- Enzymatic capture of an extrahelical thymine in the search for uracil in DNA
Jared B Parker
Department of Pharmacology and Molecular Sciences, Johns Hopkins Medical School, 725 North Wolfe Street, Baltimore, Maryland 21205, USA
Nature 449:433-7. 2007
..Here we establish for the human and Escherichia coli enzymes that discrimination of thymine and uracil is initiated by thermally induced opening of T*A and U*A base pairs and not by active participation of ..
- DNA polymerases beta and lambda bypass thymine glycol in gapped DNA structures
Ekaterina A Belousova
Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
Biochemistry 49:4695-704. 2010
Here we investigated the ability of the human X-family DNA polymerases beta and lambda to bypass thymine glycol (Tg) in gapped DNA substrates with the damage located in a defined position of the template strand...
- The guanine-thymine dinucleotide repeat polymorphism within the tenascin-C gene is associated with achilles tendon injuries
Gaonyadiwe G Mokone
UCT MRC Research Unit for Exercise Science and Sports Medicine, University of Cape Town, PO Box 115, Newlands 7725, South Africa
Am J Sports Med 33:1016-21. 2005
..The tenascin-C gene, which has been mapped to chromosome 9q32-q34, encodes for a structural component of tendons...
- Human mitochondrial DNA polymerase γ exhibits potential for bypass and mutagenesis at UV-induced cyclobutane thymine dimers
Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
J Biol Chem 287:9222-9. 2012
Cyclobutane thymine dimers (T-T) comprise the majority of DNA damage caused by short wavelength ultraviolet radiation...
- Molecular genetics of para-aminosalicylic acid resistance in clinical isolates and spontaneous mutants of Mycobacterium tuberculosis
Laboratory of Molecular Pathology of Tuberculosis, Pasteur Institute, Scientific Institute of Public Health, Brussels, Belgium
Antimicrob Agents Chemother 53:2100-9. 2009
..acid (PAS) resistance by analysis of six genes of the folate metabolic pathway and biosynthesis of thymine nucleotides (thyA, dfrA, folC, folP1, folP2, and thyX) and three N-acetyltransferase genes [nhoA, aac(1), and aac(..
- Role of RecA and the SOS response in thymineless death in Escherichia coli
Natalie C Fonville
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
PLoS Genet 6:e1000865. 2010
..documented in bacterial, yeast, and human cells, whereby cells lose viability rapidly when deprived of thymine. Despite its being the essential mode of action of important chemotherapeutic agents, and despite having been ..
- MercuryII-mediated formation of thymine-HgII-thymine base pairs in DNA duplexes
Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami Ohsawa 1 1, Hachioji, Tokyo 192 0397 Japan
J Am Chem Soc 128:2172-3. 2006
The very specific binding of the HgII ion unexpectedly and significantly stabilizes naturally occurring thymine-thymine base mispairing in DNA duplexes...
- Noncovalent SUMO-1 binding activity of thymine DNA glycosylase (TDG) is required for its SUMO-1 modification and colocalization with the promyelocytic leukemia protein
Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3 1 1 Maidashi, Higashi ku, Fukuoka, Fukuoka 812 8582, Japan
J Biol Chem 280:5611-21. 2005
..This screening resulted in the isolation of cDNAs encoding the b isoform of thymine DNA glycosylase (TDGb)...
- A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase
Istituto di Richerche di Biologia Molecolare P Angeletti, Pomezia, Italy
Nature 383:735-8. 1996
Mispairs in DNA of guanine with uracil and thymine can arise as a result of deamination of cytosine and 5-methylcytosine, respectively. In humans such mispairs are removed by thymine-DNA glycosylase (TDG)...
- Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase
UNIGEN Center for Molecular Biology, The Norwegian University of Science and Technology, Trondheim, Norway
EMBO J 15:3442-7. 1996
..of the DNA-binding groove of human UDG and the specificity for uracil over the structurally related DNA bases thymine and cytosine is conferred by shape complementarity, as well as by main chain and Asn204 side chain hydrogen bonds...
- Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota
Kevin N Kirouac
Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
EMBO J 28:1644-54. 2009
..We present three crystal structures of pol complexed with DNA containing a thymine base, paired with correct or incorrect incoming nucleotides...
- dUTP pyrophosphatase is an essential enzyme in Saccharomyces cerevisiae
M H Gadsden
Department of Biology, York University, Toronto, Ontario, Canada
EMBO J 12:4425-31. 1993
..This latter effect suggests that the extensive stable substitution of uracil for thymine in DNA leads to a general failure in macromolecular synthesis...
- Selective recognition of pyrimidine-pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators
Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D 52056 Aachen, Germany
Nucleic Acids Res 36:5000-12. 2008
..The macrocyclic bis-intercalators bind to duplexes containing mismatched thymine bases with high selectivity over the fully matched ones, whereas the acyclic model compounds are much less ..
- Efficient removal of uracil from G.U mispairs by the mismatch-specific thymine DNA glycosylase from HeLa cells
Department of Biochemistry, Istituto di Richerche di Biologia Molecolare P Angeletti, Pomezia, Italy
Proc Natl Acad Sci U S A 91:1642-6. 1994
..The enzyme, a 55-kDa polypeptide, was previously characterized as a mismatch-specific thymine DNA glycosylase and was thought to be responsible solely for the correction (to G.C) of G...
- The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites
Institute of Cell and Molecular Biology, University of Edinburgh, UK
Nature 401:301-4. 1999
..In humans, the mutation rate from 5-methylcytosine (m5C) to thymine (T) is 10-50-fold higher than other transitions and the methylated sequence CpG is consequently under-represented...
- Epigenetic regulation of transcription and virulence in Trypanosoma cruzi by O-linked thymine glucosylation of DNA
Dilrukshi K Ekanayake
Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green Street, Life Sciences Building, Athens, GA 30602 7229, USA
Mol Cell Biol 31:1690-700. 2011
..Here, we show that the glucosylated thymine DNA base (β-d-glucosyl-hydroxymethyluracil or base J) is present within sequences flanking the polycistronic ..
- Structural, energetic and dynamic properties of guanine(C8)-thymine(N3) cross-links in DNA provide insights on susceptibility to nucleotide excision repair
Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
Nucleic Acids Res 40:2506-17. 2012
..with the inflammatory response, can lead to the formation of intrastrand cross-links between guanine and thymine bases [Crean et al...
- A new chitosan-thymine conjugate: synthesis, characterization and biological activity
Department of Textile Engineering, Konkuk University, Seoul 143 701, South Korea
Int J Biol Macromol 50:493-502. 2012
..Here, we report the synthesis of a novel chitosan-thymine conjugate by the reaction between chitosan and thymine-1-yl-acetic acid followed by acylation...
- Small-molecule binding at an abasic site of DNA: strong binding of lumiflavin for improved recognition of thymine-related single nucleotide polymorphisms
N B Sankaran
Department of Chemistry, Graduate School of Science, Tohoku University, Aoba ku, Sendai 980 8578, Japan
J Phys Chem B 113:1522-9. 2009
..Lumiflavin binds selectively to thymine (T) opposite the AP site in a DNA duplex over other nucleobases...
- Does cytosine-thymine-guanine (CTG) expansion size predict cardiac events and electrocardiographic progression in myotonic dystrophy?
N R Clarke
Cardiology Department, John Radcliffe Hospital, Oxford Radcliffe NHS Trust, Oxford, UK
Heart 86:411-6. 2001
To assess whether the size of the cytosine-thymine-guanine (CTG) expansion mutation in myotonic dystrophy predicts progression of conduction system disease and cardiac events.
- Oxidation of thymine to 5-formyluracil in DNA: mechanisms of formation, structural implications, and base excision by human cell free extracts
Division for Environmental Toxicology, Norwegian Defence Research Establishment, Kjeller, Norway
Biochemistry 34:14758-64. 1995
..With this method, it is shown that 5-foU residues are formed with high frequency from thymine by quinone-sensitized UV-A photooxidation...
- New insights in the removal of the hydantoins, oxidation product of pyrimidines, via the base excision and nucleotide incision repair pathways
Groupe Réparation de l ADN, CNRS UMR8200, Universite Paris Sud, Institut de Cancerologie Gustave Roussy, Villejuif, France
PLoS ONE 6:e21039. 2011
..as 5-hydroxyhydantoin (5OH-Hyd) and 5-methyl-5-hydroxyhydantoin (5OH-5Me-Hyd), major products of cytosine and thymine oxidative degradation pathways, respectively, have been detected in cancer cells and ancient DNA...
- DNA polymorphism as an origin of adenine-thymine tract length-dependent threading intercalation rate
Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 41296 Gothenburg, Sweden
J Am Chem Soc 130:14651-8. 2008
..intercalation have recently been found to exhibit an exceptional kinetic selectivity for long polymeric adenine-thymine (AT) DNA...
- Error-free replicative bypass of thymine glycol by the combined action of DNA polymerases kappa and zeta in human cells
Jung Hoon Yoon
Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555 1061, USA
Proc Natl Acad Sci U S A 107:14116-21. 2010
b>Thymine glycol (Tg) is the most common DNA lesion of thymine induced by interaction with reactive oxygen species...
- A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex
Department of Microbiology andMolecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA
J Mol Biol 412:22-34. 2011
b>Thymine glycol (Tg) is the most common oxidation product of thymine and is known to be a strong block to replicative DNA polymerases...
- Cu2+/+ cation coordination to adenine--thymine base pair. Effects on intermolecular proton-transfer processes
Departament de Quimica, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain
J Phys Chem B 112:4817-25. 2008
Intermolecular proton-transfer processes in the Watson & Crick adenine-thymine Cu+ and Cu2+ cationized base pairs have been studied using the density functional theory (DFT) methods...
- Structural diversity and extreme stability of unimolecular Oxytricha nova telomeric G-quadruplex
Ja Yil Lee
Department of Physics and Astronomy, Seoul National University, San 56 1, Shillimdong, Kwanakgu, Seoul, 151 742, South Korea
Biochemistry 47:3389-96. 2008
..In addition to cation coordination, we propose that other factors such as base stacking and the size of the thymine loop may contribute to the stability of O. nova G-quadruplexes; this is based on the fact that the O...
- The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA
Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, S 106 91 Stockholm, Sweden
J Biol Chem 277:28491-7. 2002
..to the dampening of the base pair-opening fluctuations in A-tracts comes from the C5 methylation of the thymine base...
- Structure and activity of Y-class DNA polymerase DPO4 from Sulfolobus solfataricus with templates containing the hydrophobic thymine analog 2,4-difluorotoluene
Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 0146, USA
J Biol Chem 282:36421-33. 2007
The 2,4-difluorotoluene (DFT) analog of thymine has been used extensively to probe the relative importance of shape and hydrogen bonding for correct nucleotide insertion by DNA polymerases...
- Stalled replication fork repair and misrepair during thymineless death in Escherichia coli
Kawai J Kuong
Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
Genes Cells 15:619-34. 2010
..We found that the rate of DNA synthesis in thymine-starved cells decreases exponentially, indicating replication fork stalling...
- Kinetics of the action of thymine DNA glycosylase
T R Waters
Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
J Biol Chem 273:20007-14. 1998
The time course of removal of thymine by thymine DNA glycosylase has been measured in vitro. Each molecule of thymine DNA glycosylase removes only one molecule of thymine from DNA containing a G...
- Excision of 5-halogenated uracils by human thymine DNA glycosylase. Robust activity for DNA contexts other than CpG
Michael T Morgan
Department of Biochemistry and Molecular Biology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
J Biol Chem 282:27578-86. 2007
b>Thymine DNA glycosylase (TDG) excises thymine from G.T mispairs and removes a variety of damaged bases (X) with a preference for lesions in a CpG.X context...
- Human thymine DNA glycosylase (TDG) and methyl-CpG-binding protein 4 (MBD4) excise thymine glycol (Tg) from a Tg:G mispair
Jung Hoon Yoon
Division of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
Nucleic Acids Res 31:5399-404. 2003
The repair enzymes thymine DNA glycosylase (TDG) and methyl-CpG-binding protein 4 (MBD4) remove thymines from T:G mismatches resulting from deamination of 5-methylcytosine...
- Thymine-rich single-stranded DNA activates Mcm4/6/7 helicase on Y-fork and bubble-like substrates
Department of Cell Biology, Tokyo Metropolitan Institute of Medical Science, 18 22 Honkomagome 3 chome, Bunkyo ku, Tokyo 113 8613, Japan
EMBO J 22:6148-60. 2003
The presence of multiple clusters of runs of asymmetric adenine or thymine is a feature commonly found in eukaryotic replication origins...
- Oxidation of single-stranded oligonucleotides by carbonate radical anions: generating intrastrand cross-links between guanine and thymine bases separated by cytosines
Chemistry Department and Radiation and Solid State Laboratory, 31 Washington Place, New York University, New York, NY 10003 5180, USA
Nucleic Acids Res 36:742-55. 2008
..P1 and alkaline phosphatase and identified by LC-MS/MS as an unusual intrastrand cross-link between guanine and thymine. In order to further characterize the structure of this lesion, 5'-d(GpCpT) was exposed to CO3*- radicals, and ..
- Chemical synthesis and translesion replication of a cis-syn cyclobutane thymine-uracil dimer
Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1 3 Machikaneyama, Toyonaka, Osaka 560 8531, Japan
Nucleic Acids Res 32:1738-45. 2004
..We have synthesized a phosphoramidite building block of a cis-syn cyclobutane thymine-uracil dimer (TU), which is the deaminated form of the CPD at a TC site, and incorporated it into ..
- Glycogen synthase kinase-3 regulates IGFBP-1 gene transcription through the thymine-rich insulin response element
Department of Pathology and Neurosciences, University of Dundee, Ninewells Medical School and Hospital, Dundee, DD1 9SY United Kingdom
BMC Mol Biol 5:15. 2004
..is mediated through the regulation of a DNA element present in each of these gene promoters, that we call the Thymine-rich Insulin Response Element (TIRE)...
- Processing of thymine glycol in a clustered DNA damage site: mutagenic or cytotoxic
DNA Damage Group, Gray Institute for Radiation Oncology and Biology, University of Oxford, Oxford OX3 7DQ, UK
Nucleic Acids Res 37:4430-40. 2009
..Since thymine glycol (Tg) is non-mutagenic but a strong block to replicative polymerases, we have investigated whether clusters ..
- Oxidation of thymine to 5-formyluracil in DNA promotes misincorporation of dGMP and subsequent elongation of a mismatched primer terminus by DNA polymerase
Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
J Biol Chem 276:16501-10. 2001
5-Formyluracil (fU) is a major oxidative thymine lesion generated by ionizing radiation and reactive oxygen species. In the present study, we have assessed the influence of fU on DNA replication to elucidate its genotoxic potential...
- Method for detection of Hg2+ based on the specific thymine-Hg2+-thymine interaction in the DNA hybridization on the surface of quartz crystal microbalance
Beijing National Laboratory for Molecular Sciences BNLMS, Key Laboratory of Colloid and Interface Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
Colloids Surf B Biointerfaces 87:289-92. 2011
..was developed for the detection of mercury ions with quartz crystal microbalance (QCM), based on the specific thymine-Hg(2+)-thymine (T-Hg(2+)-T) interaction and gold nanoparticle-mediated signal amplification...
- Bond energies and attachments sites of sodium and potassium cations to DNA and RNA nucleic acid bases in the gas phase
Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Universita' della Calabria, I-87030 Arcavacata di Rende (CS, Italy
J Am Chem Soc 123:10272-9. 2001
..Structural features of the sodium and potassium complexes were found to be similar except in some uracil and thymine compounds in which the tendency of potassium ion toward monocoordination appeared evident...
- Electronic coupling mediated by stacked [Thymine-Hg-Thymine] base pairs
Alexander A Voityuk
Institucio Catalana de Recerca i Estudis Avancats, Institute of Computational Chemistry, Universitat de Girona, 17071 Girona, Spain
J Phys Chem B 110:21010-3. 2006
Very recently it has been shown that stable metal-mediated base pairs [Thymine-Hg-Thymine] can form in DNA...
- Role of human DNA polymerase κ in extension opposite from a cis-syn thymine dimer
Rodrigo Vasquez-Del Carpio
Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA
J Mol Biol 408:252-61. 2011
- A nuclear family A DNA polymerase from Entamoeba histolytica bypasses thymine glycol
Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV, Irapuato, Mexico
PLoS Negl Trop Dis 4:e786. 2010
..histolytica (EhDNApolA) localizes to the nucleus and that its biochemical properties indicate that this DNA polymerase may be involved in translesion DNA synthesis...
- Insulin-like growth factor-1-mediated AKT activation postpones the onset of ultraviolet B-induced apoptosis, providing more time for cyclobutane thymine dimer removal in primary human keratinocytes
Department of Dermatology, Faculty of Medicine, Katholieke Universiteit, B 3000 Leuven, Belgium
J Biol Chem 277:32587-95. 2002
..This delay allowed IGF-1-supplemented keratinocytes to repair significantly more cyclobutane thymine dimers than their growth factor-deprived counterparts...
- Ratiometric fluorescent chemosensor for Hg(2+) based on heptamethine cyanine containing a thymine moiety
Department of Chemistry, College of Chemistry and Chemical Engineering, and The MOE Key Laboratory of Analytical Sciences, Xiamen University, Xiamen 361005, China
Org Lett 14:1986-9. 2012
Based on a T-Hg(2+)-T binding mode, a sensitive ratiometric fluorescent chemosensor for aqueous Hg(2+) was developed with a heptamethine cyanine chromophore containing a thymine moiety.
- Pairing geometry of the hydrophobic thymine analogue 2,4-difluorotoluene in duplex DNA as analyzed by X-ray crystallography
Pradeep S Pallan
Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
J Am Chem Soc 131:12548-9. 2009
..Therefore, shape and H-bonding are inherently related, and steric constraints at a pol active site, or conferred by stacking or the DNA backbone conformation, may enable H-bonding by F...
- Repair of oxidative damage of thymine by HeLa whole-cell extracts: simultaneous analysis using a microsupport and comparison with traditional PAGE analysis
Laboratoire Lesions des Acides Nucleiques, Service de Chimie Inorganique et Biologique, CEA DSM Département de Recherche Fondamentale sur la Matière Condensée, CEA Grenoble, 17, rue des Martyrs, 38054 Grenoble Cedex 9, France
Biochimie 87:151-9. 2005
..We report in this study, the parallelized fluorescent analysis of excision of several oxidation products of thymine by cell extracts...
- Thymine at -5 is crucial for cpc promoter activity of Synechocystis sp. strain PCC 6714
School of Life Science, Tokyo University of Pharmacy and Life Science, Hachioji 192 0392 CREST, Japan
J Bacteriol 185:6477-80. 2003
..strain PCC 7942 but not the in vivo activity in Escherichia coli. This suggests that the requirement of -5T appears to be specific for a cyanobacterial RNA polymerase-promoter combination...
- Cloning and characterization of Rhodotorula glutinis thymine hydroxylase
Jonathan W Neidigh
Department of Basic Sciences, Loma Linda University School of Medicine, Alumni Hall for Basic Science, Room 101, 11021 Campus Street, Loma Linda, California 92350, USA
Chem Res Toxicol 22:885-93. 2009
b>Thymine hydroxylase (TH) is a member of the alpha-ketoglutarate-dependent nonheme iron dioxygenase family that includes a series of DNA repair proteins including alkB...
- A bridged nucleic acid, 2',4'-BNA COC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2',4'-BNA COC monomers and RNA-selective nucleic-acid recognition
Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565 0871, Japan
Nucleic Acids Res 37:1225-38. 2009
..Here, BNA(COC) consisting of 2',4'-BNA(COC) monomers bearing all four bases, namely thymine, 5-methylcytosine, adenine and guanine was efficiently synthesized and properties of duplexes containing the 2',4'..
- Ab initio base-pairing energies of an oxidized thymine product, 5-formyluracil, with standard DNA bases at the BSSE-free DFT and MP2 theory levels
David E Volk
Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555 1157, USA
Org Biomol Chem 5:1554-8. 2007
Oxidation of the thymine methyl group produces two stable products, non-mutagenic 5-hydroxymethyluracil and highly mutagenic 5-formyluracil...
- Direct measurement of the dynamics of excess electron transfer through consecutive thymine sequence in DNA
Man Jae Park
The Institute of Scientific and Industrial Research SANKEN, Osaka University, Mihogaoka 8 1, Ibaraki, Osaka 567 0047, Japan
J Am Chem Soc 133:15320-3. 2011
..In the present paper, we directly measured the rate of excess electron transfer (EET) through a consecutive thymine (T) sequence in nicked-dumbbell DNAs conjugated with a tetrathiophene derivative (4T) as an electron donor and ..
- Interaction of fission yeast ORC with essential adenine/thymine stretches in replication origins
Department of Biology, Graduate School of Science, Osaka University, 1 1 Machikaneyama cho, Toyonaka, Osaka 560 0043 Japan
Genes Cells 6:837-49. 2001
..Multiple adenine/thymine clusters are essential for replication, but no short consensus sequences are found...
- Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads
Revotar Biopharmaceuticals AG, Neuendorfstrasse 24a, D 16761 Hennigsdorf, Germany
J Comput Chem 26:352-64. 2005
..A microsolvation model explains the ion selectivity preference of K+ over Na+ in a qualitative sense...
- Preliminary observation of 99mTc-thymine imaging in breast neoplasms
Hospital Universitario Pedro Ernesto, Universidade do Estado do Rio de Janeiro, Brazil
Nucl Med Commun 22:1133-7. 2001
..In this paper, we report the labelling of a precursor, the nitrogenate base thymine, with 99mTc. It has been used to evaluate breast lesions...
- Double-proton transfer in adenine-thymine and guanine-cytosine base pairs. A post-Hartree-Fock ab initio study
Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1325 J R Lynch St, P O Box 17910, Jackson, Mississippi 39217 0510, USA
J Am Chem Soc 126:10119-29. 2004
The results of a comprehensive study on the double-proton transfer in Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs at room temperature in gas phase and with the inclusion of environmental effects are obtained...
- Structure and mechanism of hydroxyl radical-induced formation of a DNA-protein cross-link involving thymine and lysine in nucleohistone
Center for Chemical Technology, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
Cancer Res 49:3463-7. 1989
Hydroxyl radical-induced formation of a DNA-protein cross-link involving thymine and lysine in calf thymus nucleohistone in vitro is reported...
- Na+, Mg2+, and Zn2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: a correlated ab initio quantum chemical study
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Complex Molecular Systems and Biomolecules, 166 10 Prague 6, Czech Republic
J Phys Chem B 110:14515-23. 2006
Interactions of adenine, cytosine, guanine, and thymine with Na(+), Mg(2+), and Zn(2+) cations were studied using an approximate resolution of identity correlated second-order MP2 (RI-MP2) method with the TZVPP ([5s3p2d1f/3s2p1d]) basis ..
- The role of the Escherichia coli mug protein in the removal of uracil and 3,N(4)-ethenocytosine from DNA
Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
J Biol Chem 274:31034-8. 1999
The human thymine-DNA glycosylase has a sequence homolog in Escherichia coli that is described to excise uracils from U.G mismatches (Gallinari, P., and Jiricny, J...
- The addition of low numbers of 3' thymine bases can be used to improve the hybridization signal of oligonucleotides for use within arrays on nylon supports
T J Brown
Department of Microbiology, St Thomas Hospital, Guy s and St Thomas Hospital Trust, London SE1 7EH, UK
J Microbiol Methods 42:203-7. 2000
..This paper demonstrates low numbers of thymine bases added to the 3' end of oligonucleotides during synthesis can improve hybridisation signal intensity where ..
- Effects of hydration on the proton transfer mechanism in the adenine-thymine base pair
J P Cerón-Carrasco
Departamento de Química Física Facultad de Química, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain
J Phys Chem A 113:7892-8. 2009
..functional study of water catalytic effect in the double proton transfer (DPT) taking place in the adenine-thymine (AT) base pair...
- Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: destabilization of two base pairs at the lesion site
Kyle L Brown
Department of Chemistry and Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37235, USA
Nucleic Acids Res 38:428-40. 2010
The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) epimers; these modulate base excision repair...
- Photoreactivity of 5-iodouracil-containing DNA-Sso7d complex in solution: the protein-induced DNA kink causes intrastrand hydrogen abstraction from the 5-methyl of thymine at the 5' side
Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2 3 10 Surugadai, Kanda, Chiyoda, Tokyo 101 0062, Japan
J Am Chem Soc 124:2086-7. 2002
..The reactivity of the deoxyuridin-5-yl radical can be explained by the crystal structure of the d(GTAATTAC)(2)-Sso7d complex, suggesting that the interaction of DNA-Sso7d in solution is substantially similar to its crystal structure...
- Metal-mediated J coupling in DNA base pairs: relativistic DFT predictions
Department of Chemistry, University of Padova, and CNR Institute on Membrane Technology, Padova Section, Via Marzolo, 1 35131 Padova, Italy
J Am Chem Soc 129:11360-1. 2007
- Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch
CNRS UMR5250, ICMG FR2607, Departement de Chimie Moleculaire, Universite Joseph Fourier, 570 rue de la chimie, 38041 Grenoble Cedex 9, France
Nucleic Acids Res 40:5115-28. 2012
..unit of the ligand intercalates at the A-T base pair flanking the mismatch site, leading to encapsulation of its thymine residue via double stacking...
- Singlet excited-state behavior of uracil and thymine in aqueous solution: a combined experimental and computational study of 11 uracil derivatives
Laboratoire Francis Perrin, CEA DSM DRECAM SPAM CNRS URA 2453, CEA Saclay, Gif sur Yvette, France
J Am Chem Soc 128:607-19. 2006
The excited-state properties of uracil, thymine, and nine other derivatives of uracil have been studied by steady-state and time-resolved spectroscopy...
- The role of minor groove functional groups in DNA hydration
Kristen Kruger Woods
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
Nucleic Acids Res 31:1536-40. 2003
..The crystal structure reveals the ability of this modified thymine to effectively base pair with adenine in [d(CGCGAAtTCGCG)]2...
- Reduction of thymine hydroperoxide by phospholipid hydroperoxide glutathione peroxidase and glutathione transferases
Department of Biochemistry, Institute of Food Research, Norwich Laboratory, Norwich Research Park, UK
FEBS Lett 410:210-2. 1997
b>Thymine hydroperoxide (5-hydroperoxymethyluracil), a model compound representing products of oxidative damage to DNA, is a substrate for glutathione peroxidase and some isoforms of glutathione transferase...
- Thymine quintets and their higher order assemblies studied by electrospray ionization mass spectrometry and theoretical calculation
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, China
J Mass Spectrom 46:587-94. 2011
We previously reported that thymine molecules can specifically form a pentameric magic number cluster named as thymine quintet in the presence of K(+) , Rb(+) and Cs(+) ...
- Multiple mutant of Escherichia coli synthesizing virtually thymineless DNA during limited growth
H H El-Hajj
Department of Pathology, University of Michigan Medical School, Ann Arbor 48109 0602
J Bacteriol 174:4450-6. 1992
..C in minimal medium containing deoxyuridine, the multiple mutant displayed a 93 to 96% substitution of uracil for thymine in new DNA. Growth stopped after the cellular DNA had increased 1.6- to 1...
- NBD-based green fluorescent ligands for typing of thymine-related SNPs by using an abasic site-containing probe DNA
Department of Chemistry, Graduate School of Science, Tohoku University, Aoba ku, Sendai, Japan
Chembiochem 11:94-100. 2010
..N(1)-(7-nitrobenzo[c][1,2,5]oxadiazol-4-yl)propane-1,3-diamine (NBD-NH(2)) is found to bind selectively to the thymine base opposite an AP site in a DNA duplex with a binding affinity of 1.52 x 10(6) M(-1)...
- Efficient formation of the tandem thymine glycol/8-oxo-7,8-dihydroguanine lesion in isolated DNA and the mutagenic and cytotoxic properties of the tandem lesions in Escherichia coli cells
Department of Chemistry and, Environmental Toxicology Graduate Program, University of California, Riverside, California 92521 0403, USA
Chem Res Toxicol 23:11-9. 2010
..coli cells. Together, our results support that complex lesions could exert greater cytotoxic and mutagenic effects than when the composing individual lesions are present alone...
- Synthesis and characterization of a [3-15N]-labeled cis-syn thymine dimer-containing DNA duplex
Hussam M Bdour
Department of Chemistry, Washington University, St Louis, Missouri 63130, USA
J Org Chem 71:1640-6. 2006
Cis-syn thymine dimers are the major photoproducts of DNA and are the principal cause of mutations induced by sunlight...
- Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
Nat Struct Mol Biol 11:784-90. 2004
..When the 3' thymine is the templating base, the CPD is rotated out of the polymerase active site and the fingers subdomain adopts an ..
- Oxidative DNA damage following exposure to dimethylarsinous iodide: the formation of cis-thymine glycol
Department of Biochemical Toxicology, Nihon University College of Pharmacy, 7 7 1 Narashinodai, Funabashi, 274 8555, Chiba, Japan
Toxicol Lett 143:145-53. 2003
..Cis-thymine glycol was used as a biomarker of DNA oxidation damage...
- The dynamic properties of an intramolecular transition from DNA duplex to cytosine-thymine motif triplex
Department of Biochemistry G Moruzzi and National Institute for the Physics of the Matter, University of Bologna, Via Irnerio 48, Bologna 40126
Org Biomol Chem 3:575-7. 2005
We here report that the formation and breakdown of an intramolecular cytosine-thymine (CT) motif DNA triple-helix can be performed repeatedly, quickly and independently of its local concentration without performance reduction over ..
- Hydrogen bonds of RNA are stronger than those of DNA, but NMR monitors only presence of methyl substituent in uracil/thymine
Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL 1081 HV Amsterdam, The Netherlands
J Am Chem Soc 126:16718-9. 2004
..Our study shows that NMR merely probes the presence/absence of the methyl group in thymine/uracil, without any relation to the strength of the hydrogen bonds involved...
- Increased temperature and 2-methyl-2,4-pentanediol change the DNA structure of both curved and uncurved adenine/thymine-rich sequences
Niels Erik Møllegaard
Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, 2200 Copenhagen N, Denmark
Biochemistry 42:8587-93. 2003
..Thus, the rather subtle structural difference of AT regions and A-tracts in nonbent DNA versus A-tracts in bent DNA may be quantitative rather than qualitative; i.e., the structure is more persistent and/or rigid in bent DNA...
- DNA polymerases eta and kappa are responsible for error-free translesion DNA synthesis activity over a cis-syn thymine dimer in Xenopus laevis oocyte extracts
Department of Molecular Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916 5, Ikoma, Nara 630 0101, Japan
DNA Repair (Amst) 4:1252-69. 2005
..These results indicate that error-free insertion in CPD bypass is due mainly to pol eta (TLS3) in the extracts, and suggest that pol kappa (TLS4) may assist pol eta (TLS3) in error-free extension during CPD bypass...
- Expression and characterization of thymine-DNA glycosylase from Aeropyrum pernix
Xi peng Liu
School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
Protein Expr Purif 70:1-6. 2010
The recombinant thymine-DNA glycosylase (TDG) from Aeropyrum pernix (A. pernix) was expressed in Escherichia coli. The enzymatic activity of recombinant A...
- Structures of hydrated Li+-thymine and Li+-uracil complexes by IRMPD spectroscopy in the N-H/O-H stretching region
Elizabeth A L Gillis
Department of Chemistry, Memorial University of Newfoundland, St John s, Newfoundland and Labrador, Canada A1B 3X7
J Phys Chem A 113:824-32. 2009
The interaction of lithium ions with two pyrimidine nucleobases, thymine and uracil, as well as the solvation of various complexes by one and two water molecules, has been studied in the gas phase...
- Exomethylene pyranonucleosides: efficient synthesis and biological evaluation of 1-(2,3,4-trideoxy-2-methylene-beta-d-glycero-hex-3-enopyranosyl)thymine
Department of Biochemistry and Biotechnology, Laboratory of Organic Chemistry, University of Thessaly, 26 Ploutonos Street, 41221 Larissa, Greece
Bioorg Med Chem 15:5448-56. 2007
A new series of unsaturated pyranonucleosides with an exocyclic methylene group and thymine as heterocyclic base have been designed and synthesized...
- Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta
Laureen C Colis
Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, USA
Biochemistry 47:8070-9. 2008
..However, hpol eta may play a role in correct bypass of the cross-links...
- The 5-methyl group in thymine dynamically influences the structure of A-tracts in DNA at the local and global level
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 12, India
J Phys Chem B 114:5534-46. 2010
..One of the aspects under investigation has been the influence of the 5-methyl group of thymine on the properties of A-tracts...
- Thermodynamic properties of enzyme-catalyzed reactions involving cytosine, uracil, thymine, and their nucleosides and nucleotides
Robert A Alberty
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
Biophys Chem 127:91-6. 2007
..15 K, ionic strength 0.25 M, and pHs 5, 6, 7, 8, and 9 for thirty two reactions. The pKs, standard Gibbs energies of hydrolysis, and standard Gibbs energies of deamination are given for these fifteen reactants...
- Initiation of base excision repair of oxidative lesions in nucleosomes by the human, bifunctional DNA glycosylase NTH1
Department of Microbiology and Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, VT 05405, USA
Mol Cell Biol 27:8442-53. 2007
..In a construct where the minor groove of a thymine glycol lesion faced outward from the histone octamer, the human DNA glycosylase NTH1 (hNTH1) processed the lesion ..
- Triazole-linked analogue of deoxyribonucleic acid ((TL)DNA): design, synthesis, and double-strand formation with natural DNA
Department of Chemistry, Tohoku University, Aoba ku, Sendai 980 8578, Japan
Org Lett 10:3729-32. 2008
..The chain elongation reaction using copper-catalyzed Huisgen cycloaddition was successful and gave the artificial oligonucleotide that formed a stable double strand with the complementary strand of natural DNA...
- Recognition and kinetics for excision of a base lesion within clustered DNA damage by the Escherichia coli proteins Fpg and Nth
M H David-Cordonnier
Medical Research Council, Radiation and Genome Stability Unit, Harwell, Didcot, Oxon OX11 0RD, United Kingdom
Biochemistry 40:5738-46. 2001
- Mechanical tuning of molecular recognition to discriminate the single-methyl-group difference between thymine and uracil
World Premier International Center for Materials Nanoarchitectonics MANA, National Institute for Materials Science, 1 1 Namiki, Tsukuba 305 0044, Japan, JST, CREST, 1 1 Namiki, Tsukuba 305 0044, Japan
J Am Chem Soc 132:12868-70. 2010
..e., that of discriminating thymine from uracil...
- The triplet energy of thymine in DNA
Instituto de Tecnología Química UPV CSIC, Universidad Politecnica de Valencia, Avda de los naranjos s n, 46022 Valencia, Spain
J Am Chem Soc 128:6318-9. 2006
Norfloxacin (NFX) photosensitizes formation of thymine dimers (T<>T) in DNA, while its N(4') acetyl derivative (ANFX) does not...
- The absence of deoxyriboaldolase activity in a thymineless mutant of Escherichia coli strain 15: a possible explanation for the low thymine requirement of some thymineless strains
T R Breitman
Biochim Biophys Acta 138:217-20. 1967
- Crystal structure of an intermolecular 2:1 complex between adenine and thymine. Evidence for both Hoogsteen and 'quasi-Watson-Crick' interactions
Department of Organic Chemistry, Indian Institute of Science, Bangalore, India
Bioorg Med Chem Lett 20:3530-3. 2010
..The absence of a clear-cut Watson-Crick base pair raises intriguing questions about the basis of the DNA double helix...
- DNA bending by an adenine--thymine tract and its role in gene regulation
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
Proc Natl Acad Sci U S A 98:8490-5. 2001
To gain insight into the structural basis of DNA bending by adenine-thymine tracts (A-tracts) and their role in DNA recognition by gene-regulatory proteins, we have determined the crystal structure of the high-affinity DNA target of the ..
- High-resolution structure of an extended A-tract: [d(CGCAAATTTGCG)]2
Kristen Kruger Woods
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332 0400, USA
J Am Chem Soc 126:15330-1. 2004
..The crystal of [d(CGCAAATTTGCG)]2 was grown from a solution containing spermine, magnesium, and lithium. The conformation recapitulates that of "monovalent-minus" DNA...
- Retinoic acid receptors interact physically and functionally with the T:G mismatch-specific thymine-DNA glycosylase
Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS INSERM ULP, College de France, BP 163, 67404 Illkirch Cedex, France
J Biol Chem 273:20728-36. 1998
..capable of interacting with native retinoic acid receptor (RAR), we have isolated the T:G mismatch-specific thymine-DNA glycosylase (TDG), which initiates the repair of T:G mismatches caused by spontaneous deamination of ..
- Isolation and genetic characterization of a thymineless death-resistant mutant of Escherichia coli K12: identification of a new mutation (recQ1) that blocks the RecF recombination pathway
Mol Gen Genet 195:474-80. 1984
..The original mutant was shown to carry an additional mutation probably in the vicinity of the uhp locus, which was also required for the full TLD resistance of the mutant to be expressed...
- Somatic hypermutation at A.T pairs: polymerase error versus dUTP incorporation
Michael S Neuberger
Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
Nat Rev Immunol 5:171-8. 2005
..Here, we compare the popular suggestion of nucleotide mispairing through polymerase error with an alternative possibility, mutation through incorporation of dUTP (or another non-canonical nucleotide)...
- Predicting thymine dimerization yields from molecular dynamics simulations
Yu Kay Law
Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
Biophys J 94:3590-600. 2008
It was recently shown that thymine dimers in the all-thymine oligonucleotide (dT)(18) are fully formed in <1 ps after ultraviolet excitation...
- DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases
Departamento de Genetica, Universidad de Cordoba, 14071 Cordoba, Spain
Proc Natl Acad Sci U S A 103:6853-8. 2006
..Both enzymes also remove thymine, but not uracil, mismatched to guanine...
- A novel approach to DNA damage assessments: measurement of the thymine glycol lesion
Douglas T Bailey
Roswell Park Cancer Institute, Buffalo, New York 14263, USA
Radiat Res 165:438-44. 2006
..The method was applied to the measurement of the 5,6-dihydroxy-5,6-dihydrothymine (thymine glycol) lesion in the DNA of mouse fibroblast cells exposed in culture to various treatments including ionizing ..