Enzymatic capture of an extrahelical thymine in the search for uracil in DNAJared 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 ..
- Molecular genetics of para-aminosalicylic acid resistance in clinical isolates and spontaneous mutants of Mycobacterium tuberculosis
Vanessa Mathys
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 ..
- 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...
Structural diversity and extreme stability of unimolecular Oxytricha nova telomeric G-quadruplexJa 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...
- Oxidation of single-stranded oligonucleotides by carbonate radical anions: generating intrastrand cross-links between guanine and thymine bases separated by cytosines
Conor Crean
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 ..
The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNASebastian Warmlander
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
Adriana Irimia
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...
- MercuryII-mediated formation of thymine-HgII-thymine base pairs in DNA duplexes
Yoko Miyake
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...
- 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...
- Processing of thymine glycol in a clustered DNA damage site: mutagenic or cytotoxic
Sophie Bellon
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 ..
- Glycogen synthase kinase-3 regulates IGFBP-1 gene transcription through the thymine-rich insulin response element
David Finlay
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)...
- 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...
- Reduction of thymine hydroperoxide by phospholipid hydroperoxide glutathione peroxidase and glutathione transferases
Y Bao
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...
- NBD-based green fluorescent ligands for typing of thymine-related SNPs by using an abasic site-containing probe DNA
Viruthachalam Thiagarajan
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)...
- 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...
- Selective recognition of pyrimidine-pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators
Matthias Bahr
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 ..
- Oxidation of thymine to 5-formyluracil in DNA: mechanisms of formation, structural implications, and base excision by human cell free extracts
S Bjelland
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...
- 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...
- Singlet excited-state behavior of uracil and thymine in aqueous solution: a combined experimental and computational study of 11 uracil derivatives
Thomas Gustavsson
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...
- Thymine quintets and their higher order assemblies studied by electrospray ionization mass spectrometry and theoretical calculation
Bo Qiu
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(+) ...
- A new chitosan-thymine conjugate: synthesis, characterization and biological activity
Santosh Kumar
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...
- Cu2+/+ cation coordination to adenine--thymine base pair. Effects on intermolecular proton-transfer processes
Marc Noguera
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...
- 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...
- 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
Yoshihiko Yagi
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...
- The triplet energy of thymine in DNA
Francisco Bosca
, , 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 dynamic properties of an intramolecular transition from DNA duplex to cytosine-thymine motif triplex
Marco Brucale
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 ..
- Initiation of base excision repair of oxidative lesions in nucleosomes by the human, bifunctional DNA glycosylase NTH1
Amalthiya Prasad
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 ..
- 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
- 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
Bifeng Yuan
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...
- Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7
Ying Li
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 ..
- 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...
- Chemical synthesis and translesion replication of a cis-syn cyclobutane thymine-uracil dimer
Kohei Takasawa
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 (T[]U), which is the deaminated form of the CPD at a TC site, and incorporated it into ..
- 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...
- The 5-methyl group in thymine dynamically influences the structure of A-tracts in DNA at the local and global level
Arvind Marathe
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...
- Hydrogen bonds of RNA are stronger than those of DNA, but NMR monitors only presence of methyl substituent in uracil/thymine
Marcel Swart
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...
- Exomethylene pyranonucleosides: efficient synthesis and biological evaluation of 1-(2,3,4-trideoxy-2-methylene-beta-d-glycero-hex-3-enopyranosyl)thymine
George Agelis
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...
- 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...
- 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
....
- 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...
- Oxidative DNA damage following exposure to dimethylarsinous iodide: the formation of cis-thymine glycol
Kenzo Yamanaka
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...
- Crystal structure of an intermolecular 2:1 complex between adenine and thymine. Evidence for both Hoogsteen and 'quasi-Watson-Crick' interactions
Sosale Chandrasekhar
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...
- Mechanical tuning of molecular recognition to discriminate the single-methyl-group difference between thymine and uracil
Taizo Mori
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...
- 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...
- Triazole-linked analogue of deoxyribonucleic acid ((TL)DNA): design, synthesis, and double-strand formation with natural DNA
Hiroyuki Isobe
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...
- 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
S Um
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 ..
- DNA bending by an adenine--thymine tract and its role in gene regulation
J Hizver
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 ..
- 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
H Nakayama
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...
- A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase
P Gallinari
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)...
- The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping
I G Lyakhov
Intramural Research Support Program, SAIC, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA
Nucleic Acids Res 29:4892-900. 2001
..After protein binding, base pair distortion or base flipping could initiate DNA melting as the second step in DNA replication...
- A new mechanism for repairing oxidative damage to DNA: (A)BC excinuclease removes AP sites and thymine glycols from DNA
J J Lin
Department of Biochemistry, School of Medicine, University of North Carolina, Chapel Hill 27599
Biochemistry 28:7979-84. 1989
..nucleotide excision repair enzyme (A)BC excinuclease removes from DNA the two major products of oxidative damage, thymine glycol and the baseless sugar (AP site)...
- Role of DNA replication and repair in thymineless death in Escherichia coli
Pamela A Morganroth
Department of Biological Sciences, Stanford University, Stanford, CA 94305 5020, USA
J Bacteriol 188:5286-8. 2006
Inhibition of DNA replication with hydroxyurea during thymine starvation of Escherichia coli shows that active DNA synthesis is not required for thymineless death (TLD)...
- Quantum-chemical ab initio study on the adenine-difluorotoluene complex--a mimic for the adenine-thymine base pair
M Meyer
Institut fur Molekulare Biotechnologie, Jena, Germany
J Biomol Struct Dyn 15:619-24. 1997
Recent experiments have shown that difluorotoluene (F), a nonpolar isostere for thymine (T), codes efficiently and specifically for adenine (A) in DNA replication...
- Noncovalent SUMO-1 binding activity of thymine DNA glycosylase (TDG) is required for its SUMO-1 modification and colocalization with the promyelocytic leukemia protein
Hidehisa Takahashi
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)...
- 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...
- The recQ gene of Escherichia coli K12: molecular cloning and isolation of insertion mutants
K Nakayama
Mol Gen Genet 200:266-71. 1985
..We also identified the recQ gene product as a 74 kilodalton polypeptide by using the maxicell technique...
- The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites
B Hendrich
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...
- 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...
- Thymine DNA glycosylase
U Hardeland
Institute of Medical Radiobiology, University of Zurich, Paul Scherrer Institute, August Forel Strasse 7, Ch 8008 Zurich, Switzerland
Prog Nucleic Acid Res Mol Biol 68:235-53. 2001
..be mediated by a short-patch excision repair pathway, and one principal player implicated in this process may be thymine DNA glycosylase (TDG)...
- Principal causes of hot spots for cytosine to thymine mutations at sites of cytosine methylation in growing cells. A model, its experimental support and implications
E Lutsenko
463 Chemistry Building, Department of Chemistry, Wayne State University, Detroit, MI 48202 3489, USA
Mutat Res 437:11-20. 1999
..A number of hypotheses have been proposed regarding the source of the mispaired thymine and how the cells deal with the mispairs...
- DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases
Teresa Morales-Ruiz
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 thymine isostere in the templating position disrupts assembly of the closed DNA polymerase beta ternary complex
Thomas W Kirby
Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
Biochemistry 44:15230-7. 2005
..The DNA repair enzyme, DNA polymerase beta (Pol beta), is among the most discriminating, being inactive when the thymine isostere difluorotoluene (DFT) is present in the templating base position...
- Rapid exchange of A:T base pairs is essential for recognition of DNA homology by human Rad51 recombination protein
R C Gupta
Department of Genetics, Yale University, New Haven, Connecticut 06510, USA
Mol Cell 4:705-14. 1999
..Exchange of base pairs is essential for recognition of homology, and physical evidence indicates that such an exchange occurs early enough to mediate recognition...
- 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)...
- 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 ..
- The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modified DNA:RNA duplexes
S M Freier
Isis Pharmaceuticals, 2922 Faraday Avenue, Carlsbad, CA 92008, USA
Nucleic Acids Res 25:4429-43. 1997
..Among the heterocycles, C-5-substituted pyrimidines stood out as substantially increasing duplex stability...
- Methylenetetrahydrofolatereductase (MTHFR) 677C>T polymorphism and open angle glaucoma
Georg Mossbock
University Clinic for Ophthalmology, Medical University of Graz, Graz, Austria
Mol Vis 12:356-9. 2006
..It was the aim of this study to investigate a hypothesized association between this polymorphism and the presence of either POAG or PEXG...
- Preferential formation of (5S,6R)-thymine glycol for oligodeoxyribonucleotide synthesis and analysis of drug binding to thymine glycol-containing DNA
Tatsuhiko Shimizu
Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
Nucleic Acids Res 34:313-21. 2006
We previously reported the chemical synthesis of oligonucleotides containing thymine glycol, a major form of oxidative DNA damage...
- The common 677C>T gene polymorphism of methylenetetrahydrofolate reductase gene is not associated with breast cancer risk
Uwe Langsenlehner
Department of Internal Medicine, Division of Oncology, Karl Franzens University Graz, Graz, Austria
Breast Cancer Res Treat 81:169-72. 2003
..8%). Therefore, we conclude that the MTHFR 677C>T polymorphism is not associated with individual susceptibility to breast cancer...
- Substituted 1,8-naphthyridin-2(1H)-ones are superior to thymine in the recognition of adenine in duplex as well as triplex structures
Anne B Eldrup
Center for Biomolecular Recognition, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
J Am Chem Soc 124:3254-62. 2002
..Finally, and most surprisingly, we find no direct correlation between the end-stacking efficiency of this type of nucleobase and its helix stabilization when involved in Watson-Crick base pairing within a helix...
- Methylenetetrahydrofolate reductase gene polymorphisms c.677C/T and c.1298A/C are not associated with open angle glaucoma
Fumihiko Mabuchi
Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Shimokato, Yamanashi, Japan
Mol Vis 12:735-9. 2006
..To assess whether or not the c.677C/T and c.1298A/C genetic polymorphisms of the methylenetetrahydrofolate reductase (MTHFR) gene are associated with open angle glaucoma (OAG)...
- DNA glycosylase activities for thymine residues oxidized in the methyl group are functions of the hNEIL1 and hNTH1 enzymes in human cells
Qiu Mei Zhang
Laboratory of Radiation Biology, Department of Zoology, Graduate School of Science, Kyoto University, Sakyo ku, Kyoto 606 8502, Japan
DNA Repair (Amst) 4:71-9. 2005
..Similar activities were detected with hNTH1. These results indicate that hNEIL1 and hNTH1 are DNA glycosylases that excise 5-foU and 5-hmU as efficiently as Tg in human cells...
- (1S,2R/1R,2S)-ainocyclohexyl glycyl thymine PNA: synthesis, monomer crystal structures, and DNA/RNA hybridization studies
T Govindaraju
Division of Organic Chemistry (Synthesis) and Centre for Materials Characterisation (X-ray Facility, National Chemical Laboratory, Pune 411008, India
Org Lett 5:3013-6. 2003
..The PNA oligomers incorporating these show differential effects in hybridizing with complementary DNA and RNA...
- Excision of 5,6-dihydroxy-5,6-dihydrothymine, 5,6-dihydrothymine, and 5-hydroxycytosine from defined sequence oligonucleotides by Escherichia coli endonuclease III and Fpg proteins: kinetic and mechanistic aspects
C D'Ham
Laboratoire Lesions des Acides Nucleiques, Service de Chimie Inorganique et Biologique, Departement de Recherche Fondamentale sur la Matiere Condensee, CEA Grenoble, France
Biochemistry 38:3335-44. 1999
Oligonucleotides that contain a single modified pyrimidine, i.e., thymine glycol (Tg), 5,6-dihydrothymine (DHT), and 5-hydroxycytosine (5-OHC) were synthesized in order to investigate the substrate specificity and the excision mechanism ..
- Synthesis and thermodynamic studies of oligonucleotides containing the two isomers of thymine glycol
S Iwai
Department of Bioorganic Chemistry, Biomolecular Engineering Research Institute, Suita, Osaka, Japan
Chemistry 7:4343-51. 2001
b>Thymine glycol is a major type of base damage, which is formed in DNA by reactive oxygen species...
- Effect of the methylenetetrahydrofolate reductase C677T polymorphism on chemosensitivity of colon and breast cancer cells to 5-fluorouracil and methotrexate
Kyoung-Jin Sohn
Department of Medicine, University of Toronto, Toronto, Ontario, Canada
J Natl Cancer Inst 96:134-44. 2004
..The MTHFR C677T polymorphism may be a useful pharmacogenetic determinant for providing rational and effective tailored chemotherapy...
- A TDDFT study of the optical response of DNA bases, base pairs, and their tautomers in the gas phase
Argyrios Tsolakidis
Department of Physics and Division of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
J Phys Chem A 109:2373-80. 2005
..The optical response of base pairs indicates that the differences between normal and tautomeric forms in certain cases are significant enough to provide a means of identification...
- Hydrogen-bonding-induced shifts of the excitation energies in nucleic acid bases: an interplay between electrostatic and electron density overlap effects
Tomasz A Wesolowski
Department of Physical Chemistry, University of Geneva, 30 Quai Ernest Ansermet, CH 1211 Geneva 4, Switzerland
J Am Chem Soc 126:11444-5. 2004
..calculated dimerization-induced shifts of the lowest excitation energies in two model systems, adenine-thymine and guanine-cytosine base pairs, are analyzed...
- Interaction of DNA bases with silver nanoparticles: assembly quantified through SPRS and SERS
Soumen Basu
Department of Chemistry, Indian Institute of Technology, Kharagpur 721303, India
J Colloid Interface Sci 321:288-93. 2008
..the interaction between nanoscale silver particles and various DNA bases (adenine, guanine, cytosine, and thymine), which are used as molecular linkers because of their biological significance...
- [Determination of the base contents of liver DNA of rats by reversed-phase high performance liquid chromatography]
Chao Yun Wang
Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining 810001, China
Se Pu 20:348-9. 2002
..The contents were 17.4% of cytosine (C), 28.8% of adenine (A), 23.3% of guanine (G) and 25.3% of thymine (T). RSDs of the determination of these bases were 1.7%, 1.5%, 1.3% and 2.1%, respectively...
- On the structure and desorption dynamics of DNA bases adsorbed on gold: a temperature-programmed study
Mattias Ostblom
Division of Molecular Physics, Department of Physics, Chemistry and Biology, , , Sweden
J Phys Chem B 109:15150-60. 2005
The structure and desorption dynamics of mono- and multilayer samples of adenine, cytosine, guanine, and thymine on polycrystalline gold thin films are studied using temperature-programmed desorption-infrared reflection absorption ..
- Base sequence effects on transport in DNA
Esther M Conwell
Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
J Phys Chem B 110:5801-6. 2006
....
- Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy
B M Fischer
Department of Molecular and Optical Physics, , , Stefan-Meier-Str 19, D-79104 Freiburg, Germany
Phys Med Biol 47:3807-14. 2002
..Assisted by results from density-functional calculations we interpret the origin of the observed resonances as vibrations of hydrogen bonds between the molecules...
- The short vitamin D receptor is associated with increased risk for generalized aggressive periodontitis
Kyung Sook Park
Department of Biology, Sungshin Women s University, Seoul, Korea
J Clin Periodontol 33:524-8. 2006
..Vitamin D receptor (VDR) regulates both bone metabolism and inflammation-related genes, and its polymorphisms and haplotypes may affect the functional activity of the VDR protein in GAP...
- Sequence, structure and energy transfer in DNA
Thomas M Nordlund
Department of Physics, University of Alabama at Birmingham, Birmingham, AL, USA
Photochem Photobiol 83:625-36. 2007
..neighboring sequence shows (1) relatively efficient transfer from adenine compared to that from cytosine and thymine, (2) efficient transfer from guanine, but only when 2AP is at the 3' end, (3) approximate equality of ..
- Aminoethylprolyl (aep) PNA: mixed purine/pyrimidine oligomers and binding orientation preferences for PNA:DNA duplex formation
V Kumar
Division of Organic Chemistry (Synthesis, National Chemical Laboratory, Pune 411008, India
Org Lett 3:1281-4. 2001
..The thermal stabilities of the derived duplexes with DNA are found to be dependent on nucleobase and backbone stereochemistry...
- Bond energies and attachments sites of sodium and potassium cations to DNA and RNA nucleic acid bases in the gas phase
N Russo
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...
- TNF promoter polymorphisms and modulation of growth retardation and disease severity in pediatric Crohn's disease
Arie Levine
Pediatric Gastroenterology and Nutrition Unit, E Wolfson Medical Center, Holon, Israel
Am J Gastroenterol 100:1598-604. 2005
..The aim of our study was to determine whether growth retardation and disease severity in pediatric onset CD are affected by TNF promoter genotype...
- Low-energy (5-40 eV) electron-stimulated desorption of anions from physisorbed DNA bases
H Abdoul-Carime
Group of the Canadian Institutes of Health Research in the Radiation Sciences, , , 3001 12th Avenue North, Sherbrooke, , Canada, J1H 5N4
Radiat Res 155:625-33. 2001
We present the results of experiments on anion desorption from the physisorbed DNA bases adenine, thymine, guanine and cytosine induced by the impact of low-energy (5-40 eV) electrons...
- Ab initio determination of the ionization potentials of DNA and RNA nucleobases
Daniel Roca-Sanjuan
Instituto de Ciencia Molecular, Universitat de Valencia, Apartado 22085, ES 46071 Valencia, Spain
J Chem Phys 125:084302. 2006
..to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated...
- Direct assessment of interresidue forces in Watson-Crick base pairs using theoretical compliance constants
Jörg Grunenberg
Institut fur Organische Chemie, Hagenring 30, Technische Universitat Braunschweig, D 38106 Braunschweig, Germany
J Am Chem Soc 126:16310-1. 2004
..quantum mechanical calculations of interresidue potential constants for the Watson-Crick base pairs adenine-thymine (AT) and guanine-cytosine (GC), permitting a unique quantification of hydrogen bond strengths...
- Electrophilicity-based charge transfer descriptor
J Padmanabhan
Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
J Phys Chem A 111:1358-61. 2007
..Application of ECT can be extended to the interaction of any toxin with the biosystem...
- Estimation on the individual hydrogen-bond strength in molecules with multiple hydrogen bonds
Hao Dong
School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Lab of Mesoscopic Chemistry, Nanjing University, Nanjing, 210093, People s Republic of China
J Phys Chem A 111:2941-5. 2007
..by calculations on the homodimer of formylformamide and then applied to nucleic acid base pairs (adenine-thymine and guanine-cytosine) and some quadruply hydrogen-bonded dimers...
- Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold
Linette M Demers
Department of Chemistry and Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
J Am Chem Soc 124:11248-9. 2002
A comparison of the binding of DNA bases (adenine, cytosine, guanine, and thymine) and nucleosides (2'deoxyadenosine, 2'deoxycytidine, 2'deoxyguanosine, and thymidine) to gold thin films is presented...
- Vacuum-ultraviolet photoionization studies of the microhydration of DNA bases (guanine, cytosine, adenine, and thymine)
Leonid Belau
Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
J Phys Chem A 111:7562-8. 2007
..Gas-phase clusters of water with DNA bases [guanine (G), cytosine (C), adenine (A), and thymine (T)] are generated via thermal vaporization of the bases and expansion of the resultant vapor in a continuous ..
- Condensation of nucleobases at mercury/aqueous solution interface--a structural perspective using hydrogen bonding considerations
S Harinipriya
Department of Chemistry, Indian Institute of Technology, Madras, 600 036, India
J Colloid Interface Sci 250:201-12. 2002
..The applicability of the procedure to order-disorder transitions of water dipoles at Hg electrodes is also indicated...
- Pyrazolylborate-zinc-nucleobase-complexes, 2:(1) preparations and structures of Tp(Cum,Me)Zn and Tp(Ph,Me)Zn complexes
Dirk Badura
, Albertstr. 21, D-79104 Freiburg, Germany. vahrenka@ uni-freiburg.de
Inorg Chem 41:6013-9. 2002
The interactions of the nine most significant nucleobases (thymine, uracil, dihydrouracil, cytosine, adenine, guanine, diaminopurine, xanthine, hypoxanthine, in their deprotonated forms) with zinc and with themselves in pyrazolylborate ..
- Parallel DNA double helices incorporating isoG or m5isoC bases studied by FTIR, CD and molecular modeling
F Geinguenaud
, , , 74 rue Marcel Cachin, F93017 Bobigny Cedex, France
Spectrochim Acta A Mol Biomol Spectrosc 61:579-87. 2005
..In duplexes containing A-T and isoG-C or m5isoC-G base pairs shifts of the thymine C2=O2 and C4=O4 carbonyl stretching vibrations (to lower and higher wavenumbers, respectively, when compared to ..
