. The changes occur due to the imperfection of the processes that establish and maintain the marks and on account of spontaneous and stress imposed removal of marks. Cytosine methylation pattern acquired in response to abiotic or biotic stress is often inherited over one to several subsequent generations. Cytosine methylation marks affect physiological functions of plants via their effect(s) on gene expression levels. They also repress transposable elements that are abundantly present in plant genomes. The density of their distribution along chromosome lengths affects meiotic recombination rate, while their removal increases mutation rate. Transposon activation due to loss of methylation causes rearrangements such that new gene regulatory networks arise and genes for microRNAs may originate. Cytosine methylation dynamics contribute to evolutionary changes. This review presents and discusses the available evidence on origin, removal and roles of cytosine methylation and on related processes, such as RNA directed DNA methylation, imprinting, paramutation and

  19. Prebiotic cytosine synthesis: A critical analysis and implications for the origin of life

    OpenAIRE

    Shapiro, Robert

    1999-01-01

    A number of theories propose that RNA, or an RNA-like substance, played a role in the origin of life. Usually, such hypotheses presume that the Watson–Crick bases were readily available on prebiotic Earth, for spontaneous incorporation into a replicator. Cytosine, however, has not been reported in analyses of meteorites nor is it among the products of electric spark discharge experiments. The reported prebiotic syntheses of cytosine involve the reaction of cyanoacetylene (or its hydrolysis pr...

  20. Protection of intestinal damage by pretreatment with cytarabine (cytosine arabinoside)

    Energy Technology Data Exchange (ETDEWEB)

    Phelps, T.A.; Blackett, N.M.

    1979-09-01

    The circumstances in which cytarabine (cytosine arabinoside) ''protects'' intestinal epithelial stem cells against radiation have been investigated. Special attention has been given to this protective effect with radiation doses in the clinically used range in order to determine whether the protective effect might be of use in radiotherapy. It has been shown that 12 hours after cytarabine the D/sub 0/ and extrapolation number are increased when large single doses of radiation are used. To determine the effect of cytarabine at lower doses, it is necessary to use a second irradiation as an ''assay'' dose. By this means it is shown that there is more protection than can be accounted for by the change in D/sub 0/ and extrapolation number at the time of the first dose. Evidence is presented indicating that the rate of stem cell regeneration is not increased by cytarabine pretreatment. Finally, the relation between intestinal protection, bone marrow stem cell enhanced recovery and improved animal survival as a result of cytarabine pretreatment is discussed.

  1. Genome-Wide Discriminatory Information Patterns of Cytosine DNA Methylation

    Science.gov (United States)

    Sanchez, Robersy; Mackenzie, Sally A.

    2016-01-01

    Cytosine DNA methylation (CDM) is a highly abundant, heritable but reversible chemical modification to the genome. Herein, a machine learning approach was applied to analyze the accumulation of epigenetic marks in methylomes of 152 ecotypes and 85 silencing mutants of Arabidopsis thaliana. In an information-thermodynamics framework, two measurements were used: (1) the amount of information gained/lost with the CDM changes IR and (2) the uncertainty of not observing a SNP LCR. We hypothesize that epigenetic marks are chromosomal footprints accounting for different ontogenetic and phylogenetic histories of individual populations. A machine learning approach is proposed to verify this hypothesis. Results support the hypothesis by the existence of discriminatory information (DI) patterns of CDM able to discriminate between individuals and between individual subpopulations. The statistical analyses revealed a strong association between the topologies of the structured population of Arabidopsis ecotypes based on IR and on LCR, respectively. A statistical-physical relationship between IR and LCR was also found. Results to date imply that the genome-wide distribution of CDM changes is not only part of the biological signal created by the methylation regulatory machinery, but ensures the stability of the DNA molecule, preserving the integrity of the genetic message under continuous stress from thermal fluctuations in the cell environment. PMID:27322251

  2. Genome-Wide Discriminatory Information Patterns of Cytosine DNA Methylation.

    Science.gov (United States)

    Sanchez, Robersy; Mackenzie, Sally A

    2016-01-01

    Cytosine DNA methylation (CDM) is a highly abundant, heritable but reversible chemical modification to the genome. Herein, a machine learning approach was applied to analyze the accumulation of epigenetic marks in methylomes of 152 ecotypes and 85 silencing mutants of Arabidopsis thaliana. In an information-thermodynamics framework, two measurements were used: (1) the amount of information gained/lost with the CDM changes I R and (2) the uncertainty of not observing a SNP L C R . We hypothesize that epigenetic marks are chromosomal footprints accounting for different ontogenetic and phylogenetic histories of individual populations. A machine learning approach is proposed to verify this hypothesis. Results support the hypothesis by the existence of discriminatory information (DI) patterns of CDM able to discriminate between individuals and between individual subpopulations. The statistical analyses revealed a strong association between the topologies of the structured population of Arabidopsis ecotypes based on I R and on LCR, respectively. A statistical-physical relationship between I R and L C R was also found. Results to date imply that the genome-wide distribution of CDM changes is not only part of the biological signal created by the methylation regulatory machinery, but ensures the stability of the DNA molecule, preserving the integrity of the genetic message under continuous stress from thermal fluctuations in the cell environment. PMID:27322251

  3. Cytosine modifications after gamma irradiation in aerated aqueous solution of Escherichia coli DNA

    International Nuclear Information System (INIS)

    After gamma irradiation of cytosine in aerated aqueous solution and utilization of various spectrometric methods (mass spectrometry, proton nuclear magnetic resonance and infrared spectrometry) about ten new radiolysis products were identified. The formation of N-glycolylbiuret in H218O aqueous solution of irradiated cytosine at pH 4,5 indicated that the preferred 18OH hydroxyl radical attack was at C-5. The formation of trans 1-carbamoyl-4,5 dihydroxyimidazolidin-2 oxo which is the major product after cytosine pyrimidine ring rearrangement took place preferentially at neutral pH, while N-glycolylbiuret predominated at pH 4,5. The deamination pathway was predominant when cytosine was irradiated at acidic pH values (pH2) or in copper complexes. The development of a new acid hydrolysis method using fluorhydric acid stabilized in pyridine made easier the evaluation of cytosine modifications after gamma irradiation in aerated aqueous solution of E. Coli DNA-14C-2 cytosine. This hydrolytic agent removed the modified bases from the polynucleotidic chain. A difference was found between the proportion of radiolytic products removed by acid hydrolysis and by irradiation of the free base in solution

  4. Computation of Isobaric Vapor-Liquid Equilibrium Data for Binary and Ternary Mixtures of Methanol, Water, and Ethanoic Acid from T, p, x, and HmE Measurements

    Directory of Open Access Journals (Sweden)

    Daming Gao

    2012-01-01

    Full Text Available Vapor-liquid equilibrium (VLE data for the strongly associated ternary system methanol + water + ethanoic acid and the three constituent binary systems have been determined by the total pressure-temperature-liquid-phase composition-molar excess enthalpy of mixing of the liquid phase (p, T, x, HmE for the binary systems using a novel pump ebulliometer at 101.325 kPa. The vapor-phase compositions of these binary systems had been calculated from Tpx and HmE based on the Q function of molar excess Gibbs energy through an indirect method. Moreover, the experimental T, x data are used to estimate nonrandom two-liquid (NRTL, Wilson, Margules, and van Laar model parameters, and these parameters in turn are used to calculate vapor-phase compositions. The activity coefficients of the solution were correlated with NRTL, Wilson, Margules, and van Laar models through fitting by least-squares method. The VLE data of the ternary system were well predicted from these binary interaction parameters of NRTL, Wilson, Margules, and van Laar model parameters without any additional adjustment to build the thermodynamic model of VLE for the ternary system and obtain the vapor-phase compositions and the calculated bubble points.

  5. Crystal structure of bis-(tri-ethano-lamine-κ(3) N,O,O')nickel(II) bis-(3-hy-droxy-benzoate) tetra-hydrate.

    Science.gov (United States)

    Ibragimov, Aziz B

    2016-05-01

    The reaction of 3-hy-droxy-benzoic (m-hy-droxy-benzoic) acid (MHBA), tri-ethano-lamine (TEA) and Ni(NO3)2 in aqueous solution led to formation of the hydrated title salt, [Ni(C6H15NO3)2](C7H5O3)·4H2O. In the complex cation, the Ni(2+) ion is located on an inversion centre. Two symmetry-related TEA ligands occupy all coordination sites in an N,O,O'-tridentate coordination, leading to a slightly distorted NiN2O4 octa-hedron. Two ethanol groups of each TEA ligand form two five-membered chelate rings around Ni(2+), while the third ethanol group does not coordinate to the metal atom. Two MHBA(-) anions in the benzoate form are situated in the outer coordination sphere for charge compensation. An intricate network of hydrogen bonds between the free and coordinating hy-droxy groups of the TEA ligands, the O atoms of the MHBA(-) anions and the water mol-ecules leads to the formation of a two-dimensional structure extending parallel to (010). PMID:27308009

  6. Solid-phase molecular recognition of cytosine based on proton-transfer reaction. Part II. supramolecular architecture in the cocrystals of cytosine and its 5-Fluoroderivative with 5-Nitrouracil

    OpenAIRE

    Portalone Gustavo

    2011-01-01

    Abstract Background Cytosine is a biologically important compound owing to its natural occurrence as a component of nucleic acids. Cytosine plays a crucial role in DNA/RNA base pairing, through several hydrogen-bonding patterns, and controls the essential features of life as it is involved in genetic codon of 17 amino acids. The molecular recognition among cytosines, and the molecular heterosynthons of molecular salts fabricated through proton-transfer reactions, might be used to investigate ...

  7. A computational study of adenine, uracil, and cytosine adsorption upon AlN and BN nano-cages

    International Nuclear Information System (INIS)

    Density-functional theory calculations are used to investigate the interaction of Al12N12 and B12N12 clusters with the adenine (A), uracil (U), and cytosine (C) molecules. The current calculations demonstrate that these hybrid adsorbent materials are able to adsorb the adenine, uracil, and cytosine molecules through exothermic processes. Our theoretical results reveal improvement in the adsorption of adenine, uracil, and cytosine on Al12N12 and B12N12. It is observed that B12N12 is highly sensitive to adenine, uracil, and cytosine compared with Al12N12 to serve as a biochemical sensor.

  8. Single-Cell Quantification of Cytosine Modifications by Hyperspectral Dark-Field Imaging.

    Science.gov (United States)

    Wang, Xiaolei; Cui, Yi; Irudayaraj, Joseph

    2015-12-22

    Epigenetic modifications on DNA, especially on cytosine, play a critical role in regulating gene expression and genome stability. It is known that the levels of different cytosine derivatives are highly dynamic and are regulated by a variety of factors that act on the chromatin. Here we report an optical methodology based on hyperspectral dark-field imaging (HSDFI) using plasmonic nanoprobes to quantify the recently identified cytosine modifications on DNA in single cells. Gold (Au) and silver (Ag) nanoparticles (NPs) functionalized with specific antibodies were used as contrast-generating agents due to their strong local surface plasmon resonance (LSPR) properties. With this powerful platform we have revealed the spatial distribution and quantity of 5-carboxylcytosine (5caC) at the different stages in cell cycle and demonstrated that 5caC was a stably inherited epigenetic mark. We have also shown that the regional density of 5caC on a single chromosome can be mapped due to the spectral sensitivity of the nanoprobes in relation to the interparticle distance. Notably, HSDFI enables an efficient removal of the scattering noises from nonspecifically aggregated nanoprobes, to improve accuracy in the quantification of different cytosine modifications in single cells. Further, by separating the LSPR fingerprints of AuNPs and AgNPs, multiplex detection of two cytosine modifications was also performed. Our results demonstrate HSDFI as a versatile platform for spatial and spectroscopic characterization of plasmonic nanoprobe-labeled nuclear targets at the single-cell level for quantitative epigenetic screening. PMID:26505210

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-06-01

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

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

    International Nuclear Information System (INIS)

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

  11. HPLC-UV, MALDI-TOF-MS and ESI-MS/MS analysis of the mechlorethamine DNA crosslink at a cytosine-cytosine mismatch pair.

    Directory of Open Access Journals (Sweden)

    Pornchai Rojsitthisak

    Full Text Available BACKGROUND: Mechlorethamine [ClCH(2CH(2N(CH(3CH(2CH(2Cl], a nitrogen mustard alkylating agent, has been proven to form a DNA interstrand crosslink at a cytosine-cytosine (C-C mismatch pair using gel electrophoresis. However, the atomic connectivity of this unusual crosslink is unknown. METHODOLOGY/PRINCIPAL FINDINGS: HPLC-UV, MALDI-TOF-MS, and ESI-MS/MS were used to determine the atomic connectivity of the DNA C-C crosslink formed by mechlorethamine, MALDI-TOF-MS of the HPLC-purified reaction product of mechlorethamine with the DNA duplex d[CTCACACCGTGGTTC]•d[GAACCACCGTGTGAG] (underlined bases are a C-C mismatch pair indicated formation of an interstrand crosslink at m/z 9222.088 [M-2H+Na](+. Following enzymatic digestion of the crosslinked duplex by snake venom phosphodiesterase and calf intestinal phosphatase, ESI-MS/MS indicated the presence of dC-mech-dC [mech = CH(2CH(2N(CH(3CH(2CH(2] at m/z 269.2 [M](2+ (expected m/z 269.6, exact mass 539.27 and its hydrolytic product dC-mech-OH at m/z 329.6 [M](+ (expected m/z 329.2. Fragmentation of dC-mech-dC gave product ions at m/z 294.3 and 236.9 [M](+, which are both due to loss of the 4-amino group of cytosine (as ammonia, in addition to dC and dC+HN(CH(3CH = CH(2, respectively. The presence of m/z 269.2 [M](2+ and loss of ammonia exclude crosslink formation at cytosine N(4 or O(2 and indicate crosslinking through cytosine N(3 with formation of two quaternary ammonium ions. CONCLUSIONS: Our results provide an important addition to the literature, as the first example of the use of HPLC and MS for analysis of a DNA adduct at the N(3 position of cytosine.

  12. AID enzymatic activity is inversely proportional to the size of cytosine C5 orbital cloud.

    Directory of Open Access Journals (Sweden)

    Gopinath Rangam

    Full Text Available Activation induced deaminase (AID deaminates cytosine to uracil, which is required for a functional humoral immune system. Previous work demonstrated, that AID also deaminates 5-methylcytosine (5 mC. Recently, a novel vertebrate modification (5-hydroxymethylcytosine - 5 hmC has been implicated in functioning in epigenetic reprogramming, yet no molecular pathway explaining the removal of 5 hmC has been identified. AID has been suggested to deaminate 5 hmC, with the 5 hmU product being repaired by base excision repair pathways back to cytosine. Here we demonstrate that AID's enzymatic activity is inversely proportional to the electron cloud size of C5-cytosine - H > F > methyl >> hydroxymethyl. This makes AID an unlikely candidate to be part of 5 hmC removal.

  13. Cytosine deamination and the precipitous decline of spontaneous mutation during Earth's history.

    Science.gov (United States)

    Lewis, Charles A; Crayle, Jesse; Zhou, Shuntai; Swanstrom, Ronald; Wolfenden, Richard

    2016-07-19

    The hydrolytic deamination of cytosine and 5-methylcytosine residues in DNA appears to contribute significantly to the appearance of spontaneous mutations in microorganisms and in human disease. In the present work, we examined the mechanism of cytosine deamination and the response of the uncatalyzed reaction to changing temperature. The positively charged 1,3-dimethylcytosinium ion was hydrolyzed at a rate similar to the rate of acid-catalyzed hydrolysis of 1-methylcytosine, for which it furnishes a satisfactory kinetic model and a probable mechanism. In agreement with earlier reports, uncatalyzed deamination was found to proceed at very similar rates for cytosine, 1-methylcytosine, cytidine, and cytidine 5'-phosphate, and also for cytosine residues in single-stranded DNA generated from a phagemid, in which we sequenced an insert representing the gene of the HIV-1 protease. Arrhenius plots for the uncatalyzed deamination of cytosine were linear over the temperature range from 90 °C to 200 °C and indicated a heat of activation (ΔH(‡)) of 23.4 ± 0.5 kcal/mol at pH 7. Recent evidence indicates that the surface of the earth has been cool enough to support life for more than 4 billion years and that life has been present for almost as long. If the temperature at Earth's surface is assumed to have followed Newton's law of cooling, declining exponentially from 100 °C to 25 °C during that period, then half of the cytosine-deaminating events per unit biomass would have taken place during the first 0.2 billion years, and <99.4% would have occurred during the first 2 billion years. PMID:27382162

  14. Ionization of cytosine monomer and dimer studied by VUV photoionization and electronic structure calculations

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-12-14

    We report a combined theoretical and experimental study of ionization of cytosine monomers and dimers. Gas-phase molecules are generated by thermal vaporization of cytosine followed by expansion of the vapor in a continuous supersonic jet seeded in Ar. The resulting species are investigated by single photon ionization with tunable vacuum-ultraviolet (VUV) synchrotron radiation and mass analyzed using reflectron mass spectrometry. Energy onsets for the measured photoionization efficiency (PIE) spectra are 8.60+-0.05 eV and 7.6+-0.1 eV for the monomer and the dimer, respectively, and provide an estimate for the adiabatic ionization energies (AIE). The first AIE and the ten lowest vertical ionization energies (VIEs) for selected isomers of cytosine dimer computed using equation-of-motion coupled-cluster (EOM-IP-CCSD) method are reported. The comparison of the computed VIEs with the derivative of the PIE spectra, suggests that multiple isomers of the cytosine dimer are present in the molecular beam. The calculations reveal that the large red shift (0.7 eV) of the first IE of the lowest-energy cytosine dimer is due to strong inter-fragment electrostatic interactions, i.e., the hole localized on one of the fragments is stabilized by the dipole moment of the other. A sharp rise in the CH+ signal at 9.20+-0.05 eV is ascribed to the formation of protonated cytosine by dissociation of the ionized dimers. The dominant role of this channel is supported by the computed energy thresholds for the CH+ appearance and the barrierless or nearly barrierless ionization-induced proton transfer observed for five isomers of the dimer.

  15. Anomalous reaction of oxide radical ion (O) with 1, 3, 5-triazine analogue of cytosine

    International Nuclear Information System (INIS)

    The reaction of O with 1, 3, 5-triazine analogue of cytosine viz. 5-azacytosine has been studied using the pulse radiolysis technique. On addition (k2 = 1.9x109 dm3 mol-1 s-1) of O followed by the protonation of the adduct system has been proposed, and this anomalous reaction is supported by quantum chemical calculations. (author)

  16. Cytosine methylation of an ancient satellite family in the wild beet Beta procumbens.

    Science.gov (United States)

    Schmidt, Martin; Hense, Sarah; Minoche, André E; Dohm, Juliane C; Himmelbauer, Heinz; Schmidt, Thomas; Zakrzewski, Falk

    2014-01-01

    DNA methylation is an essential epigenetic feature for the regulation and maintenance of heterochromatin. Satellite DNA is a repetitive sequence component that often occurs in large arrays in heterochromatin of subtelomeric, intercalary and centromeric regions. Knowledge about the methylation status of satellite DNA is important for understanding the role of repetitive DNA in heterochromatization. In this study, we investigated the cytosine methylation of the ancient satellite family pEV in the wild beet Beta procumbens. The pEV satellite is widespread in species-specific pEV subfamilies in the genus Beta and most likely originated before the radiation of the Betoideae and Chenopodioideae. In B. procumbens, the pEV subfamily occurs abundantly and spans intercalary and centromeric regions. To uncover its cytosine methylation, we performed chromosome-wide immunostaining and bisulfite sequencing of pEV satellite repeats. We found that CG and CHG sites are highly methylated while CHH sites show only low levels of methylation. As a consequence of the low frequency of CG and CHG sites and the preferential occurrence of most cytosines in the CHH motif in pEV monomers, this satellite family displays only low levels of total cytosine methylation. PMID:24994030

  17. Effect of pH and substituents on the two-dimensional condensation of cytosine

    Czech Academy of Sciences Publication Activity Database

    span class="emphasis">Ignác, Janspan>; span class="emphasis">Vetterl, Vladimírspan>

    Spa , 2004. s. 48. [International Conference on Electrified Interfaces 2004. 11.07.2004-16.07.2004, Spa ] R&D Projects: GA AV ČR IBS5004107; GA MŠk ME 685 Keywords : cytosine * mercury electrode surface * 5-methylcytosine Subject RIV: BO - Biophysics

  18. The role of gene body cytosine modifications in MGMT expression and sensitivity to temozolomide

    Science.gov (United States)

    Moen, Erika L.; Stark, Amy L.; Zhang, Wei; Dolan, M. Eileen; Godley, Lucy A.

    2014-01-01

    The DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) is known to play a role in sensitivity to temozolomide. Promoter hypermethylation of MGMT is commonly used to predict low expression levels of MGMT in gliomas, despite observed discordance between promoter methylation and protein levels. Here, we investigated the functional role of gene body cytosine modification in regulating levels of MGMT gene expression and sensitivity to temozolomide. In 91 human glioblastoma samples, we observed significant variation in MGMT expression levels in patients with an unmethylated promoter, with higher levels of gene body cytosine modification correlating with higher gene expression levels. Furthermore, inducing hypomethylation across the MGMT gene body with decitabine corresponded with decreased levels of MGMT gene expression in lymphoblastoid and glioblastoma cell lines, indicating an important functional role for gene body cytosine modifications in maintaining gene expression. We reasoned that the decrease in MGMT expression induced by decitabine may render resistant glioblastoma cell lines more sensitive to temozolomide. Consistent with this reasoning, we found that the MGMT-expressing glioblastoma cell lines exhibiting an unmethylated MGMT promoter that were pre-treated with decitabine became significantly more sensitive to temozolomide. Overall, our results suggest a functional role for gene body cytosine modification in regulating gene expression of MGMT and indicate that pre-treating patients whose tumors have an unmethylated MGMT promoter with decitabine prior to temozolomide treatment may increase their response to therapy. PMID:24568970

  19. Cytosine methylation alteration in natural populations of Leymus chinensis induced by multiple abiotic stresses.

    Directory of Open Access Journals (Sweden)

    Yingjie Yu

    Full Text Available BACKGROUND: Human activity has a profound effect on the global environment and caused frequent occurrence of climatic fluctuations. To survive, plants need to adapt to the changing environmental conditions through altering their morphological and physiological traits. One known mechanism for phenotypic innovation to be achieved is environment-induced rapid yet inheritable epigenetic changes. Therefore, the use of molecular techniques to address the epigenetic mechanisms underpinning stress adaptation in plants is an important and challenging topic in biological research. In this study, we investigated the impact of warming, nitrogen (N addition, and warming+nitrogen (N addition stresses on the cytosine methylation status of Leymus chinensis Tzvel. at the population level by using the amplified fragment length polymorphism (AFLP, methylation-sensitive amplified polymorphism (MSAP and retrotransposon based sequence-specific amplification polymorphism (SSAP techniques. METHODOLOGY/PRINCIPAL FINDINGS: Our results showed that, although the percentages of cytosine methylation changes in SSAP are significantly higher than those in MSAP, all the treatment groups showed similar alteration patterns of hypermethylation and hypomethylation. It meant that the abiotic stresses have induced the alterations in cytosine methylation patterns, and the levels of cytosine methylation changes around the transposable element are higher than the other genomic regions. In addition, the identification and analysis of differentially methylated loci (DML indicated that the abiotic stresses have also caused targeted methylation changes at specific loci and these DML might have contributed to the capability of plants in adaptation to the abiotic stresses. CONCLUSIONS/SIGNIFICANCE: Our results demonstrated that abiotic stresses related to global warming and nitrogen deposition readily evoke alterations of cytosine methylation, and which may provide a molecular basis for rapid

  20. Clinical implications of cytosine deletion of exon 5 of P53 gene in non small cell lung cancer patients

    Directory of Open Access Journals (Sweden)

    Rashid Mir

    2016-01-01

    Full Text Available Aim: Lung cancer is considered to be the most common cancer in the world. In humans, about 50% or more cancers have a mutated tumor suppressor p53 gene thereby resulting in accumulation of p53 protein and losing its function to activate the target genes that regulate the cell cycle and apoptosis. Extensive research conducted in murine cancer models with activated p53, loss of p53, or p53 missense mutations have facilitated researchers to understand the role of this key protein. Our study was aimed to evaluate the frequency of cytosine deletion in nonsmall cell lung cancer (NSCLC patients. Methods: One hundred NSCLC patients were genotyped for P53 (exon5, codon168 cytosine deletion leading to loss of its function and activate the target genes by allele-specific polymerase chain reaction. The P53 cytosine deletion was correlated with all the clinicopathological parameters of the patients. Results and Analysis: 59% cases were carrying P53 cytosine deletion. Similarly, the significantly higher incidence of cytosine deletion was reported in current smokers (75% in comparison to exsmoker and nonsmoker. Significantly higher frequency of cytosine deletion was reported in adenocarcinoma (68.08% than squamous cell carcinoma (52.83%. Also, a significant difference was reported between p53 cytosine deletion and metastasis (64.28%. Further, the majority of the cases assessed for response carrying P53 cytosine deletion were found to show faster disease progression. Conclusion: The data suggests that there is a significant association of the P53 exon 5 deletion of cytosine in codon 168 with metastasis and staging of the disease.

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

    NARCIS (Netherlands)

    LaRowe, D.E.; Regnier, P.

    2008-01-01

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

  2. Flexible double-headed cytosine-linked 2'-deoxycytidine nucleotides. Synthesis, polymerase incorporation to DNA and interaction with DNA methyltransferases.

    Science.gov (United States)

    Kielkowski, Pavel; Cahová, Hana; Pohl, Radek; Hocek, Michal

    2016-03-15

    New types of double-headed 2'-deoxycytidine 5'-O-triphosphates (dC(XC)TPs) bearing another cytosine or 5-fluorocytosine linked through a flexible propargyl, homopropargyl or pent-1-ynyl linker to position 5 were prepared by the aqueous Sonogashira cross-coupling reactions of 5-iodo-dCTP with the corresponding (fluoro)cytosine-alkynes. The modified dC(XC)TPs were good substrates for DNA polymerases and were used for enzymatic synthesis of cytosine-functionalized DNA by primer extension or PCR. The cytosine- or fluorocytosine-linked DNA probes did not significantly inhibit DNA methyltransferases and did not cross-link to these proteins. PMID:26899597

  3. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

    OpenAIRE

    Briggs, A; Stenzel, U.; Meyer, M; Krause, J.; Kircher, M. (Manfred); Pääbo, S

    2010-01-01

    DNA sequences determined from ancient organisms have high error rates, primarily due to uracil bases created by cytosine deamination. We use synthetic oligonucleotides, as well as DNA extracted from mammoth and Neandertal remains, to show that treatment with uracil–DNA–glycosylase and endonuclease VIII removes uracil residues from ancient DNA and repairs most of the resulting abasic sites, leaving undamaged parts of the DNA fragments intact. Neandertal DNA sequences determined with this proto...

  4. The role of gene body cytosine modifications in MGMT expression and sensitivity to temozolomide

    OpenAIRE

    Moen, Erika L.; Stark, Amy L.; Zhang, Wei; Dolan, M. Eileen; Godley, Lucy A.

    2014-01-01

    The DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) is known to play a role in sensitivity to temozolomide. Promoter hypermethylation of MGMT is commonly used to predict low expression levels of MGMT in gliomas, despite observed discordance between promoter methylation and protein levels. Here, we investigated the functional role of gene body cytosine modification in regulating levels of MGMT gene expression and sensitivity to temozolomide. In 91 human glioblastoma samples, w...

  5. O2 Protonation Controls Threshold Behavior for N-Glycosidic Bond Cleavage of Protonated Cytosine Nucleosides.

    Science.gov (United States)

    Wu, R R; Rodgers, M T

    2016-06-01

    IRMPD action spectroscopy studies of protonated 2'-deoxycytidine and cytidine, [dCyd+H](+) and [Cyd+H](+), have established that both N3 and O2 protonated conformers coexist in the gas phase. Threshold collision-induced dissociation (CID) of [dCyd+H](+) and [Cyd+H](+) is investigated here using guided ion beam tandem mass spectrometry techniques to elucidate the mechanisms and energetics for N-glycosidic bond cleavage. N-Glycosidic bond cleavage is observed as the major dissociation pathways resulting in competitive elimination of either protonated or neutral cytosine for both protonated cytosine nucleosides. Electronic structure calculations are performed to map the potential energy surfaces (PESs) for both N-glycosidic bond cleavage pathways observed. The molecular parameters derived from theoretical calculations are employed for thermochemical analysis of the energy-dependent CID data to determine the minimum energies required to cleave the N-glycosidic bond along each pathway. B3LYP and MP2(full) computed activation energies for N-glycosidic bond cleavage associated with elimination of protonated and neutral cytosine, respectively, are compared to measured values to evaluate the efficacy of these theoretical methods in describing the dissociation mechanisms and PESs for N-glycosidic bond cleavage. The 2'-hydroxyl of [Cyd+H](+) is found to enhance the stability of the N-glycosidic bond vs that of [dCyd+H](+). O2 protonation is found to control the threshold energies for N-glycosidic bond cleavage as loss of neutral cytosine from the O2 protonated conformers is found to require ∼25 kJ/mol less energy than the N3 protonated analogues, and the activation energies and reaction enthalpies computed using B3LYP exhibit excellent agreement with the measured thresholds for the O2 protonated conformers. PMID:27159774

  6. The role of cytosine methylation on charge transport through a DNA strand

    International Nuclear Information System (INIS)

    Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit

  7. The role of cytosine methylation on charge transport through a DNA strand

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Jianqing, E-mail: jqqi@uw.edu; Anantram, M. P., E-mail: anantmp@uw.edu [Department of Electrical Engineering, University of Washington, Seattle, Washington 98195-2500 (United States); Govind, Niranjan, E-mail: niri.govind@pnnl.gov [William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)

    2015-09-07

    Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.

  8. The role of cytosine methylation on charge transport through a DNA strand

    Science.gov (United States)

    Qi, Jianqing; Govind, Niranjan; Anantram, M. P.

    2015-09-01

    Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Büttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter-strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchange-correlation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.

  9. The Role of Cytosine Methylation on Charge Transport through a DNA Strand

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Jianqing [Univ. of Washington, Seattle, WA (United States); Govind, Niranjan [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Anantram, M. P. [Univ. of Washington, Seattle, WA (United States)

    2015-09-04

    Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modifi-cation remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Buttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. Specifically, we compare the results generated with the widely used B3LYP exchange-correlation (XC) functional and CAM-B3LYP based tuned range-separated hybrid density functional. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that with both functionals, the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and interstrand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital (HOMO) level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with both functionals. We also study the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit. Our results suggest that the effect of the two different functionals is to alter the on-site energies of the DNA bases at the HOMO level, while the transport properties don't depend much on the two

  10. Specific and Modular Binding Code for Cytosine Recognition in Pumilio/FBF (PUF) RNA-binding Domains*♦

    OpenAIRE

    Dong, Shuyun; Wang, Yang; Cassidy-Amstutz, Caleb; Lu, Gang; Bigler, Rebecca; Jezyk, Mark R.; Li, Chunhua; Hall, Traci M. Tanaka; Wang, Zefeng

    2011-01-01

    Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificit...

  11. Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants.

    OpenAIRE

    Woodcock, D M; Crowther, P J; Doherty, J; Jefferson, S; DeCruz, E; Noyer-Weidner, M; Smith, S S; Michael, M Z; Graham, M W

    1989-01-01

    Many strains of E. coli K12 restrict DNA containing cytosine methylation such as that present in plant and animal genomes. Such restriction can severely inhibit the efficiency of cloning genomic DNAs. We have quantitatively evaluated a total of 39 E. coli strains for their tolerance to cytosine methylation in phage and plasmid cloning systems. Quantitative estimations of relative tolerance to methylation for these strains are presented, together with the evaluation of the most promising strai...

  12. Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands.

    Science.gov (United States)

    Schreiber, Jacob; Wescoe, Zachary L; Abu-Shumays, Robin; Vivian, John T; Baatar, Baldandorj; Karplus, Kevin; Akeson, Mark

    2013-11-19

    Cytosine, 5-methylcytosine, and 5-hydroxymethylcytosine were identified during translocation of single DNA template strands through a modified Mycobacterium smegmatis porin A (M2MspA) nanopore under control of phi29 DNA polymerase. This identification was based on three consecutive ionic current states that correspond to passage of modified or unmodified CG dinucleotides and their immediate neighbors through the nanopore limiting aperture. To establish quality scores for these calls, we examined ~3,300 translocation events for 48 distinct DNA constructs. Each experiment analyzed a mixture of cytosine-, 5-methylcytosine-, and 5-hydroxymethylcytosine-bearing DNA strands that contained a marker that independently established the correct cytosine methylation status at the target CG of each molecule tested. To calculate error rates for these calls, we established decision boundaries using a variety of machine-learning methods. These error rates depended upon the identity of the bases immediately 5' and 3' of the targeted CG dinucleotide, and ranged from 1.7% to 12.2% for a single-pass read. We estimate that Q40 values (0.01% error rates) for methylation status calls could be achieved by reading single molecules 5-19 times depending upon sequence context. PMID:24167260

  13. Protonation/deprotonation processes of primary products in x-irradiated cytosine derivatives: EPR and ENDOR studies at 10 K

    International Nuclear Information System (INIS)

    Recently, evidence has accumulated that cytosine is the initial electron trap in irradiated DNA. It has previously been observed that the protonation/deprotonation mechanisms and sites of the pristine purine/pyrimidine electron gain and loss centers depend upon the matrix. Local variations as e.g. water of crystallization, hydrogen bond pattern, initial protonation state of the cytosine bases, and associated counter ions may be important in the selection of reaction pathways following the initial ionization event. In response to this increased interest in the primary radical production in irradiated cytosine, five different crystalline cytosine derivatives have been investigated at 10 K following X-irradiation exposure to doses between 0.8 and 30 kGy. The techniques used are K-band EPR, ENDOR, and ENDOR-induced EPR (FSE) spectroscopy. The systems studied are: cytosine monohydrate (Cm); cytosine-HCI (C:HCl); cytidine (CR); deoxycytidine:HCI (CdR:HCl); and 2'-deoxycytidine 5'-monophosphate (5'dCMP)

  14. Cytosine hypomethylation at CHG and CHH sites in the pleiotropic mutants of Mendelian inheritance in Catharanthus roseus.

    Science.gov (United States)

    Kumari, Renu; Yadav, Gitanjali; Sharma, Vishakha; Sharma, Vinay; Kumar, Sushil

    2013-12-01

    The 5S and 18S rDNA sequences of Catharanthus roseus cv 'Nirmal' (wild type) and its leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill) single mutants and lli egd, lli ill and egd ill double mutants were characterized. The lli, egd and ill mutants of Mendelian inheritance bore the names after their most conspicuous morphological feature(s). They had been chemically induced and isolated for their salt tolerance. The double mutants were isolated as morphological segregants from crosses between single mutants. The morphological features of the two parents accompanied salt tolerance in the double mutants. All the six mutants were hypomethylated at repeat sequences, upregulated and downregulated for many genes and carried pleiotropic alterations for several traits. Here the 5S and 18S rDNAs of C. roseus were found to be relatively low in cytosine content. Cytosines were preponderantly in CG context (53%) and almost all of them were methylated (97%). The cytosines in CHH and CHG (where H = A, T or C) contexts were largely demethylated (92%) in mutants. The demethylation was attributable to reduced expression of RDR2 and DRM2 led RNA dependant DNA methylation and CMT3 led maintenance methylation pathways. Mutants had gained some cytosines by substitution of C at T sites. These perhaps arose on account of errors in DNA replication, mediated by widespread cytosine demethylation at CHG and CHH sites. It was concluded that the regulation of cytosine ethylation mechanisms was disturbed in the mutants. ILL, EGD and LLI genes were identified as the positive regulators of other genes mediating the RdDM and CMT3 pathways, for establishment and maintenance of cytosine methylation in C. roseus. PMID:24371171

  15. Cytosine hypomethylation at CHG and CHH sites in the pleiotropic mutants of Mendelian inheritance in Catharanthus roseus

    Indian Academy of Sciences (India)

    Renu Kumari; Gitanjali Yadav; Vishakha Sharma; Vinay Sharma; Sushil Kumar

    2013-12-01

    The 5S and 18S rDNA sequences of Catharanthus roseus cv ‘Nirmal’ (wild type) and its leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill) single mutants and lli egd, lli ill and egd ill double mutants were characterized. The lli, egd and ill mutants of Mendelian inheritance bore the names after their most conspicuous morphological feature(s). They had been chemically induced and isolated for their salt tolerance. The double mutants were isolated as morphological segregants from crosses between single mutants. The morphological features of the two parents accompanied salt tolerance in the double mutants. All the six mutants were hypomethylated at repeat sequences, upregulated and downregulated for many genes and carried pleiotropic alterations for several traits. Here the 5S and 18S rDNAs of C. roseus were found to be relatively low in cytosine content. Cytosines were preponderantly in CG context (53%) and almost all of them were methylated (97%). The cytosines in CHH and CHG (where H = A, T or C) contexts were largely demethylated (92%) in mutants. The demethylation was attributable to reduced expression of RDR2 and DRM2 led RNA dependant DNA methylation and CMT3 led maintenance methylation pathways. Mutants had gained some cytosines by substitution of C at T sites. These perhaps arose on account of errors in DNA replication, mediated by widespread cytosine demethylation at CHG and CHH sites. It was concluded that the regulation of cytosine methylation mechanisms was disturbed in the mutants. ILL, EGD and LLI genes were identified as the positive regulators of other genes mediating the RdDM and CMT3 pathways, for establishment and maintenance of cytosine methylation in C. roseus.

  16. Specific and modular binding code for cytosine recognition in Pumilio/FBF (PUF) RNA-binding domains.

    Science.gov (United States)

    Dong, Shuyun; Wang, Yang; Cassidy-Amstutz, Caleb; Lu, Gang; Bigler, Rebecca; Jezyk, Mark R; Li, Chunhua; Hall, Traci M Tanaka; Wang, Zefeng

    2011-07-29

    Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and the cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence. PMID:21653694

  17. Specific and Modular Binding Code for Cytosine Recognition in Pumilio/FBF (PUF) RNA-binding Domains

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Shuyun; Wang, Yang; Cassidy-Amstutz, Caleb; Lu, Gang; Bigler, Rebecca; Jezyk, Mark R.; Li, Chunhua; Tanaka Hall, Traci M.; Wang, Zefeng (NIH); (Beijing U); (UNC)

    2011-10-28

    Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and the cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence.

  18. Specific and Modular Binding Code for Cytosine Recognition in Pumilio/FBF (PUF) RNA-binding Domains*♦

    Science.gov (United States)

    Dong, Shuyun; Wang, Yang; Cassidy-Amstutz, Caleb; Lu, Gang; Bigler, Rebecca; Jezyk, Mark R.; Li, Chunhua; Hall, Traci M. Tanaka; Wang, Zefeng

    2011-01-01

    Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and the cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence. PMID:21653694

  19. Solvent effect on the anharmonic vibrational frequencies in guanine-cytosine base pair

    Science.gov (United States)

    Bende, A.; Muntean, C. M.

    2012-02-01

    We present an ab initio study of the vibrational properties of cytosine and guanine in the Watson-Crick and Hoogsteen base pair configurations. The results are obtained by considering the DFT method together with the Polarizable Continuum Model (PCM) using PBE and B3PW91 exchange-correlation functionals and triple-ζ valence basis set. We investigate the importance of anharmonic corrections for the vibrational modes taking into account the solvent effect of the water environment. In particular, the unusual anharmonic effect of the H+ vibration in the case of the Hoogsteen base pair configuration is discussed.

  20. Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine

    Directory of Open Access Journals (Sweden)

    Mahdi Bagherpoor Helabad

    2014-07-01

    Full Text Available Distortions in the DNA sequence, such as damage or mispairs, are specifically recognized and processed by DNA repair enzymes. Many repair proteins and, in particular, glycosylases flip the target base out of the DNA helix into the enzyme’s active site. Our molecular dynamics simulations of DNA with intact and damaged (oxidized methyl-cytosine show that the probability of being flipped is similar for damaged and intact methyl-cytosine. However, the accessibility of the different 5-methyl groups allows direct discrimination of the oxidized forms. Hydrogen-bonded patterns that vary between methyl-cytosine forms carrying a carbonyl oxygen atom are likely to be detected by the repair enzymes and may thus help target site recognition.

  1. H. atom and OH. radical reactions with 5-methyl-cytosine

    International Nuclear Information System (INIS)

    The reactions between either a hydrogen atom or a hydroxyl radical and 5-methyl-cytosine (5-MeCyt) are studied by using the hybrid kinetic energy meta-GGA functional MPW1B95. H. atom and OH. radical addition to positions C5 and C6 of 5-MeCyt, or OH. radical induced H-abstraction from the C5 methyl group, are explored. All systems are optimized in bulk solvent. The data presented show that the barriers to reaction are very low: ca. 7 kCal/mol for the H. atom additions and 1 kCal/mol for the reactions involving the OH. radical. Thermodynamically, the two C6 radical adducts and the H.- abstraction product are the most stable ones. The proton hyperfine coupling constants (HFCC), computed at the IEFPCM/MPW1B95/6-311++G(2d,2p) level, agree well with B3LYP results and available experimental and theoretical data on related thymine and cytosine radicals. (authors)

  2. Cytosine methylation does not affect binding of transcription factor Sp1

    International Nuclear Information System (INIS)

    DNA methylation may be a component of a multilevel control mechanism that regulates eukaryotic gene expression. The authors used synthetic oligonucleotides to investigate the effect of cytosine methylation on the binding of the transcription factor Sp1 to its target sequence (a G+C-rich sequence known as a GC box). Concatemers of double-stranded 14-mers containing a GC box successfully competed with the human metallothionein IIA promoter for binding to Sp1 in DNase I protection experiments. The presence of 5-methylcytosine in the CpG sequence of the GC box did not influence Sp1 binding. The result was confirmed using double-stranded 20-mers containing 16 base pairs of complementary sequence. Electrophoretic gel retardation analysis of annealed 28-mers containing a GC box incubated with an Sp1-containing HeLa cell nuclear extract demonstrated the formation of DNA-protein complexes; formation of these complexes was not inhibited when an oligomer without a GC box was used as a competitor. Once again, the presence of a 5-methylcytosine residue in the GC box did not influence the binding of the protein to DNA. The results therefore preclude a direct effect of cytosine methylation on Sp1-DNA interactions

  3. Crystal structure of bis­(tri­ethano­lamine-κ3 N,O,O′)nickel(II) bis­(3-hy­droxy­benzoate) tetra­hydrate

    Science.gov (United States)

    Ibragimov, Aziz B.

    2016-01-01

    The reaction of 3-hy­droxy­benzoic (m-hy­droxy­benzoic) acid (MHBA), tri­ethano­lamine (TEA) and Ni(NO3)2 in aqueous solution led to formation of the hydrated title salt, [Ni(C6H15NO3)2](C7H5O3)·4H2O. In the complex cation, the Ni2+ ion is located on an inversion centre. Two symmetry-related TEA ligands occupy all coordination sites in an N,O,O′-tridentate coordination, leading to a slightly distorted NiN2O4 octa­hedron. Two ethanol groups of each TEA ligand form two five-membered chelate rings around Ni2+, while the third ethanol group does not coordinate to the metal atom. Two MHBA− anions in the benzoate form are situated in the outer coordination sphere for charge compensation. An intricate network of hydrogen bonds between the free and coordinating hy­droxy groups of the TEA ligands, the O atoms of the MHBA− anions and the water mol­ecules leads to the formation of a two-dimensional structure extending parallel to (010). PMID:27308009

  4. Solid-phase molecular recognition of cytosine based on proton-transfer reaction. Part II. supramolecular architecture in the cocrystals of cytosine and its 5-Fluoroderivative with 5-Nitrouracil

    Directory of Open Access Journals (Sweden)

    Portalone Gustavo

    2011-09-01

    Full Text Available Abstract Background Cytosine is a biologically important compound owing to its natural occurrence as a component of nucleic acids. Cytosine plays a crucial role in DNA/RNA base pairing, through several hydrogen-bonding patterns, and controls the essential features of life as it is involved in genetic codon of 17 amino acids. The molecular recognition among cytosines, and the molecular heterosynthons of molecular salts fabricated through proton-transfer reactions, might be used to investigate the theoretical sites of cytosine-specific DNA-binding proteins and the design for molecular imprint. Results Reaction of cytosine (Cyt and 5-fluorocytosine (5Fcyt with 5-nitrouracil (Nit in aqueous solution yielded two new products, which have been characterized by single-crystal X-ray diffraction. The products include a dihydrated molecular salt (CytNit having both ionic and neutral hydrogen-bonded species, and a dihydrated cocrystal of neutral species (5FcytNit. In CytNit a protonated and an unprotonated cytosine form a triply hydrogen-bonded aggregate in a self-recognition ion-pair complex, and this dimer is then hydrogen bonded to one neutral and one anionic 5-nitrouracil molecule. In 5FcytNit the two neutral nucleobase derivatives are hydrogen bonded in pairs. In both structures conventional N-H...O, O-H...O, N-H+...N and N-H...N- intermolecular interactions are most significant in the structural assembly. Conclusion The supramolecular structure of the molecular adducts formed by cytosine and 5-fluorocytosine with 5-nitrouracil, CytNit and 5FcytNit, respectively, have been investigated in detail. CytNit and 5FcytNit exhibit widely differing hydrogen-bonding patterns, though both possess layered structures. The crystal structures of CytNit (Dpka = -0.7, molecular salt and 5FcytNit (Dpka = -2.0, cocrystal confirm that, at the present level of knowledge about the nature of proton-transfer process, there is not a strict correlation between the Dpka values

  5. Assembly of two-dimensional DNA crystals carrying N 4-[2-(tert- butyldisulfanyl)ethyl]cytosine residues

    OpenAIRE

    Eritja Casadellà, Ramón; Garibotti, Alejandra V.; Sisquella, Xavier; Martínez, Elena

    2009-01-01

    DNA Lattices carrying two cytosine residues bearing the N 4-[(tert-butyldisulfanyl)ethyl] group at the apex of hairpin topological markers are prepared for first time. We show that these residues are important for the deposition of DNA lattices on gold surfaces.

  6. Thermodynamic potential for the abiotic synthesis of Adenine, Cytosine, Guanine, Thymine, Uracil, Ribose, and Deoxyribose in hydrothermal systems

    OpenAIRE

    Larowe, D. E.; Regnier, P.

    2008-01-01

    The thermodynamic potential for the abiotic synthesis of the five common nucleobases (adenine, cytosine, guanine, thymine, and uracil) and two monosaccharides (ribose and deoxyribose) from formaldehyde and hydrogen cyanide has been quantified under temperature, pressure, and bulk composition conditions that are representative of hydrothermal systems. The activities of the precursor molecules (formaldehyde and hydrogen cyanide) required to evaluate the thermodynamics of biomolecule synthesis w...

  7. Mutation Processes in 293-Based Clones Overexpressing the DNA Cytosine Deaminase APOBEC3B.

    Directory of Open Access Journals (Sweden)

    Monica K Akre

    Full Text Available Molecular, cellular, and clinical studies have combined to demonstrate a contribution from the DNA cytosine deaminase APOBEC3B (A3B to the overall mutation load in breast, head/neck, lung, bladder, cervical, ovarian, and other cancer types. However, the complete landscape of mutations attributable to this enzyme has yet to be determined in a controlled human cell system. We report a conditional and isogenic system for A3B induction, genomic DNA deamination, and mutagenesis. Human 293-derived cells were engineered to express doxycycline-inducible A3B-eGFP or eGFP constructs. Cells were subjected to 10 rounds of A3B-eGFP exposure that each caused 80-90% cell death. Control pools were subjected to parallel rounds of non-toxic eGFP exposure, and dilutions were done each round to mimic A3B-eGFP induced population fluctuations. Targeted sequencing of portions of TP53 and MYC demonstrated greater mutation accumulation in the A3B-eGFP exposed pools. Clones were generated and microarray analyses were used to identify those with the greatest number of SNP alterations for whole genome sequencing. A3B-eGFP exposed clones showed global increases in C-to-T transition mutations, enrichments for cytosine mutations within A3B-preferred trinucleotide motifs, and more copy number aberrations. Surprisingly, both control and A3B-eGFP clones also elicited strong mutator phenotypes characteristic of defective mismatch repair. Despite this additional mutational process, the 293-based system characterized here still yielded a genome-wide view of A3B-catalyzed mutagenesis in human cells and a system for additional studies on the compounded effects of simultaneous mutation mechanisms in cancer cells.

  8. Biophysical and molecular docking insight into the interaction of cytosine β-D arabinofuranoside with human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Alam, Parvez; Chaturvedi, Sumit Kumar [Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP (India); Anwar, Tamanna [Center of Bioinformatics Research and Technology, Aligarh 202002 (India); Siddiqi, Mohammad Khursheed; Ajmal, Mohd Rehan [Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP (India); Badr, Gamal [Laboratory of Immunology & Molecular Physiology, Zoology Department, Faculty of Science, Assiut University, 71516 Assiut (Egypt); Mahmoud, Mohamed H. [Food Science and Nutrition Department, National Research Center, Dokki, Cairo (Egypt); Deanship of Scientific Research, King Saud University, Riyadh (Saudi Arabia); Hasan Khan, Rizwan, E-mail: rizwanhkhan@hotmail.com [Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP (India)

    2015-08-15

    Interaction of pharmacologically important anticancer drug cytosine β-D arabinofuranoside with human serum albumin (HSA) at physiological pH 7.4 has been studied by utilizing various spectroscopic and molecular docking strategies. Fluorescence results revealed that cytosine β-D arabinofuranoside interacts with HSA through static quenching mechanism with binding affinity of 2.4×10{sup 3} M{sup −1}. The average binding distance between drug and Trp{sup 214} of HSA was found to be 2.23 nm on the basis of the theory of Förster's energy transfer. Synchronous fluorescence data indicated that interaction of drug with HSA changed the microenvironment around the tryptophan residue. UV–visible spectroscopy and circular dichroism results deciphered the complex formation and conformational alterations in the HSA respectively. Dynamic light scattering was utilized to understand the topology of protein in absence and presence of drug. Thermodynamic parameters obtained from isothermal titration calorimetry (ΔH=−26.01 kJ mol{sup −1} and TΔS=6.5 kJ mol{sup −1}) suggested the involvement of van der Waal interaction and hydrogen bonding. Molecular docking and displacement study with site specific markers suggested that cytosine β-D arabinofuranoside binds to subdomain IB of HSA which is also known as the hemin binding site. This study will be helpful to understand the binding mechanism of cytosine β-D arabinofuranoside with HSA and associated alterations. - Highlights: • Comprehensive insight into the interaction of CBDA with HSA. • The interaction process is spontaneous and exothermic. • The main governing forces for stabilizing HSA–CBDA complex are van der Waal interaction and hydrogen bonding. • CBDA binds at subdomain IB on HSA.

  9. Genome-wide identification and comparative analysis of cytosine-5 DNA methyltransferases and demethylase families in wild and cultivated peanut

    Directory of Open Access Journals (Sweden)

    Pengfei eWang

    2016-02-01

    Full Text Available AbstractDNA methylation plays important roles in genome protection, regulation of gene expression and was associated with plants development. Plant DNA methylation pattern was mediated by cytosine-5 DNA methyltransferases and demethylase. Although the genomes of AA and BB wild peanuts have been fully sequence, these two gene families have not been studied. In this study we report the identification and analysis of putative cytosine-5 DNA methyltransferases (C5-MTases and demethylase in AA and BB wild peanuts. Cytosine-5 DNA methyltransferases in AA and BB wild peanuts could be classified in known MET, CMT and DRM2 groups based on their domain organization. This result was supported by the gene and protein structural characteristics and phylogenetic analysis. We found that some wild peanut DRM2 numbers didn’t contain UBA domain which was different from other plants such as Arabidopsis, maize, soybean. Five DNA demethylase were found in AA genome and five in BB genome. The selective pressure analysis showed that wild peanut C5-MTases gene mainly underwent purifying selection but many positive selection sites can be detected. Conversely, DNA demethylase genes mainly underwent positive selection during evolution. Additionally, the expression dynamic of cytosine-5 DNA methyltransferases and demethylase genes in different cultivated peanut tissues were analyzed. Expression result showed that cold, heat or drought stress could influence the expression level of C5-MTases and DNA demethylase genes in cultivated peanut. These results are useful for better understanding the complexity of these two gene families, and will facilitate epigenetic studies in peanut.

  10. Biophysical and molecular docking insight into the interaction of cytosine β-D arabinofuranoside with human serum albumin

    International Nuclear Information System (INIS)

    Interaction of pharmacologically important anticancer drug cytosine β-D arabinofuranoside with human serum albumin (HSA) at physiological pH 7.4 has been studied by utilizing various spectroscopic and molecular docking strategies. Fluorescence results revealed that cytosine β-D arabinofuranoside interacts with HSA through static quenching mechanism with binding affinity of 2.4×103 M−1. The average binding distance between drug and Trp214 of HSA was found to be 2.23 nm on the basis of the theory of Förster's energy transfer. Synchronous fluorescence data indicated that interaction of drug with HSA changed the microenvironment around the tryptophan residue. UV–visible spectroscopy and circular dichroism results deciphered the complex formation and conformational alterations in the HSA respectively. Dynamic light scattering was utilized to understand the topology of protein in absence and presence of drug. Thermodynamic parameters obtained from isothermal titration calorimetry (ΔH=−26.01 kJ mol−1 and TΔS=6.5 kJ mol−1) suggested the involvement of van der Waal interaction and hydrogen bonding. Molecular docking and displacement study with site specific markers suggested that cytosine β-D arabinofuranoside binds to subdomain IB of HSA which is also known as the hemin binding site. This study will be helpful to understand the binding mechanism of cytosine β-D arabinofuranoside with HSA and associated alterations. - Highlights: • Comprehensive insight into the interaction of CBDA with HSA. • The interaction process is spontaneous and exothermic. • The main governing forces for stabilizing HSA–CBDA complex are van der Waal interaction and hydrogen bonding. • CBDA binds at subdomain IB on HSA

  11. Depletion of neural stem cells from the subventricular zone of adult mouse brain using cytosine b‐Arabinofuranoside

    OpenAIRE

    Ghanbari, Amir; Esmaeilpour, Tahereh; Bahmanpour, Soghra; Golmohammadi, Mohammad Ghasem; Sharififar, Sharareh; Azari, Hassan

    2015-01-01

    Abstract Introduction Neural stem cells (NSCs) reside along the ventricular axis of the mammalian brain. They divide infrequently to maintain themselves and the down‐stream progenitors. Due to the quiescent property of NSCs, attempts to deplete these cells using antimitotic agents such as cytosine b‐Aarabinofuranoside (Ara‐C) have not been successful. We hypothesized that implementing infusion gaps in Ara‐C kill paradigms would recruit the quiescent NSCs and subsequently eliminate them from t...

  12. Nitrous acid damage to duplex deoxyribonucleic acid: distinction between deamination of cytosine residues and a novel mutational lesion.

    OpenAIRE

    Frankel, A D; Duncan, B K; Hartman, P E

    1980-01-01

    The rate of nitrous acid deamination of labeled cytosine residues in native Escherichia coli deoxyribonucleic acid was monitored in vitro by release of acid-soluble counts after treatment with uracil deoxyribonucleic acid glycosylase. The reaction exhibited a lag and was not stimulate by several agents previously shown to enhance base substitution mutagenesis during nitrous acid treatment of duplex deoxyribonucleic acid. We conclude that a significant proportion of nitrous acid induced mutage...

  13. Faithful inheritance of cytosine methylation patterns in repeated sequences of the allotetraploid tobacco correlates with the expression of DNA methyltransferase gene families from both parental genomes

    Czech Academy of Sciences Publication Activity Database

    Fulneček, Jaroslav; Matyášek, Roman; Kovařík, Aleš

    2009-01-01

    Roč. 281, č. 4 (2009), s. 407-420. ISSN 1617-4615 R&D Projects: GA ČR(CZ) GA204/06/1432; GA ČR(CZ) GA521/07/0116 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : cytosine methylation * DNA (cytosine-5) methyltransferase * allopolyploidy Subject RIV: BO - Biophysics Impact factor: 2.579, year: 2009

  14. Patterns of Cytosine Methylation in Parental Lines and Their Hybrids of Large White and Meishan Reciprocal Crosses

    Institute of Scientific and Technical Information of China (English)

    JIANG Cao-de; DENG Chang-yan; XIONG Yuan-zhu

    2004-01-01

    The extent and patterns of cytosine methylation in blood DNA were assessed, using the technique of methylation-sensitive amplified polymorphism(MSAP),in Meishan, Large White pigs and hybrids of their reciprocal crosses. In all, 1 508 fragments, each representing a recognition site cleaved by either or both of the isoschizomers, MspI and HpaII, were amplified using 20 pairs of selective primers. 10.3% of CCGG sites were methylated in Meishan pigs, 10.5% in Large White pigs, and 10.2% in the hybrids. Cytosine methylation was not significantly different among parental lines and hybrids of reciprocal crosses. Four classes of patterns were identified in a comparative assay of cytosine methylation in the parents and hybrids: (1) the same level of methylation in both parental lines and the hybrids; (2) the same level of methylation in either parent or hybrid; (3) an increased level of methylation in the hybrids compared to the parents, and (4) a decreased level of methylation in the hybrids. 11 crossspecific methylation sites were detected in F1 hybrids of Large White×Meishan, and 10 crossspecific methylation sites in the hybrid of Meishan×LargeWhite. In conclusion, (1) the whole methylation status between parental lines and hybrids was not different, but specific sites were differentially methylated; (2) specific sites were differentially methylated between reciprocal crosses; (3) demethylation and hypermethylation of many sites accounted for mostly (more than 50%) methylated sites in the hybrids compared to parental lines.

  15. Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair

    Science.gov (United States)

    Dumat, Blaise; Larsen, Anders Foller; Wilhelmsson, L. Marcus

    2016-01-01

    Herein, we report on the use of a tricyclic cytosine FRET pair, incorporated into DNA with different base pair separations, to study Z-DNA and B-Z DNA junctions. With its position inside the DNA structure, the FRET pair responds to a B- to Z-DNA transition with a distinct change in FRET efficiency for each donor/acceptor configuration allowing reliable structural probing. Moreover, we show how fluorescence spectroscopy and our cytosine analogues can be used to determine rate constants for the B- to Z-DNA transition mechanism. The modified cytosines have little influence on the transition and the FRET pair is thus an easily implemented and virtually non-perturbing fluorescence tool to study Z-DNA. This nucleobase analogue FRET pair represents a valuable addition to the limited number of fluorescence methods available to study Z-DNA and we suggest it will facilitate, for example, deciphering the B- to Z-DNA transition mechanism and investigating the interaction of DNA with Z-DNA binding proteins. PMID:26896804

  16. Variation in cytosine methylation patterns during ploidy level conversions in Eragrostis curvula.

    Science.gov (United States)

    Ochogavía, Ana C; Cervigni, Gerardo; Selva, Juan P; Echenique, Viviana C; Pessino, Silvina C

    2009-05-01

    In many species polyploidization involves rearrangements of the progenitor genomes, at both genetic and epigenetic levels. We analyzed the cytosine methylation status in a 'tetraploid-diploid-tetraploid' series of Eragrostis curvula with a common genetic background by using the MSAP (Methylation-sensitive Amplified Polymorphism) technique. Considerable levels of polymorphisms were detected during ploidy conversions. The total level of methylation observed was lower in the diploid genotype compared to the tetraploid ones. A significant proportion of the epigenetic modifications occurring during the tetraploid-diploid conversion reverted during the diploid-tetraploid one. Genetic and expression data from previous work were used to analyze correlation with methylation variation. All genetic, epigenetic and gene expression variation data correlated significantly when compared by pairs in simple Mantel tests. Dendrograms reflecting genetic, epigenetic and expression distances as well as principal coordinate analysis suggested that plants of identical ploidy levels present similar sets of data. Twelve (12) different genomic fragments displaying different methylation behavior during the ploidy conversions were isolated, sequenced and characterized. PMID:19160057

  17. Effects of intrathecal methotrexate and cytosine arabinoside on the radiation tolerance of the rat spinal cord

    International Nuclear Information System (INIS)

    The effect of intrathecally or intravenously administered methotrexate (MTX) or cytosine arabinoside (ara-C) on the early and late delayed radiation response of the rat cervical spinal cord has been studied. A technique has been developed for intrathecal administration of drugs into the rat lumbar spinal canal. When given shortly before irradiation, intrathecal ara-C significantly reduces the isoeffect doses for the early delayed white matter necrosis syndrome by a factor of 1.2-1.3, while no effect is observed for the late delayed vascular syndrome. The effect disappears when ara-C is given intravenously or 24 h after irradiation. At a maximally tolerated intrathecal MTX dose, no modification of the early or late radiation response of the spinal cord was observed. In constrast to ara-C, intravenous MTX seems to interact with the induction of the late delayed vascular damage in the rat cervical spinal cord, with a dose-modifying factor of 1.1-1.2. (Auth.)

  18. Effects of cytosine methylation on DNA morphology: An atomic force microscopy study.

    Science.gov (United States)

    Cassina, V; Manghi, M; Salerno, D; Tempestini, A; Iadarola, V; Nardo, L; Brioschi, S; Mantegazza, F

    2016-01-01

    Methylation is one of the most important epigenetic mechanisms in eukaryotes. As a consequence of cytosine methylation, the binding of proteins that are implicated in transcription to gene promoters is severely hindered, which results in gene regulation and, eventually, gene silencing. To date, the mechanisms by which methylation biases the binding affinities of proteins to DNA are not fully understood; however, it has been proposed that changes in double-strand conformations, such as stretching, bending, and over-twisting, as well as local variations in DNA stiffness/flexibility may play a role. The present work investigates, at the single molecule level, the morphological consequences of DNA methylation in vitro. By tracking the atomic force microscopy images of single DNA molecules, we characterize DNA conformations pertaining to two different degrees of methylation. In particular, we observe that methylation induces no relevant variations in DNA contour lengths, but produces measurable incremental changes in persistence lengths. Furthermore, we observe that for the methylated chains, the statistical distribution of angles along the DNA coordinate length is characterized by a double exponential decay, in agreement with what is predicted for polyelectrolytes. The results reported herein support the claim that the biological consequences of the methylation process, specifically difficulties in protein-DNA binding, are at least partially due to DNA conformation modifications. PMID:26475643

  19. A quantum chemical insight to intermolecular hydrogen bonding interaction between cytosine and nitrosamine: Structural and energetic investigations

    Science.gov (United States)

    Khalili, Behzad

    2016-03-01

    Hydrogen bond interactions which are formed during complex formation between cytosine and nitrosamine have been fully investigated using B3LYP, B3PW91 and MP2 methods in conjunction with various basis sets including 6-311++G (d,p), 6-311++G (2d,2p), 6-311++G (df,pd) and AUG-cc-pVDZ. Three regions around the most stable conformer of cytosine in the gas phase with six possible double H-bonded interactions were considered. Two intermolecular hydrogen bonds of type NC-N-HNA and O-H(N-H)C-ONA were found on the potential energy surface in a cyclic system with 8-member in CN1, CN3, CN5 and 7-member in CN2, CN4, CN6 systems. Results of binding energy calculation at all applied methods reveal that the CN1 structure is the most stable one which is formed by interaction of nitrosamine with cytosine in S1 region. The BSSE-corrected binding energy for six complex system is ranging from -23.8 to -43.6 kJ/mol at MP2/6-311++G (df,pd) level and the stability order is as CN1 > CN2 > CN3 > CN4 > CN5 > CN6 in all studied levels of theories. The NBO results reveal that the charge transfer occurred from cytosine to nitrosamine in CN1, CN3, CN5 and CN6 whereas this matter in the case of CN2 and CN4 was reversed. The relationship between BEs with red shift of H-bond involved bonds vibrational frequencies, charge transfer energies during complex formation and electron densities at H-bond BCPs were discussed. In addition activation energetic properties related to the proton transfer process between cytosine and nitrosamine have been calculated at MP2/6-311++G (df,pd) level. AIM results imply that H-bond interactions are electrostatic with partially covalent characteristic in nature.

  20. Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice

    Directory of Open Access Journals (Sweden)

    Pang Jinsong

    2009-07-01

    Full Text Available Abstract Background mPing is an endogenous MITE in the rice genome, which is quiescent under normal conditions but can be induced towards mobilization under various stresses. The cellular mechanism responsible for modulating the activity of mPing remains unknown. Cytosine methylation is a major epigenetic modification in most eukaryotes, and the primary function of which is to serve as a genome defense system including taming activity of transposable elements (TEs. Given that tissue-culture is capable of inducing both methylation alteration and mPing transposition in certain rice genotypes, it provides a tractable system to investigate the possible relationship between the two phenomena. Results mPing transposition and cytosine methylation alteration were measured in callus and regenerated plants in three rice (ssp. indica genotypes, V14, V27 and R09. All three genotypes showed transposition of mPing, though at various frequencies. Cytosine methylation alteration occurred both at the mPing-flanks and at random loci sampled globally in callus and regenerated plants of all three genotypes. However, a sharp difference in the changing patterns was noted between the mPing-flanks and random genomic loci, with a particular type of methylation modification, i.e., CNG hypermethylation, occurred predominantly at the mPing-flanks. Pearson's test on pairwise correlations indicated that mPing activity is positively correlated with specific patterns of methylation alteration at random genomic loci, while the element's immobility is positively correlated with methylation levels of the mPing's 5'-flanks. Bisulfite sequencing of two mPing-containing loci showed that whereas for the immobile locus loss of CG methylation in the 5'-flank was accompanied by an increase in CHG methylation, together with an overall increase in methylation of all three types (CG, CHG and CHH in the mPing-body region, for the active locus erasure of CG methylation in the 5'-flank was

  1. Cytosine Deaminase/5-Fluorocytosine Exposure Induces Bystander and Radiosensitization Effects in Hypoxic Glioblastoma Cells in vitro

    International Nuclear Information System (INIS)

    Purpose: Treatment of glioblastoma (GBM) is limited by therapeutic ratio; therefore, successful therapy must be specifically cytotoxic to cancer cells. Hypoxic cells are ubiquitous in GBM, and resistant to radiation and chemotherapy, and, thus, are logical targets for gene therapy. In this study, we investigated whether cytosine deaminase (CD)/5-fluorocytosine (5-FC) enzyme/prodrug treatment induced a bystander effect (BE) and/or radiosensitization in hypoxic GBM cells. Methods and Materials: We stably transfected cells with a gene construct consisting of the SV40 minimal promoter, nine copies of a hypoxia-responsive element, and the yeast CD gene. During hypoxia, a hypoxia-responsive element regulates expression of the CD gene and facilitates the conversion of 5-FC to 5-fluorouracil, a highly toxic antimetabolite. We used colony-forming efficiency (CFE) and immunofluorescence assays to assess for BE in co-cultures of CD-expressing clone cells and parent, pNeo- or green fluorescent protein-stably transfected GBM cells. We also investigated the radiosensitivity of CD clone cells treated with 5-FC under hypoxic conditions, and we used flow cytometry to investigate treatment-induced cell cycle changes. Results: Both a large BE and radiosensitization occurred in GBM cells under hypoxic conditions. The magnitude of the BE depended on the number of transfected cells producing CD, the functionality of the CD, the administered concentration of 5-FC, and the sensitivity of cell type to 5-fluorouracil. Conclusion: Hypoxia-inducible CD/5-FC therapy in combination with radiation therapy shows both a pronounced BE and a radiosensitizing effect under hypoxic conditions

  2. Cytosine arabinoside enhancement of gamma irradiation induced mutations in human T-lymphocytes

    International Nuclear Information System (INIS)

    The frequency of 6-thioguanine resistant (TGr) mutants induced in human G0 phase T-lymphocytes by 200 cGy of gamma irradiation is greatly enhanced by incubation with cytosine arabinoside (ara-C) after irradiation. The mutant frequency increased with increasing incubation time in ara-C for up to 2 hr. This mutation induction required a phenotypic expression time of 5-8 days mass culture growth, similar to that found with mutants induced by 300 cGy of irradiation alone. Southern blot analysis of 40 isolated mutant clones revealed 8 independent mutations by T-cell receptor (TCR) gene rearrangement patterns. Four of these eight showed hprt gene structural alterations (0.50). An alternative method to allow phenotypic expression was developed to minimize the isolation of hprt/TCR sibling mutants. The use of in situ expression in the microtiter dish wells resulted in the isolation of 17 independent mutations in 19 mutant clones. Ten of these 17 mutations showed hprt structural alterations (0.59). The high fraction of mutations involving structural alterations detected by Southern blot analysis is consistent with the known induction of chromosome aberrations by irradiation plus ara-C treatment. We propose that both the increase in Mf and the increase in the incidence of hprt gene structural alterations are due to the accumulation of strand breaks in repairing regions of DNA under these conditions of ara-C induced inhibition of repair. We further propose that upon release of the ara-C inhibition, these repairing regions can interact to yield both gene mutations and chromosome aberrations

  3. Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae).

    Science.gov (United States)

    Hegarty, Matthew J; Batstone, Tom; Barker, Gary L; Edwards, Keith J; Abbott, Richard J; Hiscock, Simon J

    2011-01-01

    The merger of two or more divergent genomes within an allopolyploid nucleus can facilitate speciation and adaptive evolution in flowering plants. Widespread changes to gene expression have been shown to result from interspecific hybridisation and polyploidy in a number of plant species, and attention has now shifted to determining the epigenetic processes that drive these changes. We present here an analysis of cytosine methylation patterns in triploid F(1) Senecio (ragwort) hybrids and their allohexaploid derivatives. We observe that, in common with similar studies in Arabidopsis, Spartina and Triticum, a small but significant proportion of loci display nonadditive methylation in the hybrids, largely resulting from interspecific hybridisation. Despite this, genome duplication results in a secondary effect on methylation, with reversion to additivity at some loci and novel methylation status at others. We also observe differences in methylation state between different allopolyploid generations, predominantly in cases of additive methylation with regard to which parental methylation state is dominant. These changes to methylation state in both F(1) triploids and their allohexaploid derivatives largely mirror the overall patterns of nonadditive gene expression observed in our previous microarray analyses and may play a causative role in generating those expression changes. These similar global changes to DNA methylation resulting from hybridisation and genome duplication may serve as a source of epigenetic variation in natural populations, facilitating adaptive evolution. Our observations that methylation state can also vary between different generations of polyploid hybrids suggests that newly formed allopolyploid species may display a high degree of epigenetic diversity upon which natural selection can act. PMID:21073590

  4. Effect of C5-Methylation of Cytosine on the UV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors.

    Science.gov (United States)

    Banyasz, Akos; Esposito, Luciana; Douki, Thierry; Perron, Marion; Lepori, Clément; Improta, Roberto; Markovitsi, Dimitra

    2016-05-12

    C5-methylation of cytosines is strongly correlated with UV-induced mutations detected in skin cancers. Mutational hot-spots appearing at TCG sites are due to the formation of pyrimidine cyclobutane dimers (CPDs). The present study, performed for the model DNA duplex (TCGTA)3·(TACGA)3 and the constitutive single strands, examines the factors underlying the effect of C5-methylation on pyrimidine dimerization at TCG sites. This effect is quantified for the first time by quantum yields ϕ. They were determined following irradiation at 255, 267, and 282 nm and subsequent photoproduct analysis using HPLC coupled to mass spectrometry. C5-methylation leads to an increase of the CPD quantum yield up to 80% with concomitant decrease of that of pyrimidine(6-4) pyrimidone adducts (64PPs) by at least a factor of 3. The obtained ϕ values cannot be explained only by the change of the cytosine absorption spectrum upon C5-methylation. The conformational and electronic factors that may affect the dimerization reaction are discussed in light of results obtained by fluorescence spectroscopy, molecular dynamics simulations, and quantum mechanical calculations. Thus, it appears that the presence of an extra methyl on cytosine affects the sugar puckering, thereby enhancing conformations of the TC step that are prone to CPD formation but less favorable to 64PPs. In addition, C5-methylation diminishes the amplitude of conformational motions in duplexes; in the resulting stiffer structure, ππ* excitations may be transferred from initially populated exciton states to reactive pyrimidines giving rise to CPDs. PMID:27075054

  5. Spatial and Functional Relationships Among Pol V-Associated loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome

    Energy Technology Data Exchange (ETDEWEB)

    Wierzbicki, A. T.; Cocklin, Ross; Mayampurath, Anoop; Lister, Ryan; Rowley, M. J.; Gregory, Brian D.; Ecker, Joseph R.; Tang, Haixu; Pikaard, Craig S.

    2012-08-15

    Multisubunit RNA polymerases IV and V (Pols IV and V) mediate RNA-directed DNA methylation and transcriptional silencing of retrotransposons and heterochromatic repeats in plants. We identified genomic sites of Pol V occupancy in parallel with siRNA deep sequencing and methylcytosine mapping, comparing wild-type plants with mutants defective for Pol IV, Pol V, or both Pols IV and V. Approximately 60% of Pol V-associated regions encompass regions of 24-nucleotide (nt) siRNA complementarity and cytosine methylation, consistent with cytosine methylation being guided by base-pairing of Pol IV-dependent siRNAs with Pol V transcripts. However, 27% of Pol V peaks do not overlap sites of 24-nt siRNA biogenesis or cytosine methylation, indicating that Pol V alone does not specify sites of cytosine methylation. Surprisingly, the number of methylated CHH motifs, a hallmark of RNA-directed de novo methylation, is similar in wild-type plants and Pol IV or Pol V mutants. In the mutants, methylation is lost at 50%-60% of the CHH sites that are methylated in the wild type but is gained at new CHH positions, primarily in pericentromeric regions. These results indicate that Pol IV and Pol V are not required for cytosine methyltransferase activity but shape the epigenome by guiding CHH methylation to specific genomic sites.

  6. The inhibition of DNA repair by aphidicolin or cytosine arabinoside in X-irradiated normal and xeroderma pigmentosum fibroblasts

    International Nuclear Information System (INIS)

    Normal and excision-deficient xeroderma pigmentosum fibroblasts were X-irradiated and the influence on DNA repair of either the repair inhibitor cytosine arabinoside or the specific inhibitor of DNA polymerase α, aphidicolin, investigated. The data indicated that the repair of a certain fraction of X-ray-induced lesions can be inhibited in both cell lines by both compounds. Thus, as aphidicolin blocks the operation of polymerase α, this enzyme must be involved in an excision repair pathway operating in both normal and excision-deficient xeroderma pigmentosum cells. (orig.)

  7. Inhibition of DNA repair by aphidicolin or cytosine arabinoside in X-irradiated normal and xeroderma pigmentosum fibroblasts

    Energy Technology Data Exchange (ETDEWEB)

    Waters, R.; Crocombe, K.; Mirzayans, R. (University Coll. of Swansea (UK). Dept. of Genetics)

    1981-01-01

    Normal and excision-deficient xeroderma pigmentosum fibroblasts were X-irradiated and the influence on DNA repair of either the repair inhibitor cytosine arabinoside or the specific inhibitor of DNA polymerase ..cap alpha.., aphidicolin, investigated. The data indicated that the repair of a certain fraction of X-ray-induced lesions can be inhibited in both cell lines by both compounds. Thus, as aphidicolin blocks the operation of polymerase ..cap alpha.., this enzyme must be involved in an excision repair pathway operating in both normal and excision-deficient xeroderma pigmentosum cells.

  8. The inhibition of DNA repair by aphidicolin or cytosine arabinoside in X-irradiated normal and xeroderma pigmentosum fibroblasts.

    Science.gov (United States)

    Waters, R; Crocombe, K; Mirzayans, R

    1982-05-01

    Normal and excision-deficient xeroderma pigmentosum fibroblasts were X-irradiated and the influence on DNA repair of either the repair inhibitor cytosine arabinoside or the specific inhibitor of Dna polymerase alpha, aphidicolin, investigated. The data indicated that the repair of a certain fraction of X-ray-induced lesions can be inhibited in both cell lines by both compounds. Thus, as aphidicolin blocks the operation of polymerase alpha, this enzyme must be involved in an excision repair pathway operating in both normal and excision-deficient xeroderma pigmentosum cells. PMID:6808389

  9. Clofarabine and high-dose cytosine arabinoside in the treatment of refractory or relapsed acute myeloid leukaemia

    OpenAIRE

    Tse, Eric; Anskar Y. H. Leung; Sim, Joycelyn; Lee, Harold K.K.; Liu, Herman S. Y.; Yip, Sze-Fai; Kwong, Yok-Lam

    2011-01-01

    Clofarabine (40 mg/m 2/day×5) and high-dose cytosine arabinoside (Ara-C, 1-2 g/m 2/day×5) were used in 10 men and 11 women, at a median age of 45 (22-62) years, with refractory (N=4) and relapsed (N=17) acute myeloid leukaemia, after a median of 3 (2-5) prior regimens. Grade 4 myelosuppression was observed in all cases, with two patients dying of bacterial sepsis. Nine patients achieved a complete remission. Disease status, number of prior therapies, and cytogenetic aberrations were not assoc...

  10. Pulsed magnetic field from video display terminals enhances teratogenic effects of cytosine arabinoside in mice

    Energy Technology Data Exchange (ETDEWEB)

    Chiang, H.; Wu, R.Y.; Shao, B.J.; Fu, Y.D.; Yao, G.D.; Lu, D.J. [Zhejiang Medical Univ. (China)

    1995-05-01

    Eighty-nine Swiss Webster mice were randomly divided into four groups: a control group, a pulsed magnetic field (PMF) group, a cytosine arabinoside (ara-C, a teratogen) group, and a combined PMF + ara-C group. Mice in the PMF and PMF + ara-C groups were irradiated with a PMF (a sawtooth waveform with 52 {mu}s rise time, 12{mu}s decay time, and 15.6 kHz frequency) at a peak magnetic flux density of 40 {mu}T for 4 hours daily on days 6-17 of gestation. The mice in the ara-C and the PMF + ara-C groups were injected intraperitoneally on day 9 of gestation with 10 mg/kg of ara-C. The incidence of resorption and dead fetuses was not affected by PMF but was increased by ara-C injection. The malformation incidence of cleft palate (CP) and/or cleft lip (CL) was significantly higher in all three of the treated groups than in the control group (P < 0.05). If, however, statistical analyses had been done on litters rather than on individual fetuses, they would show that the incidence of CP and/or CL in the PMF group is not significantly greater than that in the control group. A significantly higher incidence of CP and/or CL was found in the PMF + ara-C group (49%) than the ara-C alone group (26.1%). These data suggest that PMF might enhance the development of ara-C-induced CP and/or CL. The incidence of minor variations in skeletal development, including reduction of skeletal calcification and loss of skeleton, was not statistically significant in the PMF group. However, it was higher in the two ara-C-treated groups, and there was no significant difference between the ara-C alone group and the ara-C + PMF group. From these results it is concluded that the very weak embryotoxic effects of PMF exposure may be revealed and enhanced in combination with a teratogenic agent.

  11. Cytosines, but not purines, determine recombination activating gene (RAG)-induced breaks on heteroduplex DNA structures: implications for genomic instability.

    Science.gov (United States)

    Naik, Abani Kanta; Lieber, Michael R; Raghavan, Sathees C

    2010-03-01

    The sequence specificity of the recombination activating gene (RAG) complex during V(D)J recombination has been well studied. RAGs can also act as structure-specific nuclease; however, little is known about the mechanism of its action. Here, we show that in addition to DNA structure, sequence dictates the pattern and efficiency of RAG cleavage on altered DNA structures. Cytosine nucleotides are preferentially nicked by RAGs when present at single-stranded regions of heteroduplex DNA. Although unpaired thymine nucleotides are also nicked, the efficiency is many fold weaker. Induction of single- or double-strand breaks by RAGs depends on the position of cytosines and whether it is present on one or both of the strands. Interestingly, RAGs are unable to induce breaks when adenine or guanine nucleotides are present at single-strand regions. The nucleotide present immediately next to the bubble sequence could also affect RAG cleavage. Hence, we propose "C((d))C((S))C((S))" (d, double-stranded; s, single-stranded) as a consensus sequence for RAG-induced breaks at single-/double-strand DNA transitions. Such a consensus sequence motif is useful for explaining RAG cleavage on other types of DNA structures described in the literature. Therefore, the mechanism of RAG cleavage described here could explain facets of chromosomal rearrangements specific to lymphoid tissues leading to genomic instability. PMID:20051517

  12. The effects of tautomerization and protonation on the adenine-cytosine mismatches: a density functional theory study.

    Science.gov (United States)

    Masoodi, Hamid Reza; Bagheri, Sotoodeh; Abareghi, Mahsa

    2016-06-01

    In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine-cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs. PMID:26198186

  13. N4-methylation of cytosine drastically favors the formation of (6-4) photoproducts in a TCG context.

    Science.gov (United States)

    Douki, Thierry; Meador, Jarah A; Bérard, Izabel; Wack, Aude

    2015-01-01

    Methylation of cytosine is a common biological process both in prokaryotic and eukaryotic cells. In addition to 5-methylcytosine (5mC), some bacterial species contain in their genome N(4) -methylcytosine (N4mC). Methylation at C5 has been shown to enhance the formation of pyrimidine dimeric photoproducts but nothing is known of the effect of N4 methylation on UV-induced DNA damage. In the present work, we compared the yield and the nature of bipyrimidine photoproducts induced in a series of trinucleotides exhibiting a TXG sequence where X is either T, C, 5mC or N4mC. HPLC associated to tandem mass spectrometry was used to quantify cyclobutane pyrimidine dimers (CPD), (6-4) photoproducts (64PP) and their Dewar valence isomer. Methylation at position N4 was found to drastically increase the reactivity of C upon exposure to both UVC and UVB and to favor the formation of 64PP. In contrast methylation at C5 increased the yield of CPD at the expense of 64PP. In addition, enhancement of photoreactivity by C5 methylation was much higher in the UVB than in the UVC range. These results show the drastic effect of the methylation site on the photochemistry of cytosine. PMID:25319211

  14. Mutagenic Effects Induced by the Attack of NO2 Radical to the Guanine-Cytosine Base Pair

    Science.gov (United States)

    Cerón-Carrasco, José Pedro; Requena, Alberto; Zúñiga, José; Jacquemin, Denis

    2015-03-01

    We investigate the attack of the nitrogen dioxide radical (NO2) to the guanine-cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO2 radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO2-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC-NO2 radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.

  15. Killing effect of coexpressing cytosine deaminase and thymidine kinase on rat vascular smooth muscle cells

    Institute of Scientific and Technical Information of China (English)

    曹慧青; 孟宪敏; 刘冬青; 赵秀文; 丁金凤

    2004-01-01

    Background Vascular smooth muscle cell (VSMC) proliferation following arterial injury plays a critical role in a variety of vascular proliferative disorders, such as atherosclerosis and restenosis after balloon angioplasty. Herpes simplex virus-thymidine kinase (HSV-TK)/ganciclovir (GCV) and E.coli cytosine deaminase (CD)/5-fluorocytosine (5-Fc) suicide gene systems have been successfully employed in cardiovascular gene therapy, respectively. We reasoned that coexpression of both HSV-TK with CD suicide genes would lead to increased cell killing. To test this imagine, the adenoviral vectors expressing TK and/or CD genes were developed and tested on vascular smooth muscle cells. Methods Adenoviral vectors, including Ad-EF1α-CD-cytomegolovirus (CMV)-TK coexpressing both CD and TK double suicide genes, Ad-EF1α-CD and Ad-CMV-TK expressing CD and TK respectively, and control vector Ad-CMV-LacZ, were constructed and prepared with homologous recombination in RecA+E.coli cells. Integration and expression of CD and/or TK gene were identified by PCR and Western blot. Primary cultured VSMCs were infected at a multiplicity of infection (MOI) of 20 with exposure to their matching prodrugs 5-Fc and GCV. Cell mortality was measured by methyl thiazolyl tetrazolium (MTT) assays. Flow cytometry analysis was used to detect cell death. Apoptotic cells were analyzed using Hoechst 33342 fluorescence dye as a DNA probe. Genomic DNA cleavage of apoptotic VSMCs was tested by agarose gel electrophoresis. Results Recombinant adenovirus expressing CD and/or TK suicide genes were successfully constructed. Both single and double suicide genes could be integrated into adenoviral genome and expressed. Cytotoxic effects of Ad-EF1α-CD-CMV-TK double suicide genes combined with 5-Fc and GCV were higher than those of Ad-CMV-TK and Ad-EF1α-CD single gene groups. The rate of cell survival was only (9±3)% in the Ad-EF1α-CD-CMV-TK group, but (37±3)% in the Ad-CMV-TK and (46±4)% in the Ad-EF1

  16. Cyclopentenyl cytosine has biological and anti-tumour activity, but does not enhance the efficacy of gemcitabine and radiation in two animal tumour models

    NARCIS (Netherlands)

    C. van Bree; A.D. Barten-van Rijbroek; R. Leen; H.M. Rodermond; A.B.P. van Kuilenburg; H.B. Kal

    2009-01-01

    Cyclopentenyl cytosine (CPEC), targetting the de novo biosynthesis of cytidine triphosphate (CTP), increases the cytotoxicity of gemcitabine (2',2'-difluoro-2'-deoxycytidine, dFdC) alone and in combination with irradiation in several human tumour cells in vitro. We investigated whether OPEC enhances

  17. Bacillus halodurans Strain C125 Encodes and Synthesizes Enzymes from Both Known Pathways To Form dUMP Directly from Cytosine Deoxyribonucleotides

    DEFF Research Database (Denmark)

    Oehlenschlæger, Christian Berg; Løvgreen, Monika Nøhr; Reinauer, Eva;

    2015-01-01

    Analysis of the genome of Bacillus halodurans strain C125 indicated that two pathways leading from a cytosine deoxyribonucleotide to dUMP, used for dTMP synthesis, were encoded by the genome of the bacterium. The genes that were responsible, the comEB gene and the dcdB gene, encoding dCMP deaminase...

  18. Electronic Excited State and Vibrational Dynamics of Water Solution of Cytosine Observed by Time-resolved Transient Absorption Spectroscopy with Sub-10fs Deep Ultraviolet Laser Pules

    Directory of Open Access Journals (Sweden)

    Kobayashi Takayoshi.

    2013-03-01

    Full Text Available Time-resolved transient absorption spectroscopy for water solution of cytosine with sub-10fs deep ultraviolet laser pulse is reported. Ultrafast electronic excited state dynamics and coherent molecular vibrational dynamics are simultaneously observed and their relaxation mechanisms are discussed.

  19. Sensitization of prostate cancer cell lines to 5-fluorocytosine induced by a replication incompetent adenoviral vector carrying a cytosine deaminase transcription unit

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    AIM: To investigate the efficiency of cytosine deaminase adenoviral/5-fluorocytosine system on prostate cancer cell lines. METHODS: Cell culture, infectivity test and sensitivity test, observing the bystander effect and animal model experiment were carried out. RESULTS: All the established prostate cancer cell lines were eventually infectable, but ratio of vector/cell and time of exposed at which infection occurs was dependent on the cell lines. The expression of transfered cytosine deaminase gene peaked at different days, but persisted beyond 11 days. The prostate cell lines were sensitized to the 5-fluorocytosine by infection with the cytosine deaminase gene adenoviral vector, and only 5% of the LNCap and 10% of the RM-1 cells infected were required for 100% cell death. In the animal model, there was significant eradiation of tumor growth at the ratio of 400 vector particles/cell and with the systematic treatment of 5-fluorocytosine. CONCLUSION: The adenoviral vector carrying a cytosine deaminase transcription unit can sensitize the prostate cancer cell lines to 5-fluorocytosine, and the system can significantly inhibit the growth of prostatic tumor in mice.

  20. Spectroscopic (UV/VIS, Raman) and Electrophoresis Study of Cytosine-Guanine Oligonucleotide DNA Influenced by Magnetic Field.

    Science.gov (United States)

    Banihashemian, Seyedeh Maryam; Periasamy, Vengadesh; Boon Tong, Goh; Abdul Rahman, Saadah

    2016-01-01

    Studying the effect of a magnetic field on oligonucleotide DNA can provide a novel DNA manipulation technique for potential application in bioengineering and medicine. In this work, the optical and electrochemical response of a 100 bases oligonucleotides DNA, cytosine-guanine (CG100), is investigated via exposure to different magnetic fields (250, 500, 750, and 1000 mT). As a result of the optical response of CG100 to the magnetic field, the ultra-violet-visible spectrum indicated a slight variation in the band gap of CG100 of about 0.3 eV. Raman spectroscopy showed a significant deviation in hydrogen and phosphate bonds' vibration after exposure to the magnetic field. Oligonucleotide DNA mobility was investigated in the external electric field using the gel electrophoresis technique, which revealed a small decrease in the migration of CG100 after exposure to the magnetic field. PMID:26999445

  1. Spectroscopic (UV/VIS, Raman) and Electrophoresis Study of Cytosine-Guanine Oligonucleotide DNA Influenced by Magnetic Field

    Science.gov (United States)

    Banihashemian, Seyedeh Maryam; Periasamy, Vengadesh; Boon Tong, Goh; Abdul Rahman, Saadah

    2016-01-01

    Studying the effect of a magnetic field on oligonucleotide DNA can provide a novel DNA manipulation technique for potential application in bioengineering and medicine. In this work, the optical and electrochemical response of a 100 bases oligonucleotides DNA, cytosine-guanine (CG100), is investigated via exposure to different magnetic fields (250, 500, 750, and 1000 mT). As a result of the optical response of CG100 to the magnetic field, the ultra-violet-visible spectrum indicated a slight variation in the band gap of CG100 of about 0.3 eV. Raman spectroscopy showed a significant deviation in hydrogen and phosphate bonds’ vibration after exposure to the magnetic field. Oligonucleotide DNA mobility was investigated in the external electric field using the gel electrophoresis technique, which revealed a small decrease in the migration of CG100 after exposure to the magnetic field. PMID:26999445

  2. Induced Pib Expression and Resistance to Magnaporthe grisea are Compromised by Cytosine Demethylation at Critical Promoter Regions in Rice

    Institute of Scientific and Technical Information of China (English)

    Yuan Li; Qiong Xia; Hongping Kou; Dan Wang; Xiuyun Lin; Ying Wu; Chunming Xu; Shaochen Xing

    2011-01-01

    Pib is a well-characterized rice blast-resistance gene belonging to the nucleotide binding site (NBS) and leucine-rich repeat (LRR) superfamily.Expression of Pib was low under non-challenged conditions,but strongly induced by the blast-causing fungal pathogen Magnaporthe grisea,thereby conferring resistance to the pathogen.It is generally established that cytosine methylation of the promoter-region often plays a repressive role in modulating expression of the gene in question.We report here that two critical regions of the Pib promoter were heavily CG cytosine-methylated in both cultivars studied.Surprisingly,induced expression of Pib by M.grisea infection did not entail its promoter demethylation,and partial demethylation by 5-azacytidine-treatment actually reduced Pib expression relative to wildtype plants.Accordingly,the blast disease-resistance was compromised in the 5’-azaC-treated plants relative to wild-type.In contrast,the disease susceptibility was not affected by the 5’-azaC treatment in another two rice cultivars that did not contain the Pib gene,ruling out effects of other R genes and non-specific genotoxic effects by the drug-treatment as a cause for the compromised Pib-conditioned blast-resistance.Taken together,our results suggest that promoter DNA methylation plays a novel enhancing role in conditioning high-level of induced expression of the Pib gene in times of M.grisea infection,and its conferred resistance to the pathogen.

  3. Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

    Directory of Open Access Journals (Sweden)

    Vining Kelly J

    2012-01-01

    Full Text Available Abstract Background DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood. Results We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem in the reference tree species black cottonwood (Populus trichocarpa. Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq, we mapped a total of 129,360,151 36- or 32-mer reads to the P. trichocarpa reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation" had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation. Conclusions We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.

  4. Enhanced EJ Cell Killing of 125I Radiation by Combining with Cytosine Deaminase Gene Therapy Regulated by Synthetic Radio-Responsive Promoter

    OpenAIRE

    Li, Ling; Zhang, Chun-Li; Kang, Lei; Wang, Rong-fu; Yan, Ping; Zhao, Qian; Yin, Lei; Guo, Feng-qin

    2015-01-01

    Abstract Aim: To investigate the enhancing effect of radionuclide therapy by the therapeutic gene placed under the control of radio-responsive promoter. Methods: The recombinant lentivirus E8-codA-GFP, including a synthetic radiation-sensitive promoter E8, cytosine deaminase (CD) gene, and green fluorescent protein gene, was constructed. The gene expression activated by 125I radiation was assessed by observation of green fluorescence. The ability of converting 5-fluorocytosine (5-FC) to 5-flu...

  5. Detection of single base mismatches of thymine and cytosine residues by potassium permanganate and hydroxylamine in the presence of tetralkylammonium salts.

    OpenAIRE

    Gogos, J.A.; Karayiorgou, M; Aburatani, H; Kafatos, F C

    1990-01-01

    In the presence of tetramethylammonium chloride, potassium permanganate specifically modifies mismatched thymines. Similarly, the modification of mismatched cytosines by hydroxylamine was enhanced by tetraethylammonium chloride. Modification followed by piperidine cleavage permits specific identification of the T and C mismatches and by extension, when the opposite DNA strand is analyzed, of A and G mismatches as well. These reactions can be performed conveniently with DNA immobilized on Hybo...

  6. Stable transformation of Toxoplasma gondii based on a pyrimethamine resistant trifunctional dihydrofolate reductase-cytosine deaminase-thymidylate synthase gene that confers sensitivity to 5-fluorocytosine.

    Science.gov (United States)

    Fox, B A; Belperron, A A; Bzik, D J

    1999-01-01

    To improve genetic models available for the analysis of apicomplexan protozoan parasites, bacterial sequences encoding the 427 amino acid cytosine deaminase (CD) gene were fused, in-frame, to an engineered linker domain of the high level pyrimethamine resistant form of the parasite bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) gene. Toxoplasma gondii was transformed with the plasmid containing the fused pyrimethamine resistant dihydrofolate reductase-cytosine deaminase-thymidylate synthase (DHFRm2m3-CD-TS) gene and parasites were selected in a high level of pyrimethamine. Transfected parasites that acquired resistance to pyrimethamine were cloned and evaluated for expression of the CD genetic marker. CD transgenic parasites acquired a high sensitivity to 5-fluorocytosine due to the intraparasitic conversion of this non-toxic prodrug to the cytotoxic compound 5-fluorouracil. Exogenously supplied cytosine or uracil rescued the growth of CD transgenic T. gondii parasites that were cultured in the presence of cytotoxic concentrations of 5-fluorouracil or 5-fluorocytosine. Bacterial CD fused to the pyrimethamine resistant DHFR-TS marker provides a novel genetic tool for new positive and negative genetic selection strategies in several protozoan parasites. An advantage of the CD genetic marker is that it is derived from a bacterial gene and can therefore be used in nearly any parasite genetic background for negative selection. This novel system should facilitate new approaches for the development of improved model genetic systems for the biological investigation of apicomplexan parasites. PMID:10029312

  7. Low energy electron induced cytosine base release in 2′-deoxycytidine-3′-monophosphate via glycosidic bond cleavage: A time-dependent wavepacket study

    International Nuclear Information System (INIS)

    Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2′-deoxycytidine-3′-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3′ C–O bond cleavage from the lowest π* shape resonance in energy region * orbital of the base to the σ* orbital of the glycosidic N–C bond. In addition, the metastable state formed after impinging LEE (0–1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N–C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ∼35–55 fs. Comparison of salient features of the two dissociation events, i.e., 3′ C–O single strand break and glycosidic N–C bond cleavage in 3′-dCMPH molecule are also provided

  8. A new rapid amplification of cDNA ends method for extremely guanine plus cytosine-rich genes.

    Science.gov (United States)

    Shi, Xianzong; Jarvis, Donald L

    2006-09-15

    Rapid amplification of cDNA ends (RACE) is widely used to determine the 5'- and 3'-terminal nucleotide sequences of genes. Many different RACE methods have been developed to meet various requirements, but none addresses the difficult problems that arise when trying to isolate the ends of extremely guanine plus cytosine (GC)-rich genes. In this study, we found that we were unable to isolate the correct 5' or 3' end of an insect gene, which appeared to include extremely GC-rich sequences, using current RACE methods. Thus, we developed a new RACE method that can be used for this purpose. This new method entails first-strand cDNA synthesis at 70 degrees C with Thermo-X reverse transcriptase in the presence of homoectoine, followed by a polymerase chain reaction with 98 degrees C denaturation steps and Phusion DNA polymerase in the presence of 1M betaine and 5% dimethyl sulfoxide (DMSO). The use of these conditions yielded 5'- and 3'-RACE products that were approximately 80% GC over 213 and 162bp, respectively, and included shorter internal regions of 82 to 89% GC. PMID:16875657

  9. Antitumor effects and radiosensitization of cytosine deaminase and thymidine kinase fusion suicide gene on colorectal carcinoma cells

    Institute of Scientific and Technical Information of China (English)

    De-Hua Wu; Li Liu; Long-Hua Chen

    2005-01-01

    AIM: To investigate the killing effect and radiosensitization of double suicide gene mediated by adenovirus on colorectal carcinoma cells.METHODS: Colorectal carcinoma cell line SW480 was transfected with adenovirus expression vector containing cytosine deaminase (CD) and thymidine kinase (Tk) fusion gene. The expression of CD-TK fusion gene was detected by reverse transcriptase-polymerase chain reaction. The toxic effect of ganciclovir (GCV) and 5-fiuorocytosine (5FC) on infected cells was determined by MTT assay. The radiosensitization of double suicide gene was evaluated by clonogenic assay.RESULTS: After prodrugs were used, the survival rate of colorectal carcinoma cells was markedly decreased. When GCV and 5-FC were used in combination, the cytotoxicity and bystandereffect were markedly superior to a single prodrug (x2 = 30.371, P<0.01). Both GCV and 5-FC could sensitize colorectal carcinoma cells to the toxic effect of radiation, and greater radiosensitization was achieved when both prodrug were used in combination. CONCLUSION: CD-TK double suicide gene can kill and radiosensitize colorectal carcinoma cells.

  10. High preservation of CpG cytosine methylation patterns at imprinted gene loci in liver and brain of aged mice.

    Directory of Open Access Journals (Sweden)

    Silvia Gravina

    Full Text Available A gradual loss of the correct patterning of 5-methyl cytosine marks in gene promoter regions has been implicated in aging and age-related diseases, most notably cancer. While a number of studies have examined DNA methylation in aging, there is no consensus on the magnitude of the effects, particularly at imprinted loci. Imprinted genes are likely candidate to undergo age-related changes because of their demonstrated plasticity in utero, for example, in response to environmental cues. Here we quantitatively analyzed a total of 100 individual CpG sites in promoter regions of 11 imprinted and non-imprinted genes in liver and cerebral cortex of young and old mice using mass spectrometry. The results indicate a remarkably high preservation of methylation marks during the aging process in both organs. To test if increased genotoxic stress associated with premature aging would destabilize DNA methylation we analyzed two DNA repair defective mouse models showing a host of premature aging symptoms in liver and brain. However, also in these animals, at the end of their life span, we found a similarly high preservation of DNA methylation marks. We conclude that patterns of DNA methylation in gene promoters of imprinted genes are surprisingly stable over time in normal, postmitotic tissues and that the multiple documented changes with age are likely to involve exceptions to this pattern, possibly associated with specific cellular responses to age-related changes other than genotoxic stress.

  11. Computational modeling and functional analysis of Herpes simplex virus type-1 thymidine kinase and Escherichia coli cytosine deaminase fusion protein

    International Nuclear Information System (INIS)

    Herpes simplex virus type-1 thymidine kinase (HSV-1TK) and Escherichia coli cytosine deaminase (CD) fusion protein was designed using InsightII software. The structural rationality of the fusion proteins incorporating a series of flexible linker peptide was analyzed, and a suitable linker peptide was chosen for further investigated. The recombinant plasmid containing the coding regions of HSV-1TK and CD cDNA connected by this linker peptide coding sequence was generated and subsequently transfected into the human embryonic kidney 293 cells (HEK293). The Western blotting indicated that the recombinant fusion protein existed as a dimer with a molecular weight of approximately 90 kDa. The toxicity of the prodrug on the recombinant plasmid-transfected human lung cancer cell line NCIH460 was evaluated, which showed that TKglyCD-expressing cells conferred upon cells prodrug sensitivities equivalent to that observed for each enzyme independently. Most noteworthy, cytotoxicity could be enhanced by concurrently treating TKglyCD-expressing cells with prodrugs GCV and 5-FC. The results indicate that we have successfully constructed a HSV-1TKglyCD fusion gene which might have a potential application for cancer gene therapy

  12. Evidence that Natural Selection is the Primary Cause of the Guanine-cytosine Content Variation in Rice Genes

    Institute of Scientific and Technical Information of China (English)

    Xiaoli Shi; Xiyin Wang; Zhe Li; Qihui Zhu; Ji Yang; Song Ge; Jingchu Luo

    2007-01-01

    Cereal genes are classified into two distinct classes according to the guanine-cytosine (GC) content at the third codon sites (GC3). Natural selection and mutation bias have been proposed to affect the GC content. However, there has been controversy about the cause of GC variation. Here, we characterized the GC content of 1 092 paralogs and other single-copy genes in the duplicated chromosomal regions of the rice genome (ssp. indica) and classified the paralogs into GC3-rich and GC3-poor groups. By referring to out-group sequences from Arabidopsis and maize, we confirmed that the average synonymous substitution rate of the GC3-rich genes is significantly lower than that of the GC3-poor genes. Furthermore,we explored the other possible factors corresponding to the GC variation including the length of coding sequences, the number of exons in each gene, the number of genes in each family, the location of genes on chromosomes and the protein functions. Consequently, we propose that natural selection rather than mutation bias was the primary cause of the GC variation.

  13. Generation and characterization of a human single-chain fragment variable (scFv antibody against cytosine deaminase from Yeast

    Directory of Open Access Journals (Sweden)

    Tombesi Marina

    2008-09-01

    Full Text Available Abstract Background The ability of cytosine deaminase (CD to convert the antifungal agent 5-fluorocytosine (5-FC into one of the most potent and largely used anticancer compound such as 5-fluorouracil (5-FU raised considerable interest in this enzyme to model gene or antibody – directed enzyme-prodrug therapy (GDEPT/ADEPT aiming to improve the therapeutic ratio (benefit versus toxic side-effects of cancer chemotherapy. The selection and characterization of a human monoclonal antibody in single chain fragment (scFv format represents a powerful reagent to allow in in vitro and in vivo detection of CD expression in GDEPT/ADEPT studies. Results An enzymatic active recombinant CD from yeast (yCD was expressed in E. coli system and used as antigen for biopanning approach of the large semi-synthetic ETH-2 antibody phage library. Several scFvs were isolated and specificity towards yCD was confirmed by Western blot and ELISA. Further, biochemical and functional investigations demonstrated that the binding of specific scFv with yCD did not interfere with the activity of the enzyme in converting 5-FC into 5-FU. Conclusion The construction of libraries of recombinant antibody fragments that are displayed on the surface of filamentous phage, and the selection of phage antibodies against target antigens, have become an important biotechnological tool in generating new monoclonal antibodies for research and clinical applications. The scFvH5 generated by this method is the first human antibody which is able to detect yCD in routinary laboratory techniques without interfering with its enzymatic function.

  14. Infection with a Virulent Strain of Wolbachia Disrupts Genome Wide-Patterns of Cytosine Methylation in the Mosquito Aedes aegypti.

    Directory of Open Access Journals (Sweden)

    Yixin H Ye

    Full Text Available Cytosine methylation is one of several reversible epigenetic modifications of DNA that allow a greater flexibility in the relationship between genotype and phenotype. Methylation in the simplest models dampens gene expression by modifying regions of DNA critical for transcription factor binding. The capacity to methylate DNA is variable in the insects due to diverse histories of gene loss and duplication of DNA methylases. Mosquitoes like Drosophila melanogaster possess only a single methylase, DNMT2.Here we characterise the methylome of the mosquito Aedes aegypti and examine its relationship to transcription and test the effects of infection with a virulent strain of the endosymbiont Wolbachia on the stability of methylation patterns.We see that methylation in the A. aegypti genome is associated with reduced transcription and is most common in the promoters of genes relating to regulation of transcription and metabolism. Similar gene classes are also methylated in aphids and honeybees, suggesting either conservation or convergence of methylation patterns. In addition to this evidence of evolutionary stability, we also show that infection with the virulent wMelPop Wolbachia strain induces additional methylation and demethylation events in the genome. While most of these changes seem random with respect to gene function and have no detected effect on transcription, there does appear to be enrichment of genes associated with membrane function. Given that Wolbachia lives within a membrane-bound vacuole of host origin and retains a large number of genes for transporting host amino acids, inorganic ions and ATP despite a severely reduced genome, these changes might represent an evolved strategy for manipulating the host environments for its own gain. Testing for a direct link between these methylation changes and expression, however, will require study across a broader range of developmental stages and tissues with methods that detect splice variants.

  15. Potential benefits of combining cytosine deaminase/5-fluorocytosine gene therapy and irradiation for prostate cancer. Experimental study

    International Nuclear Information System (INIS)

    The purpose of this study was to investigate the potential of combining cytosine deaminase/5-fluorocytosine (CD/5-FC) gene therapy and radiation therapy (either external beam radiation or radioimmunotherapy [RIT]), for the treatment of prostate cancer. Tumor xenografts of CD-transduced LNCaP cells grown in the testes of severe combined immunodeficiency (SCID) mice were used to evaluate antitumor effect. The mice were injected intraperitoneally with 500 mg/kg of 5-FC, or with 5, 15 or 30 mg/kg of 5-fluorouracil (5-FU), for 9 days. The tumors were treated with fractionated radiation at a dose of 1 or 3 Gy/day for 3 days, or I-131 labelled anti-prostate specific antigen (anti-PSA) monoclonal antibody (mAb) administration at a subtherapeutic dose of 20 or 80 μCi. Intratumoral and serum concentrations of 5-FU were measured using high performance liquid chromatography. Mice treated with CD/5-FC gene therapy presented a significant tumor growth inhibition comparable to that obtained with 15 mg/kg, 5-FU systemic administration without marked weight loss. Treatment with CD/5-FC gene therapy resulted in higher tumor but lower serum concentrations of 5-FU than treatment with systemic 5-FU chemotherapy. An additive antitumor effect was obtained when CD/5-FC therapy was combined with 1 Gy irradiation, which by itself did not produce a significant antitumor effect. However, the efficacy of CD/5-FC therapy was not enhanced when combined with RIT, probably due to poor accumulation of the mAb as the tumor/blood ratio never exceeded 1. These findings indicate that CD/5-FC gene therapy for prostate cancer may function with enhanced antitumor effect when combined with external beam radiation. However, combining CD/5-FC gene therapy and RIT using an anti-PSA mAb may not be effective because of insufficient accumulation of the mAb at the target tumors. (author)

  16. Antitumor effect of cytosine deaminase/5-fluorocytosine suicide gene therapy system mediated by Bifidobacterium infantis on melanoma

    Institute of Scientific and Technical Information of China (English)

    Cheng YI; Ying HUANG; Zhi-ying GUO; Shu-ren WANG

    2005-01-01

    Aim: To construct a Bifidobacterium infantis/CD targeting gene therapy system and observe the antitumor effect of cytosine deaminase/5-fluorocytosine (CD/5-FC) suicide gene therapy system mediated by Bifidobacterium infantis on melanoma in vitro and in vivo. Methods: A recombinant CD/pGEX- 1LamdaT plasmid was transfected into Bifidobacterium infantis by electroporation. Bifidobac terium infantis transfected by recombinant CD/pGEX-1LamdaT plasmid was in cubated with 5-FC anaerobically. Then the supernatant fluid was collected and added to melanoma B16-F10 cells to observe the killing effect for B16-F10 cells.Mice were inoculated with melanoma B 16-F10 cells to establish animal models.The mice were then injected with 5-FC and Bifidobacterium infantis transfected by recombinant CD/pGEX-1LamdaT plasmid. Results:Two segments of approxi mate 4.9 kb and 1.3 kb were extracted from the 6.2 kb recombinant plasmid, which were equal to the size of the pGEX-1LamdaT plasmid and CD gene, respectively.Sequencing results showed that the full length and sequence of nucleotide acid of the inserted gene in extracted recombinant plasmid was completely identical to the CD gene. In vitro, B 16-F10 cells treated by supernatant fluid were remarkably damaged morphologically, and the cell growth was significantly inhibited. Experi ments on the mice melanoma model showed that after treatment with a combination of transfected Bifidobacterium infantis and 5-FC, the tumor volume was significantly inhibited compared with controls. Conclusion: The foreign gene,CD gene, was correctly inserted into pGEX-1LambdaT plasmid and transferred into Bifidobacterium infantis. CD/5-FC suicide gene therapy system mediated by Bifidobacterium infantis demonstrated a good antitumor effect on melanoma in vitro and in vivo.

  17. Hydrocortisone in culture protects the blast cells in acute myeloblastic leukemia from the lethal effects of cytosine arabinoside

    International Nuclear Information System (INIS)

    The blast cells in acute myeloblastic leukemia (AML) respond to many of the same regulatory mechanisms that control normal hemopoiesis. These include the growth factors that bind to membrane receptors and steroid hormones or vitamins that have intracellular receptors. The authors report the effects in culture of the steroid glucocorticoid hydrocortisone on freshly explanted AML blasts from patients and on two continuous AML cell lines. Only small changes in clonogenic cell numbers in suspension cultures were seen in the presence of hydrocortisone. The most striking effect of the hormone was on the sensitivity of blasts cells to cytosine arabinoside (ara-C). In contrast to the response of AML blast cells to retinoic acid, a ligand for intracellular steroid receptors that sensitizes some blast populations to ara-C, hydrocortisone reduced the toxic effects of the drug. The protective action of hydrocortisone was not mediated through the cell cycle since exposure of blasts to hydrocortisone did not affect the percentage of cells in DNA synthesis as measured with the tritiated thymidine (3HTdR) suicide technique. The hydrocortisone effect could be demonstrated using a pulse (20 min) exposure protocol. Blasts pulsed with increasing specific activities of 3HTdR showed the usual response pattern with an initial loss in plating efficiency to about 50% of control, followed by a plateau, regardless of whether the cells had been exposed to hydrocortisone. Control blasts exposed to increasing ara-C concentrations gave very similar dose-response curves; in striking contrast, blast cells cultured in hydrocortisone, then pulsed with ara-C did not lose colony-forming ability even though the same population was sensitive to 3HTdR

  18. Modification of the cerebral perfusion during a chemotherapy by arabinoside cytosine (A.R.A.C.) among patients suffering of an acute myelo-blastic leukemia (A.M.L.); Modification de la perfusion cerebrale au cours d'une chimiotherapie par cytosine arabinoside (ARAC) chez les patients atteints d'une leucemie aigue myeloblastique (LAM)

    Energy Technology Data Exchange (ETDEWEB)

    Modzelewski, R.; Vera, P. [Universite de Medecine de Rouen, QUANT.I.F-LITIS EA4108, departement de medecine nucleaire, 76 (France); Lepretre, S.; Tilly, H. [Centre Henri-Becquerel, departement d' hematologie, 76 - Rouen (France); Martinaud, O.; Hannequin, D. [CHU de Rouen, departement de neurologie, 76 (France); Habert, M.O. [CHU de la Pitie-Salpetriere, departement de medecine nucleaire, 75 - Paris (France)

    2010-07-01

    Cytosine arabinoside in high doses is a major treatment in acute myelo-blastic leukemia (A.M.L.). This treatment leads to neurological complications in 3-16% of cases, but the EEG, CT or MRI are normal.This prospective study examines brain perfusion in single photon emission tomography (SPECT) for patients receiving high dose arabinoside cytosine (H.D. A.R.A.C.). The SPECT of perfusion with hexamethyl propylene amine oxime (H.M.P.A.O.) for patients suffering of A.M.L. allowed to show a reduction of perfusion at the cerebellum level, of the occipito-parietal cortex and thalami, after conventional doses of A.R.A.C., while the patients had not any neurological accidents. (N.C.)

  19. Crystal structure of tetra­kis­[μ2-2-(di­methyl­amino)­ethano­lato-κ3 N,O:O]di-μ3-hydroxido-di­thio­cyanato-κ2 N-dichromium(III)dilead(II) di­thio­cyanate aceto­nitrile monosolvate

    Science.gov (United States)

    Rusanova, Julia A.; Semenaka, Valentyna V.; Omelchenko, Irina V.

    2016-01-01

    The tetra­nuclear complex cation of the title compound, [Cr2Pb2(NCS)2(OH)2(C4H10NO)4](SCN)2·CH3CN, lies on an inversion centre. The main structural feature of the cation is a distorted seco-norcubane Pb2Cr2O6 cage with a central four-membered Cr2O2 ring. The CrIII ion is coordinated in a distorted octa­hedron, which involves two N atoms of one bidentate ligand and one thio­cyanate anion, two μ2-O atoms of 2-(di­methyl­amino)­ethano­late ligands and two μ3-O atoms of hydroxide ions. The coordination geometry of the PbII ion is a distorted disphenoid, which involves one N atom, two μ2-O atoms and one μ3-O atom. In addition, weak Pb⋯S inter­actions involving the coordinating and non-coordinating thio­cyanate anions are observed. In the crystal, the complex cations are linked through the thio­cyanate anions via the Pb⋯S inter­actions and O—H⋯N hydrogen bonds into chains along the c axis. The chains are further linked together via S⋯S contacts. The contribution of the disordered solvent aceto­nitrile mol­ecule was removed with the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9–18] procedure in PLATON. The solvent is included in the reported mol­ecular formula, weight and density. PMID:27375871

  20. Crystal structure of tetra-kis-[μ2-2-(di-methyl-amino)-ethano-lato-κ(3) N,O:O]di-μ3-hydroxido-di-thio-cyanato-κ(2) N-dichromium(III)dilead(II) di-thio-cyanate aceto-nitrile monosolvate.

    Science.gov (United States)

    Rusanova, Julia A; Semenaka, Valentyna V; Omelchenko, Irina V

    2016-04-01

    The tetra-nuclear complex cation of the title compound, [Cr2Pb2(NCS)2(OH)2(C4H10NO)4](SCN)2·CH3CN, lies on an inversion centre. The main structural feature of the cation is a distorted seco-norcubane Pb2Cr2O6 cage with a central four-membered Cr2O2 ring. The Cr(III) ion is coordinated in a distorted octa-hedron, which involves two N atoms of one bidentate ligand and one thio-cyanate anion, two μ2-O atoms of 2-(di-methyl-amino)-ethano-late ligands and two μ3-O atoms of hydroxide ions. The coordination geometry of the Pb(II) ion is a distorted disphenoid, which involves one N atom, two μ2-O atoms and one μ3-O atom. In addition, weak Pb⋯S inter-actions involving the coordinating and non-coordinating thio-cyanate anions are observed. In the crystal, the complex cations are linked through the thio-cyanate anions via the Pb⋯S inter-actions and O-H⋯N hydrogen bonds into chains along the c axis. The chains are further linked together via S⋯S contacts. The contribution of the disordered solvent aceto-nitrile mol-ecule was removed with the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9-18] procedure in PLATON. The solvent is included in the reported mol-ecular formula, weight and density. PMID:27375871

  1. Targeted cytosine deaminase-uracil phosphoribosyl transferase suicide gene therapy induces small cell lung cancer-specific cytotoxicity and tumor growth delay

    DEFF Research Database (Denmark)

    Christensen, Camilla L; Gjetting, Torben; Poulsen, Thomas Tuxen;

    2010-01-01

    Small cell lung cancer (SCLC) is a highly malignant cancer for which there is no curable treatment. Novel therapies are therefore in great demand. In the present study we investigated the therapeutic effect of transcriptionally targeted suicide gene therapy for SCLC based on the yeast cytosine...... deaminase (YCD) gene alone or fused with the yeast uracil phosphoribosyl transferase (YUPRT) gene followed by administration of 5-fluorocytosine (5-FC) prodrug. Experimental design: The YCD gene or the YCD-YUPRT gene was placed under regulation of the SCLC-specific promoter insulinoma-associated 1 (INSM1...

  2. Effect of C5-methylation of cytosine on the photoreactivity of DNA: a joint experimental and computational study of TCG trinucleotides.

    Science.gov (United States)

    Esposito, Luciana; Banyasz, Akos; Douki, Thierry; Perron, Marion; Markovitsi, Dimitra; Improta, Roberto

    2014-08-01

    DNA methylation, occurring at the 5 position of cytosine, is a natural process associated with mutational hotspots in skin tumors. By combining experimental techniques (optical spectroscopy, HPLC coupled to mass spectrometry) with theoretical methods (molecular dynamics, DFT/TD-DFT calculations in solution), we study trinucleotides with key sequences (TCG/T5mCG) in the UV-induced DNA damage. We show how the extra methyl, affecting the conformational equilibria and, hence, the electronic excited states, increases the quantum yield for the formation of cyclobutane dimers while reducing that of (6-4) adducts. PMID:25050452

  3. A novel radiochemical approach to 1-(2'-deoxy-2'-[(18) F]fluoro-β-d-arabinofuranosyl)cytosine ((18) F-FAC).

    Science.gov (United States)

    Meyer, Jan-Philip; Probst, Katrin C; Trist, Iuni M L; McGuigan, Christopher; Westwell, Andrew D

    2014-09-01

    (18) F-FAC (1-(2'-deoxy-2'-[(18) F]fluoro-β-D-arabinofuranosyl)-cytosine) is an important 2'-fluoro-nucleoside-based positron emission tomography (PET) tracer that has been used for in vivo prediction of response to the widely used cancer chemotherapy drug gemcitabine. Previously reported synthetic routes to (18) F-FAC have relied on early introduction of the (18) F radiolabel prior to attachment to protected cytosine base. Considering the (18) F radiochemical half-life (110 min) and the technical challenges of multi-step syntheses on PET radiochemistry modular systems, late-stage radiofluorination is preferred for reproducible and reliable radiosynthesis with in vivo applications. Herein, we report the first late-stage radiosynthesis of (18) F-FAC. Cytidine derivatives with leaving groups at the 2'-position are particularly prone to undergo anhydro side-product formation upon heating because of their electron density at the 2-carbonyl pyrimidone oxygen. Our rationally developed fluorination precursor showed an improved reactivity-to-stability ratio at elevated temperatures. (18) F-FAC was obtained in radiochemical yields of 4.3-5.5% (n = 8, decay-corrected from end of bombardment), with purities ≥98% and specific activities ≥63 GBq/µmol. The synthesis time was 168 min. PMID:25257474

  4. Nanodosimetry of Auger electrons: A case study from the decay of (125)I and 0-18-eV electron stopping cross sections of cytosine.

    Science.gov (United States)

    Michaud, M; Bazin, M; Sanche, L

    2013-03-01

    Radiopharmaceuticals emitting Auger electrons are often injected into patients undergoing cancer treatment with targeted radionuclide therapy (TRT). In this type of radiotherapy, the radiation source is radial and most of the emitted primary particles are low-energy electrons (LEEs) having kinetic energies distributed mostly from zero to a few hundred electron volts with very short ranges in biological media. These LEEs generate a high density of energy deposits and clustered damage, thus offering a relative biological effectiveness comparable to that of alpha particles. In this paper, we present a simple model and corresponding measurements to assess the energy deposited near the site of the radiopharmaceuticals in TRT. As an example, a calculation is performed for the decay of a single (125)I radionuclide surrounded by a 1-nm-radius spherical shell of cytosine molecules using the energy spectrum of LEEs emitted by (125)I along with their stopping cross sections between 0 and 18 eV. The dose absorbed by the cytosine shell, which occupies a volume of 4 nm(3), is extremely high. It amounts to 79 kGy per decay of which 3%, 39%, and 58% is attributed to vibrational excitations, electronic excitations, and ionization processes, respectively. PMID:24976798

  5. Nanodosimetry of Auger electrons: A case study from the decay of 125I and 0–18-eV electron stopping cross sections of cytosine

    Science.gov (United States)

    Michaud, M.; Bazin, M.; Sanche, L.

    2013-01-01

    Radiopharmaceuticals emitting Auger electrons are often injected into patients undergoing cancer treatment with targeted radionuclide therapy (TRT). In this type of radiotherapy, the radiation source is radial and most of the emitted primary particles are low-energy electrons (LEEs) having kinetic energies distributed mostly from zero to a few hundred electron volts with very short ranges in biological media. These LEEs generate a high density of energy deposits and clustered damage, thus offering a relative biological effectiveness comparable to that of alpha particles. In this paper, we present a simple model and corresponding measurements to assess the energy deposited near the site of the radiopharmaceuticals in TRT. As an example, a calculation is performed for the decay of a single 125I radionuclide surrounded by a 1-nm-radius spherical shell of cytosine molecules using the energy spectrum of LEEs emitted by 125I along with their stopping cross sections between 0 and 18 eV. The dose absorbed by the cytosine shell, which occupies a volume of 4 nm3, is extremely high. It amounts to 79 kGy per decay of which 3%, 39%, and 58% is attributed to vibrational excitations, electronic excitations, and ionization processes, respectively. PMID:24976798

  6. Nanodosimetry of Auger electrons: A case study from the decay of 125I and 0-18-eV electron stopping cross sections of cytosine

    Science.gov (United States)

    Michaud, M.; Bazin, M.; Sanche, L.

    2013-03-01

    Radiopharmaceuticals emitting Auger electrons are often injected into patients undergoing cancer treatment with targeted radionuclide therapy (TRT). In this type of radiotherapy, the radiation source is radial and most of the emitted primary particles are low-energy electrons (LEEs) having kinetic energies distributed mostly from zero to a few hundred electron volts with very short ranges in biological media. These LEEs generate a high density of energy deposits and clustered damage, thus offering a relative biological effectiveness comparable to that of alpha particles. In this paper, we present a simple model and corresponding measurements to assess the energy deposited near the site of the radiopharmaceuticals in TRT. As an example, a calculation is performed for the decay of a single 125I radionuclide surrounded by a 1-nm-radius spherical shell of cytosine molecules using the energy spectrum of LEEs emitted by 125I along with their stopping cross sections between 0 and 18 eV. The dose absorbed by the cytosine shell, which occupies a volume of 4 nm3, is extremely high. It amounts to 79 kGy per decay of which 3%, 39%, and 58% is attributed to vibrational excitations, electronic excitations, and ionization processes, respectively.

  7. Gamma irradiation of Escherichia coli deoxyribonucleic acid labelled with carbon 14 on the carbon 2 of cytosine. Identification of the radiolysis products formed by breaking of the N-glycoside

    International Nuclear Information System (INIS)

    The effect of ionising radiations on living organisms consists mainly of an action on the deoxyribonucleic acid or DNA. The products resulting from the modification of the cytosine fragment and released from the polynucleotide chain by breaking of the N-glycoside bond were identified

  8. Effects of temperature and isotopic substitution on electron attachment dynamics of guanine-cytosine base pair: Ring-polymer and classical molecular dynamics simulations

    Science.gov (United States)

    Minoshima, Yusuke; Seki, Yusuke; Takayanagi, Toshiyuki; Shiga, Motoyuki

    2016-06-01

    The dynamical process of electron attachment to a guanine-cytosine pair in the normal (h-GC) and deuterated (d-GC) forms has been studied theoretically by semiclassical ring-polymer molecular dynamics (RPMD) simulations using the empirical valence bond model. The initially formed dipole-bound anion is converted rapidly to the valence-bound anion within about 0.1 ps in both h-GC and d-GC. However, the subsequent proton transfer in h-GC occurs with a rate five times greater than the deuteron transfer in d-GC. The change of rates with isotopic substitution and temperature variation in the RPMD simulations are quantitatively and qualitatively different from those in the classical molecular dynamics (MD) simulations, demonstrating the importance of nuclear quantum effects on the dynamics of this system.

  9. A possible prebiotic synthesis of purine, adenine, cytosine, and 4(3H)-pyrimidinone from formamide: implications for the origin of life.

    Science.gov (United States)

    Saladino, R; Crestini, C; Costanzo, G; Negri, R; Di Mauro, E

    2001-05-01

    The synthesis of prebiotic molecules is a major problem in chemical evolution as well as in any origin-of-life theory. We report here a plausible new prebiotic synthesis of naturally occurring purine and pyrimidine derivatives from formamide under catalytic conditions. In the presence of CaCO(3) and different inorganic oxides, namely silica, alumine, kaolin, and zeolite (Y type), neat formamide undergoes the formation of purine, adenine, cytosine, and 4(3H)-pyrimidinone, from acceptable to good yields. The role of catalysts showed to be not limited to the improvement of the yield but it is also relevant in providing a high selectivity in the products distribution. PMID:11377183

  10. Effects of inhibitors of DNA, RNA, and protein synthesis on frequencies and types of premature chromosome condensation from x-ray induced micronuclei. [Cytosine arabinoside, azathioprine, thymidine, trenimon

    Energy Technology Data Exchange (ETDEWEB)

    Madle, S.; Nowak, J.; Obe, G.

    1976-10-28

    Cells containing x-ray induced micronuclei were treated for a few hours before fixation with inhibitors of DNA synthesis (cytosine arabinoside; azathioprine; thymidine; trenimon), of RNA synthesis (actinomycin D; ethidium bromide), and of protein synthesis (puromycin). Only the inhibitors of DNA synthesis lead to a significant suppression of the frequencies of mitoses with micronucleus derived premature chromosome condensation (PCC). We tend to interpret the result as follows: Micronuclei that are in the G1 phase of their cell cycles are accumulated at the G1/S border or in the early S phase of their cell cycles under the influence of the inhibitors of the DNA synthesis. Micronuclei blocked in this way cannot be induced to undergo PCC and seem to disappear from the cells.

  11. Pleiotropic phenotypes of the salt-tolerant and cytosine hypomethylated leafless inflorescence, evergreen dwarf and irregular leaf lamina mutants of Catharanthus roseus possessing Mendelian inheritance

    Indian Academy of Sciences (India)

    Renu Kumari; Vishakha Sharma; Vinay Sharma; Sushil Kumar

    2013-12-01

    In Catharanthus roseus, three morphological cum salt-tolerant chemically induced mutants ofMendelian inheritance and their wild-type parent cv Nirmal were characterized for overall cytosine methylation at DNA repeats, expression of 119 protein-coding and seven miRNA-coding genes and 50 quantitative traits. The mutants, named after their principal morphological feature(s), were leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill). The Southern-blot analysis of MspI digested DNAs of mutants probed with centromeric and 5S and 18S rDNA probes indicated that, in comparison to wild type, the mutants were extensively demethylated at cytosine sites. Among the 126 genes investigated for transcriptional expression, 85 were upregulated and 41 were downregulated in mutants. All of the five genes known to be stress responsive had increased expression in mutants. Several miRNA genes showed either increased or decreased expression in mutants. The C. roseus counterparts of CMT3, DRM2 and RDR2 were downregulated in mutants. Among the cell, organ and plant size, photosynthesis and metabolism related traits studied, 28 traits were similarly affected in mutants as compared to wild type. Each of the mutants also expressed some traits distinctively. The egd mutant possessed superior photosynthesis and water retention abilities. Biomass was hyperaccumulated in roots, stems, leaves and seeds of the lli mutant. The ill mutant was richest in the pharmaceutical alkaloids catharanthine, vindoline, vincristine and vinblastine. The nature of mutations, origins of mutant phenotypes and evolutionary importance of these mutants are discussed.

  12. Pleiotropic phenotypes of the salt-tolerant and cytosine hypomethylated leafless inflorescence, evergreen dwarf and irregular leaf lamina mutants of Catharanthus roseus possessing Mendelian inheritance.

    Science.gov (United States)

    Kumari, Renu; Sharma, Vishakha; Sharma, Vinay; Kumar, Sushil

    2013-12-01

    In Catharanthus roseus, three morphological cum salt-tolerant chemically induced mutants of Mendelian inheritance and their wild-type parent cv Nirmal were characterized for overall cytosine methylation at DNA repeats, expression of 119 protein coding and seven miRNA-coding genes and 50 quantitative traits. The mutants, named after their principal morphological feature(s), were leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill). The Southern-blot analysis of MspI digested DNAs of mutants probed with centromeric and 5S and 18S rDNA probes indicated that, in comparison to wild type, the mutants were extensively demethylated at cytosine sites. Among the 126 genes investigated for transcriptional expression, 85 were upregulated and 41 were downregulated in mutants. All of the five genes known to be stress responsive had increased expression in mutants. Several miRNA genes showed either increased or decreased expression in mutants. The C. roseus counterparts of CMT3, DRM2 and RDR2 were downregulated in mutants. Among the cell, organ and plant size, photosynthesis and metabolism related traits studied, 28 traits were similarly affected in mutants as compared to wild type. Each of the mutants also expressed some traits distinctively. The egd mutant possessed superior photosynthesis and water retention abilities. Biomass was hyperaccumulated in roots, stems, leaves and seeds of the lli mutant. The ill mutant was richest in the pharmaceutical alkaloids catharanthine, vindoline, vincristine and vinblastine. The nature of mutations, origins of mutant phenotypes and evolutionary importance of these mutants are discussed. PMID:24371160

  13. Adenovirus-mediated interleukin-12 gene transfer combined with cytosine deaminase followed by 5-fluorocytosine treatment exerts potent antitumor activity in Renca tumor-bearing mice

    International Nuclear Information System (INIS)

    Therapeutic gene transfer affords a clinically feasible and safe approach to cancer treatment but a more effective modality is needed to improve clinical outcomes. Combined transfer of therapeutic genes with different modes of actions may be a means to this end. Interleukin-12 (IL-12), a heterodimeric immunoregulatory cytokine composed of covalently linked p35 and p40 subunits, has antitumor activity in animal models. The enzyme/prodrug strategy using cytosine deaminase (CD) and 5-fluorocytosine (5-FC) has been used for cancer gene therapy. We have evaluated the antitumor effect of combining IL-12 with CD gene transfer in mice bearing renal cell carcinoma (Renca) tumors. Adenoviral vectors were constructed encoding one or both subunits of murine IL-12 (Ad.p35, Ad.p40 and Ad.IL-12) or cytosine deaminase (Ad.CD). The functionality of the IL-12 or CD gene products expressed from these vectors was validated by splenic interferon (IFN)-γ production or viability assays in cultured cells. Ad.p35 plus Ad.p40, or Ad.IL-12, with or without Ad.CD, were administered (single-dose) intratumorally to Renca tumor-bearing mice. The animals injected with Ad.CD also received 5-FC intraperitoneally. The antitumor effects were then evaluated by measuring tumor regression, mean animal survival time, splenic natural killer (NK) cell activity and IFN-γ production. The inhibition of tumor growth in mice treated with Ad.p35 plus Ad.p40 and Ad.CD, followed by injection of 5-FC, was significantly greater than that in mice treated with Ad.CD/5-FC, a mixture of Ad.p35 plus Ad.p40, or Ad.GFP (control). The combined gene transfer increased splenic NK cell activity and IFN-γ production by splenocytes. Ad.CD/5-FC treatment significantly increased the antitumor effect of Ad.IL-12 in terms of tumor growth inhibition and mean animal survival time. The results suggest that adenovirus-mediated IL-12 gene transfer combined with Ad.CD followed by 5-FC treatment may be useful for treating cancers

  14. Adenovirus-mediated interleukin-12 gene transfer combined with cytosine deaminase followed by 5-fluorocytosine treatment exerts potent antitumor activity in Renca tumor-bearing mice

    Directory of Open Access Journals (Sweden)

    Kim Samyong

    2005-05-01

    Full Text Available Abstract Background Therapeutic gene transfer affords a clinically feasible and safe approach to cancer treatment but a more effective modality is needed to improve clinical outcomes. Combined transfer of therapeutic genes with different modes of actions may be a means to this end. Interleukin-12 (IL-12, a heterodimeric immunoregulatory cytokine composed of covalently linked p35 and p40 subunits, has antitumor activity in animal models. The enzyme/prodrug strategy using cytosine deaminase (CD and 5-fluorocytosine (5-FC has been used for cancer gene therapy. We have evaluated the antitumor effect of combining IL-12 with CD gene transfer in mice bearing renal cell carcinoma (Renca tumors. Methods Adenoviral vectors were constructed encoding one or both subunits of murine IL-12 (Ad.p35, Ad.p40 and Ad.IL-12 or cytosine deaminase (Ad.CD. The functionality of the IL-12 or CD gene products expressed from these vectors was validated by splenic interferon (IFN-γ production or viability assays in cultured cells. Ad.p35 plus Ad.p40, or Ad.IL-12, with or without Ad.CD, were administered (single-dose intratumorally to Renca tumor-bearing mice. The animals injected with Ad.CD also received 5-FC intraperitoneally. The antitumor effects were then evaluated by measuring tumor regression, mean animal survival time, splenic natural killer (NK cell activity and IFN-γ production. Results The inhibition of tumor growth in mice treated with Ad.p35 plus Ad.p40 and Ad.CD, followed by injection of 5-FC, was significantly greater than that in mice treated with Ad.CD/5-FC, a mixture of Ad.p35 plus Ad.p40, or Ad.GFP (control. The combined gene transfer increased splenic NK cell activity and IFN-γ production by splenocytes. Ad.CD/5-FC treatment significantly increased the antitumor effect of Ad.IL-12 in terms of tumor growth inhibition and mean animal survival time. Conclusion The results suggest that adenovirus-mediated IL-12 gene transfer combined with Ad.CD followed by

  15. Modification of the cerebral perfusion during a chemotherapy by arabinoside cytosine (A.R.A.C.) among patients suffering of an acute myelo-blastic leukemia (A.M.L.)

    International Nuclear Information System (INIS)

    Cytosine arabinoside in high doses is a major treatment in acute myelo-blastic leukemia (A.M.L.). This treatment leads to neurological complications in 3-16% of cases, but the EEG, CT or MRI are normal.This prospective study examines brain perfusion in single photon emission tomography (SPECT) for patients receiving high dose arabinoside cytosine (H.D. A.R.A.C.). The SPECT of perfusion with hexamethyl propylene amine oxime (H.M.P.A.O.) for patients suffering of A.M.L. allowed to show a reduction of perfusion at the cerebellum level, of the occipito-parietal cortex and thalami, after conventional doses of A.R.A.C., while the patients had not any neurological accidents. (N.C.)

  16. Methylation by a unique α-class N4-cytosine methyltransferase is required for DNA transformation of Caldicellulosiruptor bescii DSM6725.

    Directory of Open Access Journals (Sweden)

    Daehwan Chung

    Full Text Available Thermophilic microorganisms capable of using complex substrates offer special advantages for the conversion of lignocellulosic biomass to biofuels and bioproducts. Members of the gram-positive bacterial genus Caldicellulosiruptor are anaerobic thermophiles with optimum growth temperatures between 65°C and 78°C and are the most thermophilic cellulolytic organisms known. In fact, they efficiently use biomass non-pretreated as their sole carbon source and in successive rounds of application digest 70% of total switchgrass substrate. The ability to genetically manipulate these organisms is a prerequisite to engineering them for use in conversion of these complex substrates to products of interest as well as identifying gene products critical for their ability to utilize non-pretreated biomass. Here, we report the first example of DNA transformation of a member of this genus, C. bescii. We show that restriction of DNA is a major barrier to transformation (in this case apparently absolute and that methylation with an endogenous unique α-class N4-Cytosine methyltransferase is required for transformation of DNA isolated from E. coli. The use of modified DNA leads to the development of an efficient and reproducible method for DNA transformation and the combined frequencies of transformation and recombination allow marker replacement between non-replicating plasmids and chromosomal genes providing the basis for rapid and efficient methods of genetic manipulation.

  17. 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. PMID:26335024

  18. Selective in vivo radiosensitization by 5-fluorocytosine of human colorectal carcinoma cells transduced with the E. coli cytosine deaminase (CD) gene

    International Nuclear Information System (INIS)

    Purpose: The E. coli cytosine deaminase (CD) gene encodes an enzyme capable of converting the nontoxic prodrug 5-fluorocytosine (5-FC) to 5-fluorouracil (5-FU), a known radiosensitizer. Having previously shown that combined CD suicide gene therapy and radiation (RT) results in pronounced radiosensitization in vitro, we progressed to in vivo studies of combined therapy. Methods and Materials: WiDr human colon cancer cells were transduced in vitro with the CD gene and cells expressing CD were selected for use as xenografts in a nude mouse model. After administration of 5-FC, tumors received 10-30 Gy local field radiation (RT) and tumor growth delay was compared to control animals receiving either 5-FU, 5-FC, or RT alone. Results: Maximal growth delay was seen in mice treated with 5-FC for 6 consecutive days prior to RT. Combined treatment with 15 Gy radiation resulted in a dose-modifying factor (DMF) of 1.50, and a greater DMF was observed with higher doses of radiation. There was no appreciable toxicity using this new approach. In contrast, a similar treatment of combined 5-FU and radiation resulted in considerable toxicity and no appreciable radiosensitization. Conclusion: The present results show that combined suicide gene therapy and RT results in pronounced antitumor effect without any notable toxicity. This indicates that the CD gene may be useful in the development of novel treatment strategies combining radiation and gene therapy in the treatment of locally advanced cancers

  19. Repair pathways in mammalian cells: Incision-ligation kinetics after UV, x-rays and mutagenic chemicals. Effects of 3-aminobenzamide and hydroxyurea + cytosine arabinoside

    International Nuclear Information System (INIS)

    Repair of DNA-damage involves the combined action of several enzyme functions. With regard to the incision step different pathways exist. In nucleotide excision repair an endonuclease recognizes the lesion, cuts the DNA strand and the faulty nucleotide is excised together with a number of undamaged nucleotides. This seems to be the process which operates in mammalian cells after exposure to UV and a number of chemicals which introduce so called bulky lesions in the DNA. After exposure to X-rays and simple alkylating chemicals such as methyl methanesulfonate. The first step involves the action of a glycosylase which only removes the damaged base. The incision is exercised by an endonuclease which recognises abasic sites. In this process, i.e. base excision repair, probably only the damaged nucleotide is exchanged. When the damaged piece of DNA has been removed one would imagine that, independently of the type of lesion initially present, the same types of enzymes could be used to close the gap in the strand, this seems, however, not to be the case. In this investigation the authors used 3-aminobenzamide (BA) or hydroxy urea (HU) combined with cytosine arabinoside (ara C) to study repair of damage induced by UV and a number of mutagenic chemicals. DNA strand breaks have been measured by the DNA-unwinding technique

  20. A new nuclear function of the Entamoeba histolytica glycolytic enzyme enolase: the metabolic regulation of cytosine-5 methyltransferase 2 (Dnmt2 activity.

    Directory of Open Access Journals (Sweden)

    Ayala Tovy

    2010-02-01

    Full Text Available Cytosine-5 methyltransferases of the Dnmt2 family function as DNA and tRNA methyltransferases. Insight into the role and biological significance of Dnmt2 is greatly hampered by a lack of knowledge about its protein interactions. In this report, we address the subject of protein interaction by identifying enolase through a yeast two-hybrid screen as a Dnmt2-binding protein. Enolase, which is known to catalyze the conversion of 2-phosphoglycerate (2-PG to phosphoenolpyruvate (PEP, was shown to have both a cytoplasmatic and a nuclear localization in the parasite Entamoeba histolytica. We discovered that enolase acts as a Dnmt2 inhibitor. This unexpected inhibitory activity was antagonized by 2-PG, which suggests that glucose metabolism controls the non-glycolytic function of enolase. Interestingly, glucose starvation drives enolase to accumulate within the nucleus, which in turn leads to the formation of additional enolase-E.histolytica DNMT2 homolog (Ehmeth complex, and to a significant reduction of the tRNA(Asp methylation in the parasite. The crucial role of enolase as a Dnmt2 inhibitor was also demonstrated in E.histolytica expressing a nuclear localization signal (NLS-fused-enolase. These results establish enolase as the first Dnmt2 interacting protein, and highlight an unexpected role of a glycolytic enzyme in the modulation of Dnmt2 activity.

  1. Studies on the antitumor activity and biochemical actions of cyclopentenyl cytosine against human colon carcinoma HT-29 in vitro and in vivo.

    Science.gov (United States)

    Gharehbaghi, K; Zhen, W; Fritzer-Szekeres, M; Szekeres, T; Jayaram, H N

    1999-01-01

    Cyclopentenyl cytosine (CPEC) is cytotoxic to several tumor cell lines. CPEC inhibits CTP synthesis resulting in depletion of cytidylate pools. The aim of this study was to examine CPEC's cytotoxic and antitumor activity in vitro and in vivo against human colon carcinoma HT-29, and to relate its action on CTP synthesis. CPEC exhibits potent cytotoxicity in vitro to HT-29 cells with an LC50 (concentration that is lethal to the survival of 50% cell colonies) of 2.4 microM and 0.46 microM following 2 h and 24 h exposure, respectively. Incubation of cells with CPEC for 2 h resulted in a dose-dependent decrease in cytidylate pools. The in vivo antitumor activity of CPEC in athymic mice transplanted subcutaneously (s.c.) with 3 million HT-29 cells was examined. Antitumor activity of CPEC was elucidated in early-staged tumor, wherein CPEC (1.5 mg/kg, QD x 9 or 3 mg/kg, QOD x 9) was administered intraperitoneally (i.p.) 24 h after tumor implantation and it resulted in a significant reduction in tumor weight to 48% of control. The effect of CPEC on established solid tumors in vivo was examined in athymic mice transplanted s.c. 14 days earlier with HT-29 cells and treated i.p. with 1.5 mg/kg CPEC, QD x 5 for 4 courses, with a 10 day-interval between courses. This treatment resulted in a significant reduction in tumor weight (72%) in the treated group. HPLC analysis of HT-29 tumor obtained from mice after treatment with CPEC showed a depletion of the CTP concentration reaching a nadir at 8 h. In conclusion, the present studies demonstrate potent antitumor activity of CPEC against freshly transplanted and established human colon carcinoma which can be corroborated with the drug's biochemical actions. PMID:10069488

  2. Incorporation of [14C]-orotic acid into DNA of regenerating rat liver results in a greater specific radioactivity of DNA-5-methylcytosines than DNA-cytosines

    International Nuclear Information System (INIS)

    To examine in vivo organization of events related to 5-methylcytosine (5-MC) occurrence in DNA, they determined the distribution of orotic acid incorporation into 5-MC vs cytosine (C) of rat liver DNA during liver compensatory hyperplasia. Rats were injected with 5 μCi of [6-14C]-orotic acid at 2 h intervals from 12 to 26 h post-partial hepatectomy. After a 2-h incorporation, livers were removed, DNA was isolated by Marmur's procedure and hydrolyzed by formic acid. Individual pyrimidines were isolated, quantitated by preparative and analytical high pressure liquid chromatography, and specific radioactivities determined. Two peaks of DNA synthesis were observed: a major peak at 18 h and a smaller peak at 22-24 h. The specific radioactivity of labeled thymine in DNA was approximately twice that of labeled C from 16 to 24 h. A more complex pattern was seen for labeling in 5-MC vs C during the same period. Values for 5-MC/C ratios increased to a maximum of 1.5 from 16 to 20 h, then decreased to 1.0 from 20 to 26 h. Thus in regenerating rat liver, [14C]-orotic acid label occurred to a 1.5-fold greater extent among DNA-5-MC than DNA-C during DNA synthesis. These results suggest the existence of mechanisms for: (a) preferential DNA synthesis in regions enriched in 5-MC content, or (b) different rates of turnover for 5-MC and C during DNA replication

  3. Dihydropyrimidine Dehydrogenase Is a Prognostic Marker for Mesenchymal Stem Cell-Mediated Cytosine Deaminase Gene and 5-Fluorocytosine Prodrug Therapy for the Treatment of Recurrent Gliomas

    Science.gov (United States)

    Chung, Taemoon; Na, Juri; Kim, Young-il; Chang, Da-Young; Kim, Young Il; Kim, Hyeonjin; Moon, Ho Eun; Kang, Keon Wook; Lee, Dong Soo; Chung, June-Key; Kim, Sung-Soo; Suh-Kim, Haeyoung; Paek, Sun Ha; Youn, Hyewon

    2016-01-01

    We investigated a therapeutic strategy for recurrent malignant gliomas using mesenchymal stem cells (MSC), expressing cytosine deaminase (CD), and prodrug 5-Fluorocytosine (5-FC) as a more specific and less toxic option. MSCs are emerging as a novel cell therapeutic agent with a cancer-targeting property, and CD is considered a promising enzyme in cancer gene therapy which can convert non-toxic 5-FC to toxic 5-Fluorouracil (5-FU). Therefore, use of prodrug 5-FC can minimize normal cell toxicity. Analyses of microarrays revealed that targeting DNA damage and its repair is a selectable option for gliomas after the standard chemo/radio-therapy. 5-FU is the most frequently used anti-cancer drug, which induces DNA breaks. Because dihydropyrimidine dehydrogenase (DPD) was reported to be involved in 5-FU metabolism to block DNA damage, we compared the survival rate with 5-FU treatment and the level of DPD expression in 15 different glioma cell lines. DPD-deficient cells showed higher sensitivity to 5-FU, and the regulation of DPD level by either siRNA or overexpression was directly related to the 5-FU sensitivity. For MSC/CD with 5-FC therapy, DPD-deficient cells such as U87MG, GBM28, and GBM37 showed higher sensitivity compared to DPD-high U373 cells. Effective inhibition of tumor growth was also observed in an orthotopic mouse model using DPD- deficient U87MG, indicating that DPD gene expression is indeed closely related to the efficacy of MSC/CD-mediated 5-FC therapy. Our results suggested that DPD can be used as a biomarker for selecting glioma patients who may possibly benefit from this therapy. PMID:27446484

  4. Benzo[a]pyrene diol epoxide suppresses retinoic acid receptor-β2 expression by recruiting DNA (cytosine-5--methyltransferase 3A

    Directory of Open Access Journals (Sweden)

    Xu Xiao-Chun

    2010-04-01

    Full Text Available Abstract Tobacco smoke is an important risk factor for various human cancers, including esophageal cancer. How benzo [a]pyrene diol epoxide (BPDE, a carcinogen present in tobacco smoke as well as in environmental pollution, induces esophageal carcinogenesis has yet to be defined. In this study, we investigated the molecular mechanism responsible for BPDE-suppressed expression of retinoic acid receptor-beta2 (RAR-β2 in esophageal cancer cells. We treated esophageal cancer cells with BPDE before performing methylation-specific polymerase chain reaction (MSP to find that BPDE induced methylation of the RAR-β2 gene promoter. We then performed chromatin immunoprecipitation (ChIP assays to find that BPDE recruited genes of the methylation machinery into the RAR-β2 gene promoter. We found that BPDE recruited DNA (cytosine-5--methyltransferase 3 alpha (DNMT3A, but not beta (DNMT3B, in a time-dependent manner to methylate the RAR-β2 gene promoter, which we confirmed by reverse transcription-polymerase chain reaction (RT-PCR analysis of the reduced RAR-β2 expression in these BPDE-treated esophageal cancer cell lines. However, BPDE did not significantly change DNMT3A expression, but it slightly reduced DNMT3B expression. DNA methylase inhibitor 5-aza-2'-deoxycytidine (5-Aza and DNMT3A small hairpin RNA (shRNA vector antagonized the effects of BPDE on RAR-β2 expressions. Transient transfection of the DNMT3A shRNA vector also antagonized BPDE's effects on expression of RAR-β2, c-Jun, phosphorylated extracellular signal-regulated protein kinases 1/2 (ERK1/2, and cyclooxygenase-2 (COX-2, suggesting a possible therapeutic effect. The results of this study form the link between the esophageal cancer risk factor BPDE and the reduced RAR-β2 expression.

  5. Atypical epigenetic mark in an atypical location: cytosine methylation at asymmetric (CNN sites within the body of a non-repetitive tomato gene

    Directory of Open Access Journals (Sweden)

    Iusem Norberto D

    2011-05-01

    Full Text Available Abstract Background Eukaryotic DNA methylation is one of the most studied epigenetic processes, as it results in a direct and heritable covalent modification triggered by external stimuli. In contrast to mammals, plant DNA methylation, which is stimulated by external cues exemplified by various abiotic types of stress, is often found not only at CG sites but also at CNG (N denoting A, C or T and CNN (asymmetric sites. A genome-wide analysis of DNA methylation in Arabidopsis has shown that CNN methylation is preferentially concentrated in transposon genes and non-coding repetitive elements. We are particularly interested in investigating the epigenetics of plant species with larger and more complex genomes than Arabidopsis, particularly with regards to the associated alterations elicited by abiotic stress. Results We describe the existence of CNN-methylated epialleles that span Asr1, a non-transposon, protein-coding gene from tomato plants that lacks an orthologous counterpart in Arabidopsis. In addition, to test the hypothesis of a link between epigenetics modifications and the adaptation of crop plants to abiotic stress, we exhaustively explored the cytosine methylation status in leaf Asr1 DNA, a model gene in our system, resulting from water-deficit stress conditions imposed on tomato plants. We found that drought conditions brought about removal of methyl marks at approximately 75 of the 110 asymmetric (CNN sites analysed, concomitantly with a decrease of the repressive H3K27me3 epigenetic mark and a large induction of expression at the RNA level. When pinpointing those sites, we observed that demethylation occurred mostly in the intronic region. Conclusions These results demonstrate a novel genomic distribution of CNN methylation, namely in the transcribed region of a protein-coding, non-repetitive gene, and the changes in those epigenetic marks that are caused by water stress. These findings may represent a general mechanism for the

  6. Electron spin resonance and intermediate neglect of differential overlap molecular orbital study of the π cations of (hydroxymethyl)uracil and (hydroxymethyl)cytosine. Evidence for internal hydrogen bonding

    International Nuclear Information System (INIS)

    The π-cation radicals of 5-(hydroxymethyl)uracil (HOMeU) and 5-(hydroxymethyl)cytosine (HOMeC) have been produced by Cl2- attack in γ-irradiated basic 12 M LiCl and photoionization in basic 8 M NaClO4 glasses at low temperatures. Analysis of the ESR spectra found for these radicals shows that each of the π-cation radicals converts to another species probably by a change in a nitrogen protonation state as the temperature is raised. For example, 5-(hydroxymethyl)uracil cation shows a 28.5-G average splitting for the two hydroxymethyl-group β protons which convert upon annealing to a 36-G splitting. The splittings and the narrowness of the line widths found after annealing are suggestive of a configuration which is intramolecularly rigid and stabilized by a intramolecular hydrogen bond from the hydroxyl proton to the 4-position oxygen. The π cation of 5-(hydroxymethyl)cytosine converts to a radical with substantial spin density on the exocyclic nitrogen which again shows strong evidence for intramolecular hydrogen bonding. Final radicals are found to be produced from the π-cation radicals of (hydroxymethyl)uracil and (hydroxymethyl)cytosine by deprotonation of a methylene proton. INDO calculations for the π cation of (hydroxymethyl)uracil as a function of orientation of the hydroxyl group show that the hydrogen bond to the 4-position oxygen increases in strength by a factor of 3 upon deprotonation at the 3-position nitrogen. The hydrogen bond is therefore predicted to substantially stabilize the π-cation radical

  7. A Ser29Leu substitution in the cytosine deaminase Fca1p is responsible for clade-specific flucytosine resistance in Candida dubliniensis.

    LENUS (Irish Health Repository)

    McManus, Brenda A

    2009-11-01

    The population structure of the opportunistic yeast pathogen Candida dubliniensis is composed of three main multilocus sequence typing clades (clades C1 to C3), and clade C3 predominantly consists of isolates from the Middle East that exhibit high-level resistance (MIC(50) > or = 128 microg\\/ml) to the fungicidal agent flucytosine (5FC). The close relative of C. dubliniensis, C. albicans, also exhibits clade-specific resistance to 5FC, and resistance is most commonly mediated by an Arg101Cys substitution in the FUR1 gene encoding uracil phosphoribosyltransferase. Broth microdilution assays with fluorouracil (5FU), the toxic deaminated form of 5FC, showed that both 5FC-resistant and 5FC-susceptible C. dubliniensis isolates exhibited similar 5FU MICs, suggesting that the C. dubliniensis cytosine deaminase (Fca1p) encoded by C. dubliniensis FCA1 (CdFCA1) may play a role in mediating C. dubliniensis clade-specific 5FC resistance. Amino acid sequence analysis of the CdFCA1 open reading frame (ORF) identified a homozygous Ser29Leu substitution in all 12 5FC-resistant isolates investigated which was not present in any of the 9 5FC-susceptible isolates examined. The tetracycline-inducible expression of the CdFCA1 ORF from a 5FC-susceptible C. dubliniensis isolate in two separate 5FC-resistant clade C3 isolates restored susceptibility to 5FC, demonstrating that the Ser29Leu substitution was responsible for the clade-specific 5FC resistance and that the 5FC resistance encoded by FCA1 genes with the Ser29Leu transition is recessive. Quantitative real-time PCR analysis showed no significant difference in CdFCA1 expression between 5FC-susceptible and 5FC-resistant isolates in either the presence or the absence of subinhibitory concentrations of 5FC, suggesting that the Ser29Leu substitution in the CdFCA1 ORF is the sole cause of 5FC resistance in clade C3 C. dubliniensis isolates.

  8. Pharmacokinetic Profile and Acute Toxicological Properties of a Novel Radiosensitizer Cytosine-Phosphate-Guanosine Oligodeoxynucleotide 107 in Mice Following Intravenous and Orthotopic Administration.

    Science.gov (United States)

    Cen, Yanyan; Li, Xiaoli; Yin, Zhiwei; Yan, Zifei; Liu, Dan; Peng, Wei; Pan, Feng; Zhou, Hong

    2015-10-01

    The synthetic cytosine-phosphate-guanosine oligodeoxynucleotide 107 (CpG ODN107) is a novel radiosensitizer for glioma treatment. However, the information related to its pharmacokinetics and toxicity remains unclear. Therefore, the plasma pharmacokinetics, distribution, elimination, and acute toxicity of CpG ODN107 in mice were investigated in the present experiments. The results from the liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay showed that the plasma elimination half-life (t1/2β) of CpG ODN107 in BALB/c mice varied slightly with the dose, and it was 0.65, 0.49, and 0.50 h at the intravenous doses of 2.5, 5, and 10 mg/kg, respectively. CpG ODN107 rapidly and widely distributed in organs/tissues, except the brain and testes. The highest concentrations were found in the liver (28.6% of the administered dose after 0.5 h) and the kidneys (5.7% of the administered dose after 1 h). CpG ODN107 (0.3, 3, and 30 μg/mL) could highly bind to human and mouse plasma proteins in vitro. CpG ODN107 in the forms of prototype was excreted in urine (1.79%) and feces (0.91%), and its shortened metabolites were excreted in urine (2.1%) and feces (2.2%) within the first 24 h. The mice in vivo optical image showed CpG ODN107 labeled with Alexa Fluor 680 fluorochrome (AF680) accumulated in the brain after orthotopic injection, eliminated very slowly, and excreted in urine compared with poly T labeled with AF680. The median lethal dose (LD50) of CpG ODN107 was 75.7 mg/kg for mice; this dose only could produce apparent spleen and liver damage, in line with the distribution features of CpG ODN. In conclusion, our present pharmacokinetic and toxicity investigation will provide helpful information to further pharmacodynamic and pharmacokinetic research of CpG ODN107 and other oligodeoxynucleotide drugs in the future. PMID:26213852

  9. Selective antitumor effect of neural stem cells expressing cytosine deaminase and interferon-beta against ductal breast cancer cells in cellular and xenograft models

    Directory of Open Access Journals (Sweden)

    Bo-Rim Yi

    2014-01-01

    Full Text Available Due to their inherent tumor-tropic properties, genetically engineered stem cells may be advantageous for gene therapy treatment of various human cancers, including brain, liver, ovarian, and prostate malignancies. In this study, we employed human neural stem cells (HB1.F3; hNSCs transduced with genes expressing Escherichia coli cytosine deaminase (HB1.F3.CD and human interferon-beta (HB1.F3.CD.IFN-β as a treatment strategy for ductal breast cancer. CD can convert the prodrug 5-fluorocytosine (5-FC to its active chemotherapeutic form, 5-fluorouracil (5-FU, which induces a tumor-killing effect through DNA synthesis inhibition. IFN-β also strongly inhibits tumor growth by the apoptotic process. RT-PCR confirmed that HB1.F3.CD cells expressed CD and HB1.F3.CD.IFN-β cells expressed both CD and IFN-β. A modified transwell migration assay showed that HB1.F3.CD and HB1.F3.CD.IFN-β cells selectively migrated toward MCF-7 and MDA-MB-231 human breast cancer cells. In hNSC-breast cancer co-cultures the viability of breast cancer cells which were significantly reduced by HB1.F3.CD or HB1.F3.CD.IFN-β cells in the presence of 5-FC. The tumor inhibitory effect was greater with the HB1.F3.CD.IFN-β cells, indicating an additional effect of IFN-β to 5-FU. In addition, the tumor-tropic properties of these hNSCs were found to be attributed to chemoattractant molecules secreted by breast cancer cells, including stem cell factor (SCF, c-kit, vascular endothelial growth factor (VEGF, and VEGF receptor 2. An in vivo assay performed using MDA-MB-231/luc breast cancer mammary fat pad xenografts in immunodeficient mice resulted in 50% reduced tumor growth and increased long-term survival in HB1.F3.CD and HB1.F3.CD.IFN-β plus 5-FC treated mice relative to controls. Our results suggest that hNSCs genetically modified to express CD and/or IFN-β genes can be used as a novel targeted cancer gene therapy.

  10. Preliminary study of MR diffusion weighted imaging in nude mice models of hepatic Bel7402 tumors after adenovirus-mediated cytosine diaminase-thymidine kinase gene therapy

    International Nuclear Information System (INIS)

    Objective: To study the characteristics of DWI in nude mice models of hepatic Bel7402 tumors after treatment with adenovirus-mediated cytosine diaminase-thymidine kinase (Ad. CD-TK) double suicide gene therapy, and then to identify whether DWI can be used for assessing curative effect of postoperative tumors. Methods: Thirty nude mice models of hepatic Bel7402 tumors were successfully created using cell suspension method, after the tumor grew to more than 1 cm in diameter, 20 tumor models were treated by intratumoral administration of Ad. CD-TK for 3 days plus intraperitonea (i.p.) treatment with 5-Fc and GCV for the duration of the study.Then they were randomly divided into three groups during 5-Fc and GCV treatment. The remaining 10 tumor models were used as controls. MR scanning were performed in 10th day before and after tumor implantation in all models by using EPI-SE series and SENSE technology for treatment group. Tumor volumes and ADC values were calculated pretreatment and posttreatment. Cell apoptosis were determined by using TUNEL method. Analyze the change of ADC and apoptosis index (AI) in different times, t test was used for comparison the difference of AI and ADC values respectively. Results: After 10 days,the tumor volumes of the treatment groups and controls were respectively (724.16 ±57.45) mm3, (754.57 ± 66.84) mm3, with no significant difference (t=0.488, P >0.05). The ADC values of the treatment groups were (0.98 ±0.11) × 10-3 mm2/s,the ones of the control groups were (0.68 ±0.04) × 10-3 mm2/s; AI of the treatment groups were (23.25 ±6.57)%, the ones of the control groups were (2.57 ± 0.58)%. There were difference in both groups (t=4.473, 5.874; P<0.01). Conclusion: DWI can be effectively to monitor the early pathological changes of hepatic Bel7402 tumors after Ad. CD-TK double suicide gene therapy, and provide experimental evidences for clinical application. (authors)

  11. Clofarabine in combination with a standard remission induction regimen (cytosine arabinoside and idarubicin) in patients with previously untreated intermediate and bad-risk acute myelogenous leukemia (AML) or high-risk myelodysplastic syndrome (HR-MDS): phase I results of an ongoing phase I/II study of the leukemia groups of EORTC and GIMEMA (EORTC GIMEMA 06061/AML-14A trial)

    NARCIS (Netherlands)

    Willemze, R.; Suciu, S.; Muus, P.; Halkes, C.J.; Meloni, G.; Meert, L.; Karrasch, M.; Rapion, J.; Vignetti, M.; Amadori, S.; Witte, T.J.M. de; Marie, J.P.

    2014-01-01

    This study aims to determine the maximum tolerated dose (MTD) of clofarabine combined with the EORTC-GIMEMA 3 + 10 induction regimen (idarubicin + cytosine arabinoside) in adults with untreated acute myelogenous leukemia or high-risk myelodysplastic syndrome. In this phase I trial, 25 patients (medi

  12. Remarkable induction of UV-signature mutations at the 3'-cytosine of dipyrimidine sites except at 5'-TCG-3' in the UVB-exposed skin epidermis of xeroderma pigmentosum variant model mice.

    Science.gov (United States)

    Ikehata, Hironobu; Chang, Yumin; Yokoi, Masayuki; Yamamoto, Masayuki; Hanaoka, Fumio

    2014-10-01

    The human POLH gene is responsible for the variant form of xeroderma pigmentosum (XP-V), a genetic disease highly susceptible to cancer on sun-exposed skin areas, and encodes DNA polymerase η (polη), which is specialized for translesion DNA synthesis (TLS) of UV-induced DNA photolesions. We constructed polη-deficient mice transgenic with lacZ mutational reporter genes to study the effect of Polh null mutation (Polh(-/-)) on mutagenesis in the skin after UVB irradiation. UVB induced lacZ mutations with remarkably higher frequency in the Polh(-/-) epidermis and dermis than in the wild-type (Polh(+/+)) and heterozygote. DNA sequences of a hundred lacZ mutants isolated from the epidermis of four UVB-exposed Polh(-/-) mice were determined and compared with mutant sequences from irradiated Polh(+)(/)(+) mice. The spectra of the mutations in the two genotypes were both highly UV-specific and dominated by C→T transitions at dipyrimidines, namely UV-signature mutations. However, sequence preferences of the occurrence of UV-signature mutations were quite different between the two genotypes: the mutations occurred at a higher frequency preferentially at the 5'-TCG-3' sequence context than at the other dipyrimidine contexts in the Polh(+/+) epidermis, whereas the mutations were induced remarkably and exclusively at the 3'-cytosine of almost all dipyrimidine contexts with no preference for 5'-TCG-3' in the Polh(-/-) epidermis. In addition, in Polh(-/-) mice, a small but remarkable fraction of G→T transversions was also observed exclusively at the 3'-cytosine of dipyrimidine sites, strongly suggesting that these transversions resulted not from oxidative damage but from UV photolesions. These results would reflect the characteristics of the error-prone TLS functioning in the bypass of UV photolesions in the absence of polη, which would be mediated by mechanisms based on the two-step model of TLS. On the other hand, the deamination model would explain well the mutation

  13. Post-UV survival and mutagenesis in DNA repair-proficient and -deficient strains of Escherichia coli K-12 grown in 5-azacytidine to inhibit DNA cytosine methylation: evidence for mutagenic excision repair.

    Science.gov (United States)

    Radnedge, L; Pinney, R J

    1993-03-01

    Inhibition of cytosine methylation by growth in 5-azacytidine (5-azaC), did not affect the sensitivities to DNA damage induced by exposure to ultraviolet light (UV) of Escherichia coli K-12 strains AB1157 dcm+, which is fully DNA repair-proficient, LR68 (a dcm derivative of AB1157), JC3890 dcm+ uvrB, deficient in error-free excision repair, TK702 dcm+ umuC, deficient in error-prone repair, or TK501 dcm+ uvrB umuC, which lacks both excision repair and error-prone repair. However, growth in 5-azaC increased the post-UV survival of strains AB2463 recA(Def), AB2470 recB and AB2494 lexA(Ind-), which are deficient in the induction or expression of recombination repair or error-prone repair of DNA. Spontaneous mutation frequencies were increased in strains LR68, AB2463, AB2470 and AB2494 by growth in 5-azaC, but remained unaltered in strains AB1157, JC3890, TK702 or TK501. Growth in 5-azaC significantly increased UV-induced mutation frequencies in strains AB2463 and AB2470, significantly reduced UV-induced mutation in strain JC3890, but had little effect on UV-induced mutation in the other strains. The results suggest that 5-azaC may induce a normally error-free DNA repair pathway to become error-prone and therefore genotoxic. PMID:7683337

  14. Therapeutic trial of intensified conditioning regimen with high-dose cytosine arabinoside, cyclophosphamide and either total body irradiation or busulfan followed by allogeneic bone marrow transplantation for myelodysplastic syndrome in children

    Energy Technology Data Exchange (ETDEWEB)

    Nagatoshi, Yoshihisa; Okamura, Jun; Ikuno, Yoshiko; Akamatsu, Minoru; Tasaka, Hideko [National Kyushu Cancer Center, Fukuoka (Japan)

    1997-04-01

    Ten children with myelodysplastic syndrome underwent an allogeneic bone marrow transplantation (BMT) with an intensified conditioning regimen. The median age of the patients was 8 years (range 2-10), and included 6 males and 4 females. The subtype of the disease was refractory anemia (RA) in 4, RA with excess blasts (RAEB) in 4, RAEB in transformation (RAEB-T) in 1, and juvenile chronic myelogenous leukemia (JCML) in 1. All patients were conditioned with high-dose cytosine arabinoside (12000 mg/m{sup 2}), cyclophosphamide (120 mg/kg) and either total body irradiation (10-13.2 Gy) or busulfan (16 mg/kg or 560 mg/m{sup 2}). Cyclosporine A and/or methotrexate were used for the prophylaxis of graft-versus-host disease (GVHD). Engraftment was prompt in all but one patient. Severe acute GVHD (grade 3) (n=1), interstitial pneumonitis (n=1) and veno-occlusive disease of the liver (n=1) occurred. The disease relapsed in one patient with RAEB-T. Seven of the 10 patients were alive and disease free 2-74 months after BMT. The disease-free survival rate at 4 years was 69{+-}15%. All surviving patients were in the full performance status. The examined children with MDS tolerated this intensified conditioning regimen well. (author)

  15. 5-Azacytidine-induced reactivation of the human X chromosome-linked PGK1 gene is associated with a large region of cytosine demethylation in the 5 prime CpG island

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, R.S.; Gartler, S.M. (Univ. of Washington, Seattle (USA))

    1990-06-01

    Hamster-human cell hybrids containing an inactive human X chromosome were treated with 5-azacytidine and derived clones were examined for phosphoglycerate kinase activity and cytosine methylation in the human PGK1 (X chromosome-linked phosphoglycerate kinase) gene. Comparisons between expressing and nonexpressing clones indicated that demethylation of several methylation-sensitive restriction sites outside of the 5{prime} CpG island were unnecessary for expression. High-resolution polyacrylamide gel analysis of 25 Hpa II, Hha I, and Tha I sites revealed that all clones expressing PGK1 were unmethylated in a large region of the CpG island that includes the transcription start site and 400 base pairs upstream. Many nonexpressing clones had discontinuous patterns of demethylation. Remethylation was often observed in subclones of nonexpressing hybrids. These data suggest that a specific zone of methylation-free DNA within the PGK1 promoter is required for transcription. In addition, the presence of neighboring methylcytosines appears to decrease the heritable stability of unmethylated CpGs in this region.

  16. 5-Azacytidine-induced reactivation of the human X chromosome-linked PGK1 gene is associated with a large region of cytosine demethylation in the 5' CpG island.

    Science.gov (United States)

    Hansen, R S; Gartler, S M

    1990-01-01

    Hamster-human cell hybrids containing an inactive human X chromosome were treated with 5-azacytidine and derived clones were examined for phosphoglycerate kinase activity and cytosine methylation in the human PGK1 (X chromosome-linked phosphoglycerate kinase) gene. Comparisons between expressing and nonexpressing clones indicated that demethylation of several methylation-sensitive restriction sites outside of the 5' CpG island were unnecessary for expression. High-resolution polyacrylamide gel analysis of 25 Hpa II, Hha I, and Tha I sites revealed that all clones expressing PGK1 were unmethylated in a large region of the CpG island that includes the transcription start site and 400 base pairs upstream. Many nonexpressing clones had discontinuous patterns of demethylation. Remethylation was often observed in subclones of nonexpressing hybrids. These data suggest that a specific zone of methylation-free DNA within the PGK1 promoter is required for transcription. In addition, the presence of neighboring methylcytosines appears to decrease the heritable stability of unmethylated CpGs in this region. Images PMID:1693431

  17. Post-UV survival and mutagenesis in DNA repair-proficient and -deficient strains of Escherichia coli K-12 grown in 5-azacytidine to inhibit DNA cytosine methylation: evidence for mutagenic excision repair

    International Nuclear Information System (INIS)

    Inhibition of cytosine methylation by growth in 5-azacytidine (5-azaC), did not affect the sensitivities to DNA damage induced by exposure to ultraviolet light (UV) of Escherichia coli K-12 strains AB1157 dcm+, which is fully DNA repair-proficient, LR68 (a dcm derivative of AB1157), JC3890 dcm+ uvr B, deficient in error-free excision repair, TK702 dcm+ umuC, deficient in error-prone repair, or TK501 dcm+ uvrB umuC, which lacks both excision repair and error-prone repair. However, growth in 5-azaC increased the post-UV survival of strains AB2463 recA(Def), AB2470 recB and AB2494 lexA(Ind-), which are deficient in the induction or expression of recombination repair or error-prone repair of DNA. Spontaneous mutation frequencies were increased in strains LR68, AB2463, AB2470 and AB2494 by growth in 5-azaC, but remained unaltered in strains AB1157, JC3890, TK702 or TK501. Growth in 5-azaC significantly increased UV-induced mutation frequencies in strains AB2463 and AB2470, significantly reduced UV-induced mutation in strain JC3890, but had little effect on UV-induced mutation in the other strains. The results suggest that 5-azaC may induce a normally error-free DNA repair pathway to become error-prone and therefore genotoxic. (Author)

  18. Human Sulfatase-1 Improves the Effectiveness of Cytosine Deaminase Suicide Gene Therapy with 5-Fluorocytosine Treatment on Hepatocellular Carcinoma Cell Line HepG2 In Vitro and In Vivo

    Institute of Scientific and Technical Information of China (English)

    Xiao-Ping Yang; Ling Liu; Ping Wang; Sheng-Lin Ma

    2015-01-01

    Background:Human sulfatase-1 (Hsulf-l) is an endosulfatase that selectively removes sulfate groups from heparan sulfate proteoglycans (HSPGs),altering the binding of several growth factors and cytokines to HSPG to regulate cell proliferation,cell motility,and apoptosis.We investigated the role of combined cancer gene therapy with Hsulf-l and cytosine deaminase/5-fluorocytosine (CD/5-FC) suicide gene on a hepatocellular carcinoma (HCC) cell line,HepG2,in vitro and in vivo.Methods:Reverse transcription polymerase chain reaction and immunohistochemistry were used to determine the expression of Hsulf-1 in HCC.Cell apoptosis was observed through flow cytometry instrument and mechanism of Hsulf-1 to enhance the cytotoxicity of 5-FC against HCC was analyzed in HCC by confocal microscopy.We also establish a nude mice model of HCC to address the effect of Hsulf-1 expression on the CD/5-FC suicide gene therapy in vivo.Results:A significant decrease in HepG2 cell proliferation and an increase in HepG2 cell apoptosis were observed when Hsulf-1 expression was combined with the CD/5-FC gene suicide system.A noticeable bystander effect was observed when the Hsulf-1 and CD genes were co-expressed.Intracellular calcium was also increased after HepG2 cells were infected with the Hsulf-1 gene.In vivo studies showed that the suppression of tumor growth was more pronounced in animals treated with the Hsulf-1 plus CD than those treated with either gene therapy alone,and the combined treatment resulted in a significant increase in survival.Conclusions:Hsulf-1 expression combined with the CD/5-FC gene suicide system could be an effective treatment approach for HCC.

  19. Post-UV survival and mutagenesis in DNA repair-proficient and -deficient strains of Escherichia coli K-12 grown in 5-azacytidine to inhibit DNA cytosine methylation: evidence for mutagenic excision repair

    Energy Technology Data Exchange (ETDEWEB)

    Radnedge, L.; Pinney, R.J. (London Univ. (United Kingdom). Dept. of Pharmaceutics)

    1993-03-01

    Inhibition of cytosine methylation by growth in 5-azacytidine (5-azaC), did not affect the sensitivities to DNA damage induced by exposure to ultraviolet light (UV) of Escherichia coli K-12 strains AB1157 dcm[sup +], which is fully DNA repair-proficient, LR68 (a dcm derivative of AB1157), JC3890 dcm[sup +] uvr B, deficient in error-free excision repair, TK702 dcm[sup +] umuC, deficient in error-prone repair, or TK501 dcm[sup +] uvrB umuC, which lacks both excision repair and error-prone repair. However, growth in 5-azaC increased the post-UV survival of strains AB2463 recA(Def), AB2470 recB and AB2494 lexA(Ind[sup -]), which are deficient in the induction or expression of recombination repair or error-prone repair of DNA. Spontaneous mutation frequencies were increased in strains LR68, AB2463, AB2470 and AB2494 by growth in 5-azaC, but remained unaltered in strains AB1157, JC3890, TK702 or TK501. Growth in 5-azaC significantly increased UV-induced mutation frequencies in strains AB2463 and AB2470, significantly reduced UV-induced mutation in strain JC3890, but had little effect on UV-induced mutation in the other strains. The results suggest that 5-azaC may induce a normally error-free DNA repair pathway to become error-prone and therefore genotoxic. (Author).

  20. Human Sulfatase-1 Improves the Effectiveness of Cytosine Deaminase Suicide Gene Therapy with 5-Fluorocytosine Treatment on Hepatocellular Carcinoma Cell Line HepG2 In Vitro and In Vivo

    Directory of Open Access Journals (Sweden)

    Xiao-Ping Yang

    2015-01-01

    Full Text Available Background: Human sulfatase-1 (Hsulf-1 is an endosulfatase that selectively removes sulfate groups from heparan sulfate proteoglycans (HSPGs, altering the binding of several growth factors and cytokines to HSPG to regulate cell proliferation, cell motility, and apoptosis. We investigated the role of combined cancer gene therapy with Hsulf-1 and cytosine deaminase/5-fluorocytosine (CD/5-FC suicide gene on a hepatocellular carcinoma (HCC cell line, HepG2, in vitro and in vivo. Methods: Reverse transcription polymerase chain reaction and immunohistochemistry were used to determine the expression of Hsulf-1 in HCC. Cell apoptosis was observed through flow cytometry instrument and mechanism of Hsulf-1 to enhance the cytotoxicity of 5-FC against HCC was analyzed in HCC by confocal microscopy. We also establish a nude mice model of HCC to address the effect of Hsulf-1 expression on the CD/5-FC suicide gene therapy in vivo. Results: A significant decrease in HepG2 cell proliferation and an increase in HepG2 cell apoptosis were observed when Hsulf-1 expression was combined with the CD/5-FC gene suicide system. A noticeable bystander effect was observed when the Hsulf-1 and CD genes were co-expressed. Intracellular calcium was also increased after HepG2 cells were infected with the Hsulf-1 gene. In vivo studies showed that the suppression of tumor growth was more pronounced in animals treated with the Hsulf-1 plus CD than those treated with either gene therapy alone, and the combined treatment resulted in a significant increase in survival. Conclusions: Hsulf-1 expression combined with the CD/5-FC gene suicide system could be an effective treatment approach for HCC.

  1. Clofarabine in combination with a standard remission induction regimen (cytosine arabinoside and idarubicin) in patients with previously untreated intermediate and bad-risk acute myelogenous leukemia (AML) or high-risk myelodysplastic syndrome (HR-MDS): phase I results of an ongoing phase I/II study of the leukemia groups of EORTC and GIMEMA (EORTC GIMEMA 06061/AML-14A trial).

    Science.gov (United States)

    Willemze, R; Suciu, S; Muus, P; Halkes, C J M; Meloni, G; Meert, L; Karrasch, M; Rapion, J; Vignetti, M; Amadori, S; de Witte, T; Marie, J P

    2014-06-01

    This study aims to determine the maximum tolerated dose (MTD) of clofarabine combined with the EORTC-GIMEMA 3 + 10 induction regimen (idarubicin + cytosine arabinoside) in adults with untreated acute myelogenous leukemia or high-risk myelodysplastic syndrome. In this phase I trial, 25 patients (median age 56 years) received 5 days of clofarabine as 1-h infusion (arm A) or push injection (arm B) at the dose level of 5 × 10 or 5 × 15 mg/m(2)/day in an algorithmic dose escalation 3 + 3 design. A consolidation course (intermediate dose cytosine arabinoside, idarubicin) was planned for patients in complete remission (CR). Primary endpoint was safety and tolerance as measured by dose limiting toxicity (DLT); secondary endpoints were response rate, other grade III/IV toxicities, and hematological recovery after induction and consolidation. Five DLTs were observed (in arm A: one DLT at 10 mg/m(2)/day, three at 15 mg/m(2)/day; in arm B: one DLT at 15 mg/m(2)/day). Three patients receiving 15 mg/m(2)/day were withdrawn due to adverse events not classified as DLT. Prolonged hypoplasia was observed in five patients. CR + complete remission with incomplete recovery were achieved in 21 patients (11/12 (92 %) receiving clofarabine 10 mg/m(2)/day; 10/13 (77 %) receiving clofarabine 15 mg/m(2)/day). Clofarabine, 5 × 10 mg/m(2)/day, resulted in one DLT and no early treatment withdrawals. MTD of clofarabine combined with cytosine arabinoside and idarubicin is 5 × 10 mg/m(2)/day. PMID:24682421

  2. Cytotoxic effect of replication-competent adenoviral vectors carrying L-plastin promoter regulated E1A and cytosine deaminase genes in cancers of the breast, ovary and colon.

    Science.gov (United States)

    Akbulut, Hakan; Zhang, Lixin; Tang, Yucheng; Deisseroth, Albert

    2003-05-01

    Prodrug activating transcription unit gene therapy is one of several promising approaches to cancer gene therapy. Combining that approach with conditionally replication-competent viral vectors that are truly tumor specific has been an important objective of recent work. In this study, we report the construction of a new conditionally replication-competent bicistronic adenoviral vector in which the cytosine deaminase (CD) gene and the E1a gene are driven by the L-plastin tumor-specific promoter (AdLpCDIRESE1a). A similar vector driven by the CMV promoter has also been constructed (AdCMVCDIRESE1a) as a control. We have carried out in vitro cytotoxicity in carcinomas of the breast, ovary and colon, and in vivo efficacy studies with these vectors in an animal model of colon cancer. While the addition of the AdLpCDIRESE1a vector to established cancer cell lines showed significant cytotoxicity in tumor cells derived from carcinomas of the breast (MCF-7), colon (HTB-38) and ovary (Ovcar 5), no significant toxicity was seen in explant cultures of normal human mammary epithelial cells (HMEC) exposed to this vector. The addition of 5-fluorocytosine (5FC) significantly increased the cytotoxicity in an additive fashion of both the AdLpCDIRESE1a and AdCMVCDIRESE1a vectors as well as that of the AdLpCD replication incompetent vector to established tumor cell lines. However, no significant cytotoxicity was observed with the addition of 5FC to explant cultures of normal human mammary epithelial cells that had been exposed to the L-plastin-driven vectors. Studies with mixtures of infected and uninfected tumor cell lines showed that the established cancer cell lines infected with the AdLpCDIRESE1a vector generated significant toxicity to surrounding uninfected cells (the "bystander effect") even at a ratio of 0.25 of infected cells to infected + uninfected cells in the presence of 5FC. The injection of the AdLpCDIRESE1a vector into subcutaneous deposits of human tumor nodules in the

  3. Theoretical study of metal ion binding in modified and natural cytosine-cytosine base pairs

    Czech Academy of Sciences Publication Activity Database

    Šebera, Jakub; Sugiyama, K.; Ono, A.; Mulder, J.; Bickelhaupt, F. M.; Tanaka, Y.; Sychrovský, Vladimír; Guerra, C. F.

    2013-01-01

    Roč. 20, č. 1 (2013), s. 39-39. ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /11./. 14.03.2013-16.03.2013, Nové Hrady] R&D Projects: GA ČR GAP205/10/0228; GA ČR(CZ) GAP304/10/1951; GA TA ČR TA01011165 Institutional support: RVO:61388963 Keywords : DFT * NMR * base pair * metal-mediated Subject RIV: CF - Physical ; Theoretical Chemistry

  4. Hydroxyl Radical Reaction with the Guanine-Cytosine Base Pair:A Density Functional Theory Study%羟基自由基和鸟嘌呤-胞嘧啶碱基对反应的密度泛函理论研究

    Institute of Scientific and Technical Information of China (English)

    李敏杰; 刁玲; 寇莉; 李重杲; 陆文聪

    2015-01-01

    To address problems such as aging, mutation, and cancer, it is of great importance to understand the damage mechanism of DNA induced by hydroxyl radical. In this study, the abstraction reaction mechanism of hydroxyl radical with guanine-cytosine (GC) base pair in aqueous phase under the polarized continuum model (PCM) has been explored by using density functional theory (DFT). The results indicated that al the abstraction reactions in GC base pair were thermodynamical y exothermic, and the stability of dehydrogenation radicals decreased in the order of (H2b-GC)•>(GC-H4b)•>(GC-H6)•>(GC-H5)•~(H8-GC)•. The reaction energy of H2b abstraction pathway was the lowest among al investigated pathways, thus indicating that the reaction conversion of (H2b-GC)•was the highest. In the five hydrogen abstraction pathways, the local energy barriers with respect to the corresponding reactant complexes increased in the fol owing order:H2b(GC-H4b)•>(GC-H6)•>(GC-H5)•~(H8-GC)•,其中H2b反应路径的能量变化最大,说明该反应平衡时的转化率最高.动力学上,相对于反应复合物的局部反应能垒大小顺序是H2b

  5. Cytosine deaminase and uracil phosphoribosyl transferase inhibition of transplantation tumor gene fusion%胞嘧啶脱氨酶和尿嘧啶磷酸核糖转移酶融合基因对食管癌裸鼠移植瘤的抑制作用

    Institute of Scientific and Technical Information of China (English)

    潘雪; 李向楠; 王鹏; 侯晓旭

    2015-01-01

    Objective To study the multidrug resistance gene 1 (MDR1) promoter regulated cytosine deaminase and uracil phosphoribosyltransferase fusion gene (CD:UPRT) killing of esophageal cancer cells in nude mice EC9706 cells.Methods 0.2 ml EC9706 cells were inoculated subcutaneously in nude mice and esophageal cancer xenograft model to build and build pAdTrack-MDR1-CD:UPRT plasmids,were randomly divided into three groups of treated and observed 30 d,tumor volume was measured using the V =x × y2/2 (x long diameter,y for short diameter).Routine pathological examination of tumor tissue,immunohistochemical detection of CD protein.Results Successfully constructed subcutaneous xenograft model of esophageal cancer,treatment for 30 days,group B,group C rapid tumor growth,surface necrosis,tumor volume was (3.21 ±0.23) cm3,(3.15 ±0.22) cm3;A group of tumor growth restrained,the first 30 days volume (cm3),compared to the difference of (0.98 ±0.15) was statistically significant (P <0.05).A group of tumor cells arranged in a sparse,large areas of necrosis red dye,partially visible condensation nuclei,nuclear fragmentation;group B,group C tumor cells tightly packed,rich in blood vessels,cell morphology and cell nuclei were pleomorphic,and a large stained mitotic common.After immunohistochemical staining,A,group B tumor tissues were positive,indicating that the protein expression of CD,group C immunohistochemical staining of tumor tissue was negative.Conclusion MDR1 promoter regulated CD:UPRT/5-fluorocytosine (5-FC) fusion suicide gene system for esophageal carcinoma in nude mice xenograft significant cytotoxicity,gene therapy for esophageal cancer provides a possible approach.%目的 观察多药耐药基因1(MDR1)启动子调控的胞嘧啶脱氨酶和尿嘧啶磷酸核糖转移酶融合基因(CD:UPRT)在裸鼠体内对食管癌细胞EC9706细胞的杀伤作用.方法 0.2 ml EC9706细胞悬液接种裸鼠,构建食管癌皮下移植瘤模型及pAdTrack-MDR1-CD

  6. 穿山龙超声波醇提工艺研究%Studies on the Dioscorea Nipponica Makino of the EthanoI Extraction Process by UItrasonic

    Institute of Scientific and Technical Information of China (English)

    时光霞; 刘郁

    2014-01-01

    目的:研究穿山龙超声波醇提最佳提取工艺。方法采用超声波醇提工艺提取穿山龙中的有效成分,用高效液相色谱( HPLC)测定薯蓣皂苷含量,以薯蓣皂苷含量为考察指标,采用L9(34)正交试验法考察提取因素对有效物质含量的影响,考察因素为提取溶剂乙醇的浓度、提取温度、提取的时间,从中优选出穿山龙超声波醇提最佳提取工艺条件。结果最佳的提取工艺用80%的乙醇提取2次,每次提取时间为30min,提取温度为70℃。提取的薯蓣皂苷平均含量1.89mg・ g-1,RDS为3.592%,结论该提取工艺稳定、可靠。%OBJECTIVE To study the optimum ethanol extraction process by ultrasonic of Chuan shan-long.METHODS By Ethanol extraction by ultrasonic ,determination content of dioscin by HPLC ,the content of di-oscin as the detection targets ,the influence of extraction factors ( extraction concentration of solvent ethanol ,tempera-ture of the extraction ,and the time of the extraction number ) on the active substance content was investigated by or-thogonal design L9(34),which would optimize the extraction process.RESULTS The optimum extracting process for the Chuan shanlong was adding 80%ethanol,extracting 2 times,0.5 hours each times with extracting temperature 70℃.And the average content of dioscin was 1.89 mg・ g -1 , RSD was 3.592%.CONCLUSION The process is stable and reliable.

  7. Synthesis of Butyl Ethanoate Uing p-Toluene Sulphonic Acid as a Catalyst%对甲苯磺酸催化合成乙酸正丁酯

    Institute of Scientific and Technical Information of China (English)

    李继忠

    2003-01-01

    用对甲苯磺酸作冰乙酸和正丁醇的酯化催化剂,成功地合成了乙酸正丁酯,考察了影响反应的因素,探讨并找到了较好的反应条件:乙酸100mmol,n(冰乙酸)∶n(正丁醇)∶n(催化剂)=1∶3∶0.006,反应时间1.5h,不另加带水剂,产率达99.14%.

  8. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed M Vargas; Parker, Brian J; Rasmussen, Morten; Lindgreen, Stinus; Lilje, Berit; Tobin, Desmond J; Kelly, Theresa K; Vang, Søren; Andersson, Robin; Jones, Peter A; Hoover, Cindi A; Tikhonov, Alexei; Prokhortchouk, Egor; Rubin, Edward M; Sandelin, Albin; Gilbert, M Thomas P; Krogh, Anders; Willerslev, Eske; Orlando, Ludovic

    2014-01-01

    expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues......Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence...... the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into...

  9. Photoalkylated DNA and ultraviolet-irradiated DNA are incised at cytosines by endonuclease III.

    OpenAIRE

    Weiss, R B; Duker, N J

    1986-01-01

    Photoalkylation, the ultraviolet irradiation of DNA with isopropanol and di-tert-butylperoxide, causes a variety of base alterations. These include 8-(2-hydroxy-2-propyl)guanines, 8-(2-hydroxy-2-propyl)adenines and thymine dimers. An E. coli endonuclease against photoalkylated DNA was assayed by conversion of superhelical PM2 phage DNA to the nicked form. Enzyme activities were compared between extracts of strain BW9109 (xth-), lacking exonuclease III activity, and strain BW434 (xth-,nth-), d...

  10. [Cytosine-arabinoside in high doses in refractory acute granulocytic leukemia. Apropos of 17 cases].

    Science.gov (United States)

    Jouet, J P; Simon, M; Fenaux, P; Pollet, J P; Bauters, F

    1985-01-01

    A total of 17 patients, 6 female and 11 male (age range 13 to 56 years), received high dose Ara-C for treatment of refractory acute myelogenous leukemia. Ara-C was given at 3 g/m2 twice daily for 6 days as a 1 infusion. 1 patient (with induced acute leukemia) was treated directly, two after failure of a chemotherapy schedule containing the usual dose Ara-C, 12 for first relapse and 2 for subsequent relapse. Maximum follow up is 16 months. Beside hematological toxicity, systemic tolerance was good with no neurological of cutaneous effects. Despite preventive corticoid eyewash, ocular complications occurred in 6 cases, mild and resolvable in 5 of them. The immediate results were as follows: 3 deaths during induction (18%); 6 failures (35%); 8 complete remissions (CR) (47%). After primary chemo-resistance (two cases) failure was always noted. In 3 cases, after less than 12 infusions had been given, 2 failures and 1 very short CR were noted. In 2 patients, when doxorubicin was added to Ara-C, we observed 1 death during induction and 1 failure. Of the patients achieving CR 8 were treated by periodic courses with high dose Ara-C and 4 of them relapsed. The longest failure free duration was 11 months. Median survival duration of the 17 patients is 5 months. PMID:3862072

  11. The Dnmt3L ADD Domain Controls Cytosine Methylation Establishment during Spermatogenesis

    Directory of Open Access Journals (Sweden)

    Georgios Vlachogiannis

    2015-02-01

    Full Text Available A critical aspect of mammalian gametogenesis is the reprogramming of genomic DNA methylation. The catalytically inactive adaptor Dnmt3L is essential to ensuring this occurs correctly, but the mechanism by which it functions is unclear. Using gene targeting to engineer a single-amino-acid mutation, we show that the Dnmt3L histone H3 binding domain (ADD is necessary for spermatogenesis. Genome-wide single-base-resolution DNA methylome analysis of mutant germ cells revealed overall reductions in CG methylation at repetitive sequences and non-promoter CpG islands. Strikingly, we also observe an even more severe loss of non-CG methylation, suggesting an unexpected role for the ADD in this process. These epigenetic deficiencies were coupled with defects in spermatogonia, with mutant cells displaying marked changes in gene expression and reactivation of retrotransposons. Our results demonstrate that the Dnmt3L ADD is necessary for Dnmt3L function and full reproductive fitness.

  12. Patterns of DNA cytosine methylation between haploids and corresponding diploids in rice

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hongyu; PENG Hai; LI Yun; XU Peizhou; WANG Xudong; WU Xianjun

    2006-01-01

    Eighteen pairs of diploid-haploid twinseedlings were identified and screened out from special rice SARⅡ-628 population. Five pairs of them were selected and randomly designated as A, B, C, D and E. Simple sequence repeats (SSR) analysis showed that there was no difference among 310 sites,which indicated that there was no base mutation on DNA primary structure. DNA methylation plays an important role in gene expression regulation during growth and development stages in eukaryotes. A modified AFLP technique (methylation-sensitive AFLP, MSAP) was employed to detect the DNA methylation patterns in the 5'-CCGG sites of the five pairs of twin-seedlings. Although no methylation mutation was detected among the five diploids,forty-three methylation mutation sites were found from the corresponding haploids. The MSAP ratios,which were the ratios of MSAP sites to the total amplified sites, in five haploids were 18.79%, 19.35%,18.49%, 18.45% and 18.75%, respectively. And corresponding full methylation levels (5'-CmCGG in double strands) of those haploids were 10.58%,11.3%, 10.11%, 10.09% and 10.34%, respectively.Both MSAP and full methylation levels in the five haploids were higher than that of their corresponding diploids, which suggested that hypermethylation occurred in some 5'-CCGG sites. Five types of MASP patterns among the five pairs of twin-seedlings were detected as follows: (1) no changes, methylation levels were the same in both haploids and diploids; (2)demethylation, diploid was methylated but no methylation in the same site in haploid; (3) hypermethylation, the methylation level in haploid was higher than those in diploid; (4) hypomethylation, methylation in haploid was lower than those in diploid; (5)undecided pattern, change trend of methylation levels in haploids was not decided. The bands of 18 sites were reclaimed, then sequenced and searched on website to determine the sites of those sequences on rice chromosomes. The result showed that the methylation mutation involved the whole rice genome and 12 pairs of chromosomes. The mutation was site-related and there were different mutation sites for different haploids. Compared to diploids, the higher methylation level in haploids might be a readjusting reaction to the decrease in ploidy for the sake of survival.

  13. DNA binding of the p21 repressor ZBTB2 is inhibited by cytosine hydroxymethylation

    Energy Technology Data Exchange (ETDEWEB)

    Lafaye, Céline; Barbier, Ewa; Miscioscia, Audrey; Saint-Pierre, Christine [Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, UMR E_3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble F-38054 (France); Kraut, Alexandra; Couté, Yohann [Etude de la Dynamique des Protéomes, Biologie à Grande Echelle, UMR S_1038 CEA/INSERM/UJF-Grenoble 1, iRTSV, 17 rue des Martyrs, Grenoble F-38054 (France); Plo, Isabelle [INSERM, U1009, Institut Gustave Roussy, Université Paris 11, 114 rue Edouard Vaillant, Villejuif F-94805 (France); Gasparutto, Didier; Ravanat, Jean-Luc [Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, UMR E_3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble F-38054 (France); Breton, Jean, E-mail: jean.breton@cea.fr [Laboratoire Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, UMR E_3 CEA/UJF-Grenoble 1, INAC, 17 rue des Martyrs, Grenoble F-38054 (France)

    2014-03-28

    Highlights: • 5-hmC epigenetic modification is measurable in HeLa, SH-SY5Y and UT7-MPL cell lines. • ZBTB2 binds to DNA probes containing 5-mC but not to sequences containing 5-hmC. • This differential binding is verified with DNA sequences involved in p21 regulation. - Abstract: Recent studies have demonstrated that the modified base 5-hydroxymethylcytosine (5-hmC) is detectable at various rates in DNA extracted from human tissues. This oxidative product of 5-methylcytosine (5-mC) constitutes a new and important actor of epigenetic mechanisms. We designed a DNA pull down assay to trap and identify nuclear proteins bound to 5-hmC and/or 5-mC. We applied this strategy to three cancerous cell lines (HeLa, SH-SY5Y and UT7-MPL) in which we also measured 5-mC and 5-hmC levels by HPLC-MS/MS. We found that the putative oncoprotein Zinc finger and BTB domain-containing protein 2 (ZBTB2) is associated with methylated DNA sequences and that this interaction is inhibited by the presence of 5-hmC replacing 5-mC. As published data mention ZBTB2 recognition of p21 regulating sequences, we verified that this sequence specific binding was also alleviated by 5-hmC. ZBTB2 being considered as a multifunctional cell proliferation activator, notably through p21 repression, this work points out new epigenetic processes potentially involved in carcinogenesis.

  14. Analysis of cytosine methylation in early generations of resynthesized Brassica napus

    Institute of Scientific and Technical Information of China (English)

    RAN Li-ping; FANG Ting-ting; RONG Hao; JIANG Jin-jin; FANG Yu-jie; WANG You-ping

    2016-01-01

    DNA methylation, an important epigenetic modiifcation, serves as a key function in the polyploidization of numerous crops. In this study, early generations of resynthesizedBrassica napus (F1, S1–S3), ancestral parentsB. rapaandB. oleracea were analyzed to characterize their DNA methylation status during polyploidization, applying DNA methylation-sensitive ampliifca-tion polymorphism (MSAP) and high-performance liquid chromatography methods. InF1, 53.4% fragments were inherited from both A- and C-genomes. Besides, 5.04 and 8.87% fragments inF1 were inherited from A- and C- genome, respectively. 5.85 and 0.8% fragments were newly appeared and disappeared in resynthesizedB. napus, respectively. 13.1% of these gene sites were identiifed with methylation changes inF1, namely, hypermethylation (7.86%) and hypomethylation (5.24%). The lowest methylation status was detected inF1 (38.7%) compared with in S1–S3. In S3, 40.32% genes were methylated according to MSAP analysis. Sequencing of methylated fragments indicated that genes involved in multiple biological processes were modiifed, including transcription factors, protein modiifcation, and transporters. Expression ananlysis of DNA methyltransferase 1 andDNA methyltransferase chromomethylase 3 in different materials was consistent to the DNA methylation status. These results can generaly facilitate dissection of how DNA methylation contributes to genetic stability and improvement ofB. napus during polyploidization.

  15. Engineering the DNA cytosine-5 methyltransferase reaction for sequence-specific labeling of DNA

    OpenAIRE

    Lukinavičius, Gražvydas; Lapinaitė, Audronė; Urbanavičiūtė, Giedrė; Gerasimaitė, Rūta; Klimašauskas, Saulius

    2012-01-01

    DNA methyltransferases catalyse the transfer of a methyl group from the ubiquitous cofactor S-adenosyl-L-methionine (AdoMet) onto specific target sites on DNA and play important roles in organisms from bacteria to humans. AdoMet analogs with extended propargylic side chains have been chemically produced for methyltransferase-directed transfer of activated groups (mTAG) onto DNA, although the efficiency of reactions with synthetic analogs remained low. We performed steric engineering of the co...

  16. Long-lived fluorescence of homopolymeric guanine-cytosine DNA duplexes.

    Science.gov (United States)

    Vayá, Ignacio; Changenet-Barret, Pascale; Gustavsson, Thomas; Zikich, Dragoslav; Kotlyar, Alexander B; Markovitsi, Dimitra

    2010-09-24

    The fluorescence spectrum of the homopolymeric double helix poly(dG) x poly(dC) is dominated by emission decaying on the nanosecond time-scale, as previously reported for the alternating homologue poly(dGdC) x poly(dGdC). Thus, energy trapping over long periods of time is a common feature of GC duplexes which contrast with AT duplexes. The impact of such behaviour on DNA photodamage needs to be evaluated. PMID:20714677

  17. Small RNA-mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation

    OpenAIRE

    Zhang, Guoqiang; Estève, Pierre-Olivier; Chin, Hang Gyeong; Terragni, Jolyon; Dai, Nan; Corrêa, Ivan R.; Pradhan, Sriharsa

    2015-01-01

    Mammalian cells contain copious amounts of RNA including both coding and noncoding RNA (ncRNA). Generally the ncRNAs function to regulate gene expression at the transcriptional and post-transcriptional level. Among ncRNA, the long ncRNA and small ncRNA can affect histone modification, DNA methylation targeting and gene silencing. Here we show that endogenous DNA methyltransferase 1 (DNMT1) co-purifies with inhibitory ncRNAs. MicroRNAs (miRNAs) bind directly to DNMT1 with high affinity. The bi...

  18. Small RNA-mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation.

    Science.gov (United States)

    Zhang, Guoqiang; Estève, Pierre-Olivier; Chin, Hang Gyeong; Terragni, Jolyon; Dai, Nan; Corrêa, Ivan R; Pradhan, Sriharsa

    2015-07-13

    Mammalian cells contain copious amounts of RNA including both coding and noncoding RNA (ncRNA). Generally the ncRNAs function to regulate gene expression at the transcriptional and post-transcriptional level. Among ncRNA, the long ncRNA and small ncRNA can affect histone modification, DNA methylation targeting and gene silencing. Here we show that endogenous DNA methyltransferase 1 (DNMT1) co-purifies with inhibitory ncRNAs. MicroRNAs (miRNAs) bind directly to DNMT1 with high affinity. The binding of miRNAs, such as miR-155-5p, leads to inhibition of DNMT1 enzyme activity. Exogenous miR-155-5p in cells induces aberrant DNA methylation of the genome, resulting in hypomethylation of low to moderately methylated regions. And small shift of hypermethylation of previously hypomethylated region was also observed. Furthermore, hypomethylation led to activation of genes. Based on these observations, overexpression of miR-155-5p resulted in aberrant DNA methylation by inhibiting DNMT1 activity, resulting in altered gene expression. PMID:25990724

  19. Transitive RNA silencing signals induce cytosine methylation of a transgenic but not an endogenous target

    Czech Academy of Sciences Publication Activity Database

    Vermeersch, L.; De Winne, N.; Nolf, J.; Bleys, A.; Kovařík, Aleš; Depicker, A.

    2013-01-01

    Roč. 74, č. 5 (2013), s. 867-879. ISSN 0960-7412 R&D Projects: GA ČR GBP501/12/G090 Institutional research plan: CEZ:AV0Z50040702 Institutional support: RVO:68081707 Keywords : DIRECTED DNA METHYLATION * POTATO-VIRUS-X * DOUBLE-STRANDED-RNA Subject RIV: BO - Biophysics Impact factor: 6.815, year: 2013

  20. Cytosine arabinoside and daunorubicin induction therapy in a patient with acute myeloid leukemia on chronic hemodialysis.

    Science.gov (United States)

    Krashin, Eilon; Dolberg, Osnat J; Hellmann, Ilana; Huitema, Alwin D R; Rosing, Hilde; Ellis, Martin

    2016-09-01

    The combination of daunorubicin and cytarabine is the cornerstone of induction therapy for acute myeloid leukemia (AML). Little data are available on the optimal chemotherapy regimen for patients with AML and advanced renal failure, with some authors recommending administration of reduced daunorubicin doses. We report the case of a 54-year-old AML patient on chronic hemodialysis who was treated with a modified induction regimen with reduced-dose daunorubin. Daunorubicin levels were measured during the treatment schedule. Although daunorubicin terminal t1/2 appears to be unaffected in hemodialysis patients, the estimated 0-23 h area under the curve was comparable with that of patients receiving full-dose daunorubicin. Therefore, dose adjustment in this patient group may be prudent. PMID:27254285

  1. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed Missael Vargas;

    2014-01-01

    Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence...... expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues...

  2. Role of Glutamate 64 in the Activation of the Prodrug 5-Fluorocytosine by Yeast Cytosine Deaminase

    Czech Academy of Sciences Publication Activity Database

    Wang, J.; Sklenák, Štěpán; Liu, A.; Felczak, K.; Wu, Y.; Li, Y.; Yan, H.

    2012-01-01

    Roč. 51, č. 1 (2012), s. 475-486. ISSN 0006-2960 R&D Projects: GA AV ČR IAA400400812; GA AV ČR IAA400400908; GA ČR GA203/09/1627 Institutional research plan: CEZ:AV0Z40400503 Keywords : transition-state analog * barrier hydrogen-bond * side-chain amides Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.377, year: 2012

  3. Oral idarubicin plus cytosine arabinoside in the treatment of acute non lymphoblastic leukemia in elderly patients.

    Science.gov (United States)

    Pagano, L; Sica, S; Marra, R; Voso, M T; Storti, S; Di Mario, A; Leone, G

    1991-01-01

    Eighteen acute nonlymphoblastic leukemia patients greater than 60 yr., 12 at diagnosis and 6 in first relapse, were treated with the association of oral Idarubicin and subcutaneous Aracytin. One patient was not evaluable. Eight out of 17 patients achieved complete remission (47%), 4 patients died in induction and 5 proved resistant to treatments. Mucocutaneous and gastrointestinal toxicity was mild. The most frequent extra-hematological complications were infections. We observed an important hepatic toxicity in 1 case. PMID:1820991

  4. Photodynamical simulations of cytosine: characterization of the ultrafast bi-exponential UV deactivation

    Czech Academy of Sciences Publication Activity Database

    Barbatti, M.; Aquino, A. J. A.; Szymczak, J. J.; Nachtigallová, Dana; Lischka, H.

    2011-01-01

    Roč. 13, č. 13 (2011), s. 6145-6155. ISSN 1463-9076 R&D Projects: GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : initio calculations * excited states * nucleic acids * photodynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.573, year: 2011

  5. Overproduction from a cellulase gene with a high guanosine-plus-cytosine content in Escherichia coli.

    Science.gov (United States)

    O'Neill, G P; Kilburn, D G; Warren, R A; Miller, R C

    1986-10-01

    A recombinant exoglucanase was expressed in Escherichia coli to a level that exceeded 20% of total cellular protein. To obtain this level of overproduction, the exoglucanase gene coding sequence was fused to a synthetic ribosome-binding site, an initiating ATG, and placed under the control of the leftward promoter of bacteriophage lambda contained on the runaway replication plasmid vector pCP3 (E. Remaut, H. Tsao, and W. Fiers, Gene 22:103-113, 1983). With the exception of an inserted asparagine adjacent to the initiating ATG, the highly expressed exoglucanase is identical to the native exoglucanase. The overproduced exoglucanase can be isolated easily in an enriched form as insoluble aggregates, and exoglucanase activity can be recovered by solubilization of the aggregates in 6 M urea or 5 M guanidine hydrochloride. Since the codon usage of the exoglucanase gene is so markedly different from that of E. coli genes, the overproduction of the exoglucanase in E. coli indicates that codon usage may not be a major barrier to heterospecific gene expression in this organism. PMID:3096205

  6. Sensitivity of excision repair in normal human, xeroderma pigmentosum variant and Cockayne's syndrome fibroblasts to inhibition by cytosine arabinoside

    International Nuclear Information System (INIS)

    Inhibition of the gap-filling, polymerizing step of excision repair by 1-β-D-arabinofuranosylcytosine (ara-C) after irradiation with ultraviolet light in human diploid fibroblasts resulted in the formation of persistent DNA strand breaks in G1, G2, and plateau phase cells, but not in S phase cells. Addition of hydroxyurea to ara-C resulted in partial inhibition of repair in S phase cells. These observations can be explained either in terms of changing roles in repair for different DNA polymerases throughout the cell cycle or by the presence of a pool of deoxycytidine nucleotides during S phase equivalent to an external source of deoxycytidine at 50 μM concentration. A similar concentration dependence on ara-C was observed for inhibition of repair in normal human, xeroderma pigmentosum (XP) variant, and Cockayne's syndrome cells. Ara-C produced a similar number of breaks in normal and Cockayne's syndrome cells. Ara-C produced a similar number of breaks in normal and Cockayne's syndrome cells but slightly more in XP variant cells. Exonuclease III and S1 nuclease independently both degraded about 50% of the 3H-thymidine incorporated into repaired regions in the presence of ara-C. Sequential digestion with both enzymes degraded nearly 90% of the repaired regions. These observations can be explained if excision repair proceeds by displacing the damaged strand so that both the 3H-labeled patch and the damaged region are still ligated to high molecular weight DNA and compete for the same complementary strand during in vitro incubation with the nucleases. The amount of 3H-thymidine incorporated in DNA by repair decreased with increasing concentrations of ara-C and hydroxyurea, suggesting that the incomplete patches became shorter under these conditions. Extrapolation of the digestion kinetics with exonuclease III permits an estimate of the normal patch size of about 100 nucleotides, consistent with previous estimates

  7. Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines

    OpenAIRE

    Larson, Marilynn A.; Bressani, Rafael; Sayood, Khalid; Corn, Jacob E.; Berger, James M.; Griep, Mark A.; Hinrichs, Steven H.

    2008-01-01

    The placement of the extreme thermophile Aquifex aeolicus in the bacterial phylogenetic tree has evoked much controversy. We investigated whether adaptations for growth at high temperatures would alter a key functional component of the replication machinery, specifically DnaG primase. Although the structure of bacterial primases is conserved, the trinucleotide initiation specificity for A. aeolicus was hypothesized to differ from other microbes as an adaptation to a geothermal milieu. To dete...

  8. Photophysical and structural properties of the fluorescent nucleobase analogues of the tricyclic cytosine (tC) family

    DEFF Research Database (Denmark)

    Preus, Søren; Kilså, Kristine; Wilhelmsson, L. Marcus;

    2010-01-01

    Fundamental insight into the unique fluorescence and nucleobase-mimicking properties of the fluorescent nucleobase analogues of the tC family is not only vital in explaining the behaviour of these probes in nucleic acid environments, but will also be profitable in the development of new and......Cnitro; all of which are derivatives of a phenothiazine or phenoxazine tricyclic framework. These results strongly suggest that the non-radiative decay process dominating the fast deactivation of tCnitro is an internal conversion of a different origin than the decay pathways of tC and tCO. tCnitro is reported...

  9. The cytogenetic effect of radiation and postirradiation treatment of Chinese hamster cells with arabinoside cytosine and hydroxyurea

    International Nuclear Information System (INIS)

    A two-hour treatment of Chinese hamster cells at the G1 stage of the cell cycle with arabinoside cytocine combined with hydroxyurea after X-irradiation (50-300 cGy) produced a 2- to 4-fold increase in the frequency of chromosome aberrations. The mitotic selection method was used to synchronize the cells. The potentiating effect of inhibitors was estimated by the yield of centric exchanges decreased with increasing radiation dose. It is suggested that DNA repair processes determining a linear component of the dose-response curve are modified within the dose-range under study

  10. Antiviral activity of triazine analogues of 1- (S)-[3-hydroxy-2-(phosphonomethoxy)propyl]cytosine (Cidofovir) and related compounds

    Czech Academy of Sciences Publication Activity Database

    Krečmerová, Marcela; Holý, Antonín; Pískala, Alois; Masojídková, Milena; Andrei, G.; Naesens, L.; Neyts, J.; Balzarini, J.; De Clercq, E.; Snoeck, R.

    2007-01-01

    Roč. 50, č. 5 (2007), s. 1069-1077. ISSN 0022-2623 R&D Projects: GA AV ČR 1QS400550501; GA MŠk 1M0508 Grant ostatní: NIH(US) 1UC1 AI062540-01; René Descartes Prize-2001(XE) HPAV-2002-100096 Institutional research plan: CEZ:AV0Z40550506 Keywords : acyclic nucleoside phosphonate * cidofovir * antiviral activity Subject RIV: CC - Organic Chemistry Impact factor: 4.895, year: 2007

  11. Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs

    KAUST Repository

    Chawla, Mohit

    2013-10-10

    The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).

  12. pH-Independent triplex formation: hairpin DNA containing isoguanine or 9-deaza-9-propynylguanine in place of protonated cytosine.

    Science.gov (United States)

    Seela, Frank; Shaikh, Khalil I

    2006-11-01

    Triplex-forming oligonucleotides (TFOs) containing 2'-deoxyisoguanosine (2), 7-bromo-7-deaza-2'-deoxyisoguanosine (2) as well as the propynylated 9-deazaguanine N7-(2'-deoxyribonucleoside) were prepared. For this the phosphoramidites 9a, b of the nucleoside 1 and, the phosphoramidites 19, 20 of compound 3b were synthesized. They were employed in solid-phase oligonucleotide synthesis to yield the protected 31-mer oligonucleotides. The deblocking of the allyl-protected oligonucleotides containing 1 was carried out by Pd(0)[PPh3]4-PPh3 followed by 25% aq. NH3. Formation of the 31-mer single-stranded intramolecular triplexes was studied by UV-melting curve analysis. In the single-stranded 31-mer oligonucleotides the protonated dC in the dCH(+)-dG-dC base triad was replaced by 2'-deoxyisoguanosine (1), 7-bromo-7-deaza-2'-deoxyisoguanosine (2) and, 9-deaza-9-propynylguanine N7-(2'-deoxyribonucleoside) (3b). The replacement of protonated dC by compounds 1 and 3b resulted in intramolecular triplexes which are formed pH-independently and are stable under neutral conditions. These triplexes contain "purine" nucleosides in the third pyrimidine rich strand of the oligonucleotide hairpin. PMID:17047881

  13. Implications of fast-time scale dynamics of human DNA/RNA cytosine methyltransferases (DNMTs) for protein function

    Czech Academy of Sciences Publication Activity Database

    Evans, D. A.; Bronowska, Agnieszka Katarzyna

    2010-01-01

    Roč. 125, 3/6 (2010), s. 407-418. ISSN 1432-881X Institutional research plan: CEZ:AV0Z40550506 Keywords : MD simulations * DNA/RNA methyltransferase * enthalpy-entropy compensation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.903, year: 2010

  14. Flexible double-headed cytosine-linked 2'-deoxycytidine nucleotides. Synthesis, polymerase incorporation to DNA and interaction with DNA methyltransferases

    Czech Academy of Sciences Publication Activity Database

    Kielkowski, Pavel; Cahová, Hana; Pohl, Radek; Hocek, Michal

    2016-01-01

    Roč. 24, č. 6 (2016), s. 1268-1276. ISSN 0968-0896 R&D Projects: GA ČR GBP206/12/G151 Institutional support: RVO:61388963 Keywords : nucleosides * nucleotides * pyrimidines * DNA methyltransferases * DNA polymerases Subject RIV: CC - Organic Chemistry Impact factor: 2.793, year: 2014

  15. Hypomethylating drugs efficiently decrease cytosine methylation in telomeric DNA and activate telomerase without affecting telomere lengths in tobacco cells

    Czech Academy of Sciences Publication Activity Database

    Majerová, E.; Fojtová, M.; Mozgová, I.; Bittová, M.; Fajkus, Jiří

    2011-01-01

    Roč. 77, 4-5 (2011), s. 371-380. ISSN 0167-4412 Institutional support: RVO:68081707 Keywords : Nicotiana tabacum * Cell culture * Telomere Subject RIV: BO - Biophysics Impact factor: 4.150, year: 2011

  16. Strikingly Different Effects of Hydrogen Bonding on the Photodynamics of Individual Nucleobases in DNA: Comparison of Guanine and Cytosine

    Czech Academy of Sciences Publication Activity Database

    Zelený, T.; Ruckenbauer, M.; Aquino, A. J. A.; Müller, T.; Lankaš, Filip; Dršata, Tomáš; Hase, W. L.; Nachtigallová, Dana; Lischka, H.

    2012-01-01

    Roč. 134, č. 33 (2012), s. 13662-13669. ISSN 0002-7863 R&D Projects: GA ČR GAP208/12/1318; GA MŠk(CZ) LH11021 Grant ostatní: GA ČR(CZ) GD203/09/H046 Institutional support: RVO:61388963 Keywords : excited-state dynamics * ultrafast internal-conversion * photoinduced nonadiabatic dynamics * nonradiative decay mechanisms * MR-CI level * ab initio Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 10.677, year: 2012

  17. Alkylsulfanylphenyl derivatives of cytosine and 7-deazaadenine nucleosides, nucleotides and nucleoside triphosphates. Synthesis, polymerase incorporation to DNA and electrochemical study

    Czech Academy of Sciences Publication Activity Database

    Macíčková-Cahová, Hana; Pohl, Radek; Horáková Brázdilová, Petra; Havran, Luděk; Špaček, Jan; Fojta, Miroslav; Hocek, Michal

    2011-01-01

    Roč. 17, č. 21 (2011), s. 5833-5841. ISSN 0947-6539 R&D Projects: GA MŠk(CZ) LC06035; GA MŠk LC512; GA ČR GA203/09/0317; GA AV ČR(CZ) IAA400040901 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : DNA polymerases * electrochemistry * nucleosides * nucleotides * organosulfur compounds Subject RIV: CC - Organic Chemistry Impact factor: 5.925, year: 2011

  18. Synthesis of some N4-substituted derivatives of 1-[(S)-3-hydroxy-2-(phosphonomethoxy)propyl]cytosine (HPMPC, Cidofovir)

    Czech Academy of Sciences Publication Activity Database

    Chalupová, Šárka; Holý, Antonín; Masojídková, Milena

    2005-01-01

    Roč. 70, č. 12 (2005), 2053-2065. ISSN 0010-0765 R&D Projects: GA MŠk(CZ) 1M0508 Grant ostatní: NIH(US) 1UC1AiO62540-01 Institutional research plan: CEZ:AV0Z40550506 Keywords : HPMPC * ANP * antivirals Subject RIV: CC - Organic Chemistry Impact factor: 0.949, year: 2005

  19. Synthesis of N4-substituted derivatives of (S)-1-[3-hydroxy-2-(phosphonomethoxy)propyl]cytosine (HPMPC, Cidofovir, Vistide)

    Czech Academy of Sciences Publication Activity Database

    Chalupová, Šárka; Holý, Antonín

    Praha: ÚOCHB AV ČR, 2005 - (Hocek, M.), s. 387-388. (Collection Symposium Series. 7). ISBN 80-86241-25-4. [Chemistry of Nucleic Acid Components /13./. Špindlerův Mlýn (CZ), 03.09.2005-09.09.2005] R&D Projects: GA MŠk(CZ) 1M0508 Grant ostatní: NIH(US) 1UC1AIO62540-01 Institutional research plan: CEZ:AV0Z40550506 Keywords : HPMPC * ANP * antivirals Subject RIV: CC - Organic Chemistry

  20. A new value for mol percent guanine + cytosine of DNA for the salmonid fish pathogen Renibacterium salmoninarum.

    Science.gov (United States)

    Banner, C R; Rohovec, J S; Fryer, J L

    1991-03-15

    The mol% G + C of DNA extracted from seven different isolates of Renibacterium salmoninarum was determined. Organisms studied were from selected geographical areas (U.S.A., Canada, England and France) and were isolated from five different species of salmonid fish. The mol% G + C was determined to be 55.5, higher than the currently reported value of 53. PMID:2044940

  1. Isolation of methylcarbamoyl-adducts of adenine and cytosine following in vitro reaction of methyl isocyanate with calf thymus DNA.

    Science.gov (United States)

    Segal, A; Solomon, J J; Li, F J

    1989-01-01

    Methylisocyanate (MIC) is the direct-acting acylating compound involved in the Bhopal, India disaster which occurred on December 3rd, 1984. The accidental release of MIC resulted in at least 2000 deaths, thousands of injuries and exposure of at least 200,000 people to varying amounts of MIC. We have studied how MIC reacts with 2'-deoxyribonucleosides at pH 7.0 and 37 degrees C for 1 h. MIC acylates exocyclic amino groups resulting in the following methylcarbamoyl (MC) adducts: N6-MC-Ade (0.5% yield) and N4-MC-dCyd (6%). No adducts were detected with dThd and dGuo. UV, NMR and mass spectrometry were employed to spectroscopically characterize these adducts. MIC was reacted with calf thymus DNA (pH 7.0, 37 degrees C, 1 h) and yielded N6-MC-Ade (0.3 nmol/mg DNA) and N4-MC-dCyd (2.0 nmol/mg DNA). The inability of others to observe genetic mutations by MIC in Salmonella and Drosophila is consistent with the exocyclic adducts at N4 of Cyt and N6 of Ade where normal hydrogen bonding can occur after rotation of the methylcarbamoyl group anti to the Watson-Crick side of the molecule assuming that MIC binds to DNA within the intact cell. PMID:2731306

  2. Some clinical and laboratory variables in adult patients with chronic myeloid leukemia treated with recombinant alpha interferon + cytosine arabinoside

    International Nuclear Information System (INIS)

    Chronic myeloid leukemia is the most frequent myeloproliferative syndrome in adults. In a longitudinal retrospective study performed between January 1985 - December 2009, 46 patients in chronic phase diagnosed at the Institute of Hematology and Immunology were evaluated. They received cytoreductor agent as first treatment followed by interferon α2 + cytosar. Forty one percent showed high risk Sokal prognosis score. The most frequent clinical manifestations at diagnosis were asthenia (37 %), splenomegaly (31 %) and weigh lost (28.3 %). The partial and complete hematological response was of 26,8 % and 65.9 % after 6 months and the complete cytogenetic and molecular response was of 9.1 % and 16.3 %. The most frequent adverse reactions were: fever (34.9 %), thrombocytopenia (26.3 %) and general syndrome (23.8 %). Resistance or intolerance to INFα2 was found in 47.8 % of the patients and 90.0 % died due to progression of the disease. The 5 year overall survival was of 63.8 % and the 3 years free event survival was of 68.9 %. According to Sokal prognosis score the overall survival showed significant difference between groups (p= 0.005) but there was no significant difference for free event survival (p= 0.165). The INFα2 treatment in our patients showed better results than those obtained in different developed countries and is an effective therapeutic option in Cuba

  3. The synergistic risk effect of apolipoprotein ε4 and DNA (cytosine-5-)-methyltransferase 3 beta (DNMT3B) haplotype for Alzheimer's disease.

    Science.gov (United States)

    de Bem, Cíntia Monique Boschmann Ens; Pezzi, Julio Carlos; Borba, Ericksen Mielle; Chaves, Marcia Lorena Fagundes; de Andrade, Fabiana Michelsen; Fiegenbaum, Marilu; Camozzato, Analuiza

    2016-07-01

    Alzheimer's disease (AD) is a complex and multifactorial disease with the contribution of several genes and polymorphisms to its development. Among these genes, the APOEε4 is the best known risk factor for AD. Methylation is associated with APOE expression and AD development. Recently, we found an association of the TGG haplotype in the DNMT3B gene, one of the catalyst enzyme for methylation, with AD. Therefore, the objective of the study was to investigate whether APOEε4 and TGG haplotype have an synergistic effect on AD. The sample was composed of 212 Caucasian individuals (108 healthy controls and 104 with AD by NINCDS-ADRDA and DSM-IV-TR criteria) from southern Brazil. The genetic analyses were performed by real time PCR for TaqMan(®) assay. Multivariate logistic regression was performed categorizing groups according to presence of APOEε4 and/or TGG haplotype as an independent variable for outcome AD. The presence of TGG haplotype plus the allele APOEε4 were strongly associated with AD [OR 11.13; 95 % CI (4.25-29.16); P < 0.001]. This association had a higher risk than each risk factor alone. We found a strong association of the interaction of DNMT3B gene with the APOEε4 in this sample of AD patients. The presence of TGG haplotype and APOEε4 significantly increased the risk of developing the disease, showing an synergistic effect. PMID:27188425

  4. TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy

    Directory of Open Access Journals (Sweden)

    Dnyaneshwar B. Gophane

    2015-02-01

    Full Text Available Three 2´-deoxynucleosides containing semi-flexible spin labels, namely TA, UA and UC, were prepared and incorporated into deoxyoligonucleotides using the phosphoramidite method. All three nucleosides contain 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO connected to the exocyclic amino group; TA directly and UA as well as UC through a urea linkage. TA and UC showed a minor destabilization of a DNA duplex, as registered by a small decrease in the melting temperature, while UA destabilized the duplex by more than 10 °C. Circular dichroism (CD measurements indicated that all three labels were accommodated in B-DNA duplex. The mobility of the spin label TA varied with different base-pairing partners in duplex DNA, with the TA•T pair being the least mobile. Furthermore, TA showed decreased mobility under acidic conditions for the sequences TA•C and TA•G, to the extent that the EPR spectrum of the latter became nearly superimposable to that of TA•T. The reduced mobility of the TA•C and TA•G mismatches at pH 5 is consistent with the formation of TAH+•C and TAH+•G, in which protonation of N1 of A allows the formation of an additional hydrogen bond to N3 of C and N7 of G, respectively, with G in a syn-conformation. The urea-based spin labels UA and UC were more mobile than TA, but still showed a minor variation in their EPR spectra when paired with A, G, C or T in a DNA duplex. UA and UC had similar mobility order for the different base pairs, with the lowest mobility when paired with C and the highest when paired with T.

  5. Highly efficient generation of glutamatergic/cholinergic NT2-derived postmitotic human neurons by short-term treatment with the nucleoside analogue cytosine β-d-arabinofuranoside

    Directory of Open Access Journals (Sweden)

    Imanol González-Burguera

    2016-03-01

    Taken together, our results further reinforce the notion NT2 cells are a versatile source of neuronal phenotypes and provide a new encouraging platform for studying mechanisms of neuronal differentiation and for exploring neuronal replacement strategies.

  6. A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence.

    Science.gov (United States)

    Chia, Jyh Yea; Tan, Wen Siang; Ng, Chyan Leong; Hu, Nien-Jen; Foo, Hooi Ling; Ho, Kok Lian

    2016-01-01

    DNA methylation in a CpG context can be recognised by methyl-CpG binding protein 2 (MeCP2) via its methyl-CpG binding domain (MBD). An A/T run next to a methyl-CpG maximises the binding of MeCP2 to the methylated DNA. The A/T run characteristics are reported here with an X-ray structure of MBD A140V in complex with methylated DNA. The A/T run geometry was found to be strongly stabilised by a string of conserved water molecules regardless of its flanking nucleotide sequences, DNA methylation and bound MBD. New water molecules were found to stabilise the Rett syndrome-related E137, whose carboxylate group is salt bridged to R133. A structural comparison showed no difference between the wild type and MBD A140V. However, differential scanning calorimetry showed that the melting temperature of A140V constructs in complex with methylated DNA was reduced by ~7 °C, although circular dichroism showed no changes in the secondary structure content for A140V. A band shift analysis demonstrated that the larger fragment of MeCP2 (A140V) containing the transcriptional repression domain (TRD) destabilises the DNA binding. These results suggest that the solution structure of MBD A140V may differ from the wild-type MBD although no changes in the biochemical properties of X-ray A140V were observed. PMID:27502833

  7. Targeted cytosine deaminase-uracil phosphoribosyl transferase suicide gene therapy induces small cell lung cancer-specific cytotoxicity and tumor growth delay

    DEFF Research Database (Denmark)

    Christensen, Camilla L; Gjetting, Torben; Poulsen, Thomas Tuxen;

    2010-01-01

    deaminase (YCD) gene alone or fused with the yeast uracil phosphoribosyl transferase (YUPRT) gene followed by administration of 5-fluorocytosine (5-FC) prodrug. Experimental design: The YCD gene or the YCD-YUPRT gene was placed under regulation of the SCLC-specific promoter insulinoma-associated 1 (INSM1...

  8. INFLUENCES OF SUBSTITUTION OF BROMIDE CYTOSINE ON STABILITY OF TRIPLEX DNA%溴代胞嘧啶对三螺旋DNA稳定性的影响

    Institute of Scientific and Technical Information of China (English)

    李清; 刘次全

    1999-01-01

    研究了三螺旋DNA中胞嘧啶被5-溴胞嘧啶取代后的稳定性问题.通过建立CGC,CGBrC,BrCGC和BrCGBrC 4种模型,并采用 Insight Ⅱ软件包中的 Discover 程序进行计算模拟,发现用5-溴胞嘧啶取代三螺旋DNA分子中的胞嘧啶后,整个分子的稳定性有所降低.同时,当用5-溴胞嘧啶取代三螺旋DNA不同链上的胞嘧啶时,被取代链的碱基堆积能显著增高,导致分子链内稳定性降低,但被取代链和相邻链间相互作用能有所降低,使得链间作用趋向稳定.

  9. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.

    Czech Academy of Sciences Publication Activity Database

    Gresh, N.; Šponer, Judit E.; Devereux, M.; Gkionis, Konstantinos; de Courcy, B.; Piquemal, J.P.; Šponer, Jiří

    2015-01-01

    Roč. 119, č. 30 (2015), s. 9477-9495. ISSN 1520-6106 R&D Projects: GA ČR(CZ) GAP208/11/1822 Institutional support: RVO:68081707 Keywords : DENSITY-FUNCTIONAL THEORY * DISTRIBUTED MULTIPOLE ANALYSIS * PERTURBATION-THEORY APPROACH Subject RIV: BO - Biophysics Impact factor: 3.302, year: 2014

  10. General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility

    Czech Academy of Sciences Publication Activity Database

    Banáš, Pavel; Rulíšek, Lubomír; Hánošová, V.; Svozil, Daniel; Walter, N.G.; Šponer, Jiří; Otyepka, Michal

    2008-01-01

    Roč. 112, č. 35 (2008), s. 11177-11187. ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA MŠk(CZ) LC06030; GA AV ČR(CZ) IAA400040802; GA AV ČR 1QS500040581 Grant ostatní: NIH(US) GM62357 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : HDV ribozyme * catalysis * QM/MM calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.189, year: 2008

  11. A Pilot Feasibility Study of Oral 5-Fluorocytosine and Genetically-Modified Neural Stem Cells Expressing E.Coli Cytosine Deaminase for Treatment of Recurrent High Grade Gliomas

    Science.gov (United States)

    2015-03-02

    Adult Anaplastic Astrocytoma; Recurrent Grade III Glioma; Recurrent Grade IV Glioma; Adult Anaplastic Oligodendroglioma; Adult Brain Tumor; Adult Giant Cell Glioblastoma; Adult Glioblastoma; Adult Gliosarcoma; Adult Mixed Glioma; Recurrent Adult Brain Tumor; Adult Anaplastic Oligoastrocytoma; Recurrent High Grade Glioma

  12. Nucleoside conjugates as potential antitumor agents. 2. Synthesis and biological activity of 1-(beta-D-arabinofuranosyl)cytosine conjugates of prednisolone and prednisone.

    Science.gov (United States)

    Hong, C I; Nechaev, A; West, C R

    1979-11-01

    Two of the new anticancer drugs recently synthesized in our laboratory from conjugation of ara-C2 and several corticosteroids linked through a phosphodiester bond include prednisolone- (I) and prednisone-p-ara-C (II). They were demonstrated to be enzymatically hydrolyzed to the corresponding steroid and ara-CMP and the latter was further shown to be hydrolyzed to ara-C by phosphodiesterase I, snake venom, 5'-nucleotidase, and acid phosphatase. However, the conjugates were shown to be resistant to hydrolysis by alkaline phosphatase. The activity of conjugates I and II against L1210 lymphoid leukemia in female mice (C3D2F1/J) was significantly greater than that of ara-C alone or in combination with the steroid. In fact, when the optimum dosage of 75 (mumol/kg)/day x 5 was used, the administration of ara-C alone was followed by an increased life span (ILS) of 45%. This result is similar to that previously reported. With the same equimolar doses of mixtures of ara-C and either prednisolone or prednisone, the ILS values were 40 and 44%, respectively. However, when the conjugates were used, the ILS values were 89 and 100% respectively. These findings seem promising and have provided the bases for continued study of these new compounds. PMID:118258

  13. The Construction of a Mammalian Transfection Vector For Expression of Cytosine-5 Specific DNA Methyltransferase Gene M.Msp1 In Cultured Cells

    OpenAIRE

    ÖZDEMİR, Öztürk

    1998-01-01

    The expression vectors are designed for expression and purification of normal or recombi-nant gene of interest. There is a wide variety of stable and transferable selectable mammalian expres-sion vectors.The vector pCDM8 and its derivatives, pcDNAI/Ampicilline are widely used for cloning and analyzing of genes in higher eukaryotic cells. The vectors pRC/CMV, pcDNA3 and pRC/RSV are designed for high-level expression of recombinant genes in mammalian cells. In the present study, we have be...

  14. 基于食醋中乙醇的δ13C 值对其真伪鉴别的应用初探%AppIication of the δ13C of EthanoI in Vinegar for Distinguishing the FaIse from the Genuine

    Institute of Scientific and Technical Information of China (English)

    李鑫; 陈小珍; 姜侃; 张东雷; 尚才人; 章舒祺

    2015-01-01

    The determination method of the δ13C of ethanol in vinegar is built by LC-IRMS;the operational process of the instruments is introduced, through the selection of chromatography column,the effect of other components (sugar,acid)on the δ13C of ethanol in vinegar is detected from the perspective of peak time.The δ13C of pure CO2 reference gas is calibrated via international standard substance-sugar and the determination accuracy and stability in the linear range are investigated.16 batches of representative samples are determined;the relationship of theδ13C among ethanol in vinegar,vinegar,vinegar sediment is analyzed.Theδ13C of ethanol in vinegar is -28‰~-31‰,it is different from others,less than theδ13C of vinegar,it is stated that the loss happens in the process of transformation ofδ13C.Use the analysis method to test theδ13C of a variety of alcohol which is common in market,the δ13C is-10‰ ~ -17‰ of industrial alcohol,corn edible alcohol, starch alcohol,theδ13C is -29.1‰±1.2‰ of rice alcohol,theδ13C is -17.6‰±1.3‰ of sorghum alcohol,only the rice alcohol intervals coincide with the δ13C of ethanol in vinegar,others can be easily distinguished,the determination of the δ13C of ethanol in vinegar can play the role in distinguishing the false from the genuine.%文章新建了液相色谱联用稳定同位素比率质谱(LC-IRMS)对食醋中乙醇δ13C 值进行测定的方法。简述了仪器的运行过程,通过对色谱柱的选择,从出峰时间的角度考察了其他组分(糖、酸)对乙醇δ13C 值测定的影响,使用蔗糖标准物质标定了高纯 CO2参考气的δ13C 值并考察了线性范围下的测定重复性。对16批次代表性样品进行测定,分析食醋、食醋沉淀物、食醋中乙醇三者间δ13C 值的关系,乙醇的δ13C 值基本在-28‰~-31‰,与其余二者的δ13C 值范围有所差别,低于食醋的δ13C 值,说明了在转化过程中发生了一部分的同位素损失;对市场上常见的多种酒精的δ13C 值使用该分析方法进行测定,发现工业酒精、玉米食用酒精、淀粉酒精δ13C 值在-10‰~-17‰,大米食用酒精在-29.1‰±1.2‰,高粱食用酒精在-17.6‰±1.3‰,其中仅有大米食用酒精的δ13C 值与食醋中乙醇的δ13C 值区间重合,其他均能轻易分辨出,通过测定食醋中乙醇的δ13C 值或可起到真伪鉴别的作用。

  15. 固体超强酸TiO2/SO4 2-催化合成乙酸仲丁酯的研究%A Study on the Catalytic Synthesis of S- butyl Ethanoate by TiO2/SO4 -2 Solid Supper Strong Acid

    Institute of Scientific and Technical Information of China (English)

    龙德清

    2001-01-01

    研究了以固体超强酸TiO2/SO4 2-为催化剂,乙酸和仲丁醇为原料合成乙酸仲丁酯,考察了影响反应的因素.结果表明:TiO2/SO4 2-催化剂用量为2.0 g、醇酸体积比为1.5、反应时间为1.5 h、带水剂苯的用量为8 mL是最适宜的反应条件,脂化率达97.6%.

  16. Densities and isobaric vapor-liquid equilibria for the mixtures formed by four butyl esters and 1-butanol

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, E.; Ortega, J. [Univ. of Las Palmas de Gran Canaria (Spain)

    1996-01-01

    Densities of 298.15 K and the vapor-liquid equilibria for 1-butanol + butyl methanoate, + butyl ethanoate, + butyl propanoate, and + butyl butanoate have been measured at 101.32 kPa in small capacity ebulliometer. All results were found to be thermodynamically consistent with a point-to-point test. The mixtures containing butyl methanoate and butyl ethanoate show azeotropes at T = 379.14 K, x = 0.871 and T = 389.64 K, x = 0.222, respectively. Different group-contribution methods were applied to these mixtures.

  17. 胡芦巴种子不同溶剂提取物及提取工艺对植物果实致病菌的抑菌作用初探

    Institute of Scientific and Technical Information of China (English)

    邵明昱; 王颖; 崔新仪; 杨晓君

    2011-01-01

    [ Objective ] The purpose of this writing is to expIore the antibacteriaI activity of the extract from the seeds of Trigonella foenum -graecum L. For pIant disease caused by bacteria and screen out the best soIvent extraction process. [ Method ] Extract was taken from seeds of Trigonella foenum - graecum L. By ethanoI, ethyI acetate and water to expIore the impact of colletrotrichum gloeosporioildes, Valsa mali and Jujube rotten bacteria by it. Result The different extracted soIvents from the seeds of Trigonella foenum -graecum L. Have antibacteriaI effects for colletrotrichum gloeosporioildes and Valsa mali and Jujube rotten bacteria, and the best antimicrobiaI effect is the extract by ethanoI. The best technics to extract the soIvent from the seeds of Trigonella foenum - graecum L. Is to use 80% ethanoI. The ratio of the IiGuid - soIid is l:l5 , at 60 ℃ for 2 h extraction. [ conclusion ] The extracted soIvents form the seeds of Trigonella foenum -graecum L. Have the bacteriostatic effect in the order Iike this ethanoI concentration > extraction time > extraction temperature > IiGuid - solid ratio.

  18. Using Gene Arrays as Tools to Develop Alfalfa as a Biomass Crop

    Science.gov (United States)

    Alfalfa has considerable potential as a biomass feedstock for producing cellulosic ethanol. The model that we propose for alfalfa as a biomass crop involves stripping leaves from stems. The leaves would be used as a protein supplement for livestock while the stems would be used for cellulosic ethano...

  19. Tissue specificity of methylation of cytosines in regulatory regions of four genes located in the locus FXYD5-COX7A1 of human chromosome 19: correlation with their expression level.

    Science.gov (United States)

    Chalaya, T V; Akopov, S B; Nikolaev, L G; Sverdlov, E D

    2006-03-01

    In this study, we compared degree of methylation of selected CpG sites in CCGG sequences located in promoter regions of four human genes with expression level of these genes in several human cell lines and tissues. These genes were subdivided into two groups according to the dependence of their expression on CpG methylation in the 5 -regions. The first group, characterized by clear correlation of methylation with the transcription level, includes housekeeping gene COX6B (the absence of methylation unambiguously correlates with expression) and urothelium-specific uroplakin gene (the methylation coincides with absence of expression). The second group includes genes that are expressed in many, but not all tissues and cells. For these genes (LEAP-1 and ATP4A), there was no correlation between methylation and expression. It is possible that methylation provides some basal level of gene repression, which is overcome by binding of tissue-specific transcription factors, whereas lack of methylation gives the opportunity for gene expression in various cells and tissues. PMID:16545066

  20. Extent of Intramolecular pi Stacks in Aqueous Solution in Mixed-Ligand Copper(II) Complexes Formed by Heteroaromatic Amines and 1-[2-(Phosphonomethoxy)ethyl]cytosine (PMEC), a Relative of Antivirally Active Acyclic Nucleotide Analogues (Part 72)

    Czech Academy of Sciences Publication Activity Database

    Blindauer, C. A.; Sigel, A.; Operschall, B. P.; Holý, Antonín; Sigel, H.

    2013-01-01

    Roč. 639, 8-9 (2013), s. 1661-1673. ISSN 0044-2313 Institutional support: RVO:61388963 Keywords : nucleotide analogues * antivirals * complex stabilities * isomers * equilibria * mixed ligand complexes Subject RIV: CC - Organic Chemistry Impact factor: 1.251, year: 2013

  1. Electron Detachment as a Probe of Intrinsic Nucleobase Dynamics in Dianion-Nucleobase Clusters: Photoelectron Spectroscopy of the Platinum II Cyanide Dianion Bound to Uracil, Thymine, Cytosine and Adenine

    Energy Technology Data Exchange (ETDEWEB)

    Sen, Ananya; Hou, Gao-Lei; Wang, Xue B.; Dessent, Caroline

    2015-08-05

    We report the first low-temperature photodetachment photoelectron spectra of isolated gas-phase complexes of the platinum II cyanide dianion bound to nucleobases. These systems are model systems for understanding platinum-complex photodynamic therapies, and knowledge of the intrinsic photodetachment properties is crucial for understanding their broader photophysical properties. Well-resolved, distinct peaks are observed in the spectra consistent with the complexes where the Pt(CN)42- moiety is largely intact. The adiabatic electron detachment energies for the dianion-nucleobase complexes are measured to be between 2.39-2.46 eV. The magnitudes of the repulsive Coulomb barriers of the complexes are estimated to be between 1.9 and 2.1 eV, values that are lower than for the bare Pt(CN)42- dianion as a result of charge solvation by the nucleobases. In addition to the resolved spectral features, broad featureless bands indicative of delayed electron detachment are observed in the 193 nm photodetachment spectra of the four nucleobase-dianion complexes, and also in the 266 nm spectra of the Pt(CN)42-∙thymine and Pt(CN)42-∙adenine complexes. The selective excitation of these features in the 266 nm spectra is attributed to one-photon excitation of [Pt(CN)42-∙T]* and [Pt(CN)42-∙A]* long-lived excited states that can effectively couple to the electron detachment continuum, producing strong electron detachment signals. We attribute the resonant electron detachment bands observed here for Pt(CN)42-∙T and Pt(CN)42-∙A but not for Pt(CN)42-∙U and Pt(CN)42-∙C to fundamental differences in the individual nucleobase photophysics following 266 nm excitation. This indicates that the Pt(CN)42- dianion in the Pt(CN)42-∙M clusters can be viewed as a “dynamic tag” which has the propensity to emit electrons when the attached nucleobase disaplys a long-lived excited state.

  2. Economic and environmental impacts of U.S. corn ethanol production and use

    OpenAIRE

    Tiffany, Douglas G.

    2009-01-01

    For many years, U.S. policy initiatives and incentives have favored the production of ethanol from corn. The goals have been to increase corn prices and farmer income, enhance rural employment through encouragement of value-added businesses, increase energy security, and produce additives and/or fuels capable of reducing tailpipe pollutants and greenhouse gases. The Energy Policy Act of 2005 established annual goals via a renewable fuels standard that would have increased production of ethano...

  3. Evaluation of Antibacterial Effects of Lecanora muralis SP. Extract on Staphylococcus Aureus and Salmonella Typhimurium in in-vitro and in animal model

    OpenAIRE

    Shahrzad Nasisri Semnani; Mehdi Rahnema; Hasan Ghasempour; Hamed Alizadeh

    2014-01-01

     Background & Objective: Staphylococcus aureus and Salmonella typhimurium are among important causes of infection and antibiotic resistance. It is essential to find antimicrobial compounds against them. The objective of this study is to evaluate the antibacterial activity of Lecanora muralis SP. extracts on Staphylococcus aureus and Salmonella typhimurium in in-vitro and in animal model.Materials & Methods: In this study, aquatic, acetonic, and ethanoic extracts ...

  4. INFLUENCE OF SOLUBLE PROTEINS ON THE ADHERENCE OF PARTICULATE SOILS

    OpenAIRE

    Toure, Yetioman; Rouxhet, Paul; Dupont-Gillain, Christine; Sindic, Marianne

    2013-01-01

    Adsorbed compounds from food and pharmaceutical mixtures may influence interactions at interfaces and thus fouling and cleaning. In this study, quartz particles (10 to 30µm) were used as a model soil for examining the effect of dissolved proteins on the cleanability of substrates after soiling and drying. Glass and stainless steel pretreated by UV-Ozone (StSteel-UVO) were used as model hydrophilic substrates, while hydrophobic substrates were represented by stainless steel cleaned with ethano...

  5. Inhibitory effect of Allium sativum and Zingiber officinale extracts on clinically important drug resistant pathogenic bacteria

    OpenAIRE

    Gull Iram; Saeed Mariam; Shaukat Halima; Aslam Shahbaz M; Samra Zahoor; Athar Amin M

    2012-01-01

    Abstract Background Herbs and spices are very important and useful as therapeutic agent against many pathological infections. Increasing multidrug resistance of pathogens forces to find alternative compounds for treatment of infectious diseases. Methods In the present study the antimicrobial potency of garlic and ginger has been investigated against eight local clinical bacterial isolates. Three types of extracts of each garlic and ginger including aqueous extract, methanol extract and ethano...

  6. Acute Toxicity Study and Antipyretic Effect of the Brown Alga Turbinaria Conoides (J. Agardh) Kuetz

    OpenAIRE

    Kumar, S Sadish; Kumar, Y; Khan, M. S. Y; J Anbu; Sam, K G

    2009-01-01

    The active principles of brown alga, Turbinaria conoides (J.Agardh) Kuetz. (Sargassaceae) was extracted with n-hexane, cyclohexane, methanol and ethanol-water (1:1) and investigated for acute toxicity and antipyretic activity. Phytochemical analysis of the extracts revealed the presence of steroids, flavonoids and reducing sugars. Acute toxicity study was performed in Wistar rats after administration of extracts orally. No mortality was observed up to the dose of 5g/kg for methanol and ethano...

  7. Using high hydrodynamic fluctuations to obtain water-ethanol mixtures

    OpenAIRE

    Шурчкова, Юлія Олександрівна; Дубовкіна, Ірина Олександрівна

    2016-01-01

    The analysis of the processes that occur in binary systems of water-ethanol: hydration, association, formation of hydrogen bonds. The research of the properties of water systems, namely water-ethanol mixtures processed by discrete-pulsed input of energy are presented. The results of experimental research of the effect of high-frequency oscillations in the hydrodynamic physic-chemical parameters of water systems are obtained. The reductions in the amount of dissolved oxygen in the water-ethano...

  8. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Pedersen, Marianne Terndrup;

    2011-01-01

    Enzymes catalysing the methylation of the 5-position of cytosine (mC) have essential roles in regulating gene expression and maintaining cellular identity. Recently, TET1 was found to hydroxylate the methyl group of mC, converting it to 5-hydroxymethyl cytosine (hmC). Here we show that TET1 binds...

  9. ISS immune modulation, vaccination and the regulation of arthritis

    NARCIS (Netherlands)

    Ronaghy, Arash

    2007-01-01

    Bacterial DNA contains unique unmethylated CpG motifs. The cytosine-phosphate-guanisine (CpG) sequence of this motif has an unmethylated cytosine which is suppressed or methylated in mammalian DNA. Synthetic oligodeoxynucleotides containing these CpG (CpG-ODN) motifs are called Immunostimulatory DNA

  10. AcEST: BP918468 [AcEST

    Lifescience Database Archive (English)

    Full Text Available _id Q94F88 Definition sp|Q94F88|CMT3_ARATH DNA (cytosine-5)-methyltransfera...ive DNA (cytosine-5)-methyltransferase... 33 0.34 sp|Q8BHJ6|SERC5_MOUSE Serine incorporator 5 ... Sequences producing significant alignments: (bits) Value sp|Q94F88|CMT3_ARATH DNA (cytosine-5)-methyltra...>sp|Q9ARI6|CMT2_MAIZE DNA (cytosine-5)-methyltransferase 2 OS=Zea mays GN=ZMET5 PE=2 SV=1 Length = 915 Score = 43.5 bit...ive DNA (cytosine-5)-methyltransferase CMT1 OS=Arabidopsis thaliana GN=CMT1 PE=5 SV=2 Leng

  11. The effects of prepubertal gonadectomy and binge-like ethanol exposure during adolescence on ethanol drinking in adult male and female rats

    OpenAIRE

    Sherrill, Luke K.; Koss, Wendy A.; Foreman, Emily S.; Gulley, Joshua M.

    2010-01-01

    The pubertal surge in gonadal hormones that occurs during adolescence may impact the long-term effects of early alcohol exposure and sex differences in drinking behavior in adulthood. We investigated this hypothesis by performing sham or gonadectomy surgeries in Long Evans rats around postnatal day (P) 20. From P35–45, males and females were given saline or 3.0 g/kg ethanol using a binge-like model of exposure (8 injections total). As adults (P100), they were trained to self-administer ethano...

  12. Evaluation of the Wound-healing Activity of Ethanolic Extract of Morinda citrifolia L. Leaf

    OpenAIRE

    Anderson Maxwell; Steve Sandiford; Shivananda Nayak, B

    2007-01-01

    Morinda citrifolia L. (noni) is one of the most important traditional Polynesian medicinal plants. The primary indigenous use of this plant appears to be of the leaves, as a topical treatment for wound healing. The ethanol extract of noni leaves (150 mg kg−1 day−1) was used to evaluate the wound-healing activity on rats, using excision and dead space wound models. Animals were randomly divided into two groups of six for each model. Test group animals in each model were treated with the ethano...

  13. Synthesis, characterization and biological activities of novel chalcone derivatives, containing 4, 7-ethanoisoindole-1,3-dione units

    OpenAIRE

    Mustafa Ceylan; İsa Karaman; Meryem Keçeci Sarıkaya

    2013-01-01

    Novel chalcone derivatives, containing 4, 7-ethanoisoindole-1,3-dione units were synthesized starting from 1,3-cyclohexadine (4) and maleic anhydride (5). Addition of maleic anhydride (5) to 1,3-cyclehexadine (4) gave an endo-adduct, 3a,4,7,7a-tetrahydro-4,7-ethano-2-benzofuran-1,3-dione (6), in 90% yield. Heating the solution of the adduct dione (6) and 1-(4-aminophenyl)ethanone (7) in the presence of Et 3N in toluene at 110 oC for 24 hours afforded 2-(4-acetylphenyl)-3a,4,7,7a-tetrahydro-1H...

  14. Tetrakis[μ3-2-(piperidin-1-yl)ethanolato]tetrakis[chloridocopper(II)

    OpenAIRE

    Mei Luo; Yong-Hua Huang; Jing-Cheng Zhang

    2014-01-01

    In the title tetra­nuclear compound, [Cu4(C7H14NO)4Cl4], each CuII cation is N,O-chelated by a piperidineethanolate anion and coordinated by a Cl− anion and two O atoms from neighboring piperidine­ethano­late anions in a distorted NO3Cl square-pyramidal geometry. The deprotonated hydroxyl groups of the piperidineethanolate anions bridge CuII cations, forming the tetra­nuclear complex. All piperidine rings display a chair conformation. In the crystal, there are no significant inter­molecular i...

  15. Solvolysis of the Tumor-Inhibiting Ru(III)-Complex trans-Tetrachlorobis(Indazole)Ruthenate(III)

    OpenAIRE

    Pieper, Thomas; Peti, Wolfgang; BERNHARD K. KEPPLER

    2000-01-01

    The ruthenium(III) complex Hlnd trans-[RuCl4,(ind)2], with two trans-standing indazole (ind) ligands bound to ruthenium via nitrogen, shows remarkable activity in different tumor models in vitro and in vivo. The solvolysis of the complex trans-[RuCl4,(ind)2]- has been investigated by means of spectroscopic techniques (UV/vis, NMR)in different solvents. We investigated the indazolium as well as the sodium salt, the latter showing improved solubility in water. In aqueous acetonitrile and ethano...

  16. Sinalbin degradation products in mild yellow mustard paste

    Directory of Open Access Journals (Sweden)

    Paunović Dragana

    2012-01-01

    Full Text Available Sinalbin degradation products in mild yellow mustard paste were investigated. The analyzed material consisted of a mild yellow mustard paste condiment and ground white mustard seeds which were originally used in the mustard paste production process. The samples were extracted in a Soxhlet extraction system and analyzed by gas chromatography - mass spectrometry (GC-MS technique. The only sinalbin degradation product in ground mustard seeds was 2-(4-hydroxyphenylacetonitrile. The most abundant sinalbin degradation product in yellow mustard paste was 4-(hydroxymethylphenol. Other compounds identified in this sample were: 4-methyl phenol, 4-ethyl phenol, 4-(2-hydroxyethylphenol and 2-(4-hydroxyphenyl ethanoic acid.

  17. Discrepancies between the rate constants for the reactions of hydroxyl radicals with ferrocenyl-substituted carboxylic acids determined by direct measurement and by competition with thiocyanate-ion

    International Nuclear Information System (INIS)

    The rate constants for the reaction of OH radical with 3-ferrocenyl-propanoate and 2-ferrocenyl-ethanoate have been determined using competition with thiocyanate ion. However, the corrections involved in these determinations were large, ranging up to 38.5%, and we have, therefore, considered it necessary to attempt the direct measurement of these rate constants by pulse radiolysis. In this communication we report these direct measurements of the rate constants for these reactions and compare the values so obtained with those determined by competition with thiocyanate ion. We also report similar measurements for the reaction of OH with ferrocenylformate. (author)

  18. Studies on the Analgesic Potential of leaf Extracts of Allium humile on Swiss albino mice

    OpenAIRE

    Kamini Singh; Raveesh Kumar Gangwar; Garima Singh; Vikash S. Jadon; Shashi Ranjan

    2014-01-01

    Allium humile is a medicinal plant found at the Alpine Himalayas of Uttarakhand at altitute of 2500-3000 meters height of sea level. In India, Allium humile, is used by local people as a spice and in ethano-medicine. In the present study, Allium humile leaves were explored for their analgesic potential on experimental model and compared to standard drugs. Allium humile at the doses of 100 mg/kg and aspirin 25 mg/kg exhibited significant (p>0.05) inhibition of the control writhes at the rate o...

  19. Crystal structure of a four-stranded intercalated DNA: d(C4)

    Science.gov (United States)

    Chen, L.; Cai, L.; Zhang, X.; Rich, A.

    1994-01-01

    The crystal structure of d(C4) solved at 2.3-A resolution reveals a four-stranded molecule composed of two interdigitated or intercalated duplexes. The duplexes are held together by hemiprotonated cytosine-cytosine base pairs and are parallel stranded, but the two duplexes point in opposite directions. The molecule has a slow right-handed twist of 12.4 degrees between covalently linked cytosine base pairs, and the base stacking distance is 3.1 A. This is in general agreement with the NMR studies. A biological role for DNA in this conformation is suggested.

  20. Substituent group effects on reorganization and activation energies: Theoretical study of charge transfer reaction through DNA

    Science.gov (United States)

    Khan, Arshad

    2010-02-01

    The density functional theory (DFT) calculations (B3LYP) with aug-cc-pVDZ basis sets on various substituted neutral and radical cationic guanine-cytosine (GC ∗+) base pairs suggest that an electron-withdrawing ring deactivating substituent group like -NO 2, -COOH attached to a G ring lowers the reorganization/activation energy values whereas an electron releasing ring activating group like -OH increases these values. An electron releasing , but a ring deactivating group -F, exhibits its effect in between the above two extreme cases. A weak electron releasing, ring activating methyl group, as well as substituent groups attached to C (cytosine)-ring show almost no effect.

  1. Novel biophysical determination of miRNAs related to prostate and head and neck cancers

    Czech Academy of Sciences Publication Activity Database

    Hudcová, K.; Trnková, L.; Kejnovská, Iva; Vorlíčková, Michaela; Gumulec, J.; Kizek, R.; Masarik, M.

    2015-01-01

    Roč. 44, č. 3 (2015), s. 131-138. ISSN 0175-7571 Institutional support: RVO:68081707 Keywords : SQUAMOUS-CELL CARCINOMA * ELIMINATION VOLTAMMETRY * CYTOSINE SIGNALS Subject RIV: BO - Biophysics Impact factor: 2.219, year: 2014

  2. Assignment of the human cytidine deaminase (CDA) gene to chromosome 1 band p35-p36.2

    Energy Technology Data Exchange (ETDEWEB)

    Saccone, S.; Andreozzi, L.; Della Valle, G. [Universita di Pavia (Italy)] [and others

    1994-08-01

    The enzyme cytidine deaminase (EC 3.5.4.12; CDA) catalyzes the hydrolytic deamination of cytidine or deoxycytidine to uridine or deoxyuridine, respectively. It can also catalyze the deamination of cytosine nucleoside analogues such as cytosine arabinoside and 5-azacytidine, which results in a loss of their cytotoxic and antitumor activity. Cytosine arabinoside is used in the treatment of acute myeloid leukemia, and the antileukemic activity of the drug is dependent on phosphorylation by deoxycytidine kinase. The occurrence of clinical cytosine arabinoside resistance is one of the main problems in the successful treatment of acute myeloid leukemia. Resistance to the drug has been ascribed to functional deoxycytidine kinase deficiency and to increased expression of the CDA gene. In this study, we report on the isolation of a CDA genomic fragment and its use as a probe for the chromosomal localization of the human CDA gene by in situ hybridization. 9 refs., 1 fig.

  3. Protein (Viridiplantae): 308801991 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available LTVDPANQQYASVRALLLDPSCSGSGTEVNRGDIMLREALCDDNDDENEVDAADHDRVEKLAAFQKKALTHAFNFPEVQRVSYSTCSVYEKENEEVVRDVMGAANERGFKLVHALPAWHRRGIA...TREDAARAVGALFAAAATRTRGASIKARTLAPHVRHKRATHAVTCETIKHARTIKSVFADACEDLRALVDEDAGESEGKETFRRRGEAYVYAYETLFGNGRGLERWEGGEGCAIARENE...DVDALIDTLLVFPAGTDLHAHRLVKSGGVVLQGRASCLPAAALAPERGWACIDGCAAPGNKTTQLAAMVGREGGVYAFDADAKRLKRLKENATTTGSHAIIRAKCQDF...IDGLSESQARCLIRADPTEDDMEGFFVAVFERDVERTRSKGCELPPSNPNAAAAKAESERDKKKRSMKHATIAQPVYAKKKSKGGKPAPLFR ... ...A and rRNA cytosine-C5-methylase (nucleolar protein NOL1/NOP2) (ISS) Ostreococcus tauri MNILSPPHSPPPMSRARAPDAVTLNE

  4. Fragile X-Associated Disorders (FXD): A Handbook for Families, Health Care Providers, Counselors, and Educators

    Science.gov (United States)

    ... Genetics of Fragile X-Associated Disorders Cytosine (C) Guanine (G) Methyl Group CGG Start Codon Repeats Promoter ... FXPOI may have inadequate, but not absent, ovarian function such as in POF. FXPOI includes a spectrum ...

  5. Cardiac manifestations of myotonic dystrophy type 1

    DEFF Research Database (Denmark)

    Petri, Helle; Vissing, John; Witting, Nanna; Bundgaard, Henning; Køber, Lars

    2012-01-01

    To estimate the degree of cardiac involvement regarding left ventricular ejection fraction, conduction abnormalities, arrhythmia, risk of sudden cardiac death (SCD) and the associations between cardiac involvement and cytosine-thymine-guanine (CTG)-repeat, neuromuscular involvement, age and gender...

  6. Pyrimidine-specific chemical reactions useful for DNA sequencing.

    OpenAIRE

    Rubin, C M; Schmid, C. W.

    1980-01-01

    Potassium permanganate reacts selectively with thymidine residues in DNA (1) while hydroxylamine hydrochloride at pH 6 specifically attacks cytosine (2). We have adopted these reactions for use with the chemical sequencing method developed by Maxam and Gilbert (3).

  7. Protein (Viridiplantae): 308803957 [

    Lifescience Database Archive (English)

    Full Text Available XP_003079291.1 33090:404 3041:4055 1035538:2460 13792:2460 70447:1625 70448:2249 Cytosine deamin ... ase FCY1 and related enzymes ... (ISS) Ostreococcus tauri MVTRVSIDASTSRIRPRMAHDGFTD ...

  8. Non-CpG methylation of the PGC-1alpha promoter through DNMT3B controls mitochondrial density

    DEFF Research Database (Denmark)

    Barres, Romain; Osler, Megan E; Yan, Jie;

    2009-01-01

    Epigenetic modification through DNA methylation is implicated in metabolic disease. Using whole-genome promoter methylation analysis of skeletal muscle from normal glucose-tolerant and type 2 diabetic subjects, we identified cytosine hypermethylation of peroxisome proliferator-activated receptor...

  9. Application of Markov chain to the pattern of mitochondrial deoxyribonucleic acid mutations

    Science.gov (United States)

    Vantika, Sandy; Pasaribu, Udjianna S.

    2014-03-01

    This research explains how Markov chain used to model the pattern of deoxyribonucleic acid mutations in mitochondrial (mitochondrial DNA). First, sign test was used to see a pattern of nucleotide bases that will appear at one position after the position of mutated nucleotide base. Results obtained from the sign test showed that for most cases, there exist a pattern of mutation except in the mutation cases of adenine to cytosine, adenine to thymine, and cytosine to guanine. Markov chain analysis results on data of mutations that occur in mitochondrial DNA indicate that one and two positions after the position of mutated nucleotide bases tend to be occupied by particular nucleotide bases. From this analysis, it can be said that the adenine, cytosine, guanine and thymine will mutate if the nucelotide base at one and/or two positions after them is cytosine.

  10. Ligation Bias in Illumina Next-Generation DNA Libraries

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel;

    2013-01-01

    Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products,...

  11. Estimation of the methylation pattern distribution from deep sequencing data

    OpenAIRE

    Lin, Peijie; Forêt, Sylvain; Wilson, Susan R; Burden, Conrad J.

    2015-01-01

    Background Bisulphite sequencing enables the detection of cytosine methylation. The sequence of the methylation states of cytosines on any given read forms a methylation pattern that carries substantially more information than merely studying the average methylation level at individual positions. In order to understand better the complexity of DNA methylation landscapes in biological samples, it is important to study the diversity of these methylation patterns. However, the accurate quantific...

  12. Epigenetic responses to drought stress in rice (Oryza sativa L.)

    OpenAIRE

    Gayacharan; Joel, A. John

    2013-01-01

    Cytosine methylation polymorphism plays a key role in gene regulation, mainly in expression of genes in crop plants. The differential expression of cytosine methylation over drought stress response was analyzed in rice using drought susceptible but agronomically superior lines IR 20 and CO 43, and drought tolerant genotypes PL and PMK 3 and their F1 hybrids. The parents and hybrids were subjected to two moisture regimes viz., one under drought condition and another under control condition. Th...

  13. ISS immune modulation, vaccination and the regulation of arthritis

    OpenAIRE

    Ronaghy, Arash

    2007-01-01

    Bacterial DNA contains unique unmethylated CpG motifs. The cytosine-phosphate-guanisine (CpG) sequence of this motif has an unmethylated cytosine which is suppressed or methylated in mammalian DNA. Synthetic oligodeoxynucleotides containing these CpG (CpG-ODN) motifs are called Immunostimulatory DNA Sequences (ISS). Our goal is to gain a better understanding of how ISS, a TLR9 agonist, modulates the immune response and how this response may influence chronic inflammation in those with Juvenil...

  14. Direct Base-to-Base Transitions in ssDNA Revealed by Tip-Enhanced Raman Scattering

    CERN Document Server

    Lin, Xiu-Mei; Singh, Prabha; Siegmann, Michael; Kupfer, Stephan; Zhang, Zhenglong; Gräfe, Stefanie; Deckert, Volker

    2016-01-01

    In the present contribution, specifically designed single-stranded DNA (ssDNA) sequences composed of adenine and cytosine were used as nanometric rulers to target the maximum achievable spatial resolution of tip-enhanced Raman spectroscopy (TERS) under ambient conditions. By stepping along a strand with a TERS tip, the obtained spectra allowed for a clear spectral discrimination including conformational information of the nucleobases, and even sharp adenine-cytosine transitions were detected repeatedly with a spatial resolution below 1 nm.

  15. Direct homo- and hetero-interactions of MeCP2 and MBD2

    OpenAIRE

    Becker, A; Allmann, L.; Hofstaetter, M.; Casa, V.; Weber, P; Lehmkuhl, A.; Herce, H.D.; Cardoso, M.C.

    2013-01-01

    Epigenetic marks like methylation of cytosines at CpG dinucleotides are essential for mammalian development and play a major role in the regulation of gene expression and chromatin architecture. The methyl-cytosine binding domain (MBD) protein family recognizes and translates this methylation mark. We have recently shown that the level of MeCP2 and MBD2, two members of the MBD family, increased during differentiation and their ectopic expression induced heterochromatin clustering in vivo. As ...

  16. The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis

    OpenAIRE

    Ausin, Israel; Greenberg, Maxim V. C.; Li, Carey Fei; Jacobsen, Steven E.

    2012-01-01

    Cytosine DNA methylation is an epigenetic mark frequently associated with silencing of genes and transposons. In Arabidopsis, the establishment of cytosine DNA methylation is performed by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2). DRM2 is guided to target sequences by small interfering RNAs (siRNAs) in a pathway termed RNA-directed DNA methylation (RdDM). We performed a screen for mutants that affect the establishment of DNA methylation by investigating genes that contain predicted RNA-in...

  17. Nucleoprotein-based nanoscale assembly

    OpenAIRE

    Smith, Steven S.; Niu, Luming; Baker, David J.; Wendel, John A.; Kane, Susan E.; Joy, Darrin S.

    1997-01-01

    A system for addressing in the construction of macromolecular assemblies can be based on the biospecificity of DNA (cytosine-5) methyltransferases and the capacity of these enzymes to form abortive covalent complexes at targeted 5-fluorocytosine residues in DNA. Using this system, macromolecular assemblies have been created using two representative methyltransferases: M·HhaI and M·MspI. When 5-fluorocytosine (F) is placed at the targeted cytosine in each recognition sequence in a synthetic ol...

  18. Sequence analysis and editing for bisulphite genomic sequencing projects

    OpenAIRE

    Carr, IM; Valleley, EMA; Cordery, SF; Markham, AF; Bonthron, DT

    2007-01-01

    Bisulphite genomic sequencing is a widely used technique for detailed analysis of the methylation status of a region of DNA. It relies upon the selective deamination of unmethylated cytosine to uracil after treatment with sodium bisulphite, usually followed by PCR amplification of the chosen target region. Since this two-step procedure replaces all unmethylated cytosine bases with thymine, PCR products derived from unmethylated templates contain only three types of nucleotide, in unequal prop...

  19. The infrared spectrum and structure of the type I complex of silver and DNA.

    OpenAIRE

    DiRico, D E; Keller, P B; Hartman, K. A.

    1985-01-01

    Infrared spectroscopy was used to study films of the type I complex of Ag+ and DNA as a function of hydration with the following conclusions. Ag+ binds to guanine residues but not to cytosine or thymine residues. Cytosine becomes protonated as Ag+ binds to guanine. (These conclusions confirm previous models.) The type I complex remains in the B family of structures with slight modifications of the sugar-phosphate geometry. This modified B structure remains stable at lower values of hydration ...

  20. Metabolism of pyrimidine bases and nucleosides in the coryneform bacteria Brevibacterium ammoniagenes and Micrococcus luteus.

    OpenAIRE

    Auling, G; Moss, B

    1984-01-01

    The metabolism of exogenous pyrimidine bases and nucleosides was investigated in Brevibacterium ammoniagenes and Micrococcus luteus with fluorinated analogs and radioactive precursors. Salvage of thymine and thymidine was found in M. luteus, but not in B. ammoniagenes. Exogenous uracil or uracil nucleosides, but not cytosine or cytosine nucleosides, were nucleic acid precursors for both bacteria. By examining the possible nucleoside-metabolizing enzymes, it can be suggested that the pyrimidin...

  1. Influence of x-rays on the deamination of cytidine compounds in yeasts

    International Nuclear Information System (INIS)

    The investigation of deamination of cytidine, cytosine, and cytidine nucleotides (CMP, CDP and CTP) was carried out on yeast Candida guilliermondii. It has been shown, that after exposure to X-ray the value of deamination of (CTD) was decreased, and the value of deamination of cytosine was increased. The increase of deamination level was detected in presence of all substrates besides cytidine after the post radiation repair of cells

  2. Genetic variations in the human cannabinoid receptor gene are associated with happiness.

    Directory of Open Access Journals (Sweden)

    Masahiro Matsunaga

    Full Text Available Happiness has been viewed as a temporary emotional state (e.g., pleasure and a relatively stable state of being happy (subjective happiness level. As previous studies demonstrated that individuals with high subjective happiness level rated their current affective states more positively when they experience positive events, these two aspects of happiness are interrelated. According to a recent neuroimaging study, the cytosine to thymine single-nucleotide polymorphism of the human cannabinoid receptor 1 gene is associated with sensitivity to positive emotional stimuli. Thus, we hypothesized that our genetic traits, such as the human cannabinoid receptor 1 genotypes, are closely related to the two aspects of happiness. In Experiment 1, 198 healthy volunteers were used to compare the subjective happiness level between cytosine allele carriers and thymine-thymine carriers of the human cannabinoid receptor 1 gene. In Experiment 2, we used positron emission tomography with 20 healthy participants to compare the brain responses to positive emotional stimuli of cytosine allele carriers to that of thymine-thymine carriers. Compared to thymine-thymine carriers, cytosine allele carriers have a higher subjective happiness level. Regression analysis indicated that the cytosine allele is significantly associated with subjective happiness level. The positive mood after watching a positive film was significantly higher for the cytosine allele carriers compared to the thymine-thymine carriers. Positive emotion-related brain region such as the medial prefrontal cortex was significantly activated when the cytosine allele carriers watched the positive film compared to the thymine-thymine carriers. Thus, the human cannabinoid receptor 1 genotypes are closely related to two aspects of happiness. Compared to thymine-thymine carriers, the cytosine allele carriers of the human cannabinoid receptor 1 gene, who are sensitive to positive emotional stimuli, exhibited greater

  3. PSE extrakce rostlinného materiálu pro potravinářské účely

    OpenAIRE

    Holasová, Petra

    2009-01-01

    Ve vzorcích sušených listů rostliny Stevia rebaudiana Bertoni byly identifikovány a kvantifikovány flavonoidy. Obsah flavonolů (kaemferol, kvercetin, myricetin, rutin) a flavonů (apigenin, luteolin) byl porovnáván ve 3 vzorcích (standardní listy Stevia rebaudiana Bertoni, Stevia rebaudiana Bertoni pěstovaná v Ukrajině a v České republice), které byly extrahovány třemi extrakčními metodami (PSE, extrakce ultrazvukem, extrakce dle Soxhleta) za použití 2 polárních rozpouštědel, methanol a ethano...

  4. Endophytic fungi found in association with Bacopa monnieri as potential producers of industrial enzymes and antimicrobial bioactive compounds

    Directory of Open Access Journals (Sweden)

    Meenu Katoch

    2014-10-01

    Full Text Available This study aimed to screen the endophytic fungal species of ethano-medicinal plant Bacopa monnieri (L. Pennell for their ability to produce antimicrobial substances against Bacillus subtilis, Pseudomonas aeroginosa, Salmonella typhimurium, Escherichia coli, Klebsiella pneumonia, Staphylococcus aureus, and Candida albicans. Endophytes were also screened for their ability to produce amylase, cellulase, protease and lipase to evaluate their ecological role within the host plant. Twenty-six endophytes were isolated and seventeen were identified. All the isolated endophytes exhibited amylolytic activity. Lipolytic, cellulolytic, proteolytic activity was shown by 98, 28 and 31% isolates, respectively. Similarly, all the endophytes (100% exhibited significant antimicrobial activity against K. pneumonia, while seventeen endophytes (89.5% were active against S. aureus. Fourteen endophytes (78.9% showed significant antimicrobial activity against B. subtilis and C. albicans. Eleven (57.8%, nine (50%, four (21% endophytes were active against S. typhimurium, E. coli and P. aeruginosa, respectively.

  5. Selective solid phase extraction for separation and preconcentration of palladium from Gold Ore and anode slime after complexation with a N{sub 4}O{sub 2} mixed donor ligand derivative

    Energy Technology Data Exchange (ETDEWEB)

    Bulut, Volkan Numan [Macka Vocational School, Karadeniz Technical University, Macka/ Trabzon (Turkey); Tufekci, Mehmet; Duran, Celal; Kantekin, Halit [Faculty of Arts and Sciences, Department of Chemistry, Karadeniz Technical University, Trabzon (Turkey); Soylak, Mustafa [Faculty of Science, Department of Chemistry, Erciyes University, Kayseri (Turkey)

    2010-07-15

    A selective and sensitive method for the preconcentration, separation, and determination of palladium with flame atomic absorption spectrometry using 4,15-bis[(4-methylphenyl)sulfonyl]-20,21-dinitro-2,3,4,5,6,7,9,10,12,13,14,15,16,17-tetradecahydro-8,11-ethano-1,18,4,8,11,15-benzodioxa tetraaza cycloicosine (TNACIN) on XAD-2010 was developed. TNACIN-Pd(II) complex formed acidic aqueous solution (0.075-0.100 M HNO{sub 3}) was accumulated on XAD-2010 and then eluted with 1 M HCl in acetone. The effects of some analytical parameters including pH, TNACIN amount, sample volume, eluent type, and concentration, sample flow rate and matrix ions were studied for optimization of the method. Detection limit and precision were calculated for Pd(II). This method was also verified with CRM and internal standard, and satisfactory results were obtained. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  6. 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 ...

  7. CRISPR/Cas9-mediated phage resistance is not impeded by the DNA modifications of phage T4.

    Directory of Open Access Journals (Sweden)

    Stephanie J Yaung

    Full Text Available Bacteria rely on two known DNA-level defenses against their bacteriophage predators: restriction-modification and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-CRISPR-associated (Cas systems. Certain phages have evolved countermeasures that are known to block endonucleases. For example, phage T4 not only adds hydroxymethyl groups to all of its cytosines, but also glucosylates them, a strategy that defeats almost all restriction enzymes. We sought to determine whether these DNA modifications can similarly impede CRISPR-based defenses. In a bioinformatics search, we found naturally occurring CRISPR spacers that potentially target phages known to modify their DNA. Experimentally, we show that the Cas9 nuclease from the Type II CRISPR system of Streptococcus pyogenes can overcome a variety of DNA modifications in Escherichia coli. The levels of Cas9-mediated phage resistance to bacteriophage T4 and the mutant phage T4 gt, which contains hydroxymethylated but not glucosylated cytosines, were comparable to phages with unmodified cytosines, T7 and the T4-like phage RB49. Our results demonstrate that Cas9 is not impeded by N6-methyladenine, 5-methylcytosine, 5-hydroxymethylated cytosine, or glucosylated 5-hydroxymethylated cytosine.

  8. AcEST: BP914879 [AcEST

    Lifescience Database Archive (English)

    Full Text Available BlastX Result : TrEMBL tr_hit_id A9RVR7 Definition tr|A9RVR7|A9RVR7_PHYPA Cytosine-specific methyltransferase OS=Physcomitrella pat...se OS=Br... 164 3e-39 >tr|A9RVR7|A9RVR7_PHYPA Cytosine-specific methyltransferase OS=Physcomitrella patens subsp. pat...s) Value sp|P34881|DNMT1_ARATH DNA (cytosine-5)-methyltransferase AthI OS... 179 8e-45 sp|O33945|CATR_ACILW Probable cat1 operon tra...se OS=Or... 196 7e-49 tr|Q7Y1I7|Q7Y1I7_ORYSJ Cytosine-specific methyltransferase OS=Or... 196 7e-49 tr|B8B7V4|B8B7V4_ORYSI Putat...|Q69W70|Q69W70_ORYSJ Cytosine-specific methyltransferase OS=Or... 195 9e-49 tr|B1Q3J7|B1Q3J7_ORYSJ Putative cytos

  9. Micrococcus luteus correndonucleases. II. Mechanism of action of two endonucleases specific for DNA containing pyrimidine dimers

    International Nuclear Information System (INIS)

    Py--Py correndonucleases I and II from Micrococcus luteus act exclusively on thymine-thymine, cytosine-cytosine, and thymine-cytosine cyclobutyl dimers in DNA, catalyzing incision 5' to the damage and generating 3'-hydroxyl and 5'-phosphoryl termini. Both enzymes initiate excision of pyrimidine dimers in vitro by correxonucleases and DNA polymerase I. The respective incised DNAs, however, differ in their ability to act as substrate for phage T4 polynucleotide ligase or bacterial alkaline phosphatase, suggesting that each endonuclease is specific for a conformationally unique site. The possibility that their respective action generates termini which represent different degrees of single strandedness is suggested by the unequal protection by Escherichia coli binding protein from the hydrolytic action of exonuclease VII

  10. AcEST: DK950254 [AcEST

    Lifescience Database Archive (English)

    Full Text Available 4964|RSC1_SCHPO Chromatin structure-remodeling complex subu... 37 0.11 sp|P26358|DNMT1_HUMAN DNA (cytosine-5)-methyltr...DNA (cytosine-5)-methyltransferase... 33 0.92 sp|P53236|RSC1_YEAST Chromatin structure-remodeling complex su...bu... 33 1.6 sp|Q92072|DNMT1_CHICK DNA (cytosine-5)-methyltransferase 1 OS=Ga... 33 1.6 sp|Q06488|RSC2_YEAST Chromatin structure-re...s vinifera Align length 142 Score (bit) 206.0 E-value 1.0e-51 Report BLASTX 2.2.19 [Nov-02-2008] Reference: Altschul, Step... (bit) 52.8 E-value 1.0e-06 Report BLASTX 2.2.19 [Nov-02-2008] Reference: Altschul, Stephen F.

  11. Mutagenic and Cytotoxic Properties of Oxidation Products of 5-Methylcytosine Revealed by Next-Generation Sequencing

    OpenAIRE

    Xi-Wen Xing; Yu-Li Liu; Mario Vargas; Yinsheng Wang; Yu-Qi Feng; Xiang Zhou; Bi-Feng Yuan

    2013-01-01

    5-methylcytosine (5-mC) can be sequentially oxidized to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-foC), and finally to 5-carboxylcytosine (5-caC), which is thought to function in active DNA cytosine demethylation in mammals. Although the roles of 5-mC in epigenetic regulation of gene expression are well established, the effects of 5-hmC, 5-foC and 5-caC on DNA replication remain unclear. Here we report a systematic study on how these cytosine derivatives (5-hmC, 5-foC and 5-caC) pe...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-06-15

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

  13. An in silico study of the protonated DNA triplex: In vivo stability of C +GC in a DNA triple helix

    Science.gov (United States)

    Jung, Jiwon; Lee, Sang Hak

    2010-07-01

    Protonated DNA base pairs, particularly the Cytosine-Guanine-Cytosine (CGC) triple pairs, were investigated its relative energetics by theoretical calculations. The energetic stabilities of C +GC and CG +C are almost the same in the gas phase, although the C +G pair is more stable than CG + by ca. 1150 cm -1 (3.34 kcal/mol). It is to be noted, however, that only C +GC was found in vivo, which seems to indicate different chemical environments for the triple pairs in vivo.

  14. Methylation Patterns of Papillomavirus DNA, Its Influence on E2 Function, and Implications in Viral Infection

    OpenAIRE

    Kim, Kitai; Garner-Hamrick, Peggy A.; Fisher, Chris; Lee, Denis; Lambert, Paul F.

    2003-01-01

    The biological activities of the papillomavirus E2 protein in transcription, replication, and maintenance of the papillomavirus genome rely on the E2 protein's ability to bind that genome specifically. The E2 binding sites (E2BSs), located within the long control region (LCR) of human papillomavirus (HPV) genomes, contain potential sites for 5′methylation at cytosine (CpG) residues. The E2 protein's capacity to bind E2BS in vitro is inhibited by methylation of these cytosines (59). Herein, we...

  15. Synthesis and Structural Study of Some Pyrimidinium Hexafluoridosilicates.

    Science.gov (United States)

    Pevec, Andrej

    2015-01-01

    The synthesis and spectroscopic characterization of some pyrimidinium hexafluoridosilicate salts with the formula (RH)2[SiF]6 (where R = 2-aminopyrimidine (1), cytosine (2) and 5-cyanocytosine (3)) is obtained in the reaction of SiO2 with hydrofluoric acid solution and subsequent addition of 2-aminopyrimidine, cytosine or 4-amino-2-chloropyrimidine-5-carbonitrile. The crystal structures of 1 and 3 have been determined by single-crystal X‒ray diffraction analysis. The combination of N‒H···F hydrogen bonds along with π‒π interactions between aromatic rings resulted in supramolecular architecture of cations and anions in the solid state. PMID:26085410

  16. Purification and characterization of DNA methyltransferases from Neisseria gonorrhoeae.

    OpenAIRE

    Piekarowicz, A; Yuan, R.; Stein, D C

    1988-01-01

    Three DNA methyltransferases, M.NgoAI, and M.NgoBI and M.NgoBII, free of any nuclease activities were isolated from Neisseria gonorrhoeae strains WR220 and MUG116 respectively. M.NgoAI recognizes the sequence 5' GGCC 3' and methylates the first 5' cytosine on both strands. M.NgoBI and M.NgoBII recognize 5' TCACC 3' and 5' GTAN5CTC 3' respectively. M.NgoBII methylates cytosine on only one strand to produce 5' GTAN5mCTC 3'.

  17. Understanding the effect of the nature of the nucleobase in the loops on the stability of the i-motif structure.

    Science.gov (United States)

    Benabou, Sanae; Garavís, Miguel; Lyonnais, Sébastien; Eritja, Ramon; González, Carlos; Gargallo, Raimundo

    2016-03-01

    The nature and the length of loops connecting cytosine tracts in i-motif structures may affect their stability. In this work, the influence of the nature of the nucleobases located in two of the loops of an intramolecular i-motif is studied using spectroscopy, separation techniques, and multivariate data analysis. The insertion of bases other than thymine induces an additional acid-base equilibrium with pKa ∼ 4.5. The presence of two guanine bases in the loops, placed opposite to each other, decreases the thermal stability of the structure. In contrast, thymine and cytosine bases in these positions stabilize the structure. PMID:26957024

  18. Evidence for non-CpG methylation in mammals

    DEFF Research Database (Denmark)

    Yan, Jie; Zierath, Juleen R; Barres, Romain

    2011-01-01

    In mammals, the existence of cytosine methylation on non-CpG sequences is controversial. Here, we adapted a LuminoMetric-based Assay (LUMA) to determine global non-CpG methylation levels in rodent and human tissues. We observed that......In mammals, the existence of cytosine methylation on non-CpG sequences is controversial. Here, we adapted a LuminoMetric-based Assay (LUMA) to determine global non-CpG methylation levels in rodent and human tissues. We observed that...

  19. The evidence for functional non-CpG methylation in mammalian cells

    OpenAIRE

    Patil, Vibha; Ward, Robyn L.; Hesson, Luke B

    2014-01-01

    In mammalian genomes, the methylation of cytosine residues within CpG dinucleotides is crucial to normal development and cell differentiation. However, methylation of cytosines in the contexts of CpA, CpT, and CpC (non-CpG methylation) has been reported for decades, yet remains poorly understood. In recent years, whole genome bisulphite sequencing (WGBS) has confirmed significant levels of non-CpG methylation in specific tissues and cell types. Non-CpG methylation has several properties that ...

  20. Data for the morphometric characterization of NT2-derived postmitotic neurons.

    Science.gov (United States)

    González-Burguera, Imanol; Ricobaraza, Ana; Aretxabala, Xabier; Barrondo, Sergio; García Del Caño, Gontzal; López de Jesús, Maider; Sallés, Joan

    2016-06-01

    NTERA2/D1 human teratocarcinoma progenitors induced to differentiate into postmitotic neurons by either long-term treatment with retinoic acid or short-term treatment with the nucleoside analog cytosine β-D-arabinofuranoside were subjected to morphometric analysis and compared. Our data provide a methodological and conceptual framework for future investigations aiming at distinguishing neuronal phenotypes on the basis of morphometric analysis. Data presented here are related to research concurrently published in "Highly Efficient Generation of Glutamatergic/Cholinergic NT2-Derived Postmitotic Human Neurons by Short-Term treatment with the Nucleoside Analogue Cytosine β-D-Arabinofuranoside" [1]. PMID:27158648

  1. Oxidative damage to 5-methylcytosine in DNA.

    OpenAIRE

    Zuo, S; Boorstein, R J; Teebor, G.W.

    1995-01-01

    Exposure of pyrimidines of DNA to ionizing radiation under aerobic conditions or oxidizing agents results in attack on the 5,6 double bond of the pyrimidine ring or on the exocyclic 5-methyl group. The primary product of oxidation of the 5,6 double bond of thymine is thymine glycol, while oxidation of the 5-methyl group yields 5-hydroxymethyluracil. Oxidation of the 5,6 double bond of cytosine yields cytosine glycol, which decomposes to 5-hydroxycytosine, 5-hydroxyuracil and uracil glycol, al...

  2. Archease from Pyrococcus abyssi improves substrate specificity and solubility of a tRNA m5C methyltransferase

    DEFF Research Database (Denmark)

    Auxilien, Sylvie; El Khadali, Fatima; Rasmussen, Anette;

    2007-01-01

    reading frame (PAB1947), which is shown here to encode a tRNA m(5)C methyltransferase. In vitro, the purified recombinant methyltransferase catalyzes m(5)C formation at several cytosines within tRNAs with preference for C49. The specificity of the methyltransferase is increased by the archease...

  3. Epigenetic Vestiges of Early Developmental Adversity: Childhood Stress Exposure and DNA Methylation in Adolescence

    Science.gov (United States)

    Essex, Marilyn J.; Boyce, W. Thomas; Hertzman, Clyde; Lam, Lucia L.; Armstrong, Jeffrey M.; Neumann, Sarah M. A.; Kobor, Michael S.

    2013-01-01

    Fifteen-year-old adolescents (N = 109) in a longitudinal study of child development were recruited to examine differences in DNA methylation in relation to parent reports of adversity during the adolescents' infancy and preschool periods. Microarray technology applied to 28,000 cytosine-guanine dinucleotide sites within DNA derived from buccal…

  4. Characterization of Nucleobase Analogue FRET Acceptor tCnitro

    DEFF Research Database (Denmark)

    Preus, Søren; Börjesson, Karl; Kilså, Kristine; Albinsson, Bo; Wilhelmsson, L. Marcus

    2010-01-01

    The fluorescent nucleobase analogues of the tricyclic cytosine (tC) family, tC and tCO, possess high fluorescence quantum yields and single fluorescence lifetimes, even after incorporation into double-stranded DNA, which make these base analogues particularly useful as fluorescence resonance ener...

  5. Excited-state hydrogen atom abstraction initiates the photochemistry of beta-2 '-deoxycytidine

    Czech Academy of Sciences Publication Activity Database

    Szabla, Rafal; Campos, J.; Šponer, Judit E.; Gora, R.W.; Sutherland, J.D.

    2015-01-01

    Roč. 6, č. 3 (2015), s. 2035-2043. ISSN 2041-6520 R&D Projects: GA ČR(CZ) GA14-12010S Institutional support: RVO:68081707 Keywords : ULTRAFAST IR SPECTROSCOPY * CONICAL INTERSECTIONS * CYTOSINE DERIVATIVES Subject RIV: BO - Biophysics Impact factor: 9.211, year: 2014

  6. Gene : CBRC-MDOM-08-0077 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MDOM-08-0077 Novel 8 D UNKNOWN TPRXL_HUMAN 2e-11 62% gb|EEE27844.1| DNA ... mismatch repair pro ... -11 65% gnl|UG|Mdm#S36542801 Monodelphis domestica DNA ... (cytosine-5-)-methyltransferase (DNMT1), mRNA /cds ...

  7. Neuroblastoma: the Escherichia coli of neurobiology

    International Nuclear Information System (INIS)

    Changes in morphology in various clonal lines of neuroblastoma cells are described. Morphological changes were induced by FUDR, cytosine arabinoside, x radiation, and hypertonic culture media. Biochemical changes induced by x radiation and other agents in neuroblastoma cultures are tabulated. These changes include increased and decreased activities of acetyl cholinesterase, choline acetyltransferase, tyrosine hydroxylase, glutamate dehydrogenase, and lactate dehydrogenase. (U.S.)

  8. Eukaryotic DNA repair is blocked at different steps by inhibitors of DNA topoisomerases and of DNA polymerases α and β

    International Nuclear Information System (INIS)

    Inhibitors of (a) DNA topoisomerases (novobiocin and nalidixic acid) and of (b) eukaryotic DNA polymerases α (cytosine arabinoside) and β (dideoxythymidine) blocked different steps of DNA repair, demonstrated by the effects of the inhibitors on the relaxation of supercoiled DNA nucleoids following treatment of human cell cultures with ultraviolet light (1-3 J/m2) or MNNG (5 or 20 μM) and the subsequent restoration of the supercoiled nucleoids during repair incubation. Inhibition of repair by novobiocin was partially reversible; upon its removal from the culture medium, the nucleoid DNA of repairing cells became relaxed. The DNA polymerase inhibitors allowed the initial relaxation of DNA after treatment of the cells with ultraviolet or MNNG but delayed the regeneration of rapidly-sedimenting (supercoiled) nucleoid DNA for 2-4 h. Dideoxythymidine (1 mM) was more effective than cytosine arabinoside (1 μM) in producing this delay, but neither inhibitor by itself blocked repair permanently. Incubation of ultraviolet-irradiated cells with 1 μM cytosine arabinoside plus 1 mM dideoxythymidine blocked the completion of repair for 24 h, whereas incubation with 10 μM cytosine arabinoside or 5 mM dideoxythymidine produced only temporary repair delays of 2-4 h. Thus, it is likely that the two DNA polymerase inhibitors act upon separate targets and that both targets are involved in repair. (Auth.)

  9. Growth hormone dose in growth hormone-deficient adults is not associated with IGF-1 gene polymorphisms

    NARCIS (Netherlands)

    S. Meyer; S. Schaefer (Stephan); D. Ivan (Diana); L. Stolk (Lisette); P.P. Arp (Pascal); A.G. Uitterlinden (André); P.P. Nawroth (Peter); U. Plöckinger (Ursula); G.K. Stalla (Günter); U. Tuschy (Ulrich); M.M. Weber (Matthias); W.J. Weise (Wolfgang); A. Pfützner (Andreas); P. Kann (P.)

    2009-01-01

    textabstractAims: Several SNPs and a microsatellite cytosine-adenine repeat promoter polymorphisms of the IGF-1 gene have been reported to be associated with circulating IGF-1 serum concentrations. Variance in IGF-1 concentrations due to genetic variations may affect different response to growth hor

  10. Few constraints limit the design of quinone methide-oligonucleotide self-adducts for directing DNA alkylation†

    OpenAIRE

    Rossiter, Clifford S.; Modica, Emilia; Kumar, Dalip; Rokita, Steven E

    2010-01-01

    Nucleotide sequences minimally containing adenosine, cytosine or guanosine are sufficient to form intrastrand oligonucleotide quinone methide self-adducts reversibly for subsequent alkylation of complementary DNA. The general lack of sequence restrictions should now allow for alkylation of most any target of interest although reaction is most efficient when the self-adducts contain guanine residues and do not form hairpin structures.

  11. A Prebiotic Chemistry Experiment on the Adsorption of Nucleic Acids Bases onto a Natural Zeolite

    Science.gov (United States)

    Anizelli, Pedro R.; Baú, João Paulo T.; Gomes, Frederico P.; da Costa, Antonio Carlos S.; Carneiro, Cristine E. A.; Zaia, Cássia Thaïs B. V.; Zaia, Dimas A. M.

    2015-09-01

    There are currently few mechanisms that can explain how nucleic acid bases were synthesized, concentrated from dilute solutions, and/or protected against degradation by UV radiation or hydrolysis on the prebiotic Earth. A natural zeolite exhibited the potential to adsorb adenine, cytosine, thymine, and uracil over a range of pH, with greater adsorption of adenine and cytosine at acidic pH. Adsorption of all nucleic acid bases was decreased in artificial seawater compared to water, likely due to cation complexation. Furthermore, adsorption of adenine appeared to protect natural zeolite from thermal degradation. The C=O groups from thymine, cytosine and uracil appeared to assist the dissolution of the mineral while the NH2 group from adenine had no effect. As shown by FT-IR spectroscopy, adenine interacted with a natural zeolite through the NH2 group, and cytosine through the C=O group. A pseudo-second-order model best described the kinetics of adenine adsorption, which occurred faster in artificial seawaters.

  12. Molecular Data for a Biochemical Model of DNA Radiation Damage: Electron Impact Ionization and Dissociative Ionization of DNA Bases and Sugar-Phosphate Backbone

    Science.gov (United States)

    Dateo, Christopher E.; Fletcher, Graham D.

    2004-01-01

    As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is found that the total ionization cross sections of C3'- and C5'-deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3'- and C5'-deoxyribose-phospate cross sections, differing by less than 10%. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-Hl)(+), with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 17.1 eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage.

  13. Genomic uracil and human disease

    DEFF Research Database (Denmark)

    Hagen, Lars; Pena Diaz, Javier; Kavli, Bodil;

    2006-01-01

    Uracil is present in small amounts in DNA due to spontaneous deamination of cytosine and incorporation of dUMP during replication. While deamination generates mutagenic U:G mismatches, incorporated dUMP results in U:A pairs that are not directly mutagenic, but may be cytotoxic. In most cells, mut...

  14. Novel mutation in 16S rRNA associated with streptomycin dependence in Mycobacterium tuberculosis.

    OpenAIRE

    Honoré, N; Marchal, G.; Cole, S T

    1995-01-01

    Molecular characterization of a streptomycin-dependent mutant of Mycobacterium tuberculosis revealed the presence of a novel mutation in the rrs gene encoding 16S rRNA. Insertion of an additional cytosine in the 530 loop of 16S rRNA, a region known to be involved in streptomycin susceptibility and resistance, was associated with streptomycin dependence.

  15. DNA methylation profiling using HpaII tiny fragment enrichment by ligation-mediated PCR (HELP)

    OpenAIRE

    Suzuki, Masako; Greally, John M.

    2010-01-01

    The HELP assay is a technique that allows genome-wide analysis of cytosine methylation. Here we describe the assay, its relative strengths and weaknesses, and the transition of the assay from a microarray to massively-parallel sequencing-based foundation.

  16. Energy dependence of effective atomic numbers for photon energy absorption and photon interaction: Studies of some biological molecules in the energy range 1 keV-20 MeV

    DEFF Research Database (Denmark)

    Manohara, S.R.; Hanagodimath, S.M.; Gerward, Leif

    2008-01-01

    , linolenic, arachidonic, and arachidic acids), nucleotide bases (adenine, guanine, cytosine, uracil, and thymine), and carbohydrates (glucose, sucrose, raffinose, and starch). The Z(PEA, eff) and Z(PI, eff) values have been found to change with energy and composition of the biological molecules. The energy...

  17. Divergence of Pumilio/fem-3 mRNA Binding Factor (PUF) Protein Specificity through Variations in an RNA-binding Pocket*

    Science.gov (United States)

    Qiu, Chen; Kershner, Aaron; Wang, Yeming; Holley, Cynthia P.; Wilinski, Daniel; Keles, Sunduz; Kimble, Judith; Wickens, Marvin; Hall, Traci M. Tanaka

    2012-01-01

    mRNA control networks depend on recognition of specific RNA sequences. Pumilio-fem-3 mRNA binding factor (PUF) RNA-binding proteins achieve that specificity through variations on a conserved scaffold. Saccharomyces cerevisiae Puf3p achieves specificity through an additional binding pocket for a cytosine base upstream of the core RNA recognition site. Here we demonstrate that this chemically simple adaptation is prevalent and contributes to the diversity of RNA specificities among PUF proteins. Bioinformatics analysis shows that mRNAs associated with Caenorhabditis elegans fem-3 mRNA binding factor (FBF)-2 in vivo contain an upstream cytosine required for biological regulation. Crystal structures of FBF-2 and C. elegans PUF-6 reveal binding pockets structurally similar to that of Puf3p, whereas sequence alignments predict a pocket in PUF-11. For Puf3p, FBF-2, PUF-6, and PUF-11, the upstream pockets and a cytosine are required for maximal binding to RNA, but the quantitative impact on binding affinity varies. Furthermore, the position of the upstream cytosine relative to the core PUF recognition site can differ, which in the case of FBF-2 originally masked the identification of this consensus sequence feature. Importantly, other PUF proteins lack the pocket and so do not discriminate upstream bases. A structure-based alignment reveals that these proteins lack key residues that would contact the cytosine, and in some instances, they also present amino acid side chains that interfere with binding. Loss of the pocket requires only substitution of one serine, as appears to have occurred during the evolution of certain fungal species. PMID:22205700

  18. Divergence of Pumilio/fem-3 mRNA binding factor (PUF) protein specificity through variations in an RNA-binding pocket.

    Science.gov (United States)

    Qiu, Chen; Kershner, Aaron; Wang, Yeming; Holley, Cynthia P; Wilinski, Daniel; Keles, Sunduz; Kimble, Judith; Wickens, Marvin; Hall, Traci M Tanaka

    2012-02-24

    mRNA control networks depend on recognition of specific RNA sequences. Pumilio-fem-3 mRNA binding factor (PUF) RNA-binding proteins achieve that specificity through variations on a conserved scaffold. Saccharomyces cerevisiae Puf3p achieves specificity through an additional binding pocket for a cytosine base upstream of the core RNA recognition site. Here we demonstrate that this chemically simple adaptation is prevalent and contributes to the diversity of RNA specificities among PUF proteins. Bioinformatics analysis shows that mRNAs associated with Caenorhabditis elegans fem-3 mRNA binding factor (FBF)-2 in vivo contain an upstream cytosine required for biological regulation. Crystal structures of FBF-2 and C. elegans PUF-6 reveal binding pockets structurally similar to that of Puf3p, whereas sequence alignments predict a pocket in PUF-11. For Puf3p, FBF-2, PUF-6, and PUF-11, the upstream pockets and a cytosine are required for maximal binding to RNA, but the quantitative impact on binding affinity varies. Furthermore, the position of the upstream cytosine relative to the core PUF recognition site can differ, which in the case of FBF-2 originally masked the identification of this consensus sequence feature. Importantly, other PUF proteins lack the pocket and so do not discriminate upstream bases. A structure-based alignment reveals that these proteins lack key residues that would contact the cytosine, and in some instances, they also present amino acid side chains that interfere with binding. Loss of the pocket requires only substitution of one serine, as appears to have occurred during the evolution of certain fungal species. PMID:22205700

  19. Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations

    Science.gov (United States)

    Yang, Bo; Rodgers, M. T.

    2015-08-01

    Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m5dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m5dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m5dCyd)H+(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

  20. Comparative acute freshwater hazard assessment and preliminary PNEC development for eight fluorinated acids.

    Science.gov (United States)

    Hoke, Robert A; Bouchelle, Laurie D; Ferrell, Barbra D; Buck, Robert C

    2012-05-01

    Short-term 48, 72 and 96-h aquatic toxicity tests were conducted to evaluate the acute toxicity of eight fluorinated acids to the cladoceran, Daphnia magna, the green alga, Pseudokirchneriella subcapitata, and the rainbow trout, Oncorhynchus mykiss or the fathead minnow, Pimephales promelas. The eight fluorinated acids studied were tridecafluorohexyl ethanoic acid (6:2 FTCA), heptadecafluorooctyl ethanoic acid (8:2 FTCA), 2H-dodecafluoro-2-octenoic acid (6:2 FTUCA), 2H-hexadecafluoro-2-decenoic acid (8:2 FTUCA), 2H,2H,3H,3H-undecafluoro octanoic acid (5:3 acid), 2H,2H,3H,3H-pentadecafluoro decanoic acid (7:3 acid), n-perfluoropentanoic acid (PFPeA) and n-perfluorodecanoic acid (PFDA). The results of the acute toxicity tests conducted during this study suggest that the polyfluorinated acids, 8:2 FTCA, 8:2 FTUCA, 6:2 FTCA, 6:2 FTUCA, 7:3 acid and 5:3 acid, and the perfluorinated acids PFPeA and PFDA, are generally of low to medium concern based on evaluation of their acute freshwater toxicity (EC/LC50s typically between 1 and >100 mg L(-1)) using the USEPA TSCA aquatic toxicity evaluation paradigm. For the polyfluorinated acids, aquatic toxicity generally decreased as the number of fluorinated carbons decreased and as the overall carbon chain length decreased from 12 to 8. Acute aquatic toxicity of the 5 and 10 carbon perfluorocarboxylic acids (EC/LC50s between 10.6 and >100 mg L(-1)) was greater or similar to that of the 6-9 carbon perfluorocarboxylic acids (EC/LC50s>96.5 mg L(-1)). This study also provides the first report of the acute aquatic toxicity of the 5:3 acid (EC/LC50s of 22.5 to >103 mg L(-1)) which demonstrated less aquatic toxicity than the 7:3 acid (EC/LC50s of 0.4-32 mg L(-1)). The cladoceran, D. magna and the green alga, P. subcapitata had generally similar EC50 values for a given substance while fish were typically equally or less sensitive with the exception that PFPeA was most toxic to fish. Predicted no-effect concentrations (PNECs) were

  1. π-Radical to σ-Radical Tautomerization in One-Electron-Oxidized 1-Methylcytosine and Its Analogs.

    Science.gov (United States)

    Adhikary, Amitava; Kumar, Anil; Bishop, Casandra T; Wiegand, Tyler J; Hindi, Ragda M; Adhikary, Ananya; Sevilla, Michael D

    2015-09-01

    In this work, iminyl σ-radical formation in several one-electron-oxidized cytosine analogs, including 1-MeC, cidofovir, 2'-deoxycytidine (dCyd), and 2'-deoxycytidine 5'-monophosphate (5'-dCMP), were investigated in homogeneous, aqueous (D2O or H2O) glassy solutions at low temperatures by employing electron spin resonance (ESR) spectroscopy. Upon employing density functional theory (DFT) (DFT/B3LYP/6-31G* method), the calculated hyperfine coupling constant (HFCC) values of iminyl σ-radical agree quite well with the experimentally observed ones, thus confirming its assignment. ESR and DFT studies show that the cytosine iminyl σ-radical is a tautomer of the deprotonated cytosine π-cation radical [cytosine π-aminyl radical, C(N4-H)(•)]. Employing 1-MeC samples at various pHs ranging from ca. 8 to 11, ESR studies show that the tautomeric equilibrium between C(N4-H)(•) and the iminyl σ-radical at low temperature is too slow to be established without added base. ESR and DFT studies agree that, in the iminyl σ-radical, the unpaired spin is localized on the exocyclic nitrogen (N4) in an in-plane pure p-orbital. This gives rise to an anisotropic nitrogen hyperfine coupling (Azz = 40 G) from N4 and a near isotropic β-nitrogen coupling of 9.7 G from the cytosine ring nitrogen at N3. Iminyl σ-radical should exist in its N3-protonated form, as the N3-protonated iminyl σ-radical is stabilized in solution by over 30 kcal/mol (ΔG = -32 kcal/mol) over its conjugate base, the N3-deprotonated form. This is the first observation of an isotropic β-hyperfine ring nitrogen coupling in an N-centered DNA radical. Our theoretical calculations predict that the cytosine iminyl σ-radical can be formed in double-stranded DNA by a radiation-induced ionization-deprotonation process that is only 10 kcal/mol above the lowest energy path. PMID:26237072

  2. Target-controlled formation of silver nanoclusters in abasic site-incorporated duplex DNA for label-free fluorescence detection of theophylline

    Science.gov (United States)

    Park, Ki Soo; Oh, Seung Soo; Soh, H. Tom; Park, Hyun Gyu

    2014-08-01

    A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to the cytosine nucleobase is prevented. Consequently, fluorescent silver nanoclusters are not formed causing a significant reduction of the fluorescence signal. By employing this new sensor, theophylline can be highly selectively detected at a concentration as low as 1.8 μM. Finally, the diagnostic capability and practical application of this sensor were demonstrated by its use in detecting theophylline in human blood serum.A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to

  3. Pretargeting in tumored mice with radiolabeled morpholino oligomer showing low kidney uptake

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Guozheng; He, Jiang; Dou, Shuping; Gupta, Suresh; Vanderheyden, Jean-Luc; Rusckowski, Mary; Hnatowich, Donald J. [Division of Nuclear Medicine, Department of Radiology, University of Massachusetts Medical School, 55 Lake Avenue North, MA 01655-0243, Worcester (United States)

    2004-03-01

    We have recently shown that accumulation in mouse kidneys of technetium-99m labeled phosphorodiamidate morpholinos (MORFs) increases with the number of cytosines in the base sequence. To improve tumor/kidney ratios in tumored mice, pretargeting studies were performed with a cytosine-free MORF. An 18-mer MORF (5'-TCTTCTACTTCACAACTA) was conjugated to the anti-CEA antibody MN14 (Immunomedics) and administered to nude mice bearing LS174T tumors. Thereafter, the {sup 99m}Tc-labeled cytosine-free cMORF (5'-TAGTTGTGAAGTAGAAGA-amide-MAG{sub 3}) was administered. For comparison, the identical study was repeated but with our original pair of 18-mer MORFs (5'-GGGTGTACGTCACAACTA-conjugated MN14 and {sup 99m}Tc-labeled 5'-TAGTTGTGACGTACACCC-amide-MAG{sub 3}). Surface plasmon resonance was used to show that the hybridization affinities of the original and the modified pair of MORFs were essentially equal. Hybridization of the cytosine-free cMORF-{sup 99m}Tc to MN14-MORF was demonstrated in vitro by size-exclusion high-performance liquid chromatography. At 3 h, kidney levels in normal mice were 2.0%ID/organ for the modified cMORF vs. 4.1%ID/organ for the original cMORF sequence, while at 24 h, these values were 0.9% vs 1.8%ID/organ. Pretargeting studies in tumored mice receiving 25 {mu}g of conjugated antibody, 0.5 {mu}g of labeled cMORF 48 h later, followed by imaging and sacrifice at 3 h showed that kidney levels were reduced using the cytosine-free cMORF. Moreover, tumor accumulation was about 3.6%ID/g and was independent of sequence. The whole-body images clearly reflected the improved tumor to kidney ratios. By choosing a cytosine-free base sequence for pretargeting studies, kidney accumulation of cMORF-{sup 99m}Tc was reduced without adversely influencing tumor accumulation. The lowering of kidney radioactivity levels in this way may be important to reduce toxicity to this organ in connection with pretargeting radiotherapy studies. (orig.)

  4. Pretargeting in tumored mice with radiolabeled morpholino oligomer showing low kidney uptake.

    Science.gov (United States)

    Liu, Guozheng; He, Jiang; Dou, Shuping; Gupta, Suresh; Vanderheyden, Jean-Luc; Rusckowski, Mary; Hnatowich, Donald J

    2004-03-01

    We have recently shown that accumulation in mouse kidneys of technetium-99m labeled phosphorodiamidate morpholinos (MORFs) increases with the number of cytosines in the base sequence. To improve tumor/kidney ratios in tumored mice, pretargeting studies were performed with a cytosine-free MORF. An 18-mer MORF (5'-TCTTCTACTTCACAACTA) was conjugated to the anti-CEA antibody MN14 (Immunomedics) and administered to nude mice bearing LS174T tumors. Thereafter, the (99m)Tc-labeled cytosine-free cMORF (5'-TAGTTGTGAAGTAGAAGA-amide-MAG(3)) was administered. For comparison, the identical study was repeated but with our original pair of 18-mer MORFs (5'-GGGTGTACGTCACAACTA-conjugated MN14 and (99m)Tc-labeled 5'-TAGTTGTGACGTACACCC-amide-MAG(3)). Surface plasmon resonance was used to show that the hybridization affinities of the original and the modified pair of MORFs were essentially equal. Hybridization of the cytosine-free cMORF-(99m)Tc to MN14-MORF was demonstrated in vitro by size-exclusion high-performance liquid chromatography. At 3 h, kidney levels in normal mice were 2.0%ID/organ for the modified cMORF vs. 4.1%ID/organ for the original cMORF sequence, while at 24 h, these values were 0.9% vs 1.8%ID/organ. Pretargeting studies in tumored mice receiving 25 microg of conjugated antibody, 0.5 microg of labeled cMORF 48 h later, followed by imaging and sacrifice at 3 h showed that kidney levels were reduced using the cytosine-free cMORF. Moreover, tumor accumulation was about 3.6%ID/g and was independent of sequence. The whole-body images clearly reflected the improved tumor to kidney ratios. By choosing a cytosine-free base sequence for pretargeting studies, kidney accumulation of cMORF-(99m)Tc was reduced without adversely influencing tumor accumulation. The lowering of kidney radioactivity levels in this way may be important to reduce toxicity to this organ in connection with pretargeting radiotherapy studies. PMID:14691611

  5. Integrated basic treatment of activated carbon for enhanced CO2 selectivity

    Science.gov (United States)

    Adelodun, Adedeji Adebukola; Jo, Young-Min

    2013-12-01

    We attempted the use of three chemical agents viz nitric acid (HN), calcium nitrate (CaN) and calcium ethanoate (CaEt) to achieve enhanced CO2 selective adsorption by activated carbon (AC). In dry phase treatment, microporous coconut shell-based carbon (CS) exhibits higher CO2 capacity than coal-based. However, upon wet-phase pre-treatment, modified CS samples showed lesser CO2 adsorption efficiency. Surface characterization with X-ray photoelectron spectroscopy confirms the presence of calcium and amine species on the samples with integrated treatment (A-CaN). These samples recorded the highest low-level CO2 capture despite calcinated CaEt-doped samples (C-CaEt) showing the highest value for pure and high level CO2 adsorption capacities. The slope and linearity values of isobaric desorption were used to estimate the proportion of CO2 chemisorbed and heterogeneity of the adsorbents’ surfaces respectively. Consequently, integrated basic impregnation provides the most efficient adsorbents for selective adsorption of both indoor and outdoor CO2 levels.

  6. Integrated basic treatment of activated carbon for enhanced CO2 selectivity

    International Nuclear Information System (INIS)

    We attempted the use of three chemical agents viz nitric acid (HN), calcium nitrate (CaN) and calcium ethanoate (CaEt) to achieve enhanced CO2 selective adsorption by activated carbon (AC). In dry phase treatment, microporous coconut shell-based carbon (CS) exhibits higher CO2 capacity than coal-based. However, upon wet-phase pre-treatment, modified CS samples showed lesser CO2 adsorption efficiency. Surface characterization with X-ray photoelectron spectroscopy confirms the presence of calcium and amine species on the samples with integrated treatment (A-CaN). These samples recorded the highest low-level CO2 capture despite calcinated CaEt-doped samples (C-CaEt) showing the highest value for pure and high level CO2 adsorption capacities. The slope and linearity values of isobaric desorption were used to estimate the proportion of CO2 chemisorbed and heterogeneity of the adsorbents’ surfaces respectively. Consequently, integrated basic impregnation provides the most efficient adsorbents for selective adsorption of both indoor and outdoor CO2 levels.

  7. Changes of phosphorylation of cAMP response element binding protein in rat nucleus accumbens after chronic ethanol intake: naloxone reversal

    Institute of Scientific and Technical Information of China (English)

    LIJing; LIYue-Hua; YUANXiao-Ru

    2003-01-01

    AIM: To study the changes in the expression and phosphorylation of cAMP response element binding protein(CREB) in the rat nucleus accumbens after chronic ethanol intake and its withdrawal. METHODS: Ethanol wasgiven in drinking water at the concentration of 6 % (v/v), for one month. Changes in the levels of CREB andphospho-CREB (p-CREB) protein in the nucleus accumbens were measured by immunohistochemistry methods.RESULTS: Ethanol given to rats in drinking water decreased the level of p-CREB protein in the nucleus accumbens(-75 %) at the time of exposure to ethanol. The decrement of p-CREB protein in the nucleus accumbens remainedat 24 h (-35 %) and 72 h (-28 %) of ethanol withdrawal, which recovered toward control level after 7 d of ethanolwithdrawal. However, chronic ethanol, as well as ethanol withdrawal failed to produce any significant alteration inthe level of CREB protein in the nucleus accumbens. Naloxone (alone) treatment of rats had no effect on the levelsof CREB and p-CREB protein in the nucleus accumbens. However, when naloxone was administered concurrentlywith ethanol treatment, it antagonized the down-regulation of p-CREB protein in the nucleus accumbens (142 %) ofrats exposed to ethanol. CONCLUSION: A long-term intake of ethanol solution down-regulates the phosphoryla-tion of CREB in the nucleus accumbens, and those changes can be reversed by naloxone, which may be one kindof the molecular mechanisms associated with ethano1 dependence.

  8. Studies on the Analgesic Potential of leaf Extracts of Allium humile on Swiss albino mice

    Directory of Open Access Journals (Sweden)

    Kamini Singh

    2014-09-01

    Full Text Available Allium humile is a medicinal plant found at the Alpine Himalayas of Uttarakhand at altitute of 2500-3000 meters height of sea level. In India, Allium humile, is used by local people as a spice and in ethano-medicine. In the present study, Allium humile leaves were explored for their analgesic potential on experimental model and compared to standard drugs. Allium humile at the doses of 100 mg/kg and aspirin 25 mg/kg exhibited significant (p>0.05 inhibition of the control writhes at the rate of 64.25%, 44.54%, 44.54% and 59.89% respectively when compared to that of control. Thus, methanolic extract of the plant can be fully explored for its analgesic potential which has not been reported so far. The plant extract showed a relative low toxicity hence justifies the folkloric use of plant by the local people in Western Himalayan region for curing inflammation and painful conditions.

  9. Bio-electrochemical synthesis of commodity chemicals by autotrophic acetogens utilizing CO_{2} for environmental remediation

    Indian Academy of Sciences (India)

    GUGAN JABEEN; ROBINA FAROOQ

    2016-09-01

    Bio-electrochemical synthesis (BES) is a technique in which electro-autotrophic bacteria such as Clostridiumljungdahlii utilize electric currents as an electron source from the cathode to reduce CO_{2} to extracellular, multicarbon,exquisite products through autotrophic conversion. The BES of volatile fatty acids and alcohols directly fromCO_{2} is a sustainable alternative for non-renewable, petroleum-based polymer production. This conversion ofCO_{2} implies reduction of greenhouse gas emissions. The synthesis of heptanoic acid, heptanol, hexanoic acidand hexanol, for the first time, by Clostridium ljungdahlii was a remarkable achievement of BES. In ourstudy, these microorganisms were cultivated on the cathode of a bio-electrochemical cell at −400 mV by aDC power supply at 37°C, pH 6.8, and was studied for both batch and continuous systems. Pre-enrichment ofbio-cathode enhanced the electroactivity of cells and resulted in maximizing extracellular products in lesstime. The main aim of the research was to investigate the impact of low-cost substrate CO_{2}, and the longercathode recovery range was due to bacterial reduction of CO_{2} to multicarbon chemical commodities withelectrons driven from the cathode. Reactor design was simplified for cost-effectiveness and to enhance energyefficiencies. The Columbic recovery of ethanoic acid, ethanol, ethyl butyrate, hexanoic acid, heptanoic acidand hexanol being in excess of 80% proved that BES was a remarkable technology.

  10. Labeling and biodistribution of therapeutic radiopharmaceutical for brain cancer 125I-Nimotuzumab in normal mice

    International Nuclear Information System (INIS)

    Nimotuzumab is a monoclonal antibody which known giving contribution in anti proliferation, pro apoptosis and antiangionik effect on the therapy of brain cancer (glioma). The labeling of monoclonal antibody nimotuzumab with 125I which radiate auger electrons has been done with idogen method. The best result of radiochemical purity (97%) was shown in fraction 6 with the mol ratio of nimotuzumab towards potassium iodide and iodogen was 1 : 2 : 1200. Radiochemical purity was examined by paper chromatography with whatman paper no. 1 as the stationary phase and ethano!-butanol-ammonium hydroxide with a ratio of 3 : 2 : 1 as the mobile phase. Rf Values for 125I-nimotuzumab is 0.0, while Rf value of 125I .is 0.9. The biodistribution result on normal mice for 72 hours showed that 125I-nimotuzumab not only has a long half-life time but also has high accumulation in liver (1.97 + 1.18%), kidney (0.82 + 0.28%) and muscle (0.61+ 0.98%). The highest accumulation in brain on normal mice (0.128 + 0.06 %) occurred 24 hours after injection. Based on the therapeutic effects and organ accumulation on normal mice, 125I-nimotuzumab could be potentially used for brain cancer therapy. (author)

  11. Bio-electrochemical synthesis of commodity chemicals by autotrophic acetogens utilizing CO2 for environmental remediation.

    Science.gov (United States)

    Jabeen, Gugan; Farooq, Robina

    2016-09-01

    Bio-electrochemical synthesis (BES) is a technique in which electro-autotrophic bacteria such as Clostridium ljungdahlii utilize electric currents as an electron source from the cathode to reduce CO2 to extracellular, multicarbon, exquisite products through autotrophic conversion. The BES of volatile fatty acids and alcohols directly from CO2 is a sustainable alternative for non-renewable, petroleum-based polymer production. This conversion of CO2 implies reduction of greenhouse gas emissions. The synthesis of heptanoic acid, heptanol, hexanoic acid and hexanol, for the first time, by Clostridium ljungdahlii was a remarkable achievement of BES. In our study, these microorganisms were cultivated on the cathode of a bio-electrochemical cell at -400 mV by a DC power supply at 37 degree Centrigrade, pH 6.8, and was studied for both batch and continuous systems. Pre-enrichment of bio-cathode enhanced the electroactivity of cells and resulted in maximizing extracellular products in less time. The main aim of the research was to investigate the impact of low-cost substrate CO2, and the longer cathode recovery range was due to bacterial reduction of CO2 to multicarbon chemical commodities with electrons driven from the cathode. Reactor design was simplified for cost-effectiveness and to enhance energy efficiencies. The Columbic recovery of ethanoic acid, ethanol, ethyl butyrate, hexanoic acid, heptanoic acid and hexanol being in excess of 80 percent proved that BES was a remarkable technology. PMID:27581929

  12. Characterization of Ge Nano structures Embedded Inside Porous Silicon for Photonics Application

    International Nuclear Information System (INIS)

    In this work we prepared germanium nano structures by means of filling the material inside porous silicon (PS) using conventional and cost effective technique, thermal evaporator. The PS acts as patterned substrate. It was prepared by anodization of silicon wafer in ethanoic hydrofluoric acid (HF). A Ge layer was then deposited onto the PS by thermal evaporation. This was followed by deposition of Si layer by thermal evaporation and anneal at 650 degree Celsius for 30 min. The process was completed by Ni metal deposition using thermal evaporator followed by metal annealing of 400 degree Celsius for 10 min to form metal semiconductor metal (MSM) photodetector. Structural analysis of the samples was performed using energy dispersive x-ray analysis (EDX), scanning electron microscope (SEM), X-ray diffraction (XRD) and Raman spectroscopy (RS). EDX spectrum suggests the presence of Ge inside the pores structure. Raman spectrum showed that good crystalline structure of Ge can be produced inside silicon pores with a phase with the diamond structure by (111), (220) and (400) reflections. Finally current-voltage (I-V) measurement of the MSM photodetector was carried out and showed lower dark currents compared to that of Si control device. Interestingly the device showed enhanced current gain compared to Si device which can be associated with the presence of Ge nano structures in the porous silicon. (author)

  13. Thermodynamic study of (alkyl esters+α,ω-alkyl dihalides) I: HmE and VmE for 25 binary mixtures {xCu-1H2u-1CO2C2H5+(1-x)α,ω-ClCH2(CH2)v-2CH2Cl}, where u=1 to 5, α=1 and v=ω=2 to 6

    International Nuclear Information System (INIS)

    This article presents the experimental data of HmE and VmE, obtained at atmospheric pressure and at a temperature of 298.15K, for a set of 25 binary mixtures composed of the first 5 ethyl alkanoates (methanoate to pentanoate) and five α,ω-dichloroalkanes (1,2-dichloroethane to 1,6-dichlorohexane). Quantitatively, and with only a few exceptions, small values are obtained for the excess properties and the results imply that specific interactions exist between both types of compounds, with exothermic process for most mixtures, but with the exception of some that contain ethyl methanoate and ethanoate. The change in enthalpies with increasing length of the dichloroalkane chain for the same ester is regular, and also the change in HmE with the acid portion of the ethyl ester. However, the change in excess volumes does not present such a regular variation. A behavioural structural model is established to explain the results of the excess properties. Experimental values of HmE and VmE were correlated, as a function of ester concentration, x with a new expression which uses the so-called active fraction as a variable and which, in turn, is a function of this concentration. The application of two versions of the UNIFAC group contribution models produces no good estimations of HmE.

  14. Synthesis, characterization and biological activities of novel chalcone derivatives, containing 4, 7-ethanoisoindole-1,3-dione units

    Directory of Open Access Journals (Sweden)

    Mustafa Ceylan

    2013-09-01

    Full Text Available Novel chalcone derivatives, containing 4, 7-ethanoisoindole-1,3-dione units were synthesized starting from 1,3-cyclohexadine (4 and maleic anhydride (5. Addition of maleic anhydride (5 to 1,3-cyclehexadine (4 gave an endo-adduct, 3a,4,7,7a-tetrahydro-4,7-ethano-2-benzofuran-1,3-dione (6, in 90% yield. Heating the solution of the adduct dione (6 and 1-(4-aminophenylethanone (7 in the presence of Et 3N in toluene at 110 oC for 24 hours afforded 2-(4-acetylphenyl-3a,4,7,7a-tetrahydro-1H-4,7-ethanoisoindole-1,3-dione (8 in high yield. Piperidine-catalyzed addition of benzaldehyde derivatives (9a-i to the compound 8 in CH 2Cl 2 at 55 oC gave the expected chalcone derivatives (10-i in the range of 42% - 96% yields. The antibacterial activities of the chalcone derivatives (10a-i were evaluated against human pathogenic microorganism and the compounds showed low activity compared to the standard, name of the standard.

  15. Thermodynamic study of (alkyl esters+{alpha},{omega}-alkyl dihalides) I: H{sub m}{sup E} and V{sub m}{sup E} for 25 binary mixtures {l_brace}xC{sub u-1}H{sub 2u-1}CO{sub 2}C{sub 2}H{sub 5}+(1-x){alpha},{omega}-ClCH{sub 2}(CH{sub 2}){sub v-2}CH{sub 2}C= l{r_brace}, where u=1 to 5, {alpha}=1 and v={omega}=2 to 6

    Energy Technology Data Exchange (ETDEWEB)

    Ortega, J. [Laboratorio de Termodinamica y Fisicoquimica de Fluidos, Parque Cientifico-Tecnologico, Campus Universitario Tafira, Universidad de Las Palmas de Gran Canaria, 35071-Las Palmas de Gran Canaria, Canary Islands (Spain)]. E-mail: jortega@dip.ulpgc.es; Marrero, E. [Laboratorio de Termodinamica y Fisicoquimica de Fluidos, Parque Cientifico-Tecnologico, Campus Universitario Tafira, Universidad de Las Palmas de Gran Canaria, 35071-Las Palmas de Gran Canaria, Canary Islands (Spain); Toledo, F.J. [Laboratorio de Termodinamica y Fisicoquimica de Fluidos, Parque Cientifico-Tecnologico, Campus Universitario Tafira, Universidad de Las Palmas de Gran Canaria, 35071-Las Palmas de Gran Canaria, Canary Islands (Spain); Espiau, F. [Laboratorio de Termodinamica y Fisicoquimica de Fluidos, Parque Cientifico-Tecnologico, Campus Universitario Tafira, Universidad de Las Palmas de Gran Canaria, 35071-Las Palmas de Gran Canaria, Canary Islands (Spain)

    2005-12-15

    This article presents the experimental data of H{sub m}{sup E} and V{sub m}{sup E}, obtained at atmospheric pressure and at a temperature of 298.15K, for a set of 25 binary mixtures composed of the first 5 ethyl alkanoates (methanoate to pentanoate) and five {alpha},{omega}-dichloroalkanes (1,2-dichloroethane to 1,6-dichlorohexane). Quantitatively, and with only a few exceptions, small values are obtained for the excess properties and the results imply that specific interactions exist between both types of compounds, with exothermic process for most mixtures, but with the exception of some that contain ethyl methanoate and ethanoate. The change in enthalpies with increasing length of the dichloroalkane chain for the same ester is regular, and also the change in H{sub m}{sup E} with the acid portion of the ethyl ester. However, the change in excess volumes does not present such a regular variation. A behavioural structural model is established to explain the results of the excess properties. Experimental values of H{sub m}{sup E} and V{sub m}{sup E} were correlated, as a function of ester concentration, x with a new expression which uses the so-called active fraction as a variable and which, in turn, is a function of this concentration. The application of two versions of the UNIFAC group contribution models produces no good estimations of H{sub m}{sup E}.

  16. Integrated basic treatment of activated carbon for enhanced CO{sub 2} selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Adelodun, Adedeji Adebukola; Jo, Young-Min, E-mail: ymjo@khu.ac.kr

    2013-12-01

    We attempted the use of three chemical agents viz nitric acid (HN), calcium nitrate (CaN) and calcium ethanoate (CaEt) to achieve enhanced CO{sub 2} selective adsorption by activated carbon (AC). In dry phase treatment, microporous coconut shell-based carbon (CS) exhibits higher CO{sub 2} capacity than coal-based. However, upon wet-phase pre-treatment, modified CS samples showed lesser CO{sub 2} adsorption efficiency. Surface characterization with X-ray photoelectron spectroscopy confirms the presence of calcium and amine species on the samples with integrated treatment (A-CaN). These samples recorded the highest low-level CO{sub 2} capture despite calcinated CaEt-doped samples (C-CaEt) showing the highest value for pure and high level CO{sub 2} adsorption capacities. The slope and linearity values of isobaric desorption were used to estimate the proportion of CO{sub 2} chemisorbed and heterogeneity of the adsorbents’ surfaces respectively. Consequently, integrated basic impregnation provides the most efficient adsorbents for selective adsorption of both indoor and outdoor CO{sub 2} levels.

  17. Modelling of quantum yields in photocatalytic membrane reactors immobilising titanium dioxide

    Directory of Open Access Journals (Sweden)

    Riccardo Bianchi

    2006-08-01

    Full Text Available For some model molecules (methanoic and ethanoic acids, methane, and phenol, systematic investigations of quantum yields were carried out in the present paper, as a function of concentration and of absorbed radiant power. Quantum yields Φ∞, calculated from rates, followed an apparently Langmuirian function of initial concentration C0, by which Φ∞ values at “infinite” concentration could be obtained. By having thus established that quantum yields of photomineralisation Φ∞ are independent of radiation wavelength, within the absorption range of semiconductor, but depend on radiant power, such a dependency was experimentally investigated. For all the investigated molecules, the maximum allowable values reached in the low radiant power range clearly appeared as a plateau. On the contrary, at high radiant power values, another plateau, at a value of about 1/4-1/5 with respect to the maximum value, was evident. This was interpreted on the basis of a competition kinetics of hydroxyl radicals with themselves, leading to hydrogen peroxide formation, other than with substrate or intermediate molecules leading to full mineralisation. Modelling of quantum yields as a function of concentration and radiant power thus allows a fully consistent and trustworthy design of photoreactors.

  18. QUERCETIN CONTENT AND ANTIOXIDANT ACTIVITY OF ARMENIAN CRATAEGUS LAEVIGATA, PLANTAGO MAJOR AND ARTEMISIA ABSINTHIUM PLANTS EXTRACTS

    Directory of Open Access Journals (Sweden)

    Vardapetyan H

    2014-05-01

    Full Text Available In present study in vitro antioxidant properties of ethanolic extracts of Armenian plants Crataegus laevigata, Plantago major and Artemisia absinthium was investigated by DPPH stable radical chemical model with simultaneous monitoring of the total flavonoids and selected polyphenolic compounds content. Experimental results indicates that ethanolic extract of Crataegus laevigata exhibit the highest radical scavenging activity in neutralization of DPPH with an IC50 value of 12.5 ± 0.08 µl, while the lowest activity was reported in Plantago major extract (IC50 = 45 ± 0.1 µl and IC50 of Artemisia absinthium extract was 35 ± 0.1 µl. Present study also demonstrates a possible relationship between quercetin content and antioxidant activity of extracts. Crataegus laevigata ethanoic extract showed highest antiradical potential as well as the highest concentration of quercetin (7.47 ± 0.2 µg/ml and it can be proposed as a potential sources of natural antioxidants and bioactive phytopharmaceuticals.

  19. Hepatoprotective Effect of Aqueous Acetone Extract of Sida alba L. (Malvaceae Against Alcohol Induced Liver Damage in albinos Wistar Rats

    Directory of Open Access Journals (Sweden)

    K. Konaté

    2011-02-01

    Full Text Available The present study was conducted to evaluate the hepatoprotective effects of aqueous acetone extract of Sida alba. (Malvaceae an herbal plant used in Burkina Faso to treat traditionally hepatics affections in albinos Wistar rats. Animals were treated by gavage during 28 days with different doses of aqueous acetone extracts of Sida alba. (75, 100, 150 mg/kg suspended in 35% ethanol. Control groups received alcohol 35% and water. In vivo administration of 35% ethano l for 28 days results an activity of liver marker enzymes (AST, ALT, ALP, glucose, triglycerides, total cholesterol, total bilirubin and direct bilirubin in serum as compared with rats which received water (control water. However, administrations of 35% ethanol along with aqueous acetone extract decreased the activities of liver markers enzyme in serum comparatively to the control water group (p0.05 and p<0.05. This study revealed that Sida alba presents a hepatoprotective potential and this plant could be traditionally exploited in the treatment of affection hepatics.

  20. Synthesis of Novel Metal Ion Sensors Based on DNA-Metal Interactions

    Institute of Scientific and Technical Information of China (English)

    Akira Ono; Shiqi Cao; Humika Togashi; Yoko Miyake

    2005-01-01

    @@ 1Introduction The interactions of metal ions with nucleic acids, nucleosides, and nucleo-bases have been extensively investigated[1,2]. We have reported that thymine-thymine (T-T) and cytosine-cytosine (C- C) miss base pairs in DNA duplexes highly selectively capture HgⅡ ion and Ag Ⅰ ion, which result in formations of metal-mediated base pairs, T-HgⅡ -T and C-AgⅠ -C, in duplexes[3]. The phenomenon is expected to be useful for a variety of studies such as synthesis of nano-wires containing metal ions, developing metal-ion sensing methods, etc.Here, we report novel oligodeoxyribonucleotide (ODN)-based sensors that detect HgⅡ ions and AgⅠ ions in aqueous solutions.

  1. Pulmonary complications of induction therapy for acute myeloid leukemia in adults. Findings of chest X-rays and computed tomography

    International Nuclear Information System (INIS)

    To exclude pulmonary complications, 359 chest radiographs and 50 computed tomographs of the lung were performed in 95 patients suffering from acute myeloid leukemia. The radiological findings were registered, described and correlated with clinical findings in the present study on 2395 days of observation. Results: In summary, 52 patients showed alterations of the lung. Pulmonary hyperhydration was seen in 21 cases, bacterial pneumonia was found in 18 cases, invasive pulmonary aspergillosis was documented in 14 cases, and 5 cases of severe haemorrhage were seen. An unexplained pulmonary edema in 13 patients with interstitial and alveolar infiltrates is considered to be a complication of treatment with cytosine-arabinoside. Conclusion: The results demonstrate that chest X-ray and computed tomography have a high impact in detection and treatment of pulmonary complications following intensive chemotherapy. We may expect the development of diffuse opacity following administration of cytosine-arabinoside in medium-sized doses. (orig.)

  2. An Integrated Workflow for DNA Methylation Analysis

    Institute of Scientific and Technical Information of China (English)

    Pingchuan Li; Feray Demirci; Gayathri Mahalingam; Caghan Demirci; Mayumi Nakano; Blake C.Meyers

    2013-01-01

    The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes.DNA methylation has a demonstrated role in the genome stability and protection,regulation of gene expression and many other aspects of genome function and maintenance.BS-seq is a relatively unbiased method for profiling the DNA methylation,with a resolution capable of measuring methylation at individual cytosines.Here we describe,as an example,a workflow to handle DNA methylation analysis,from BS-seq library preparation to the data visualization.We describe some applications for the analysis and interpretation of these data.Our laboratory provides public access to plant DNA methylation data via visualization tools available at our "Next-Gen Sequence" websites (http://mpss.udel.edu),along with small RNA,RNA-seq and other data types.

  3. Electron Attachment to DNA and RNA Nucleobases: An EOMCC Investigation

    CERN Document Server

    Dutta, Chintya Kumar; Vaval, Nayana; Pal, Sourav

    2014-01-01

    We report a benchmark theoretical investigation of both adiabatic and vertical electron affinities of five DNA and RNA nucleobases: adenine, guanine, cytosine, thymine and uracil using state-of-the-art equation of motion coupled cluster (EOMCC) method. We have calculated the vertical electron affinity values of first five electron attached states of the DNA and RNA nucleobases and only the first electron attached state is found to be energetically accessible in gas phase. An analysis of the natural orbitals shows that the first electron attached states of uracil and thymine are valence-bound type and undergo significant structural changes on attachment of excess electron, which is reflected in the deviation of the adiabatic electron affinity from the vertical one. On the other hand, the first electron attached state of cytosine, adenine and guanine are dipole-bound type and their structure remain unaffected on attachment of an extra electron, which results in small deviation of adiabatic electron affinity fro...

  4. Genome-wide mapping of DNA methylation in the human malaria parasite Plasmodium falciparum

    Science.gov (United States)

    Ponts, Nadia; Fu, Lijuan; Harris, Elena Y.; Zhang, Jing; Chung, Duk-Won D.; Cervantes, Michael C.; Prudhomme, Jacques; Atanasova-Penichon, Vessela; Zehraoui, Enric; Bunnik, Evelien; Rodrigues, Elisandra M.; Lonardi, Stefano; Hicks, Glenn R.; Wang, Yinsheng; Le Roch, Karine G.

    2014-01-01

    SUMMARY Cytosine DNA methylation is an epigenetic mark in most eukaryotic cells that regulates numerous processes, including gene expression and stress responses. We performed a genome-wide analysis of DNA methylation in the human malaria parasite Plasmodium falciparum. We mapped the positions of methylated cytosines and identified a single functional DNA methyltransferase, PfDNMT, that may mediate these genomic modifications. These analyses revealed that the malaria genome is asymmetrically methylated, in which only one DNA strand is methylated, and shares common features with undifferentiated plant and mammalian cells. Notably, core promoters are hypomethylated and transcript levels correlate with intra-exonic methylation. Additionally, there are sharp methylation transitions at nucleosome and exon-intron boundaries. These data suggest that DNA methylation could regulate virulence gene expression and transcription elongation. Furthermore, the broad range of action of DNA methylation and uniqueness of PfDNMT suggest that the methylation pathway is a potential target for anti-malarial strategies. PMID:24331467

  5. TET1 Suppresses Cancer Invasion by Activating the Tissue Inhibitors of Metalloproteinases

    Directory of Open Access Journals (Sweden)

    Chih-Hung Hsu

    2012-09-01

    Full Text Available Tumor suppressor gene silencing through cytosine methylation contributes to cancer formation. Whether DNA demethylation enzymes counteract this oncogenic effect is unknown. Here, we show that TET1, a dioxygenase involved in cytosine demethylation, is downregulated in prostate and breast cancer tissues. TET1 depletion facilitates cell invasion, tumor growth, and cancer metastasis in prostate xenograft models and correlates with poor survival rates in breast cancer patients. Consistently, enforced expression of TET1 reduces cell invasion and breast xenograft tumor formation. Mechanistically, TET1 suppresses cell invasion through its dioxygenase and DNA binding activities. Furthermore, TET1 maintains the expression of tissue inhibitors of metalloproteinase (TIMP family proteins 2 and 3 by inhibiting their DNA methylation. Concurrent low expression of TET1 and TIMP2 or TIMP3 correlates with advanced node status in clinical samples. Together, these results illustrate a mechanism by which TET1 suppresses tumor development and invasion partly through downregulation of critical gene methylation.

  6. TALEored Epigenetics: A DNA-Binding Scaffold for Programmable Epigenome Editing and Analysis.

    Science.gov (United States)

    Kubik, Grzegorz; Summerer, Daniel

    2016-06-01

    Epigenetic modification of the cytosine 5-position is an important regulator of gene expression with essential roles in genome stability, development, and disease. In addition to 5-methylcytosine (mC), the oxidized mC derivatives 5-hydroxymethyl-, 5-formyl-, and 5-carboxylcytosine (hmC, fC, and caC) have recently been discovered. These are intermediates of an active demethylation pathway but might also represent new epigenetic marks with individual biological roles. This increase in chemical complexity of DNA-encoded information has created a pressing need for new approaches that allow reading and editing of this information. Transcription-activator-like effectors (TALEs) are DNA-binding domains with programmable sequence selectivity that enable the direct reading of epigenetic cytosine modifications but can also guide enzymatic editing domains to genomic loci of choice. Here, we review recent advances in employing TALEs for these applications. PMID:26972580

  7. Detection and monitoring of hypermethylated RASSF1A in serum from patients with metastatic breast cancer

    DEFF Research Database (Denmark)

    Kristiansen, Søren; Nielsen, Dorte; Söletormos, Georg

    2016-01-01

    different locations of methylation in the RASSF1A gene among patients. One common method for detection of hypermethylated genes is sodium bisulfite conversion of non-methylated cytosine to uracil, followed by detection with PCR. However, the method relies on full conversion of all non-methylated cytosines......, cause strand breaks, and loss of DNA. Alternatively, methylation-sensitive restriction enzymes have been used to digest genomic DNA, as well as sodium bisulfite-treated DNA. By flanking different regions of the RASSF1A with different PCR primer pairs, we analyzed for methylated genomic regions resistant...... subjects, these four regions gave a specificity of 100 %. Among these four regions, the primer pair with the highest PCR efficacy was selected to monitor the RASSF1A concentration in 31 collected serum samples. The spiked DNA was then used to calculate the tumor RASSF1A concentrations independent of...

  8. Modulation of CpG oligodeoxynucleotide-mediated immune stimulation by locked nucleic acid (LNA)

    DEFF Research Database (Denmark)

    Vollmer, Jörg; Jepsen, Jan Stenvang; Uhlmann, Eugen; Schetter, Christian; Jurk, Marion; Wader, Tanja; Wüllner, Meike; Krieg, Arthur M; Stenvang, Jan

    2004-01-01

    Locked nucleic acid (LNA) is an RNA derivative that when introduced into oligodeoxynucleotides (ODN), mediates high efficacy and stability. CpG ODNs are potent immune stimulators and are recognized by toll-like receptor-9 (TLR9). Some phosphorothioate antisense ODNs bearing CpG dinucleotides have...... been shown to possess immune modulatory capacities. We investigated the effects of LNA substitutions on immune stimulation mediated by antisense ODN G3139 or CpG ODN 2006. LNA ODNs were tested for their ability to stimulate cytokine secretion from human immune cells or TLR9-dependent signaling....... Phosphorothioate chimeric LNA/DNA antisense ODNs with phosphodiester-linked LNA nucleobases at both ends showed a marked decrease of immune modulation with an increasing number of 3' and 5' LNA bases. In addition, guanosine-LNA and cytosine-LNA or simply cytosine-LNA substitutions in the CpG dinucleotides of ODN...

  9. Systemic chemotherapy of advanced head and neck malignancies.

    Science.gov (United States)

    Dowell, K E; Armstrong, D M; Aust, J B; Cruz, A B

    1975-04-01

    Several Phase II chemotherapy protocols were evaluated in patients with advanced malignancies; 158 were evaluable head and neck cases. The protocols were as follows: five-drug combination (COMFP), four-drug (COMF), (CCNU, Adriamycin, DTIC, and cytosine arabinoside. Insufficient numbers and data were received to adequately evaluate Yoshi 864, 5 Azacytidine, porfiromycin, BCNU, and Azaserine. Significant responses to therapy were noted in the four and five-drug combinations in which 30-44% of the patients had 50% or greater regression, with an average duration of 2.2 months. Adriamycin and CCNU demonstrated lesser antitumor effects, while DTIC and cytosine arabinoside did not demonstrate significant antitumor activity in the head and neck areas. Usual toxicity consisted largely of nausea and vomiting, leukopenia, and thrombocytopenia. Alopecia was not pronouced in Adriamycin-treated patients. It appears that combination chemotherapy had a higher response rate compared to single agents used in the different cooperative protocols. PMID:1116105

  10. Síntesis y actividad antimicrobiana de derivados de 4,6-diaminopirimidinas análogos de citosina

    Directory of Open Access Journals (Sweden)

    Gricela Lobo

    2012-09-01

    Full Text Available A new synthesis of novel 4,6-diaminopyrimidines 2a-j, cytosine analogous, is described. This involves the base-assisted cyclization reaction of benzylidenemalononitriles 1a-j (BMNs with urea. Compounds 1a-j were prepared by a Knoevenagel condensation reaction from benzaldehyde and malononitrile using EtOH as solvent at room temperature conditions. The antimicrobial activity against Gram-positive microorganisms: Staphylococcus aureus (ATCC 25923 and Bacillus cereus (ATCC 14579 and Gram-negative: Escherichia coli (ATCC 35218 and Pseudomonas aeruginosa (ATCC 27853 and th yeast Candida tropicalis (MLDM 372 is also reported. The compounds 2c, 2e, 2f, 2g, 2i and 2j are considered wide spectrum. Antimicrobial activity, Benzylidenemalononitriles (BMNs, Cytosine, Diaminopyrimidine, Urea,

  11. Chemotherapeutic treatment for leukemia in a bearded dragon (Pogona vitticeps).

    Science.gov (United States)

    Jankowski, Gwen; Sirninger, Jeffrey; Borne, Jessica; Nevarez, Javier G

    2011-06-01

    A 4.5-yr-old, captive-bred, male bearded dragon (Pogona vitticeps) presented for lethargy, anorexia, and increased mucoid salivation with upper respiratory clicks. Diagnostics were declined and the bearded dragon was prescribed ceftazidime 20 mg/kg i.m. q 72 hr. The patient presented again 1 wk later with a marked monocytosis, heterophilia, and lymphocytosis, and a clinical diagnosis of chronic monocytic leukemia was made. Chemotherapy with cytosine arabinoside (100 mg/m2 over 48 hr i.v.) was initiated. Forty-four hours into the treatment the dragon became acutely unresponsive and died within 1 hr. Adverse effects as a result of i.v. cytosine arabinoside therapy were not identified despite previous reports suggestive that the drug induces renal failure. PMID:22946414

  12. Radiation effects on DNA methylation in mice

    International Nuclear Information System (INIS)

    Effects of ionizing radiation on DNA methylation in liver, brain and spleen were examined by high performance liquid chromatography (HPLC). The total methylated cytosine level in the genome was reduced within 8 hours after 3.8 Gy of irradiation in liver of adult mice. But no appreciable effect was observed in brain and spleen. When mice were irradiated at newborn, liver DNA revealed no change in methylated cytosine level. Even though slight effects of radiation were detected in he methylation of the c-myc and c-fos genes, they were only temporary and no long-term effects were observed. These data suggest that the effect of radiation on DNA methylation in vivo is not prevailing a DNA damage, but rather influenced much through biological parameters. (author)

  13. Optoelectronic studies on heterocyclic bases of deoxyribonucleic acid for DNA photonics.

    Science.gov (United States)

    El-Diasty, Fouad; Abdel-Wahab, Fathy

    2015-10-01

    The optoelectronics study of large molecules, particularly π-stacking molecules, such as DNA is really an extremely difficult task. We perform first electronic structure calculations on the heterocyclic bases of 2'-deoxyribonucleic acid based on Lorentz-Fresnel dispersion theory. In the UV-VIS range of spectrum, many of the optoelectronic parameters for DNA four bases namely adenine, guanine, cytosine and thymine are calculated and discussed. The results demonstrate that adenine has the highest hyperpolarizability, whereas thymine has the lowest hyperpolarizability. Cytosine has the lower average oscillator energy and the higher lattice energy. Thymine infers the most stable nucleic base with the lower phonon energy. Thymine also has the highest average oscillator energy and the lower lattice energy. Moreover, the four nucleic acid bases have large band gap energies less than 5 eV with a semiconducting behavior. Guanine shows the smallest band gap and the highest Fermi level energy, whereas adenine elucidates the highest band gap energy. PMID:26117785

  14. Deoxyribonucleic acid (DNA methylation and its impact in generation of Cancer

    Directory of Open Access Journals (Sweden)

    Rajeswari J

    2014-07-01

    Full Text Available The arrangement of genes in the chromosome is dependent on histone modifications, deoxyribonucleic acid (DNA binding proteins and methylation of cytosines within 51–cytosine-phosphate-Guanine–31 (CpG dinucleotides. DNA methylation can modify the gene activity without changing the gene sequence. Aberrant hypomethylation and hypermethylations, causal or heritable gene expressions play an important role in tumour initiation and progression. Global hypomethylation at some part of genome and hypermethylation at the promoter regions of the tumour suppressor genes could generate mutations in several types of cancers. Reversal or inhibition of DNA methylation mechanism provides a promising improvement in the treatment of cancer along with chemotherapy. A combined approach utilising epigenetic treatment along with standard chemotherapy appears to hold promise as a future therapy.

  15. Sequence specificity of DNA cleavage by Micrococcus luteus γ endonuclease

    International Nuclear Information System (INIS)

    DNA fragments of defined sequence have been used to determine the sites of cleavage by γ-endonuclease activity in extracts prepared from Micrococcus luteus. End-labeled DNA restriction fragments of pBR322 DNA that had been irradiated under nitrogen in the presence of potassium iodide or t-butanol were treated with M. luteus γ endonuclease and analyzed on irradiated DNA preferentially at the positions of cytosines and thymines. DNA cleavage occurred immediately to the 3' side of pyrimidines in irradiated DNA and resulted in fragments that terminate in a 5'-phosphoryl group. These studies indicate that both altered cytosines and thymines may be important DNA lesions requiring repair after exposure to γ radiation

  16. Tight-binding parameters for charge transfer along DNA

    CERN Document Server

    Hawke, L G D; Simserides, C

    2009-01-01

    We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wavefunctions and energies of DNA bases are discussed and then used for calculating the corresponding wavefunctions of the two B-DNA base-pairs (adenine-thymine and guanine-cytosine). The obtained HOMO and LUMO energies of the bases are in good agreement with available experimental values. Our results are then used for estimating the complete set of charge transfer parameters between neighboring bases and also between successive base-pairs, considering all possible combinations between them, for both electrons and holes. The calculated microscopic quantities can be used in mesoscopic theoretical models of electron or hole transfer along the DNA double helix, as they provide the necessar...

  17. The MBD protein family – reading an epigenetic mark?

    OpenAIRE

    Dhasarathy, Archana; Wade, Paul A.

    2008-01-01

    A family of proteins conserved throughout the eukaryotic lineage is characterized by the presence of a common sequence motif – the methyl CpG binding domain, or MBD. This sequence motif corresponds to a structural domain which, in some but not all cases, confers the ability to bind methylated cytosine residues in the context of the dinucleotide 5’ CG 3’. Mammals have five well characterized members of this family, each with unique biological characteristics. Recently, much progress has been m...

  18. Pulmonary complications of induction therapy for acute myeloid leukemia in adults. Findings of chest X-rays and computed tomography; Pulmonale Komplikationen der Induktionstherapie bei akuter myeloischer Leukaemie des Erwachsenen. Befunde in Thoraxuebersichtsaufnahme und Computertomographie

    Energy Technology Data Exchange (ETDEWEB)

    Kirchner, J.; Huettmann, C.; Jacobi, V. [Univ. Frankfurt am Main (Germany). Inst. fuer Roentgendiagnostik; Boehme, A. [Frankfurt Univ. (Germany). Medizinische Klinik 3

    1998-03-01

    To exclude pulmonary complications, 359 chest radiographs and 50 computed tomographs of the lung were performed in 95 patients suffering from acute myeloid leukemia. The radiological findings were registered, described and correlated with clinical findings in the present study on 2395 days of observation. Results: In summary, 52 patients showed alterations of the lung. Pulmonary hyperhydration was seen in 21 cases, bacterial pneumonia was found in 18 cases, invasive pulmonary aspergillosis was documented in 14 cases, and 5 cases of severe haemorrhage were seen. An unexplained pulmonary edema in 13 patients with interstitial and alveolar infiltrates is considered to be a complication of treatment with cytosine-arabinoside. Conclusion: The results demonstrate that chest X-ray and computed tomography have a high impact in detection and treatment of pulmonary complications following intensive chemotherapy. We may expect the development of diffuse opacity following administration of cytosine-arabinoside in medium-sized doses. (orig.) [Deutsch] Zum Ausschluss pulmonaler Komplikationen durchgefuehrte Thoraxuebersichtsaufnahmen (n=359) und computertomographische Untersuchungen der Lunge (n=50) von 95 Patienten mit akuter myeloischer Leukaemie werden in der vorliegenden Arbeit systematisch erfasst, beschrieben und mit den klinischen Symptomen an insgesamt 2395 Beobachtungstagen korreliert. Ergebnisse: Hierbei wiesen 52 Patienten Lungenveraenderungen auf. Eine pulmonale Ueberwaesserung wurde in 21 Faellen beobachtet, bakterielle Pneumonien in 18 Faellen, eine invasive pulmonale Aspergillose in 14 Faellen. Es wurden 5 Lungenblutungen beobachtet. Ein bei 13 Patienten aufgetretenes unklares Lungenoedem mit diffuser interstitieller Zeichnungsvermehrung und auch alveolaerer Komponente wird von uns als Komplikation der Anwendung von Cytosin-Arabinosid angenommen. Schlussfolgerung: Thoraxuebersichtsaufnahme und Computertomographie besitzen einen hohen Stellenwert bei der Erkennung

  19. Shedding and Reversion of Oral Polio Vaccine Type 3 in Mexican Vaccinees: Comparison of Mutant Analysis by PCR and Enzyme Cleavage to a Real-Time PCR Assay▿

    OpenAIRE

    Gnanashanmugam, Devasena; Falkovitz-Halpern, Meira S.; Dodge, Anthony; Fang, Melanie; Wong, Lisa J.; Esparza, Melissa; Hammon, Rebecca; Rivas-Merelles, Enrique E.; Santos, Jose I.; Maldonado, Yvonne

    2007-01-01

    A uracil-to-cytosine mutation at nucleotide position 472 of oral poliovirus vaccine type 3 (OPV3) contributes to the development of vaccine-associated paralytic poliomyelitis (VAPP). To analyze OPV3 shedding patterns, we previously used the multistep method of mutant analysis by PCR and enzyme cleavage (MAPREC). This involves conventional reverse transcription-PCR to detect OPV3, followed by a restriction digest to quantify position 472 reversion. Real-time PCR detects and quantifies nucleic ...

  20. Estrogen directly activates AID transcription and function

    OpenAIRE

    Pauklin, Siim; Sernández, Isora V.; Bachmann, Gudrun; Ramiro, Almudena R.; Petersen-Mahrt, Svend K.

    2009-01-01

    The immunological targets of estrogen at the molecular, humoral, and cellular level have been well documented, as has estrogen's role in establishing a gender bias in autoimmunity and cancer. During a healthy immune response, activation-induced deaminase (AID) deaminates cytosines at immunoglobulin (Ig) loci, initiating somatic hypermutation (SHM) and class switch recombination (CSR). Protein levels of nuclear AID are tightly controlled, as unregulated expression can lead to alterations in th...

  1. DNA Methylation Alterations at 5′-CCGG Sites in the Interspecific and Intraspecific Hybridizations Derived from Brassica rapa and B. napus

    OpenAIRE

    Wanshan Xiong; Xiaorong Li; Donghui Fu; Jiaqin Mei; Qinfei Li; Guanyuan Lu; Lunwen Qian; Yin Fu; Joseph Onwusemu Disi; Jiana Li; Wei Qian

    2013-01-01

    DNA methylation is an important regulatory mechanism for gene expression that involved in the biological processes of development and differentiation in plants. To investigate the association of DNA methylation with heterosis in Brassica, a set of intraspecific hybrids in Brassica rapa and B. napus and interspecific hybrids between B. rapa and B. napus, together with parental lines, were used to monitor alterations in cytosine methylation at 5'-CCGG sites in seedlings and buds by methylation-...

  2. The roles of APE1, APE2, DNA polymerase β and mismatch repair in creating S region DNA breaks during antibody class switch

    OpenAIRE

    Schrader, Carol E.; Guikema, Jeroen E.J.; Wu, Xiaoming; Stavnezer, Janet

    2008-01-01

    Immunoglobulin class switch recombination (CSR) occurs by an intrachromosomal deletion requiring generation of double-stranded DNA breaks (DSBs) in immunoglobulin switch region DNA. The initial steps of DSB formation have been elucidated: cytosine deamination by activation-induced cytidine deaminase (AID) and the generation of abasic sites by uracil-DNA glycosylase (UNG). We show that abasic sites are converted into single-strand breaks (SSBs) by apurinic/apyrimidinic endonucleases (APE1 and ...

  3. Optimized method for methylated DNA immuno-precipitation

    OpenAIRE

    Carlos Guerrero-Bosagna; Per Jensen

    2015-01-01

    Methylated DNA immunoprecipitation (MeDIP) is one of the most widely used methods to evaluate DNA methylation on a whole genome scale, and involves the capture of the methylated fraction of the DNA by an antibody specific to methyl-cytosine. MeDIP was initially coupled with microarray hybridization to detect local DNA methylation enrichments along the genome. More recently, MeDIP has been coupled with next generation sequencing, which highlights its current and future applicability. In previo...

  4. Analyse phosphoprotéomique pour la recherche de biomarqueurs : développements et applications

    OpenAIRE

    Negroni, Luc

    2013-01-01

    Proteomic is a method of choice for biomarker research, without a priori, it establishes a directory of proteins that are expressed in a cell, tissue or an entire organism. This approach has been implemented for proteomic analysis of colon cancer cells and phosphoproteomic analysis of liver biopsies.The study of colon cancer cells transformed by the cytosine deaminase and treated with the prodrug 5-fluorocytosine was performed by two-dimensional electrophoresis. Image analysis allowed the qua...

  5. Differential adsorption of nucleic acid bases: Relevance to the origin of life

    OpenAIRE

    Sowerby, Stephen J.; Cohn, Corey A; Heckl, Wolfgang M.; Holm, Nils G

    2001-01-01

    The adsorption of organic molecules onto the surfaces of inorganic solids has long been considered a process relevant to the origin of life. We have determined the equilibrium adsorption isotherms for the nucleic acid purine and pyrimidine bases dissolved in water on the surface of crystalline graphite. The markedly different adsorption behavior of the bases describes an elutropic series: guanine > adenine > hypoxanthine > thymine > cytosine > uracil. We propose th...

  6. Palladium Electrodes for Molecular Tunnel Junctions

    OpenAIRE

    Chang, Shuai; Sen, Suman; Zhang, Peiming; Gyarfas, Brett; Ashcroft, Brian; Lefkowitz, Steven; Peng, Hongbo; Lindsay, Stuart

    2012-01-01

    Gold has been the metal of choice for research on molecular tunneling junctions, but it is incompatible with CMOS fabrication because it forms deep level traps in silicon. Palladium electrodes do not contaminate silicon, and also give higher tunnel current signals in the molecular tunnel junctions we have studied. The result is cleaner signals in a recognition-tunneling junction that recognizes the four natural DNA bases as well as 5-methyl cytosine, with no spurious background signals. More ...

  7. Atomic Structures of the Molecular Components in DNA and RNA based on Bond Lengths as Sums of Atomic Radii

    OpenAIRE

    Heyrovska, Raji

    2007-01-01

    The interpretation by the author in recent years of bond lengths as sums of the relevant atomic or ionic radii has been extended here to the bonds in the skeletal structures of adenine, guanine, thymine, cytosine, uracil, ribose, deoxyribose and phosphoric acid. On examining the bond length data in the literature, it has been found that the averages of the bond lengths are close to the sums of the corresponding atomic covalent radii of carbon, nitrogen, oxygen, hydrogen and phosphorus. Thus, ...

  8. 16S rRNA Mutation Associated with Tetracycline Resistance in a Gram-Positive Bacterium

    OpenAIRE

    Ross, Jeremy I.; Eady, E Anne; Cove, Jonathan H.; Cunliffe, William J.

    1998-01-01

    A genetic basis for tetracycline resistance in cutaneous propionibacteria was suggested by comparing the nucleotide sequences of the 16S rRNA genes from 16 susceptible and 21 resistant clinical isolates and 6 laboratory-selected tetracycline-resistant mutants of a susceptible strain. Fifteen clinical isolates resistant to tetracycline were found to have cytosine instead of guanine at a position cognate with Escherichia coli 16S rRNA base 1058 in a region important for peptide chain terminatio...

  9. DNA Methylation

    OpenAIRE

    Alokail, Majed S.; Alenad, Amal M

    2015-01-01

    The DNA of E. coli contains 19,120 6-methyladenines and 12,045 5-methylcytosines in addition to the four regular bases and these are formed by the postreplicative action of three DNA methyltransferases. The majority of the methylated bases are formed by the Dam and Dcm methyltransferases encoded by the dam (DNA adenine methyltransferase) and dcm (DNA cytosine methyltransferase) genes. Although not essential, Dam methylation is important for strand discrimination during repair of replication e...

  10. EG-01EPIGENETIC INACTIVATION OF ARGININE BIOSYNTHESIS PATHWAY IN PAEDIATRIC HIGH GRADE GLIOMA

    OpenAIRE

    Channathodiyil, Prasanna; Kardooni, Hoda; Khozoie, Combiz; Nelofer, Syed; Darling, John; Morris, Mark; Warr, Tracy

    2014-01-01

    Aberrant cellular metabolism contributes significantly to the growth and proliferation of several tumour types. Identification of genes that control critical metabolic pathways is a major factor in the development of novel therapies that target metabolic defects in tumour cells. Our aim is to identify such genes in paediatric high grade glioma that are altered due to promoter hyper-methylation of cytosine residues in CpG dinucleotides. Genome wide DNA methylation profiling using Illumina infi...

  11. Systemic mastocytosis with associated acute myelogenous leukemia

    OpenAIRE

    Zhrebker, Leah; Cooper, Barry; Krause, John R.

    2014-01-01

    Systemic mastocytosis (SM) is a condition associated with a clonal neoplastic proliferation of mast cells. Approximately 40% of patients with SM present with an associated clonal hematological non–mast cell lineage disorder. Patients presenting with SM–acute myeloid leukemia (AML) have the worst prognosis. We present a case of a 62-year-old woman who was diagnosed with SM-AML. After initial treatment with a standard regimen of cytosine arabinoside (Ara-C)/idarubicin, her bone marrow showed re...

  12. APOBEC enzymes: mutagenic fuel for cancer evolution and heterogeneity

    OpenAIRE

    Swanton, Charles; McGranahan, Nicholas; Starrett, Gabriel J.; Harris, Reuben S.

    2015-01-01

    Deep sequencing technologies are revealing the complexities of cancer evolution, casting light on mutational processes fuelling tumor adaptation, immune escape, and treatment resistance. Understanding mechanisms driving cancer diversity is a critical step toward developing strategies to attenuate tumor evolution and adaptation. One emerging mechanism fuelling tumor diversity and subclonal evolution is genomic DNA cytosine deamination catalyzed by APOBEC3B and at least one other APOBEC family ...

  13. Protein (Viridiplantae): 225433302 [

    Lifescience Database Archive (English)

    Full Text Available XP_002282386.1 33090:1773 35493:7072 131221:7072 3193:7072 58023:1787 78536:984 58024:984 3398:9 ... 505 3602:505 3603:505 29760:505 PREDICTED: histone-lysine ... N-methyltransferase, H3 lysine -9, H3 lysine -27, H4 ... lysine -20 and cytosine specific SUVH2 Vitis vinifera MGSL ...

  14. Capillary Electrophoresis in the Presence of Fosfomycin

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Fosfomyein, a sodim salt of cis-(3-methyloxiranyl) phosphonic acid, was used as electrolyte in binary methanol-water media for capillary electrophoresis. The variety of electroosmotic flow with pH*,methanol concentration and ionic strength was investigated. The migration behavior of nine bases was examined under various conditions, and the separation of thymine, cytosine, 5-flurouracil, 4,6-diamino-pyrimidine, purine was accomplished.

  15. The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals

    Science.gov (United States)

    Background: APOBEC3 (A3) proteins deaminate DNA cytosines and block the replication of retroviruses and retrotransposons. Each A3 gene encodes a protein with one or two conserved zinc-coordinating motifs (Z1, Z2 or Z3). The presence of one A3 gene in mice (Z2-Z3) and seven in humans, A3A-H (Z1a, Z2a...

  16. DNA Methylation in Skeletal Muscle Stem Cell Specification, Proliferation, and Differentiation

    OpenAIRE

    Rhianna C. Laker; Ryall, James G.

    2016-01-01

    An unresolved and critically important question in skeletal muscle biology is how muscle stem cells initiate and regulate the genetic program during muscle development. Epigenetic dynamics are essential for cellular development and organogenesis in early life and it is becoming increasingly clear that epigenetic remodeling may also be responsible for the cellular adaptations that occur in later life. DNA methylation of cytosine bases within CpG dinucleotide pairs is an important epigenetic mo...

  17. AID-mediated diversification within the IgL locus of chicken DT40 cells is restricted to the transcribed IgL gene

    OpenAIRE

    Gopal, Anjali R.; Fugmann, Sebastian D.

    2007-01-01

    Somatic hypermutation (SHM) and gene conversion (GCV) are closely related processes that increase the diversity the primary immunoglobulin repertoire. In both processes the activation-induced cytidine deaminase (AID) converts cytosine residues to uracils within the DNA of the immunoglobulin (Ig) genes in a transcription-dependent manner, and subsequent error-prone repair processes lead to changes in the antigen recognition site of the encoded receptors. This activity is specifically recruited...

  18. Maintenance of genomic imprinting by G9a/GLP complex of histone methyltransferases in embryonic stem (ES) cells

    OpenAIRE

    Zhang, Tuo

    2014-01-01

    DNA methylation refers to an addition of a methyl group to the 5 position of the cytosine pyrimidine ring. As the best characterized epigenetic mark, DNA methylation plays an important role in a plethora of biological functions, including gene repression, genomic imprinting, silencing of retro-transposons and X chromosome inactivation. Genomic imprinting refers to the mono-allelic expression of certain genes according to their parent-of-origin. In mammals, the expression of ...

  19. Absolute total and partial cross sections for ionization of nucleobases by proton impact in the Bragg peak velocity range

    OpenAIRE

    Tabet, J.; Eden, S.; Feil, S.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.; Ouaskit, S.; Märk, T.D.

    2010-01-01

    We present experimental results for 80 keV proton impact ionization of nucleobases (adenine, cytosine, thymine and uracil) based on an event by event analysis of the different ions produced combined with an absolute target density determination. We are able to disentangle in detail the various proton ionization channels from mass analyzed product ion signals in coincidence with the charge-analyzed projectile. Thus, for the first time, cross sections and fragmentation patterns are compared for...

  20. Radio-sensitization of gliomas by intracellular generation of 5-fluorouracil potentiates prodrug activator gene therapy with a retroviral replicating vector

    OpenAIRE

    Takahashi, Masamichi; Valdes, Gilmer; Hiraoka, Kei; Inagaki, Akihito; Kamijima, Shuichi; Micewicz, Ewa; Gruber, Harry E.; Robbins, Joan M.; Jolly, Douglas J.; McBride, William H.; Iwamoto, Keisuke S.; Kasahara, Noriyuki

    2014-01-01

    A tumor-selective non-lytic retroviral replicating vector (RRV), Toca 511, and an extended-release formulation of 5-fluorocytosine (5-FC), Toca FC, are currently being evaluated in clinical trials in patients with recurrent high-grade glioma (NCT01156584, NCT01470794, NCT01985256). Tumor-selective propagation of this RRV enables highly efficient transduction of glioma cells with cytosine deaminase (CD), which serves as a prodrug activator for conversion of the anti-fungal prodrug 5-FC to the ...

  1. Molecular Mechanism of Immunoglobulin Gene Conversion in Chicken DT40 Cells

    OpenAIRE

    Saribasak, Huseyin

    2006-01-01

    Immunoglobulin (Ig) gene conversion is one of three B cell specific processes which create the repertoire of antigen receptors in B cells. The process involves the unidirectional transfer of sequences from pseudogene V segments into the rearranged V gene. There are general and lymphoid-specific trans-acting factors as well as cis-acting elements involved in this process. Gene conversion is most likely initiated by AID mediated cytosine deamination. If the resulting uracils need to be further ...

  2. CRISPR/Cas9-Mediated Phage Resistance Is Not Impeded by the DNA Modifications of Phage T4

    OpenAIRE

    Yaung, Stephanie J.; Kevin M Esvelt; Church, George M

    2014-01-01

    Bacteria rely on two known DNA-level defenses against their bacteriophage predators: restriction-modification and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) systems. Certain phages have evolved countermeasures that are known to block endonucleases. For example, phage T4 not only adds hydroxymethyl groups to all of its cytosines, but also glucosylates them, a strategy that defeats almost all restriction enzymes. We sought to determine whether the...

  3. Implementation of Quantum Logic Gates by Nuclear Magnetic Resonance Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    DU Jiang-Feng; WU Ji-Hui; SHI Ming-Jun; HAN Liang; ZHOU Xian-Yi; YE Bang-Jiao; WENG Hui-Ming; HAN Rong-Dian

    2000-01-01

    Using nuclear magnetic resonance techniques with a solution of cytosine molecules, we show an implementation of certain quantum logic gates (including NOT gate, square-root of NOT gate and controlled-NOT gate), which have central importance in quantum computing. In addition, experimental results show that nuclear magnetic resonance spectroscopy can efficiently measure the result of quantum computing without attendant wave-function collapse.

  4. 5-azacytidine and 5-azadeoxycytidine inhibit human immunodeficiency virus type 1 replication in vitro.

    OpenAIRE

    Bouchard, J.; Walker, M. C.; Leclerc, J M; Lapointe, N; Beaulieu, R.; Thibodeau, L

    1990-01-01

    Chemotherapeutic agents which affect the integration, stability, or inducibility of the human immunodeficiency virus (HIV) provirus would have considerable value in treating acquired immunodeficiency syndrome. Two nucleoside analogs of cytosine, 5-azacytidine and 5-azadeoxycytidine, which seem to have such value because of their capabilities to affect both the stability and the methylation patterns of the nucleic acids into which they are incorporated, were tested for their ability to inhibit...

  5. Site-specific mutagenesis by triple helix-forming oligonucleotides containing a reactive nucleoside analog

    OpenAIRE

    Nagatsugi, Fumi; Sasaki, Shigeki; Miller, Paul S.; Seidman, Michael M.

    2003-01-01

    The specific recognition of homopurine–homo pyrimidine regions in duplex DNA by triplex-forming oligonucleotides (TFOs) provides an attractive strategy for genetic manipulation. Alkylation of nucleobases with functionalized TFOs would have the potential for site-directed mutagenesis. Recently, we demonstrated that a TFO bearing 2-amino-6-vinylpurine derivative, 1, achieves triplex-mediated reaction with high selectivity toward the cytosine of the G-C target site. In this report, we have inves...

  6. Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes

    OpenAIRE

    Bentin, Thomas; Hansen, Georg I.; Nielsen, Peter E.

    2006-01-01

    Sequence-selective recognition of double-stranded (ds) DNA by homopyrimidine peptide nucleic acid (PNA) oligomers can occur by major groove triplex binding or by helix invasion via triplex P-loop formation. We have compared the binding of a decamer, a dodecamer and a pentadecamer thymine–cytosine homopyrimidine PNA oligomer to a sequence complementary homopurine target in duplex DNA using gel-shift and chemical probing analyses. We find that all three PNAs form stable triplex invasion complex...

  7. Efficient and Stereoselective Synthesis of C-(β-2'-Deoxynucleosides)

    Institute of Scientific and Technical Information of China (English)

    WU,Qin-Pei; REES,B.Colin

    2004-01-01

    @@ The formation of triplex DNA is, in principle, an effective way of regulating the expression of selected genes.[1]Many cytosine mimics were investigated to form triplex DNA, e.g., 2-amino-(2'-deoxy-β-D-ribofuranosyl)pyridine (9)was proved to have some effectiveness in stabilizing triplex DNA under neutral conditions.[2] Stereoselective synthesis of 9 was achieved starting from 2-deoxyribose.

  8. Double suicide genes selectively kill human umbilical vein endothelial cells

    OpenAIRE

    Liu Lunxu; Wang Yanping; Mei Longyong; Jia Weiguo; Che Guowei

    2011-01-01

    Abstract Background To construct a recombinant adenovirus containing CDglyTK double suicide genes and evaluate the killing effect of the double suicide genes driven by kinase domain insert containing receptor (KDR) promoter on human umbilical vein endothelial cells. Methods Human KDR promoter, Escherichia coli (E. coli) cytosine deaminase (CD) gene and the herpes simplex virus-thymidine kinase (TK) gene were cloned using polymerase chain reaction (PCR). Plasmid pKDR-CDglyTK was constructed wi...

  9. Soluble β-glucan from Grifola frondosa induces tumor regression in synergy with TLR9 agonist via dendritic cell-mediated immunity.

    Science.gov (United States)

    Masuda, Yuki; Nawa, Daiki; Nakayama, Yoshiaki; Konishi, Morichika; Nanba, Hiroaki

    2015-12-01

    The maturation of dendritic cells into more-immunostimulatory dendritic cells by stimulation with different combinations of immunologic agents is expected to provide efficient, adoptive immunotherapy against cancer. Soluble β-glucan maitake D-fraction, extracted from the maitake mushroom Grifola frondosa, acts as a potent immunotherapeutic agent, eliciting innate and adoptive immune responses, thereby contributing to its antitumor activity. Here, we evaluated the efficacy of maitake D-fraction, in combination with a Toll-like receptor agonist, to treat tumors in a murine model. Our results showed that maitake D-fraction, in combination with the Toll-like receptor 9 agonist, cytosine-phosphate-guanine oligodeoxynucleotide, synergistically increased the expression of dendritic cell maturation markers and interleukin-12 production in dendritic cells, but it did not increase interleukin-10 production, generating strong effector dendritic cells with an augmented capacity for efficiently priming an antigen-specific, T helper 1-type T cell response. Maitake D-fraction enhances cytosine-phosphate-guanine oligodeoxynucleotide-induced dendritic cell maturation and cytokine responses in a dectin-1-dependent pathway. We further showed that a combination therapy using cytosine-phosphate-guanine oligodeoxynucleotide and maitake D-fraction was highly effective, either as adjuvants for dendritic cell vaccination or by direct administration against murine tumor. Therapeutic responses to direct administration were associated with increased CD11c(+) dendritic cells in the tumor site and the induction of interferon-γ-producing CD4(+) and CD8(+) T cells. Our results indicate that maitake D-fraction and cytosine-phosphate-guanine oligodeoxynucleotide synergistically activated dendritic cells, resulting in tumor regression via an antitumor T helper cell 1-type response. Our findings provide the basis for a potent antitumor therapy using a novel combination of immunologic agents for

  10. Nucleotide Capacitance Calculation for DNA Sequencing

    OpenAIRE

    Lu, Jun-Qiang; Zhang, X.-G.

    2008-01-01

    Using a first-principles linear response theory, the capacitance of the DNA nucleotides, adenine, cytosine, guanine, and thymine, are calculated. The difference in the capacitance between the nucleotides is studied with respect to conformational distortion. The result suggests that although an alternate current capacitance measurement of a single-stranded DNA chain threaded through a nanogap electrode may not be sufficient to be used as a standalone method for rapid DNA sequencing, the capaci...

  11. Elimination Voltammetry with Linear Scan as a New Detection Method for DNA Sensors

    OpenAIRE

    Rene Kizek*; David Potesil; Vojtech Adam; Jitka Petrlova; Frantisek Jelen; Libuse Trnkova

    2005-01-01

    The paper describes successful coupling of adsorptive transfer stripping (AdTS) and elimination voltammetry with linear scan (EVLS) for the resolution of reduction signals of cytosine (C) and adenine (A) residues in hetero-oligodeoxynucleotides (ODNs). Short ODNs (9-mers and 20-mers) were adsorbed from a small volume on a hanging mercury drop electrode (HMDE). After washing of the ODN-modified electrode by water and its transferring to an electrochemical cell, voltammetric curves were measure...

  12. Nuclear quadrupole resonance of 14N and 2H in pyrimidines, purines, and their nucleosides

    Science.gov (United States)

    Rabbani, S. R.; Edmonds, D. T.; Gosling, P.

    Using nuclear quadrupole double-resonance techniques, nitrogen-14 and deuterium nuclear quadrupole coupling constants and asymmetry parameters have been measured in uracil, 5-bromouracil, cytosine, adenine, xanthine, hypoxanthine, their nucleosides, 2-aminopyrimidine, and benzimidazole. Zeeman studies and the detection of the simultaneous transitions of neighboring nuclei allowed in many cases a complete assignment of the observed spectral lines to particular 14N and 2D sites.

  13. Hereditary Amyloid Cardiomyopathy Caused by a Variant Apolipoprotein A1

    OpenAIRE

    Hamidi Asl, Ladan; Liepnieks, Juris J.; Hamidi Asl, Kamran; Uemichi, Tomoyuki; Moulin, Georges; Desjoyaux, Emmanuel; Loire, Robert; Delpech, Marc; Grateau, Gilles; Benson, Merrill D.

    1999-01-01

    Autosomal dominant hereditary amyloidosis with a unique cutaneous and cardiac presentation and death from heart failure by the sixth or seventh decade was found to be associated with a previously unreported point mutation (thymine to cytosine, nt 1389) in exon 4 of the apolipoprotein A1 (apoA1) gene. The predicted substitution of proline for leucine at amino acid position 90 was confirmed by structural analysis of amyloid protein isolated from cardiac deposits of amyloid. The subunit protein ...

  14. A new transthyretin variant (Ser 24) associated with familial amyloid polyneuropathy.

    OpenAIRE

    Uemichi, T; Gertz, M A; Benson, M D

    1995-01-01

    An American kindred with systemic amyloidosis presenting with carpal tunnel syndrome, peripheral neuropathy, and cardiomyopathy is reported. The transthyretin gene of a patient was analysed by direct DNA sequencing and both cytosine and thymine were present at the first base of codon 24. This new point mutation in exon 2 results in the amino acid substitution of serine for proline in the A-B loop of the transthyretin molecule. DNA testing for this mutant allele by restriction fragment length ...

  15. Epigenetic modifications associated with prenatal environmental risk factors for neurodevelopmental psychiatric disorders

    OpenAIRE

    Basil, Paul

    2014-01-01

    Maternal Immune activation (MIA) has been highlighted to be a risk factor for neurodevelopmental disorders like schizophrenia and autism. Epidemiological studies have confirmed this association and studies on animal models from our group and others consistently support this relationship. The functions of genes implicated in the pathophysiology of neurodevelopmental disorders are known to be modulated by epigenetic changes such as DNA cytosine methylation. These epigenetic ‘marks’ can be modif...

  16. Bisprimer-A program for the design of primers for bisulfite-based genomic sequencing of both plant and mammalian DNA samples

    Czech Academy of Sciences Publication Activity Database

    Kováčová, Viera; Janoušek, Bohuslav

    2012-01-01

    Roč. 103, č. 2 (2012), s. 308-312. ISSN 0022-1503 R&D Projects: GA ČR(CZ) GA521/08/0932; GA ČR(CZ) GD204/09/H002 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : bisulfite * cytosine methylation * DNA methylation Subject RIV: BO - Biophysics Impact factor: 1.995, year: 2012

  17. Compromised telomere maintenance in hypomethylated Arabidopsis thaliana plants

    Czech Academy of Sciences Publication Activity Database

    Ogrocká, A.; Polanská, P.; Majerová, E.; Janeba, Zlatko; Fajkus, Jiří; Fojtová, M.

    2014-01-01

    Roč. 42, č. 5 (2014), s. 2919-2931. ISSN 0305-1048 Grant ostatní: GA ČR(CZ) GAP501/11/0596; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:61388963 ; RVO:68081707 Keywords : DNA methylation * cytosine methylation * mammalian telomeres Subject RIV: CE - Biochemistry; BO - Biophysics (BFU-R) Impact factor: 9.112, year: 2014

  18. Epigenetic switches of tobacco transgenes associate with transient redistribution of histone marks in callus culture

    Czech Academy of Sciences Publication Activity Database

    Křížová, Kateřina; Depicker, A.; Kovařík, Aleš

    2013-01-01

    Roč. 8, č. 6 (2013), s. 666-676. ISSN 1559-2294 R&D Projects: GA ČR(CZ) GPP501/11/P667; GA ČR(CZ) GBP501/12/G090; GA ČR(CZ) GA13-10057S Institutional support: RVO:68081707 Keywords : JMJC DOMAIN PROTEIN * DNA METHYLATION * CYTOSINE METHYLATION Subject RIV: BO - Biophysics Impact factor: 5.108, year: 2013

  19. Refining the Neuberger Model: uracil processing by activated B cells

    OpenAIRE

    Maul, Robert W.; Gearhart, Patricia J.

    2014-01-01

    During the immune response, B cells undergo a programmed mutagenic cascade to promote increased affinity and expanded antibody function. The two processes, somatic hypermutation (SHM) and class switch recombination (CSR), are initiated by the protein activation-induced deaminase (AID), which converts cytosine to uracil in the immunoglobulin loci. The presence of uracil in DNA promotes DNA mutagenesis though a subset of DNA repair proteins. Two distinct mechanisms have been proposed to control...

  20. 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 (function of the photon energy.

  1. A new usage of functionalized oligodeoxynucleotide probe for site-specific modification of a guanine base within RNA

    OpenAIRE

    Onizuka, Kazumitsu; Taniguchi, Yosuke; Sasaki, Shigeki

    2010-01-01

    Site-specific modification of RNA is of great significance to investigate RNA structure, function and dynamics. Recently, we reported a new method for sequence- and cytosine-selective chemical modification of RNA based on the functional group transfer reaction of the 1-phenyl-2-methylydene-1,3-diketone unit of the 6-thioguanosine base incorporated in the oligodeoxynucleotide probe. In this study, we describe that the functionality transfer rate is greatly enhanced and the selectivity is shift...

  2. Visual motion processing deficits in infants with the fragile X premutation

    OpenAIRE

    Gallego, Pamela K; Burris, Jessica L.; Rivera, Susan M.

    2014-01-01

    Background Fragile X syndrome (FXS) results from a trinucleotide repeat expansion (full mutation >200 cytosine-guanine-guanine (CGG) repeats) in the FMR1 gene, leading to a reduction or absence of the gene’s protein product, fragile X mental retardation protein (FMRP), ultimately causing cognitive and behavioral impairments that are characteristic of the syndrome. In our previous work with infants and toddlers with FXS, we have been able to describe much about their cognitive and visual proce...

  3. Immunofluorescent staining reveals hypermethylation of microchromosomes in the central bearded dragon, Pogona vitticeps

    OpenAIRE

    Domaschenz, Renae; Livernois, Alexandra M.; Rao, Sudha; Ezaz, Tariq; Deakin, Janine E

    2015-01-01

    Background Studies of model organisms have demonstrated that DNA cytosine methylation and histone modifications are key regulators of gene expression in biological processes. Comparatively little is known about the presence and distribution of epigenetic marks in non-model amniotes such as non-avian reptiles whose genomes are typically packaged into chromosomes of distinct size classes. Studies of chicken karyotypes have associated the gene-richness and high GC content of microchromosomes wit...

  4. How do eubacterial organisms manage aggregation-prone proteome?

    OpenAIRE

    Rishi Das Roy; Manju Bhardwaj; Vasudha Bhatnagar; Kausik Chakraborty; Debasis Dash

    2014-01-01

    Eubacterial genomes vary considerably in their nucleotide composition. The percentage of genetic material constituted by guanosine and cytosine (GC) nucleotides ranges from 20% to 70%.  It has been posited that GC-poor organisms are more dependent on protein folding machinery. Previous studies have ascribed this to the accumulation of mildly deleterious mutations in these organisms due to population bottlenecks. This phenomenon has been supported by protein folding simulations, which showed t...

  5. Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity

    OpenAIRE

    Pinto, Yishay; Gabay, Orshay; Arbiza, Leonardo; Sams, Aaron J.; Keinan, Alon; Levanon, Erez Y.

    2016-01-01

    The gradual accumulation of mutations by any of a number of mutational processes is a major driving force of divergence and evolution. Here, we investigate a potentially novel mutational process that is based on the activity of members of the AID/APOBEC family of deaminases. This gene family has been recently shown to introduce—in multiple types of cancer—enzyme-induced clusters of co-occurring somatic mutations caused by cytosine deamination. Going beyond somatic mutations, we hypothesized t...

  6. Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA

    OpenAIRE

    Laszlo, Andrew H; Derrington, Ian M.; Brinkerhoff, Henry; Langford, Kyle W.; Nova, Ian C.; Samson, Jenny Mae; Bartlett, Joshua J.; Pavlenok, Mikhail; Gundlach, Jens H.

    2013-01-01

    Cells attach a methyl group (—CH3) to certain cytosines in DNA to control gene expression. These methylation patterns change over time and can be related to cell differentiation and diseases such as cancer. Existing methylation detection techniques are not ideal for clinical use. We pulled single-stranded DNA molecules through the biological pore MspA and found that ion currents passing through the pore reveal the methylation sites with high confidence. Hydroxymethylation, which differs from ...

  7. Wheat Hybridization and Polyploidization Results in Deregulation of Small RNAs

    OpenAIRE

    Kenan-Eichler, Michal; Leshkowitz, Dena; Tal, Lior; Noor, Elad; Melamed-Bessudo, Cathy; Feldman, Moshe; Levy, Avraham A.

    2011-01-01

    Speciation via interspecific or intergeneric hybridization and polyploidization triggers genomic responses involving genetic and epigenetic alterations. Such modifications may be induced by small RNAs, which affect key cellular processes, including gene expression, chromatin structure, cytosine methylation and transposable element (TE) activity. To date, the role of small RNAs in the context of wide hybridization and polyploidization has received little attention. In this work, we performed h...

  8. Next-generation sequencing offers new insights into DNA degradation

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren; Orlando, Ludovic Antoine Alexandre; Willerslev, Eske

    2012-01-01

    rates that previously were obtained only from extrapolations of results from in vitro kinetic experiments performed over short timescales. For example, recent next-generation sequencing of ancient DNA reveals purine bases as one of the main targets of postmortem hydrolytic damage, through base......The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation...

  9. Linking active DNA demethylation by Thymine DNA Glycosylase with epigenetic regulation of gene expression

    OpenAIRE

    Wirz, Annika

    2014-01-01

    The correct regulation of epigenetic modifications is crucial for cell plasticity and the establishment of cell identity. The underlying molecular mechanisms are not clear, but a role for DNA repair proteins has been implicated in this context, the investigation of which was the overall aim of my PhD thesis. The Thymine DNA Glycosylase (TDG) was described to excise the deamination products of cytosine (C) and 5-methylcytosine (5-mC), thereby initiating base excision repair (BER; Nedderman...

  10. Factors to preserve CpG-rich sequences in methylated CpG islands

    OpenAIRE

    Miyahara, Hiroki; Hirose, Osamu; Satou, Kenji; Yamada, Yoichi

    2015-01-01

    Background Mammalian CpG islands (CGIs) normally escape DNA methylation in all adult tissues and developmental stages. However, in our previous study we unexpectedly identified many methylated CGIs in human peripheral blood leukocytes. Methylated CpG dinucleotides convert to TpG dinucleotides through deaminization of their cytosine bases more frequently than hypomethylated CpG dinucleotides. Therefore, we wondered how methylated CGIs in germline or non-germline cells maintain their CpG-rich s...

  11. Non-canonical uracil processing in DNA gives rise to double-strand breaks and deletions: relevance to class switch recombination

    OpenAIRE

    Bregenhorn, Stephanie; Kallenberger, Lia; Artola-Borán, Mariela; Peña-Diaz, Javier; Jiricny, Josef

    2016-01-01

    During class switch recombination (CSR), antigen-stimulated B-cells rearrange their immunoglobulin constant heavy chain (CH) loci to generate antibodies with different effector functions. CSR is initiated by activation-induced deaminase (AID), which converts cytosines in switch (S) regions, repetitive sequences flanking the CH loci, to uracils. Although U/G mispairs arising in this way are generally efficiently repaired to C/Gs by uracil DNA glycosylase (UNG)-initiated base excision repair (B...

  12. Mechanism of interferon action: Simian virus 40-specific early polypeptides synthesized in untreated and interferon-treated monkey kidney cells

    OpenAIRE

    Kingsman, Susan M.; Smith, Mark D; Samuel, Charles E.

    1980-01-01

    The effect of interferon treatment on proteins synthesized in simian virus 40 (SV40)-infected cells in the presence of cytosine arabinoside was investigated. The following results were obtained: (i) In addition to previously described large tumor (T) antigen (94 kilodaltons) and small tumor (t) antigen (19 kilodaltons), a 62-kilodalton polypeptide was immunoprecipitated by SV40 anti-T antiserum from extracts of infected CV-1 and BSC-1 monkey kidney cells and transformed SV3T3 mouse cells. The...

  13. The use of permanganate as a sequencing reagent for identification of 5-methylcytosine residues in DNA.

    OpenAIRE

    Fritzsche, E; Hayatsu, H; Igloi, G L; Iida, S.; Kössel, H

    1987-01-01

    The use of permanganate as a reagent for DNA sequencing by chemical degradation has been studied with respect to its specificity for 5-methylcytosine residues. At weakly acidic pH and room temperature, 0.2 mM potassium permanganate reacts preferentially with thymine, 5-methylcytosine, and to a lesser extent with purine residues, while cytosine remains essentially intact. Permanganate oxidation is, therefore, a suitable DNA sequencing reaction for positive discrimination between 5-methylcytosi...

  14. Thymine Photodimers. Two-dimensional NMR and photo-CIDNP studies

    OpenAIRE

    Kemmink, Johan

    1987-01-01

    De erfelijke eigenschappen van levende organismen zijn vastgelegd in DNA molekulen in de vorm van een specifieke volgorde van de basen adenine, cytosine, guanine en thymine. Het essentieel voor de ontwikkeling van levende organisemen, dat de DNA molekulen zeer vaak gedupliceerd kunnen worden zoder dat de vastgelegde code noemenswaardig veranderd. Dit vereist een extreem hoge stabiliteit van het DNA molekuul. In schijnbare tegenspraak hiermee is het feit, dat het DNA wordt blootgesteld aan een...

  15. Prognostic Value of AML1/ETO Fusion Transcripts in Patients with Acute Myelogenous Leukemia

    OpenAIRE

    Cho, Eun Kyung; Bang, Soo Mee; Ahn, Jeong Yeal; Yoo, Seung Min; Park, Pil Whan; Seo, Yieh Hea; Shin, Dong Bok; Lee, Jae Hoon

    2003-01-01

    Background The t (8;21) (q22;q22), which produces the fusion gene AML1/ETO, is associated with relatively good prognosis and, in particular, with a good response to cytosine arabinoside. Analysis of t (8;21) positive leukemic blasts has shown characteristic morphological and immunological features. We performed this study to investigate the incidence of AML1/ETO rearrangement in adult acute myelogenous leukemia (AML), especially in M2 subtype, to make a comparison of clinical, morphological a...

  16. p53 Represses Class Switch Recombination to IgG2a through its Antioxidant Function1

    OpenAIRE

    Guikema, Jeroen E. J.; Schrader, Carol E.; Brodsky, Michael H.; Linehan, Erin K.; Richards, Adam; El Falaky, Nahla; Li, Daniel H.; Sluss, Hayla K.; Szomolanyi-Tsuda, Eva; Stavnezer, Janet

    2010-01-01

    Immunoglobulin class switch recombination (CSR) occurs in activated mature B cells, and causes an exchange of the IgM isotype for IgG, IgE or IgA isotypes, which increases the effectiveness of the humoral immune response. DNA double-stranded breaks (DSBs) in recombining switch (S) regions, where CSR occurs, are required for recombination. Activation-induced cytidine deaminase (AID) initiates DSB formation by deamination of cytosines in S regions. This reaction requires reactive oxygen species...

  17. Nasal delivery of Japanese cedar pollen Cryj1 by using self-gelling immunostimulatory DNA for effective induction of immune responses in mice.

    OpenAIRE

    Ishii-Mizuno, Yumiko; Umeki, Yuka; Takahashi, Yuki; Kato, Yukinori; Takabayashi, Tetsuji; Fujieda, Shigeharu; Takakura, Yoshinobu; Nishikawa, Makiya

    2015-01-01

    To develop an immunotherapeutic vaccine for treatment of allergic rhinitis, we developed a controlled release formulation of Cryj1, a major Japanese cedar pollen allergen, with immunostimulatory potency. Two sets of hexapod-like structured DNA (hexapodna) were prepared using six oligodeoxynucleotides (ODNs) each, including ODNs with an unmethylated cytosine-phosphate-guanine (CpG) sequence (CpG motif), to obtain an immunostimulatory DNA hydrogel (sDNA hydrogel). A non-immunostimulatory DNA hy...

  18. LINE-1 Hypomethylation in a Choline-Deficiency-Induced Liver Cancer in Rats: Dependence on Feeding Period

    Directory of Open Access Journals (Sweden)

    2006-01-01

    Full Text Available Chronic feeding of methyl-donor (methionine, choline, folic acid, and vitamin B12 deficient diet induces hepatocellular carcinoma formation in rats. Previous studies have shown that promoter CpG islands in various cancer-related genes are aberrantly methylated in this model. Moreover, the global genome in methyl-donor-deficient diet fed rats contains a lesser amount of 5-methylcytosine than control livers. It is speculated that more than 90% of all 5-methylcytosines lie within the CpG islands of the transposons, including the long/short interspersed nucleotide elements (LINE and SINE. It is considered that the 5-methylcytosines in LINE-1 limit the ability of retrotransposons to be activated and transcribed; therefore, the extent of hypomethylation of LINE-1 could be a surrogate marker for aberrant methylation in other tumor-related genes as well as genome instability. Additionally, LINE-1 methylation status has been shown to be a good indicator of genome-wide methylation. In this study, we determined cytosine methylation status in the LINE-1 repetitive sequences of rats fed a choline-deficient (CD diet for various durations and compared these with rats fed a choline-sufficient (CS diet. The methylation status of LINE-1 was assessed by the combined bisulfite restriction analysis (COBRA method, where the amount of bisulfite-modified and RsaI-cleaved DNA was quantified using gel electrophoresis. Progressive hypomethylation was observed in LINE-1 of CD livers as a function of feeding time; that is, the amount of cytosine in total cytosine (methylated and unmethylated increased from 11.1% (1 week to 19.3% (56 weeks, whereas in the control CS livers, it increased from 9.2% to 12.9%. Hypomethylation in tumor tissues was slightly higher (6% than the nontumorous surrounding tissue. The present result also indicates that age is a factor influencing the extent of cytosine methylation.

  19. Theoretical study of chemical reactions in solution

    International Nuclear Information System (INIS)

    Quantum chemical calculations in solution are becoming more and more important in chemistry. Reference interaction site model self-consistent field (RISM-SCF) is one of the powerful approaches to perform quantum chemical calculations in solution. In this work, we developed a new generation of RISM-SCF, where a robust fitting method was newly introduced. We applied the new method to tautomerization reaction of cytosine in aqueous phase. Our calculation reproduced experimentally obtained relative stabilities and relative free energies correctly

  20. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine

    OpenAIRE

    Iqbal, Khursheed; Jin, Seung-Gi; Pfeifer, Gerd P; Szabó, Piroska E.

    2011-01-01

    Genome-wide erasure of DNA cytosine-5 methylation has been reported to occur along the paternal pronucleus in fertilized oocytes in an apparently replication-independent manner, but the mechanism of this reprogramming process has remained enigmatic. Recently, considerable amounts of 5-hydroxymethylcytosine (5hmC), most likely derived from enzymatic oxidation of 5-methylcytosine (5mC) by TET proteins, have been detected in certain mammalian tissues. 5hmC has been proposed as a potential interm...

  1. Sequence Classification: 891958 [

    Lifescience Database Archive (English)

    Full Text Available ondrial glycosylase/lyase that specifically excises 7,8-dihydro-8-oxoguanine residues located opposite cytosine or thymine residues... in DNA, repairs oxidative damage to mitochondrial DNA; Ogg1p || http://www.ncbi.nlm.nih.gov/protein/6323580 ... ...Non-TMB Non-TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|6323580|ref|NP_013651.1| Mitoch

  2. Identification of a new HLA-G allele, HLA-G*01:19, by cloning and phasing.

    Science.gov (United States)

    Wang, W Y; Tian, W

    2016-08-01

    A new HLA-G allelic variant, HLA-G*01:19, was identified in a southern Chinese Han population by polymerase chain reaction-sequence-based typing (PCR-SBT), cloning and phasing. HLA-G*01:19 differs from HLA-G*01:04:01 by a nonsynonymous cytosine at position 99 in exon 2, resulting in amino acid change from valine to leucine at codon 34 of the mature HLA-G molecule. PMID:27277539

  3. Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

    OpenAIRE

    McCutcheon, John P.; McDonald, Bradon R.; Moran, Nancy A

    2009-01-01

    Author Summary The genetic code, which relates DNA sequence to protein sequence, is nearly universal across all life. Examples of recodings do exist, but new instances are rare. Genomes that exhibit recodings typically have other extreme properties, including reduced size, reduced gene sets, and low guanine plus cytosine (GC) content. The most common recoding event, the reassignment of UGA to Tryptophan instead of Stop (Stop→Trp), was previously known from several mitochondrial and one bacter...

  4. Comprehensive Analysis of MGMT Promoter Methylation: Correlation with MGMT Expression and Clinical Response in GBM

    OpenAIRE

    Shah, Nameeta; Lin, Biaoyang; Sibenaller, Zita; Ryken, Timothy; Lee, Hwahyung; Yoon, Jae-Geun; Rostad, Steven; Foltz, Greg

    2011-01-01

    O6-methylguanine DNA-methyltransferase (MGMT) promoter methylation has been identified as a potential prognostic marker for glioblastoma patients. The relationship between the exact site of promoter methylation and its effect on gene silencing, and the patient's subsequent response to therapy, is still being defined. The aim of this study was to comprehensively characterize cytosine-guanine (CpG) dinucleotide methylation across the entire MGMT promoter and to correlate individual CpG site met...

  5. Nucleotide Variability in the 5-Enolpyruvylshikimate-3-Phosphate Synthase Gene from Eleusine indica (L.) Gaertn

    OpenAIRE

    J.L. Chong; R. Wickneswari; Ismail, B. S.; S. Salmijah

    2008-01-01

    This study reports the results of the partial DNA sequence analysis of the 5-enolpyruvyl-shikimate-3-phosphate synthase (EPSPS) gene in glyphosate-resistant (R) and glyphosate-susceptible (S) biotypes of Eleusine indica (L.) Gaertn from Peninsular Malaysia. Sequencing results revealed point mutation at nucleotide position 875 in the R biotypes of Bidor, Chaah and Temerloh. In the Chaah R population, substitution of cytosine (C) to adenine (A) resulted in the change of threonine (Thr106) to pr...

  6. Tight-binding parameters for charge transfer along DNA

    OpenAIRE

    Hawke, L. G.D.; Kalosakas, G.; Simserides, C.

    2009-01-01

    We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wavefunctions and energies of DNA bases are discussed and then used for calculating the corresponding wavefunctions of the two B-DNA base-pairs (adenine-thymine and gua...

  7. 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.

  8. DNA Methylation Profiling of the Human Major Histocompatibility Complex: A Pilot Study for the Human Epigenome Project

    Directory of Open Access Journals (Sweden)

    Rakyan Vardhman K

    2004-01-01

    Full Text Available The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine-guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated, tissue specificity, inter-individual variation, and correlation with independent gene expression data.

  9. GPU-BSM: a GPU-based tool to map bisulfite-treated reads.

    Directory of Open Access Journals (Sweden)

    Andrea Manconi

    Full Text Available Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads.

  10. DNA abasic site-directed formation of fluorescent silver nanoclusters for selective nucleobase recognition

    Energy Technology Data Exchange (ETDEWEB)

    Ma Kun; Cui Qinghua; Liu Guiying; Wu Fei; Xu Shujuan; Shao Yong, E-mail: yshao@zjnu.cn [Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang (China)

    2011-07-29

    DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation related diseases. Various methods for SNP detection have been proposed and many are already in use. Here, we find that the abasic site (AP site) in the DNA duplex can be developed as a capping scaffold for the generation of fluorescent silver nanoclusters (Ag NCs). As a proof of concept, the DNA sequences from fragments near codon 177 of cancer supression gene p53 were used as a model for SNP detection by in situ formed Ag NCs. The formation of fluorescent Ag NCs in the AP site-containing DNA duplex is highly selective for cytosine facing the AP site and guanines flanking the site and can be employed in situ as readout for SNP detection. The fluorescent signal-on sensing for SNP based on this inorganic fluorophore is substantially advantageous over the previously reported signal-off responses using low-molecular-weight organic ligands. The strong dependence of fluorescent Ag NC formation on the sequences surrounding the AP site was successfully used to identify mutations in codon 177 of cancer supression gene p53. We anticipate that this approach will be employed to develop a practical SNP detection method by locating an AP site toward the midway cytosine in a target strand containing more than three consecutive cytosines.

  11. DNA abasic site-directed formation of fluorescent silver nanoclusters for selective nucleobase recognition

    International Nuclear Information System (INIS)

    DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation related diseases. Various methods for SNP detection have been proposed and many are already in use. Here, we find that the abasic site (AP site) in the DNA duplex can be developed as a capping scaffold for the generation of fluorescent silver nanoclusters (Ag NCs). As a proof of concept, the DNA sequences from fragments near codon 177 of cancer supression gene p53 were used as a model for SNP detection by in situ formed Ag NCs. The formation of fluorescent Ag NCs in the AP site-containing DNA duplex is highly selective for cytosine facing the AP site and guanines flanking the site and can be employed in situ as readout for SNP detection. The fluorescent signal-on sensing for SNP based on this inorganic fluorophore is substantially advantageous over the previously reported signal-off responses using low-molecular-weight organic ligands. The strong dependence of fluorescent Ag NC formation on the sequences surrounding the AP site was successfully used to identify mutations in codon 177 of cancer supression gene p53. We anticipate that this approach will be employed to develop a practical SNP detection method by locating an AP site toward the midway cytosine in a target strand containing more than three consecutive cytosines.

  12. DNA abasic site-directed formation of fluorescent silver nanoclusters for selective nucleobase recognition

    Science.gov (United States)

    Ma, Kun; Cui, Qinghua; Liu, Guiying; Wu, Fei; Xu, Shujuan; Shao, Yong

    2011-07-01

    DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation related diseases. Various methods for SNP detection have been proposed and many are already in use. Here, we find that the abasic site (AP site) in the DNA duplex can be developed as a capping scaffold for the generation of fluorescent silver nanoclusters (Ag NCs). As a proof of concept, the DNA sequences from fragments near codon 177 of cancer supression gene p53 were used as a model for SNP detection by in situ formed Ag NCs. The formation of fluorescent Ag NCs in the AP site-containing DNA duplex is highly selective for cytosine facing the AP site and guanines flanking the site and can be employed in situ as readout for SNP detection. The fluorescent signal-on sensing for SNP based on this inorganic fluorophore is substantially advantageous over the previously reported signal-off responses using low-molecular-weight organic ligands. The strong dependence of fluorescent Ag NC formation on the sequences surrounding the AP site was successfully used to identify mutations in codon 177 of cancer supression gene p53. We anticipate that this approach will be employed to develop a practical SNP detection method by locating an AP site toward the midway cytosine in a target strand containing more than three consecutive cytosines.

  13. The absence of tertiary interactions in a self-assembled DNA crystal structure.

    Science.gov (United States)

    Nguyen, Nam; Birktoft, Jens J; Sha, Ruojie; Wang, Tong; Zheng, Jianping; Constantinou, Pamela E; Ginell, Stephan L; Chen, Yi; Mao, Chengde; Seeman, Nadrian C

    2012-04-01

    DNA is a highly effective molecule for controlling nanometer-scale structure. The convenience of using DNA lies in the programmability of Watson-Crick base-paired secondary interactions, useful both to design branched molecular motifs and to connect them through sticky-ended cohesion. Recently, the tensegrity triangle motif has been used to self-assemble three-dimensional crystals whose structures have been determined; sticky ends were reported to be the only intermolecular cohesive elements in those crystals. A recent communication in this journal suggested that tertiary interactions between phosphates and cytosine N(4) groups are responsible for intermolecular cohesion in these crystals, in addition to the secondary and covalent interactions programmed into the motif. To resolve this issue, we report experiments challenging this contention. Gel electrophoresis demonstrates that the tensegrity triangle exists in conditions where cytosine-PO(4) tertiary interactions seem ineffective. Furthermore, we have crystallized a tensegrity triangle using a junction lacking the cytosine suggested for involvement in tertiary interactions. The unit cell is isomorphous with that of a tensegrity triangle crystal reported earlier. This structure has been solved by molecular replacement and refined. The data presented here leave no doubt that the tensegrity triangle crystal structures reported earlier depend only on base pairing and covalent interactions for their formation. PMID:22434713

  14. Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing

    Science.gov (United States)

    Lee, Myeong H.; Sankey, Otto F.

    2009-01-01

    We report a first-principles study of electron ballistic transport through a molecular junction containing deoxycytidine-monophosphate (dCMP) connected to metal electrodes. A guanidinium ion and guanine nucleobase are tethered to gold electrodes on opposite sides to form hydrogen bonds with the dCMP molecule providing an electric circuit. The circuit mimics a component of a potential device for sequencing unmodified single-stranded DNA. The molecular conductance is obtained from DFT Green's function scattering methods and is compared to estimates from the electron tunneling decay constant obtained from the complex band structure. The result is that a complete molecular dCMP circuit of 'linker((CH2)2)-guanidinium-phosphate-deoxyribose-cytosine-guanine' has a very low conductance (of the order of fS) while the hydrogen-bonded guanine-cytosine base-pair has a moderate conductance (of the order of tens to hundreds of nS). Thus, while the transverse electron transfer through base-pairing is moderately conductive, electron transfer through a complete molecular dCMP circuit is not. The gold Fermi level is found to be aligned very close to the HOMO for both the guanine-cytosine base-pair and the complete molecular dCMP circuit. Results for two different plausible geometries of the hydrogen-bonded dCMP molecule reveal that the conductance varies from fS for an extended structure to pS for a slightly compressed structure.

  15. Anhydrous crystals of DNA bases are wide gap semiconductors

    Science.gov (United States)

    Maia, F. F.; Freire, V. N.; Caetano, E. W. S.; Azevedo, D. L.; Sales, F. A. M.; Albuquerque, E. L.

    2011-05-01

    We present the structural, electronic, and optical properties of anhydrous crystals of DNA nucleobases (guanine, adenine, cytosine, and thymine) found after DFT (Density Functional Theory) calculations within the local density approximation, as well as experimental measurements of optical absorption for powders of these crystals. Guanine and cytosine (adenine and thymine) anhydrous crystals are predicted from the DFT simulations to be direct (indirect) band gap semiconductors, with values 2.68 eV and 3.30 eV (2.83 eV and 3.22 eV), respectively, while the experimentally estimated band gaps we have measured are 3.83 eV and 3.84 eV (3.89 eV and 4.07 eV), in the same order. The electronic effective masses we have obtained at band extremes show that, at low temperatures, these crystals behave like wide gap semiconductors for electrons moving along the nucleobases stacking direction, while the hole transport are somewhat limited. Lastly, the calculated electronic dielectric functions of DNA nucleobases crystals in the parallel and perpendicular directions to the stacking planes exhibit a high degree of anisotropy (except cytosine), in agreement with published experimental results.

  16. Degenerative minimalism in the genome of a psyllid endosymbiont.

    Science.gov (United States)

    Clark, M A; Baumann, L; Thao, M L; Moran, N A; Baumann, P

    2001-03-01

    Psyllids, like aphids, feed on plant phloem sap and are obligately associated with prokaryotic endosymbionts acquired through vertical transmission from an ancestral infection. We have sequenced 37 kb of DNA of the genome of Carsonella ruddii, the endosymbiont of psyllids, and found that it has a number of unusual properties revealing a more extreme case of degeneration than was previously reported from studies of eubacterial genomes, including that of the aphid endosymbiont Buchnera aphidicola. Among the unusual properties are an exceptionally low guanine-plus-cytosine content (19.9%), almost complete absence of intergenic spaces, operon fusion, and lack of the usual promoter sequences upstream of 16S rDNA. These features suggest the synthesis of long mRNAs and translational coupling. The most extreme instances of base compositional bias occur in the genes encoding proteins that have less highly conserved amino acid sequences; the guanine-plus-cytosine content of some protein-coding sequences is as low as 10%. The shift in base composition has a large effect on proteins: in polypeptides of C. ruddii, half of the residues consist of five amino acids with codons low in guanine plus cytosine. Furthermore, the proteins of C. ruddii are reduced in size, with an average of about 9% fewer amino acids than in homologous proteins of related bacteria. These observations suggest that the C. ruddii genome is not subject to constraints that limit the evolution of other known eubacteria. PMID:11222582

  17. Biomolecule-assisted synthesis of porous PtPd alloyed nanoflowers supported on reduced graphene oxide with highly electrocatalytic performance for ethanol oxidation and oxygen reduction

    International Nuclear Information System (INIS)

    Graphical abstract: A facile co-reduction wet-chemical approach was developed for synthesis of porous PtPd alloyed nanoflowers uniformly supported on reduced graphene oxide in the presence of cytosine as a structure-directing agent. The as-obtained nanocomposites displayed enhanced electrocatalytic activity for ethanol oxidation and oxygen reduction reactions. - Highlights: • Porous PtPd alloyed nanoflowers supported on reduced graphene oxide were prepared by a simple, facile, and green co-reduction wet-chemical method. • Cytosine as a model biomolecule was employed for directing synthesis of porous PtPd alloyed nanoflowers. • The nanocomposites showed improved electrocatalytic activity and better stability for ethanol oxidation and oxygen reduction. - Abstract: In this work, we have prepared porous PtPd alloyed nanoflowers uniformly supported on reduced graphene oxide by a simple and facile wet-chemical method, with the assistance of cytosine as a structure-directing agent. The products were mainly characterized by transmission electron microscopy, X-ray diffraction and X-ray photoelectron spectroscopy. The as-prepared nanocomposites displayed improved electrocatalytic performances toward ethanol oxidation in alkaline media and oxygen reduction in acidic media, which make it a promising electrocatalyst in fuel cells

  18. Nucleotide discrimination with DNA immobilized in the MspA nanopore.

    Science.gov (United States)

    Manrao, Elizabeth A; Derrington, Ian M; Pavlenok, Mikhail; Niederweis, Michael; Gundlach, Jens H

    2011-01-01

    Nanopore sequencing has the potential to become a fast and low-cost DNA sequencing platform. An ionic current passing through a small pore would directly map the sequence of single stranded DNA (ssDNA) driven through the constriction. The pore protein, MspA, derived from Mycobacterium smegmatis, has a short and narrow channel constriction ideally suited for nanopore sequencing. To study MspA's ability to resolve nucleotides, we held ssDNA within the pore using a biotin-NeutrAvidin complex. We show that homopolymers of adenine, cytosine, thymine, and guanine in MspA exhibit much larger current differences than in α-hemolysin. Additionally, methylated cytosine is distinguishable from unmethylated cytosine. We establish that single nucleotide substitutions within homopolymer ssDNA can be detected when held in MspA's constriction. Using genomic single nucleotide polymorphisms, we demonstrate that single nucleotides within random DNA can be identified. Our results indicate that MspA has high signal-to-noise ratio and the single nucleotide sensitivity desired for nanopore sequencing devices. PMID:21991340

  19. 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.

  20. Characterization of Partial Coding Region Fibroin Gene on Wild Silkmoth Cricula trifenestrata Helfer (Lepidoptera: Saturniidae

    Directory of Open Access Journals (Sweden)

    Suriana

    2011-04-01

    Full Text Available The study was conducted to characterize coding region of wild silkmoth C. trifenestrata partial fibroin gene, and detect these gene potential as molecular marker. A total of six larvae C. trifenestrata were collected from Bogor, Purwakarta and Bantul Regency. Genomic DNA was extracted from silk gland individual larvae, then amplified by PCR method and sequenced. DNA sequenced result was 986 nucleotide partial fibroin gene of C. trifenestrata, which are comprising complete coding region of first exon (42 nucleotide, an intron (113 nucleotide, and partial of second was exon (831 nucleotide. Only coding region was characterized. Results showed that first exon very conserved in C. trifenestrata. These gene consisted of 31%, thymine, 28% guanine, 21% cytosine, and 19% adenine. Cytosine and thymine (sites of 25th and 35th respectively were marker for C. trifenestrata species. The first exon encoding 14 amino acids. Valine amino acid (12th site was marker to the species C. trifenestrata. The partial second exon consisted of guanine (32.7%, alanine (26.5%, thymine (21% and cytosine (19.7%. These region encoded 277 amino acids, which were dominated by the alanine (27.8% and glycine (21.66%. Alanine formed polyalanine sequence with different motifs namely: AAAAAAASS, AAAAAAAAAAAGSSG, AAAAAAAAAAAAGSGTGFGGYDS, AAAAAAAAAAGSSGRGGYDGVDGGYGSGSS, and AAAAAAAAAAAAGSSGRGLGGYDGWVDDGYGSGSGS.

  1. Genetic analysis of the cardiac methylome at single nucleotide resolution in a model of human cardiovascular disease.

    Directory of Open Access Journals (Sweden)

    Michelle D Johnson

    2014-12-01

    Full Text Available Epigenetic marks such as cytosine methylation are important determinants of cellular and whole-body phenotypes. However, the extent of, and reasons for inter-individual differences in cytosine methylation, and their association with phenotypic variation are poorly characterised. Here we present the first genome-wide study of cytosine methylation at single-nucleotide resolution in an animal model of human disease. We used whole-genome bisulfite sequencing in the spontaneously hypertensive rat (SHR, a model of cardiovascular disease, and the Brown Norway (BN control strain, to define the genetic architecture of cytosine methylation in the mammalian heart and to test for association between methylation and pathophysiological phenotypes. Analysis of 10.6 million CpG dinucleotides identified 77,088 CpGs that were differentially methylated between the strains. In F1 hybrids we found 38,152 CpGs showing allele-specific methylation and 145 regions with parent-of-origin effects on methylation. Cis-linkage explained almost 60% of inter-strain variation in methylation at a subset of loci tested for linkage in a panel of recombinant inbred (RI strains. Methylation analysis in isolated cardiomyocytes showed that in the majority of cases methylation differences in cardiomyocytes and non-cardiomyocytes were strain-dependent, confirming a strong genetic component for cytosine methylation. We observed preferential nucleotide usage associated with increased and decreased methylation that is remarkably conserved across species, suggesting a common mechanism for germline control of inter-individual variation in CpG methylation. In the RI strain panel, we found significant correlation of CpG methylation and levels of serum chromogranin B (CgB, a proposed biomarker of heart failure, which is evidence for a link between germline DNA sequence variation, CpG methylation differences and pathophysiological phenotypes in the SHR strain. Together, these results will

  2. On the role of Fe3+ ions in FexOy/C catalysts for hydrogen production from the photodehydrogenation of ethanol

    International Nuclear Information System (INIS)

    Graphical abstract: In FexOy/C photocatalyts important effect of Fe3+ ions in the photodehydrogenation of the ethano was noticed. -- Highlights: • Iron oxides supported on carbon are photoactive catalysts. • Photoactivity in dehydrogenation of ethanol depends of the amount of Fe3+ ions present in the catalysts. • The capacity of UV–vis absorbance by the FexOy/C catalysts is significantly dependent of the amount of Fe3+ ions. • A maximum of rate constant, K = 2125 μmol h−1, was obtained from the sample with 30 wt% Fe. -- Abstract: FexOy/C photocatalysts at different iron content were prepared by the incipient wet impregnation method and calcined at 773 K. The photocatalysts were characterized by means of nitrogen adsorption–desorption isotherms, surface fractal dimension, non-local density functional theory, X-ray diffraction, Rietveld refinement and UV–vis spectroscopy. The photocatalytic activity was evaluated using the photodehydrogenation of ethanol as a model reaction for the production of hydrogen. The specific surface areas of FexOy/C substrates, with 15, 20 and 30 wt% iron content, diminished from 638 to 490 m2/g, as the iron content increased. X-ray diffraction analysis showed that iron oxides coexist as wustite and magnetite in samples with Fe contents of 15 and 20 wt%; for sample with 30 wt% Fe, wustite, magnetite and hematite phases were observed. The photophysical, textural and structural properties were modified by the hematite phase formed by thermal treatment. The Rietveld refinements denoted changes in occupancy of Fe3+ and Fe2+ in FexOy crystallites. A relationship between the Fe3+ ions content and the reactivity for the hydrogen production from the photodehydrogenation of ethanol (from 1360 to 2125 μmol h−1), was evidenced

  3. Unraveling the complexity of the interactions of DNA nucleotides with gold by single molecule force spectroscopy

    Science.gov (United States)

    Bano, Fouzia; Sluysmans, Damien; Wislez, Arnaud; Duwez, Anne-Sophie

    2015-11-01

    Addressing the effect of different environmental factors on the adsorption of DNA to solid supports is critical for the development of robust miniaturized devices for applications ranging from biosensors to next generation molecular technology. Most of the time, thiol-based chemistry is used to anchor DNA on gold - a substrate commonly used in nanotechnology - and little is known about the direct interaction between DNA and gold. So far there have been no systematic studies on the direct adsorption behavior of the deoxyribonucleotides (i.e., a nitrogenous base, a deoxyribose sugar, and a phosphate group) and on the factors that govern the DNA-gold bond strength. Here, using single molecule force spectroscopy, we investigated the interaction of the four individual nucleotides, adenine, guanine, cytosine, and thymine, with gold. Experiments were performed in three salinity conditions and two surface dwell times to reveal the factors that influence nucleotide-Au bond strength. Force data show that, at physiological ionic strength, adenine-Au interactions are stronger, asymmetrical and independent of surface dwell time as compared to cytosine-Au and guanine-Au interactions. We suggest that in these conditions only adenine is able to chemisorb on gold. A decrease of the ionic strength significantly increases the bond strength for all nucleotides. We show that moderate ionic strength along with longer surface dwell period suggest weak chemisorption also for cytosine and guanine.Addressing the effect of different environmental factors on the adsorption of DNA to solid supports is critical for the development of robust miniaturized devices for applications ranging from biosensors to next generation molecular technology. Most of the time, thiol-based chemistry is used to anchor DNA on gold - a substrate commonly used in nanotechnology - and little is known about the direct interaction between DNA and gold. So far there have been no systematic studies on the direct

  4. Synthesis, Characterization and Weak Intramolecular Interactions of Porphyrins Bearing Nucleobases

    Institute of Scientific and Technical Information of China (English)

    阮文娟; 李瑛; 赵小菁; 王传忠; 朱志昂; 缪方明

    2003-01-01

    5,10, 15-Triphenyl-20-{2- [α- (adenine-9 ) acetylamino]} phenyl porphyrin ( 1 ), 5,10, 15-triphenyl-20-{2-[α-(cytosine-1)acetylamino]} phenyl porphyrin (2), 5, 10, 15-triphenyl-20-{4-[α-(cytosine-1)ethoxy]} phenyl porphyrin (3) and their zinc complexes Zn-1, Zn-2 and Zn-3 have been prepared and characterized by 1H NMR spectra, elemental analyses, electronic absorption spectra and mass spectra (FAB). Intramolecular π-π interactions and intramolecular metal-~ interaction for 1, 2, Zn-1,and Zn-2 have been investigated by several methods. 1H NMR studies demonstrate that the porphyrin π-system in 1 and 2 is parallel to the adenine and the cytosine aromatic ring, respectively. The electronic absorption spectral properties of free porphyrin derivatives and their zinc complexes have been compared with those of H2TPP and ZnTPP. The results show that the UV-vis spectra of 1 and 2 are the same as that of H2TPP,whereas the spectra of their zinc complexes show 7 nm red shifts of the Soret bands compared to that of ZnTPP. The emission spectra of Zn-1 and Zn-2 are independent of excitation wavelength. From combination of the evidence of absorption and emission spectra it is suggested the existence of intramolecular metal-π interaction in Zn-1 and Zn-2. The results of conformational analysis agreed quite nicely with that of experiments, thus it was further to validate the experimental conclusions.

  5. Use of MSAP markers to analyse the effects of salt stress on DNA methylation in rapeseed (Brassica napus var. oleifera.

    Directory of Open Access Journals (Sweden)

    Gianpiero Marconi

    Full Text Available Excessive soil salinity is a major ecological and agronomical problem, the adverse effects of which are becoming a serious issue in regions where saline water is used for irrigation. Plants can employ regulatory strategies, such as DNA methylation, to enable relatively rapid adaptation to new conditions. In this regard, cytosine methylation might play an integral role in the regulation of gene expression at both the transcriptional and post-transcriptional levels. Rapeseed, which is the most important oilseed crop in Europe, is classified as being tolerant of salinity, although cultivars can vary substantially in their levels of tolerance. In this study, the Methylation Sensitive Amplified Polymorphism (MSAP approach was used to assess the extent of cytosine methylation under salinity stress in salinity-tolerant (Exagone and salinity-sensitive (Toccata rapeseed cultivars. Our data show that salinity affected the level of DNA methylation. In particular methylation decreased in Exagone and increased in Toccata. Nineteen DNA fragments showing polymorphisms related to differences in methylation were sequenced. In particular, two of these were highly similar to genes involved in stress responses (Lacerata and trehalose-6-phosphatase synthase S4 and were chosen to further characterization. Bisulfite sequencing and quantitative RT-PCR analysis of selected MSAP loci showed that cytosine methylation changes under salinity as well as gene expression varied. In particular, our data show that salinity stress influences the expression of the two stress-related genes. Moreover, we quantified the level of trehalose in Exagone shoots and found that it was correlated to TPS4 expression and, therefore, to DNA methylation. In conclusion, we found that salinity could induce genome-wide changes in DNA methylation status, and that these changes, when averaged across different genotypes and developmental stages, accounted for 16.8% of the total site

  6. OmpF, a nucleotide-sensing nanoprobe, computational evaluation of single channel activities

    Science.gov (United States)

    Abdolvahab, R. H.; Mobasheri, H.; Nikouee, A.; Ejtehadi, M. R.

    2016-09-01

    The results of highthroughput practical single channel experiments should be formulated and validated by signal analysis approaches to increase the recognition precision of translocating molecules. For this purpose, the activities of the single nano-pore forming protein, OmpF, in the presence of nucleotides were recorded in real time by the voltage clamp technique and used as a means for nucleotide recognition. The results were analyzed based on the permutation entropy of current Time Series (TS), fractality, autocorrelation, structure function, spectral density, and peak fraction to recognize each nucleotide, based on its signature effect on the conductance, gating frequency and voltage sensitivity of channel at different concentrations and membrane potentials. The amplitude and frequency of ion current fluctuation increased in the presence of Adenine more than Cytosine and Thymine in milli-molar (0.5 mM) concentrations. The variance of the current TS at various applied voltages showed a non-monotonic trend whose initial increasing slope in the presence of Thymine changed to a decreasing one in the second phase and was different from that of Adenine and Cytosine; e.g., by increasing the voltage from 40 to 140 mV in the 0.5 mM concentration of Adenine or Cytosine, the variance decreased by one third while for the case of Thymine it was doubled. Moreover, according to the structure function of TS, the fractality of current TS differed as a function of varying membrane potentials (pd) and nucleotide concentrations. Accordingly, the calculated permutation entropy of the TS, validated the biophysical approach defined for the recognition of different nucleotides at various concentrations, pd's and polarities. Thus, the promising outcomes of the combined experimental and theoretical methodologies presented here can be implemented as a complementary means in pore-based nucleotide recognition approaches.

  7. Binding of the antitumor drug nogalamycin and its derivatives to DNA: Structural comparison

    International Nuclear Information System (INIS)

    The three-dimensional molecular structures of the complexes between a novel antitumor drug nogalamycin and its derivative U-58872 with a modified DNA hexamer d[m5CGT(pS)Am5CG] have been determined at 1.7- and 1.8-angstrom resolution, respectively, by X-ray diffraction analyses. Both structures (in space group P61) have been refined with constrained refinement procedure to final R factors of 0.208 (3386 reflections) and 0.196 (2143 reflections). In both complexes, two nogalamycins bind to the DNA hexamer double helix in a 2:1 ratio with the elongated aglycon chromophore intercalated between the CpG steps at both ends of the helix. The aglycon chromophore spans across the GC Watson-Crick base pairs with its nogalose lying in the minor groove and the aminoglucose lying in the major groove of the distorted B-DNA double helix. Most of the sugars remain in the C2'-endo pucker family, except three deoxycytidine residues (terminal C1, C7, and internal C5). All nucleotides are in the anti conformation. Specific hydrogen bonds are found in the complex between the drug and guanine-cytosine bases in both grooves of the helix. One hydroxyl group of the aminoglucose donates a hydrogen bond to the N7 of guanine, while the other receives a hydrogen bond from the N4 amino group of cytosine. The orientation of these two hydrogen bonds suggests that nogalamycin prefers a GC base pair with its aglycon chromophore intercalating at the 5'-side of a guanine (between NpG), or at the 3'-side of a cytosine (between CpN) with the sugars pointing toward the GC base pair. The binding of nogalamycin to DNA requires that the base pairs in DNA open up transiently to allow the bulky sugars to go through, suggesting that nogalamycin prefers GC sequences embedded in a stretch of AT sequences

  8. Epigenetic estimation of age in humpback whales.

    Science.gov (United States)

    Polanowski, Andrea M; Robbins, Jooke; Chandler, David; Jarman, Simon N

    2014-09-01

    Age is a fundamental aspect of animal ecology, but is difficult to determine in many species. Humpback whales exemplify this as they have a lifespan comparable to humans, mature sexually as early as 4 years and have no reliable visual age indicators after their first year. Current methods for estimating humpback age cannot be applied to all individuals and populations. Assays for human age have recently been developed based on age-induced changes in DNA methylation of specific genes. We used information on age-associated DNA methylation in human and mouse genes to identify homologous gene regions in humpbacks. Humpback skin samples were obtained from individuals with a known year of birth and employed to calibrate relationships between cytosine methylation and age. Seven of 37 cytosines assayed for methylation level in humpback skin had significant age-related profiles. The three most age-informative cytosine markers were selected for a humpback epigenetic age assay. The assay has an R(2) of 0.787 (P = 3.04e-16) and predicts age from skin samples with a standard deviation of 2.991 years. The epigenetic method correctly determined which of parent-offspring pairs is the parent in more than 93% of cases. To demonstrate the potential of this technique, we constructed the first modern age profile of humpback whales off eastern Australia and compared the results to population structure 5 decades earlier. This is the first epigenetic age estimation method for a wild animal species and the approach we took for developing it can be applied to many other nonmodel organisms. PMID:24606053

  9. A Phytase-Based Reporter System for Identification of Functional Secretion Signals in Bifidobacteria.

    Directory of Open Access Journals (Sweden)

    Annika Osswald

    Full Text Available Health-promoting effects have been attributed to a number of Bifidobacterium sp. strains. These effects as well as the ability to colonise the host depend on secreted proteins. Moreover, rational design of protein secretion systems bears the potential for the generation of novel probiotic bifidobacteria with improved health-promoting or therapeutic properties. To date, there is only very limited data on secretion signals of bifidobacteria available. Using in silico analysis, we demonstrate that all bifidobacteria encode the major components of Sec-dependent secretion machineries but only B. longum strains harbour Tat protein translocation systems. A reporter plasmid for secretion signals in bifidobacteria was established by fusing the coding sequence of the signal peptide of a sialidase of Bifidobacterium bifidum S17 to the phytase gene appA of E. coli. The recombinant strain showed increased phytase activity in spent culture supernatants and reduced phytase levels in crude extracts compared to the control indicating efficient phytase secretion. The reporter plasmid was used to screen seven predicted signal peptides in B. bifidum S17 and B. longum E18. The tested signal peptides differed substantially in their efficacy to mediate protein secretion in different host strains. An efficient signal peptide was used for expression and secretion of a therapeutically relevant protein in B. bifidum S17. Expression of a secreted cytosine deaminase led to a 100-fold reduced sensitivity of B. bifidum S17 to 5-fluorocytosine compared to the non-secreted cytosine deaminase suggesting efficient conversion of 5-fluorocytosine to the cytotoxic cancer drug 5-fluorouracil by cytosine deaminase occurred outside the bacterial cell. Selection of appropriate signal peptides for defined protein secretion might improve therapeutic efficacy as well as probiotic properties of bifidobacteria.

  10. Association of TCF7L2 Genetic Polymorphisms with Type 2 Diabetes Mellitus in the Uygur Population of China

    Science.gov (United States)

    Yao, Hua; Wang, Zhiqiang; Wang, Tingting; Ma, Yan; Su, Yinxia; Ma, Qi; Wang, Li; Zhu, Jun

    2015-01-01

    Background: Genetic polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene have been reported to be strongly associated with type 2 diabetes mellitus (T2DM) in Icelandic, Danish and American populations and further replicated in other European populations, African Americans, Mexican Americans, and Asian populations. The aim of the present study was to investigate the association of TCF7L2 gene polymorphisms with T2DM in a Uygur population of China. Methods: 877 T2DM patients and 871 controls were selected for the present study. Two single nucleotide polymorphisms (SNPs) (rs12255372 and rs7901695) were genotyped by using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The associations of SNPs and haplotypes with T2DM and linkage disequilibrium (LD) structure of the TCF7L2 gene were analyzed. Results: For total participants and male, the distribution of rs12255372 alleles and the dominant model (Guanine Guanine (GG) genotype vs. Guanine Thymine (GT) genotype + Thymine Thymine (TT) genotype) showed significant difference between T2DM and control subjects (for allele: p = 0.013 and p = 0.002, respectively; for dominant model: p = 0.028 and p = 0.008, respectively). The distribution of rs7901695 alleles and the dominant model (TT genotype vs. Thymine Cytosine (TC) genotype + Cytosine Cytosine (CC) genotype) for total participants and male showed significant difference between T2DM and control subjects (for allele: both p = 0.001; for dominant model: p = 0.006 and p = 0.008, respectively). Conclusions: Our data suggested that the genetic polymorphisms of the TCF7L2 gene were associated with T2DM in the Uygur population of China. PMID:26393635

  11. Changes in liver cell DNA methylation status in diabetic mice affect its FT-IR characteristics.

    Directory of Open Access Journals (Sweden)

    Benedicto de Campos Vidal

    Full Text Available Lower levels of cytosine methylation have been found in the liver cell DNA from non-obese diabetic (NOD mice under hyperglycemic conditions. Because the Fourier transform-infrared (FT-IR profiles of dry DNA samples are differently affected by DNA base composition, single-stranded form and histone binding, it is expected that the methylation status in the DNA could also affect its FT-IR profile.The DNA FT-IR signatures obtained from the liver cell nuclei of hyperglycemic and normoglycemic NOD mice of the same age were compared. Dried DNA samples were examined in an IR microspectroscope equipped with an all-reflecting objective (ARO and adequate software.Changes in DNA cytosine methylation levels induced by hyperglycemia in mouse liver cells produced changes in the respective DNA FT-IR profiles, revealing modifications to the vibrational intensities and frequencies of several chemical markers, including νas -CH3 stretching vibrations in the 5-methylcytosine methyl group. A smaller band area reflecting lower energy absorbed in the DNA was found in the hyperglycemic mice and assumed to be related to the lower levels of -CH3 groups. Other spectral differences were found at 1700-1500 cm(-1 and in the fingerprint region, and a slight change in the DNA conformation at the lower DNA methylation levels was suggested for the hyperglycemic mice. The changes that affect cytosine methylation levels certainly affect the DNA-protein interactions and, consequently, gene expression in liver cells from the hyperglycemic NOD mice.

  12. Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control.

    Science.gov (United States)

    Lee, Hwan Young; Yoo, Ji-Eun; Park, Myung Jin; Chung, Ukhee; Shin, Kyoung-Jin

    2006-01-01

    We have established a high-quality mtDNA control region sequence database for Koreans. To identify polymorphic sites and to determine their frequencies and haplotype frequencies, the complete mtDNA control region was sequenced in 593 Koreans, and major length variants of poly-cytosine tracts in HV2 and HV3 were determined in length heteroplasmic individuals by PCR analysis using fluorescence-labeled primers. Sequence comparison showed that 494 haplotypes defined by 285 variable sites were found when the major poly-cytosine tract genotypes were considered in distinguishing haplotypes, whereas 441 haplotypes were found when the poly-cytosine tracts were ignored. Statistical parameters indicated that analysis of partial mtDNA control region which encompasses the extended regions of HV1 and HV2, CA dinucleotide repeats in HV3 and nucleotide position 16497, 16519, 456, 489 and 499 (HV1ex+HV2ex+HV3CA+5SNPs) and the analysis of another partial mtDNA control region including extended regions of HV1 and HV2, HV3 region and nucleotide position 16497 and 16519 (HV1ex+HV2ex+HV3+2SNPs) can be used as efficient alternatives for the analysis of the entire mtDNA control region in Koreans. Also, we collated the basic informative SNPs, suggested the important mutation motifs for the assignment of East Asian haplogroups, and classified 592 Korean mtDNAs (99.8%) into various East Asian haplogroups or sub-haplogroups. Haplogroup-directed database comparisons confirmed the absence of any major systematic errors in our data, e.g., a mix-up of site designations, base shifts or mistypings. PMID:16177905

  13. Effect of copper ions on voltammetric signals of aminopurines at a carbon electrode

    Directory of Open Access Journals (Sweden)

    Frantisek Jelen

    2010-12-01

    Full Text Available Electrochemical oxidations of aminopurines (adenine–Ade, 2–aminopurine, 2AP, 2,6–diaminopurine, 2,6–DAP and theircomplexes with Cu(I on carbon electrodes (pencil–PeGE wereinvestigated by means of linear sweep voltammetry (LSV andelimination voltammetry with linear scan (EVLS. We found thatthe Cu(I–purine complex was formed not only by aminopurines butalso by purine. On the other hand the complex is not formed in thecase of imidazol or cytosine. The results showed that carbonelectrodes in connection with EVLS can be an excellent prototypefor cheap and fast working sensor for aminopurines in the presenceof copper.

  14. Uracil-DNA glycosylase-deficient yeast exhibit a mitochondrial mutator phenotype

    OpenAIRE

    Chatterjee, Aditi; Keshav K Singh

    2001-01-01

    Mutations in mitochondrial DNA (mtDNA) have been reported in cancer and are involved in the pathogenesis of many mitochondrial diseases. Uracil-DNA glycosylase, encoded by the UNG1 gene in Saccharomyces cerevisiae, repairs uracil in DNA formed due to deamination of cytosine. Our study demonstrates that inactivation of the UNG1 gene leads to at least a 3-fold increased frequency of mutations in mtDNA compared with the wild-type. Using a Ung1p–green fluorescent protein (GFP) fusion construct, w...

  15. Active DNA demethylation by oxidation and repair

    Institute of Scientific and Technical Information of China (English)

    Zhizhong Gong; Jian-Kang Zhu

    2011-01-01

    DNA methylation and demethylation are increasingly recognized as important epigenetic factors in both plants and animals.DNA methylation,which is catalyzed by DNA methyltransferases (DNMTs),is a relatively stable and heritable modification that controls gene expression,cellular differentiation,genomic imprinting,paramutation,transposon movement,X-inactivation,and embryogenesis [1].The methylation of cytosine to 5-methylcytosine (5mC) is an important example of DNA modification in animals and plants.This highlight concerns DNA demethylation mechanisms in mammals and whether they are similar to that in plants.

  16. Improved negative selection protocol for Plasmodium berghei in the rodent malarial model

    Directory of Open Access Journals (Sweden)

    Orr Rachael Y

    2012-03-01

    Full Text Available Abstract An improved methodology is presented here for transgenic Plasmodium berghei lines that express the negative selectable marker yFCU (a bifunctional protein that combines yeast cytosine deaminase and uridyl phosphoribosyl transferase (UPRT and substitutes delivery of selection drug 5-fluorocytosine (5FC by intraperitoneal injection for administration via the drinking water of the mice. The improved methodology is shown to be as effective, less labour-intensive, reduces animal handling and animal numbers required for successful selection thereby contributing to two of the "three Rs" of animal experimentation, namely refinement and reduction.

  17. Perturbation of maintenance and de novo DNA methylation in vitro by UVB (280-340 nm)-induced pyrimidine photodimers.

    OpenAIRE

    Becker, F F; Holton, P.; Ruchirawat, M; Lapeyre, J N

    1985-01-01

    The effect of pyrimidine photodimers on transmethylation reactions catalyzed by a highly purified rat liver DNA (cytosine-5-)-methyltransferase (EC 2.1.1.37) that exhibits maintenance and de novo methylation activities was studied in vitro, using the viral substrates M13 mp9 replicative form (RF) DNA and the hemimethylated analog formed from primed synthesis of phage DNA in the presence of 2'-deoxy-5-methylcytidine 5'-triphosphate. These DNAs were irradiated with UVB (280-340 nm) at 900-3600 ...

  18. Formation of covalent complexes between human O6-alkylguanine-DNA alkyltransferase and BCNU-treated defined length synthetic oligodeoxynucleotides.

    OpenAIRE

    Brent, T P; Remack, J S

    1988-01-01

    Repair of chloroethylnitrosourea (CENU)-induced precursors of DNA interstrand cross-links by O6-alkylguanine-DNA alkyltransferase (GAT or GATase) appears to be a factor in tumor resistance to therapy with this class of antineoplastic drugs. Since human GAT is highly specific for O6-guanine, yet the probable cross-link structure is N'-Guanine N3-cytosine ethane, rearrangement of the initial O6-guanine adduct via O6,N1ethanoguanine has been proposed. We suggested that GAT reaction with this int...

  19. AcEST: DK952277 [AcEST

    Lifescience Database Archive (English)

    Full Text Available TST38A01NGRL0013_K15 505 Adiantum capillus-veneris mRNA. clone: TST38A01NGRL0013_K15. 5' end seq ... : 31 VLHVVIP---YPRAREQGTSLMAFQHQEEEDLAFAAA--YEDDTPTPSG *RPSLVPRIGK 195 VL VV+ YP + E+G ++ + E++ L F A E++ ... KREEEELVTNGGRVLLVAKQAS 385 Query: 196 SMVPIQTDVIFVTPSG EELNSRAQLPLFLKSNKGSPSISE 315 ++ Q V EELN LF + + GS ... 383 Query: 82 TKCPAPSLLDRV 47 T P D V Sbjct: 384 TGPSG PVTPDGV 395 >sp|Q08J23|NSUN2_HUMAN tRNA (cytosine-5 ... (53%), Gaps = 6/124 (4%) Frame = +1 Query: 142 DTPTPSG *RPSLVPRIGKSMVPIQTDVIFVTPSG EELNSRAQLPLFLKSNKGSPSISE ...

  20. A constitutional de novo mutation in exon 8 of the p53 gene in a patient with multiple primary malignancies.

    OpenAIRE

    Speiser, P.; Gharehbaghi-Schnell, E.; Eder, S; Haid, A.; Kovarík, J.; Nenutil, R.; Sauter, G.; Schneeberger, C. H.; Vojtesek, B.; Wiltschke, C. H.; Zeillinger, R.

    1996-01-01

    We report a constitutional point mutation of codon 278 in exon 8 of the TP53 gene that has not yet been described as a germ-line mutation. A 52-year-old female developed multiple primary malignancies (liposarcoma, breast cancer, malignant histiocytoma, occult adenocarcinoma). The mutation found in her tumour and peripheral blood lymphocyte DNA is a cytosine to thymine transition at the second position of codon 278 resulting in an amino acid exchange from proline to leucine in the DNA-binding ...

  1. Palladium electrodes for molecular tunnel junctions.

    Science.gov (United States)

    Chang, Shuai; Sen, Suman; Zhang, Peiming; Gyarfas, Brett; Ashcroft, Brian; Lefkowitz, Steven; Peng, Hongbo; Lindsay, Stuart

    2012-10-26

    Gold has been the metal of choice for research on molecular tunneling junctions, but it is incompatible with complementary metal-oxide-semiconductor fabrication because it forms deep level traps in silicon. Palladium electrodes do not contaminate silicon, and also give higher tunnel current signals in the molecular tunnel junctions that we have studied. The result is cleaner signals in a recognition-tunneling junction that recognizes the four natural DNA bases as well as 5-methyl cytosine, with no spurious background signals. More than 75% of all the recorded signal peaks indicate the base correctly. PMID:23037952

  2. Palladium electrodes for molecular tunnel junctions

    International Nuclear Information System (INIS)

    Gold has been the metal of choice for research on molecular tunneling junctions, but it is incompatible with complementary metal–oxide–semiconductor fabrication because it forms deep level traps in silicon. Palladium electrodes do not contaminate silicon, and also give higher tunnel current signals in the molecular tunnel junctions that we have studied. The result is cleaner signals in a recognition-tunneling junction that recognizes the four natural DNA bases as well as 5-methyl cytosine, with no spurious background signals. More than 75% of all the recorded signal peaks indicate the base correctly. (paper)

  3. Atomic Structures of the Molecular Components in DNA and RNA based on Bond Lengths as Sums of Atomic Radii

    CERN Document Server

    Heyrovska, Raji

    2007-01-01

    The interpretation by the author in recent years of bond lengths as sums of the relevant atomic or ionic radii has been extended here to the bonds in the skeletal structures of adenine, guanine, thymine, cytosine, uracil, ribose, deoxyribose and phosphoric acid. On examining the bond length data in the literature, it has been found that the averages of the bond lengths are close to the sums of the corresponding atomic covalent radii of carbon, nitrogen, oxygen, hydrogen and phosphorus. Thus, the conventional molecular structures have been resolved here, for the first time, into probable atomic structures.

  4. Animal Models in Studies of Cardiotoxicity Side Effects from Antiblastic Drugs in Patients and Occupational Exposed Workers

    Directory of Open Access Journals (Sweden)

    Monica Lamberti

    2014-01-01

    Full Text Available Cardiotoxicity is an important side effect of cytotoxic drugs and may be a risk factor of long-term morbidity for both patients during therapy and also for staff exposed during the phases of manipulation of antiblastic drugs. The mechanism of cardiotoxicity studied in vitro and in vivo essentially concerns the formation of free radicals leading to oxidative stress, with apoptosis of cardiac cells or immunologic reactions, but other mechanisms may play a role in antiblastic-induced cardiotoxicity. Actually, some new cytotoxic drugs like trastuzumab and cyclopentenyl cytosine show cardiotoxic effects. In this report we discuss the different mechanisms of cardiotoxicity induced by antiblastic drugs assessed using animal models.

  5. Signatures of molecular recognition from the topography of electrostatic potential

    Indian Academy of Sciences (India)

    Dhimoy K Roy; P Balanarayan; Shridhar R Gadre

    2009-09-01

    The recognition of interaction between two molecules is analysed via the topography of their molecular electrostatic potentials (MESP). The point of recognition between two species is proposed to be the geometry at which there is a change in the nature of the set of MESP critical points of one of the molecules vis-a-vis with its MESP topography at infinite separation. These results are presented for certain model systems such as pyridine and benzene dimers, cytosine-guanine and adenine-thymine base pairs in various orientations of approach of the two species.

  6. Human placental DNA methyltransferase: DNA substrate and DNA binding specificity.

    OpenAIRE

    Wang, R.Y.; Huang, L. H.; Ehrlich, M

    1984-01-01

    We have partially purified a DNA methyltransferase from human placenta using a novel substrate for a highly sensitive assay of methylation of hemimethylated DNA. This substrate was prepared by extensive nick translation of bacteriophage XP12 DNA, which normally has virtually all of its cytosine residues replaced by 5-methylcytosine (m5C). Micrococcus luteus DNA was just as good a substrate if it was first similarly nick translated with m5dCTP instead of dCTP in the polymerization mixture. At ...

  7. [Delayed diagnosis of juvenile Huntington's diseases: case report].

    Science.gov (United States)

    Meza Escobar, Luis Enrique; Orozco, Jorge Luis; Takeuchi, Yuri; Ariza, Yoseth; Pachajoa, Harry

    2014-02-01

    Huntington's disease is a neurodegenerative disease that is clinically manifested as mood and personality changes, loss of cognitive functions and choreiform movements. The pattern of inheritance is autosomic dominant. It is due to the gradual expansion of a cytosine, adenine, guanine trinucleotide in a gene that codifies the protein Huntington. The molecular diagnosis must be performed to confirm the diagnosis. Genetic counseling must be carefully done due to the high suicide risk among these patients. We present the case of a fourteen-year-old male with a severe disease, poor social support and an unclear pattern of inheritance. PMID:24566795

  8. Nail-patella syndrome—a novel mutation in the LMX1B gene

    OpenAIRE

    Nair, Rajesh R.; Unni, Vavullipathy N.; Indu, Kadevalappil N.; Nampoothiri, Sheela; Mathew, Anil; Kurian, George; Vimala, Avadaiammal

    2013-01-01

    Nail-patella syndrome (NPS) is an autosomal-dominant pleiotropic disorder characterized by dyplasia of finger nails, skeletal anomalies and frequently renal disease. In the reported case, genetic analysis revealed a new missense mutation in the homeodomain of LMX1B, presumed to abolish DNA binding (c.725T>C, p.Val242Ala). A missense mutation at codon 725 was identified, where thymine was replaced by cytosine which led to the replacement of valine by alanine at position 242. It was not detecte...

  9. Alterations of 5-Hydroxymethylcytosine in Human Cancers

    Directory of Open Access Journals (Sweden)

    Ali Yesilkanal

    2013-06-01

    Full Text Available Prior to 2009, 5-methylcytosine (5-mC was thought to be the only biologically significant cytosine modification in mammalian DNA. With the discovery of the TET enzymes, which convert 5-methylcytosine (5-mC to 5-hydroxymethylcytosine (5-hmC, however, intense interest has emerged in determining the biological function of 5-hmC. Here, we review the techniques used to study 5-hmC and evidence that alterations to 5-hmC physiology play a functional role in the molecular pathogenesis of human cancers.

  10. A novel process for the synthesis of 'Designed Molecular Precursor' (DMP) of thorium useful for broad application spectrum

    International Nuclear Information System (INIS)

    For the first time (Patent application filed in India vide N/F No-0018NF2015) a novel process for the synthesis of 'Designed Molecular Precursor' (DMP) of thorium has been developed, which involves the unique combination of two different (dual) capping agents, one is biomolecule: Cytosine and other is non biomolecule: cetyl trimethyl ammonium bromide. The DMP essentially consists of hybrid nanosized thorium oxalate and alkaline thorate whose application lies in the area of making thorium metal, densified thorium oxide, carbide and nitride, anhydrous thorium complexes and thorium boron silicates glasses. (author)

  11. Mammalian 5’ C-rich telomeric overhangs are a mark of recombination-dependent telomere maintenance

    OpenAIRE

    Oganesian, Liana; Karlseder, Jan

    2011-01-01

    Recent evidence for 5’ cytosine (C)-rich overhangs at the telomeres of the nematode C. elegans provided the impetus to re-examine the end structure of mammalian telomeres. Two-dimensional (2D) gel electrophoresis, Single Telomere Length Analysis (STELA) and strand-specific exonuclease assays revealed the presence of a 5’ C-rich overhang at the telomeres of human and mouse chromosomes. C-overhangs were prominent in G1/S arrested as well as terminally differentiated cells, indicating that they ...

  12. Triple helix structures: sequence dependence, flexibility and mismatch effects.

    Science.gov (United States)

    Sun, J S; Mergny, J L; Lavery, R; Montenay-Garestier, T; Hélène, C

    1991-12-01

    By means of molecular modelling, electrostatic interactions are shown to play an important role in the sequence-dependent structure of triple helices formed by a homopyrimidine oligonucleotide bound to a homopurine. homopyrimidine sequence on DNA. This is caused by the presence of positive charges due to the protonation of cytosines in the Hoogsteen-bonded strand, required in order to form C.GxC+ triplets. Energetic and conformational characteristics of triple helices with different sequences are analyzed and discussed. The effects of duplex mismatches on the triple helix stability are investigated via thermal dissociation using UV absorption. PMID:1815635

  13. APOBEC3G Impairs the Multimerization of the HIV-1 Vif Protein in Living Cells

    OpenAIRE

    Batisse, Julien; Guerrero, Santiago Xavier; Bernacchi, Serena; Richert, Ludovic; Godet, Julien; Goldschmidt, Valérie; Mély, Yves; Marquet, Roland; de Rocquigny, Hugues; Paillart, Jean-Christophe

    2013-01-01

    The HIV-1 viral infectivity factor (Vif) is a small basic protein essential for viral fitness and pathogenicity. Vif allows productive infection in nonpermissive cells, including most natural HIV-1 target cells, by counteracting the cellular cytosine deaminases APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G [A3G]) and A3F. Vif is also associated with the viral assembly complex and packaged into viral particles through interactions with the viral genomic RNA and t...

  14. HIV-1 Vif binds to APOBEC3G mRNA and inhibits its translation

    OpenAIRE

    Mercenne, Gaëlle; Bernacchi, Serena; Richer, Delphine; Bec, Guillaume; Henriet, Simon; Paillart, Jean-Christophe; Marquet, Roland

    2009-01-01

    The HIV-1 viral infectivity factor (Vif) allows productive infection of non-permissive cells (including most natural HIV-1 targets) by counteracting the cellular cytosine deaminases APOBEC-3G (hA3G) and hA3F. The Vif-induced degradation of these restriction factors by the proteasome has been extensively studied, but little is known about the translational repression of hA3G and hA3F by Vif, which has also been proposed to participate in Vif function. Here, we studied Vif binding to hA3G mRNA ...

  15. Characterization of RNA binding and chaperoning activities of HIV-1 Vif protein: Importance of the C-terminal unstructured tail

    OpenAIRE

    Sleiman, Dona; Bernacchi, Serena; Xavier Guerrero, Santiago; Brachet, Franck; Larue, Valéry; Paillart, Jean-Christophe; Tisné, Carine

    2014-01-01

    The viral infectivity factor (Vif) is essential for the productive infection and dissemination of HIV-1 in non-permissive cells, containing the cellular anti-HIV defense cytosine deaminases APOBEC3 (A3G and A3F). Vif neutralizes the antiviral activities of the APOBEC3G/F by diverse mechanisms including their degradation through the ubiquitin/proteasome pathway and their translational inhibition. In addition, Vif appears to be an active partner of the late steps of viral replication by interac...

  16. Importance of the proline-rich multimerization domain on the oligomerization and nucleic acid binding properties of HIV-1 Vif

    OpenAIRE

    Bernacchi, Serena; Mercenne, Gaëlle; Tournaire, Clémence; Marquet, Roland; Paillart, Jean-Christophe

    2010-01-01

    The HIV-1 viral infectivity factor (Vif) is required for productive infection of non-permissive cells, including most natural HIV-1 targets, where it counteracts the antiviral activities of the cellular cytosine deaminases APOBEC-3G (A3G) and A3F. Vif is a multimeric protein and the conserved proline-rich domain 161PPLP164 regulating Vif oligomerization is crucial for its function and viral infectivity. Here, we expressed and purified wild-type Vif and a mutant protein in which alanines were ...

  17. Hemimethylated duplex DNAs prepared from 5-azacytidine-treated cells.

    OpenAIRE

    Jones, P A; Taylor, S M

    1981-01-01

    Duplex heavy-light (HL) DNAs synthesized in the presence of brdUrd and methylation inhibitors were separated from bulk cellular DNA by CsCl density gradient centrifugation and analysed for 5-methylcytosine (5mC) contents by HPLC. DNAs synthesized in the presence of 5 mM ethionine or 2 mg/ml cycloleucine were not detectably hypomethylated, was undermethylated with respect to control DNA. The heavy, or H-strand, in which up to 5% of the cytosine residues were replaced by intact 5-azacytosine, w...

  18. 5-Azacytidine acts directly on both erythroid precursors and progenitors to increase production of fetal hemoglobin.

    OpenAIRE

    Humphries, R K; Dover, G; Young, N S; Moore, J G; Charache, S.; Ley, T; Nienhuis, A W

    1985-01-01

    The effect of 5-azacytidine on erythroid precursors and progenitors was studied in nine patients with sickle cell anemia or severe thalassemia. Each patient received the drug intravenously for 5 or 7 d. 5-Azacytidine caused a four- to sixfold increase in gamma-messenger RNA concentration in bone marrow cells of eight of the nine patients and decreased the methylation frequency of a specific cytosine residue in the gamma-globin gene promoter in all nine patients. Within 2 d of the start of dru...

  19. Genetic analysis of the 5-azacytidine sensitivity of Escherichia coli K-12.

    OpenAIRE

    Bhagwat, A S; Roberts, R. J.

    1987-01-01

    DNA containing 5-azacytidine (5-azaC) has been shown to form stable detergent-resistant complexes with cytosine methylases. We reasoned that if 5-azaC treatment causes protein-DNA cross-links in vivo, then mutations in DNA repair and recombination genes may increase the sensitivity of a cell to 5-azaC. We found that although recA (defective) and lexA (induction-negative) mutants of Escherichia coli were very sensitive to the drug, mutations in uvrA and ung genes had little effect on cell leth...

  20. 5-Azacytidine stimulates fetal hemoglobin synthesis in anemic baboons.

    OpenAIRE

    DESIMONE, J.; Heller, P; Hall, L; Zwiers, D

    1982-01-01

    In an attempt to stimulate Hb F synthesis in baboons by means other than erythropoietic stress, we considered the possibility that an agent that inhibits methylation of CpG sequences in DNA may be effective. 5-Azacytidine, a cytosine analogue that cannot be methylated, is such an agent. Animals whose packed red cell volume was maintained at approximately 20% by bleeding were given 10 daily intravenous injections of the drug (6 mg/kg) in 12 days. Hb F levels in these animals started to increas...

  1. 5-Azacytidine Induces Transgene Silencing by DNA Methylation in Chinese Hamster Cells

    OpenAIRE

    Broday, Limor; Lee, Yong-Woo; Costa, Max

    1999-01-01

    The cytosine analog 5-azacytidine (5-AzaC) is a demethylating agent that is also known to induce mutagenesis in mammalian cells. In this study, the mutagenic potential of this drug was tested in the G10 and G12 transgenic Chinese hamster cell lines, which have a single bacterial gpt gene integrated into the genome at different sites, with its expression driven by a simian virus 40 (SV40) promoter. We show that the mutation frequencies following a 48-h exposure to different concentrations of 5...

  2. Activation of Innate Immunity in Healthy Macaca mulatta Macaques by a Single Subcutaneous Dose of GMP CpG 7909: Safety Data and Interferon-Inducible Protein-10 Kinetics for Humans and Macaques▿

    OpenAIRE

    Stewart, V. Ann; McGrath, Shannon; Krieg, Arthur M.; Larson, Noelle S.; Angov, Evelina; Christopher L. Smith; Brewer, Thomas G; Heppner, D Gray

    2007-01-01

    Following a demonstration that mouse-optimized cytosine-guanosine dinucleotide (CpG) oligodeoxynucleotides stimulated innate immune protection against intracellular pathogens, we tested the ability of CpG 7909, a primate-optimized Toll-like receptor 9 (TLR9) agonist, to stimulate rhesus macaques to produce interferon-inducible protein-10 (IP-10), a biomarker of immune activation. This study was performed prior to a similar trial with humans in order to facilitate the development of CpG 7909 a...

  3. Synthesis and triplex formation of oligonucleotides containing 8-thioxodeoxyadenosine and 5-methyl-2-thiodeoxycytosine.

    Science.gov (United States)

    Ohkubo, Akihiro; Miyata, Kenichi; Tsunoda, Hirosuke; Seio, Kohji; Sekine, Mitsuo

    2009-01-01

    For more effective DNA triplex formation under neutral conditions, we synthesized triplex-forming oligonucleotides (TFO) containing 8-thioxodeoxyadenine (s(8)A) residues in place of the protonated cytosines (Cs) required for the third base pairing with DNA duplexes. Consequently, it was found that s(8)A exhibited much stronger hybridization ability than C under neutral conditions when four s(8)A bases were arranged in a consecutive sequence. Moreover, we also synthesized TFOs containing 5-methyl-2-thiocytosines and examined their ability of triplex formation. PMID:19749240

  4. Super-specific DNA methylation by a DNA methyltransferase coupled with a triple helix-forming oligonucleotide

    OpenAIRE

    Maluszynska-Hoffman, Maria

    2008-01-01

    In this work, an engineered variant of the DNA cytosine-C5 methyltransferase (MTase) M.SssI has been conjugated with a triple helix-forming oligonucleotide (TFO) and the properties of the enzyme-TFO conjugate were evaluated using a variety of biochemical and biophysical methods. M.SssI is the only known prokaryotic DNA MTase which shares the 5’-CG-3’ recognition sequence (CpG) with mammalian DNA MTases. It has been rendered a super-specific MTase by conjugation with a TFO designed to bind a t...

  5. Inhibition of thymus cell proliferation: possibilities of elociting natural cell death with the organ and its contribution to the induced interphase death

    International Nuclear Information System (INIS)

    Parallelism was noted between the suppression of proliferation and the amount of cells dying in mouse thymus after the effects inducing cell destruction. However, inhibition of DNA synthesis under the effect of nontoxic doses of arabinoside cytosine increased insignificantly the number of dying cells as compared to normal. This indicated the absence of the masking effect of reutilization of degradation products of dying cells, minor amounts of cells normally dying in the thymus and their insignificant contribution to the induced cell death after the effects leading to inhibition of cell proliferation

  6. A Case of Juvenile Huntington Disease in a 6-Year-Old Boy

    Directory of Open Access Journals (Sweden)

    Jun-Sang Sunwoo

    2010-10-01

    Full Text Available Huntington disease is a neurodegenerative disorder distinguished by the triad of dominant inheritance, choreoathetosis and dementia, usually with onset in the fourth and fifth decades. It is caused by an unstable cytosine-adenine-guanine (CAG trinucleotide repeat expansion in the gene IT15 in locus 4p16.3. Juvenile HD that constitutes about 3% to 10% of all patients is clinically different from adult-onset form and characterized by a larger number of CAG repeats typically exceeding 60. We report a case of a 6-year-old boy with myoclonic seizure and 140 CAG repeats confirmed by molecular genetic analysis.

  7. Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes

    OpenAIRE

    Chae, Heejoon; Park, Jinwoo; Lee, Seong-Whan; Nephew, Kenneth P.; Kim, Sun

    2013-01-01

    CpG islands are GC-rich regions often located in the 5′ end of genes and normally protected from cytosine methylation in mammals. The important role of CpG islands in gene transcription strongly suggests evolutionary conservation in the mammalian genome. However, as CpG dinucleotides are over-represented in CpG islands, comparative CpG island analysis using conventional sequence analysis techniques remains a major challenge in the epigenetics field. In this study, we conducted a comparative a...

  8. Final Report: Theoretical Studies on Radiation-Induced Transformations in Nucleic Acid Bases, May 1, 1993 - April 30, 1996

    Energy Technology Data Exchange (ETDEWEB)

    Adamowicz, Ludwik

    1996-04-30

    In the proposal we identified several elemental molecular properties related to the effects observed in genetic material exposed to ionizing irradiation, and we studied them by means of the ab-initio quantum chemistry. The chemistry of irradiation is complex and biological consequences are significant. This includes cell death, mutations, carcinogenic transformations, etc. In the proposal we theoretically modeled several elemental processes related to the radiolysis of components of the nucleic acids, i.e., the pyrimidine nucleobases cytosine, uracine and thymine. Based on the state-of-the-art ab-initio calculations, we obtained information on the structural and spectroscopic properties of transition intermediate reactants.

  9. Indoleamine 2,3-dioxygenase specific, cytotoxic T cells as immune regulators

    DEFF Research Database (Denmark)

    Sørensen, Rikke Bæk; Hadrup, Sine Reker; Svane, Inge Marie; Hjortso, Mads Christian; Straten, Per Thor; Andersen, Mads Hald

    2011-01-01

    Indoleamine 2,3-dioxygenase (IDO) is an immunoregulatory enzyme that is implicated in suppressing T-cell immunity in normal and pathologic settings. Here, we describe that spontaneous cytotoxic T-cell reactivity against IDO exists not only in patients with cancer but also in healthy persons. We...... caused an increase in the production of the proinflammatory cytokines IL-6 and tumor necrosis factor-alpha while decreasing the IL-10 production. Finally, the addition of IDO-inducing agents (ie, the TLR9 ligand cytosine-phosphate- guanosine, soluble cytotoxic T lymphocyte-associated antigen 4, or...

  10. Optical Characterization of Oligonucleotide DNA Influenced by Magnetic Fields

    Directory of Open Access Journals (Sweden)

    Seyedeh Maryam Banihashemian

    2013-09-01

    Full Text Available UV-VIS spectroscopic analysis of oligonucleotide DNA exposed to different magnetic fields was performed in order to investigate the relationship between DNA extinction coefficients and optical parameters according to magnetic-field strength. The results with the oligonucleotides adenine-thymine 100 mer (AT-100 DNA and cytosine-guanine 100 mer (CG-100 DNA indicate that the magnetic field influences DNA molar extinction coefficients and refractive indexes. The imaginary parts of the refractive index and molar extinction coefficients of the AT-100 and CG-100 DNA decreased after exposure to a magnetic field of 750 mT due to cleavage of the DNA oligonucleotides into smaller segments.

  11. Soil Bacterial Community Shift Correlated with Change from Forest to Pasture Vegetation in a Tropical Soil

    OpenAIRE

    Nüsslein, Klaus; Tiedje, James M

    1999-01-01

    The change in vegetative cover of a Hawaiian soil from forest to pasture led to significant changes in the composition of the soil bacterial community. DNAs were extracted from both soil habitats and compared for the abundance of guanine-plus-cytosine (G+C) content, by analysis of abundance of phylotypes of small-subunit ribosomal DNA (SSU rDNA) amplified from fractions with 63 and 35% G+C contents, and by phylogenetic analysis of the dominant rDNA clones in the 63% G+C content fraction. All ...

  12. Multiway study of hybridization in nanoscale semiconductor labeled DNA based on fluorescence resonance energy transfer

    DEFF Research Database (Denmark)

    Gholami, Somayeh; Kompany Zare, Mohsen

    2013-01-01

    The resolution of the ternary-binary complex competition of a target sequence and of its two complementary probes in sandwich DNA hybridization is reported. To achieve this goal, Fluorescence Resonance Energy Transfer (FRET) between oligonucleotide-functionalized quantum dot (QD) nanoprobes (QD...... first time. Equilibrium constants illustrated that the extent of hybridization in one side on the target strand depends on hybridization conditions on the other side of the strand. Effects of guanine (G) and cytosine (C) contents of strands on the extent and rate of hybridization were investigated. In...

  13. Synthesis of chemically modified DNA.

    Science.gov (United States)

    Shivalingam, Arun; Brown, Tom

    2016-06-15

    Naturally occurring DNA is encoded by the four nucleobases adenine, cytosine, guanine and thymine. Yet minor chemical modifications to these bases, such as methylation, can significantly alter DNA function, and more drastic changes, such as replacement with unnatural base pairs, could expand its function. In order to realize the full potential of DNA in therapeutic and synthetic biology applications, our ability to 'write' long modified DNA in a controlled manner must be improved. This review highlights methods currently used for the synthesis of moderately long chemically modified nucleic acids (up to 1000 bp), their limitations and areas for future expansion. PMID:27284032

  14. Analysis of intra-genomic GC content homogeneity within prokaryotes

    DEFF Research Database (Denmark)

    Bohlin, J; Snipen, L; Hardy, S.P.;

    2010-01-01

    Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how...... the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organism's environment and phylogeny. We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content of...

  15. CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI

    OpenAIRE

    Wojciechowski, Marek; Czapinska, Honorata; Bochtler, Matthias

    2013-01-01

    Cytosine methylation promotes deamination. In eukaryotes, CpG methylation is thought to account for CpG underrepresentation. Whether scarcity of CpGs in prokaryotic genomes is diagnostic for methylation is not clear. Here, we report that Mycoplasms tend to be CpG depleted and to harbor a family of constitutively expressed or phase variable CpG-specific DNA methyltransferases. The very CpG poor Mycoplasma penetrans and its constitutively active CpG-specific methyltransferase M.MpeI were chosen...

  16. DNA Scaffolded Silver Clusters: A Critical Study

    OpenAIRE

    Bidisha Sengupta; Christa Corley; Keith Cobb; Anthony Saracino; Steffen Jockusch

    2016-01-01

    Fluorescent silver nanoclusters (Ag-NCs) are in prominence as novel sensing materials due to their biocompatibility, photostability, and molecule-like optical properties. The present work is carried out on an array (17 sequences) of 16 bases long cytosine rich, single stranded DNA templates 5′-C3XiC3XiiC3XiiiC3Xiv-3′ where i, ii, iii, iv correspond to T/G/C deoxynucleobases (with default base A). Among all the oligonucleotides, a sequence C3AC3AC3TC3G (3T4G) has been identified, which grows t...

  17. Interaction of quinones with three pyrimidine bases: A laser flash photolysis study

    International Nuclear Information System (INIS)

    The interaction between three different pyrimidine bases, uracil (U), cytosine (C) and thymine (T) and two quinones, 2-methyl-1,4-naphthoquinone or menadione (MQ) and 9,10-anthraquinone (AQ) have been studied using laser flash photolysis technique in organic homogeneous medium. The three pyrimidines have revealed a difference in their extent of reactivity towards the quinones, which has been attributed to their structural difference. Our works have revealed that the difference in structural dimension of the quinones is also responsible for affecting the reactivity of these pyrimidines in homogeneous medium.

  18. A temperate phage of Streptomyces azureus.

    OpenAIRE

    Ogata, S; Suenaga, H; Hayashida, S.

    1985-01-01

    A new phage, SAt1, was isolated from soil on Streptomyces azureus ATCC 14921. This phage was able to lysogenize S. azureus. The percentage of lysogenic responses was ca. 10%. Electron microscopic observation showed that this phage belonged to group B of Bradley's morphological classification. The molecular mass of SAt1 DNA was ca. 24 megadaltons. The guanine-plus-cytosine content and the density of SAt1 DNA were ca. 71% and 1.724 g/cm3, respectively. A cleavage map of SAt1 DNA was constructed...

  19. A stimulator of proliferation of spleen colony-forming cells (CFU-S) in the bone marrow of irradiated rats

    International Nuclear Information System (INIS)

    The presence and activity of a spleen colony - forming cell (CFU-S) proliferation stimulator was investigated in rat bone marrow after irradiation. The dose dependent increase in cytosine arabinoside induced cell dealth of normal mouse bone marrow. The results demonstrate the existence of a CFU-S proliferation stimulator in rat bone marrow similar to that originally found as a macrophage product in regenarating mouse bone marrow. The CFU-S proliferation stimulator activity was not associated with the presence of interleukin - 1,2, or 6 like activities in the material tested

  20. True single-molecule DNA sequencing of a Pleistocene horse bone

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Ginolhac, Aurelien; Raghavan, Maanasa;

    2011-01-01

    -preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous DNA sequences derived from the horse is higher among the Helicos data than Illumina data. This result indicates that the molecular biology tools used to generate sequencing...... standard Helicos DNA template preparation protocol further increase the proportion of horse DNA for this sample by 3-fold. Comparison of Helicos-specific biases and sequence errors in modern DNA with those in ancient DNA also reveals extensive cytosine deamination damage at the 3' ends of ancient templates...