deoxyadenine nucleotides

Summary

Summary: Adenine nucleotides which contain deoxyribose as the sugar moiety.

Top Publications

  1. ncbi Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade
    P Li
    Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 75235, USA
    Cell 91:479-89. 1997
  2. pmc Mechanisms of mutagenesis in vivo due to imbalanced dNTP pools
    Dinesh Kumar
    Department of Medical Biochemistry and Biophysics, Umea University, SE 901 87 Umea, Sweden
    Nucleic Acids Res 39:1360-71. 2011
  3. pmc Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase
    Kevin A Fiala
    Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
    J Mol Biol 365:590-602. 2007
  4. ncbi Increased expression of Apaf-1 and procaspase-3 and the functionality of intrinsic apoptosis apparatus in non-small cell lung carcinoma
    Evzen Krepela
    Department of Molecular and Cellular Pneumology, University Hospital Bulovka, CZ 18081 Prague 8, Czech Republic
    Biol Chem 385:153-68. 2004
  5. ncbi Comprehensive model for allosteric regulation of mammalian ribonucleotide reductase: refinements and consequences
    Ossama B Kashlan
    Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104 6323, USA
    Biochemistry 42:1696-706. 2003
  6. ncbi Pre-steady-state kinetic studies of the fidelity of human DNA polymerase mu
    Michelle P Roettger
    Department of Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
    Biochemistry 43:13827-38. 2004
  7. ncbi Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential
    Joseph M Krahn
    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, P O Box 12233, Research Triangle Park, NC 27709, USA
    Structure 11:121-7. 2003
  8. ncbi Evaluating the contribution of base stacking during translesion DNA replication
    Edmunds Z Reineks
    Department of Pharmacology and the Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
    Biochemistry 43:393-404. 2004
  9. pmc Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization
    James Wesley Fairman
    Department of Biochemistry, University of Tennessee, Knoxville, TN, USA
    Nat Struct Mol Biol 18:316-22. 2011
  10. pmc Termination of DNA synthesis by N6-alkylated, not 3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates
    Weidong Wu
    LaserGen, Inc, Houston, TX 77054, USA
    Nucleic Acids Res 35:6339-49. 2007

Research Grants

  1. CARDIAC CONTRACTILE KINETICS
    Michael Regnier; Fiscal Year: 2009
  2. Repair of DNA Damages Induced by Ionizing Radiation
    Susan Wallace; Fiscal Year: 2009
  3. 9th International Workshop on "Radiation Damage to DNA"
    Susan Wallace; Fiscal Year: 2006
  4. Molecular Models of Adenosine Signaling and Asthma
    Michael Blackburn; Fiscal Year: 2008
  5. Phase I Clinical Trials of Anti-Cancer Agents
    Francis Giles; Fiscal Year: 2007
  6. Engineering DNA nicking endonucleases
    Shuang yong Xu; Fiscal Year: 2006
  7. A Genetic System Able to Screen for Active DNA Demethylation
    Shuang yong Xu; Fiscal Year: 2006
  8. A universal DNA endonuclease
    Shuang yong Xu; Fiscal Year: 2005
  9. Cloning and Engineering of Nicking enzymes
    Shuang yong Xu; Fiscal Year: 2004
  10. ADENOSINE SIGNALING AND LUNG INFLAMMATION
    Michael Blackburn; Fiscal Year: 2001

Detail Information

Publications164 found, 100 shown here

  1. ncbi Cytochrome c and dATP-dependent formation of Apaf-1/caspase-9 complex initiates an apoptotic protease cascade
    P Li
    Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 75235, USA
    Cell 91:479-89. 1997
    ....
  2. pmc Mechanisms of mutagenesis in vivo due to imbalanced dNTP pools
    Dinesh Kumar
    Department of Medical Biochemistry and Biophysics, Umea University, SE 901 87 Umea, Sweden
    Nucleic Acids Res 39:1360-71. 2011
    ..An interesting mutational strand bias is observed in one rnr1 strain, suggesting that the S-phase checkpoint selectively prevents replication errors during leading strand replication...
  3. pmc Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase
    Kevin A Fiala
    Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
    J Mol Biol 365:590-602. 2007
    ..This unprecedented base-stacking pattern can be applied to subsequent blunt-end additions only if all incorporated dAMPs are extrahelical, leading to predominantly single non-templated dATP incorporation...
  4. ncbi Increased expression of Apaf-1 and procaspase-3 and the functionality of intrinsic apoptosis apparatus in non-small cell lung carcinoma
    Evzen Krepela
    Department of Molecular and Cellular Pneumology, University Hospital Bulovka, CZ 18081 Prague 8, Czech Republic
    Biol Chem 385:153-68. 2004
    ....
  5. ncbi Comprehensive model for allosteric regulation of mammalian ribonucleotide reductase: refinements and consequences
    Ossama B Kashlan
    Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104 6323, USA
    Biochemistry 42:1696-706. 2003
    ....
  6. ncbi Pre-steady-state kinetic studies of the fidelity of human DNA polymerase mu
    Michelle P Roettger
    Department of Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
    Biochemistry 43:13827-38. 2004
    ..In addition to a slow and distributive DNA polymerase activity, Polmu was identified to possess a weak strand-displacement activity. The potential biological roles of Polmu are discussed...
  7. ncbi Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential
    Joseph M Krahn
    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, P O Box 12233, Research Triangle Park, NC 27709, USA
    Structure 11:121-7. 2003
    ..Our results provide insights into the mechanisms employed by polymerases to select the complementary dNTP...
  8. ncbi Evaluating the contribution of base stacking during translesion DNA replication
    Edmunds Z Reineks
    Department of Pharmacology and the Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
    Biochemistry 43:393-404. 2004
    ..These kinetic differences are interpreted with regard to the differences in various structural components between the two enzymes and are consistent with the proposed model for DNA polymerization...
  9. pmc Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization
    James Wesley Fairman
    Department of Biochemistry, University of Tennessee, Knoxville, TN, USA
    Nat Struct Mol Biol 18:316-22. 2011
    ..Site-directed mutagenesis and functional assays confirm that hexamerization is a prerequisite for inhibition by dATP. Our data indicate a mechanism for regulating RR activity by dATP-induced oligomerization...
  10. pmc Termination of DNA synthesis by N6-alkylated, not 3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates
    Weidong Wu
    LaserGen, Inc, Houston, TX 77054, USA
    Nucleic Acids Res 35:6339-49. 2007
    ..A five-base experiment, illustrating the exquisite, stepwise addition through a homopolymer repeat, demonstrates the applicability of the N(6)-(2-nitrobenzyl)-dATP as an ideal RT for CRT sequencing...
  11. ncbi A kinetic study on the influence of nucleoside triphosphate effectors on subunit interaction in mouse ribonucleotide reductase
    R Ingemarson
    Department of Medical Biochemistry and Biophysics, Umea University, Sweden
    Biochemistry 35:8603-9. 1996
    ....
  12. ncbi Synthesis of 8-bromo-, 8-methyl- and 8-phenyl-dATP and their polymerase incorporation into DNA
    Hana Cahová
    Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead and IOCB Research Center, Flemingovo nam 2, CZ 16610, Prague 6, Czech Republic
    Org Biomol Chem 6:3657-60. 2008
    ....
  13. ncbi Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase beta
    Christopher A Dunlap
    Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
    Biochemistry 41:11226-35. 2002
    ..Stopped flow of incorrect dNTP incorporation and the reverse reaction are also reported, which provide useful information to the mechanism of Pol beta...
  14. ncbi Dynamics of translesion DNA synthesis catalyzed by the bacteriophage T4 exonuclease-deficient DNA polymerase
    A J Berdis
    Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
    Biochemistry 40:7180-91. 2001
    ..Extension from the G:abasic or A:abasic site mispair generates significant elemental effects (between 5 and 20) and suggests that chemistry is at least partially rate-limiting for extension beyond either mispair...
  15. pmc Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosine
    Cynthia L Hendrickson
    Department of Chemistry and Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32611 7200, USA
    Nucleic Acids Res 32:2241-50. 2004
    ..Each interpretation is significant for understanding the planetary biology of polymerases...
  16. ncbi Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism
    M R Sawaya
    Department of Chemistry, University of California, San Diego 92093 0317
    Science 264:1930-5. 1994
    ..The location of Mn2+ and deoxyadenosine triphosphate in pol beta confirms the role of the invariant aspartates in metal ion and deoxynucleoside triphosphate binding...
  17. pmc Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes
    S Datta
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
    J Bacteriol 185:4280-4. 2003
    ..These observations provide a framework for exploring the known properties of the RecA proteins...
  18. pmc DNA synthesis across an abasic lesion by human DNA polymerase iota
    Deepak T Nair
    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
    Structure 17:530-7. 2009
    ..These different patterns of hydrogen bonds, as well as stacking interactions, may underlie Poliota's small preference for insertion of dGTP over other nucleotides opposite this common lesion...
  19. ncbi Negative regulation of the Apaf-1 apoptosome by Hsp70
    A Saleh
    Center for Apoptosis Research and Department of Microbiology and Immunology, Kimmel Cancer Institute, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
    Nat Cell Biol 2:476-83. 2000
    ..On the basis of these results, we propose that resistance to apoptosis exhibited by stressed cells and some tumours, which constitutively express high levels of Hsp70, may be due in part to modulation of Apaf-1 function by Hsp70...
  20. ncbi Evading the proofreading machinery of a replicative DNA polymerase: induction of a mutation by an environmental carcinogen
    R A Perlow
    Department of Biology, New York University, 100 Washington Square East Room 1009M, New York, NY 10003, USA
    J Mol Biol 309:519-36. 2001
    ....
  21. pmc Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase
    Luis G Brieba
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    EMBO J 23:3452-61. 2004
    ..This explains why translesion synthesis is permitted without proofreading of an 8oG.dA mismatch, thus providing insight into the high mutagenic potential of 8oG...
  22. pmc Bacillus subtilis RecU Holliday-junction resolvase modulates RecA activities
    Begona Carrasco
    Departmento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia, CSIC C Darwin 3, Campus Universidad Autonoma de Madrid, 28049 Madrid, Spain
    Nucleic Acids Res 33:3942-52. 2005
    ....
  23. ncbi Pre-steady-state kinetic characterization of the DinB homologue DNA polymerase of Sulfolobus solfataricus
    Janina Cramer
    Max Planck Institut fur molekulare Physiologie, Abteilung Physikalische Biochemie, Otto Hahn Strasse 11, Dortmund 44227, Germany
    J Biol Chem 280:40552-8. 2005
    ..Thus, unlike replicative polymerases, an "induced fit" mechanism to select and incorporate nucleotides during DNA polymerization could not be detected for Dbh...
  24. ncbi A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine
    Luis G Brieba
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Massachusetts 02115, USA
    Structure 13:1653-9. 2005
    ..We propose that Lys536 acts as a steric and/or electrostatic filter that attenuates the miscoding potential of 8oG by normally interfering with the binding of 8oG in a syn conformation that pairs with dATP...
  25. ncbi Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution
    Farid J Ghadessy
    MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
    Nat Biotechnol 22:755-9. 2004
    ..Such 'unfussy' polymerases have immediate utility, as we demonstrate by the generation of microarray probes with up to 20-fold brighter fluorescence...
  26. ncbi Structure of the large subunit of class Ib ribonucleotide reductase from Salmonella typhimurium and its complexes with allosteric effectors
    Malin Uppsten
    Department of Molecular Biosciences section of Structure Biology, Uppsala Biomedical Center, Swedish University of Agricultural Sciences, Box 590, Sweden
    J Mol Biol 330:87-97. 2003
    ..The low affinity for ATP at the specificity site is explained by a tyrosine, which hinders nucleotides containing a 2'-OH group to bind...
  27. ncbi Injection of exogenous RNA in amphibian oocytes leads to RNA level fluctuations which are sensitive to cordycepin, an RNA chain elongation terminator
    Nicole Montreau
    Laboratoire de Biologie du Developpement, Universite Pierre et Marie Curie, CNRS, UMR 7622, 9, quai Saint Bernard, 75251 Paris, France
    C R Biol 326:1135-47. 2003
    ..Cordycepin prevent increases in RNA levels indicating the involvement of an RNA synthesis. These results indicate the existence of an in vivo post-transcriptional RNA amplification mechanism during the early development of amphibians...
  28. pmc A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4)
    Lihua Wang
    Biology Department, New York University, New York, NY 10003, USA
    Nucleic Acids Res 34:785-95. 2006
    ..Possible relevance of our new major groove structure for AAF-dG to other polymerases, lesion repair and solution conformations are discussed...
  29. ncbi Molecular dynamics of a food carcinogen-DNA adduct in a replicative DNA polymerase suggest hindered nucleotide incorporation and extension
    Ling Zhang
    Department of Chemistry, New York University, New York, New York 10003, USA
    Chem Res Toxicol 18:1347-63. 2005
    ..Polymerase stalling would be the more common outcome and in vivo could lead to switch to an error-prone bypass polymerase...
  30. ncbi Four-color multiplex reverse transcription polymerase chain reaction--overcoming its limitations
    Kent Persson
    Gene Expression Division, Bio Rad Laboratories, Hercules, CA 94547, USA
    Anal Biochem 344:33-42. 2005
    ..This study shows that multiplexing is a feasible approach applicable to most qRT-PCR assays performed with total RNA, independent of the expression levels of the genes under scrutiny...
  31. ncbi Regioselective syntheses of 7-nitro-7-deazapurine nucleosides and nucleotides for efficient PCR incorporation
    Tomohiko Kawate
    Variagenics Inc, Cambridge, MA 02139, USA
    Org Lett 7:3865-8. 2005
    ..These modified nucleosides were converted to nucleotide triphosphates, each of which can replace the corresponding, naturally occurring triphosphate to support PCR amplification. [structure: see text]..
  32. ncbi Multiple enzyme activities of Escherichia coli MutT protein for sanitization of DNA and RNA precursor pools
    Riyoko Ito
    Department of Physiological Science and Molecular Biology, Fukuoka Dental College, Fukuoka 814 0193, Japan
    Biochemistry 44:6670-4. 2005
    ..These multiple enzyme activities of the MutT protein would facilitate the high fidelity of DNA and RNA syntheses...
  33. ncbi Human mitochondrial DNA polymerase holoenzyme: reconstitution and characterization
    A A Johnson
    Institute for Cellular and Molecular Biology, A4800, MBB 3 122, University of Texas at Austin, Austin, Texas 78712, USA
    Biochemistry 39:1702-8. 2000
    ....
  34. ncbi Biodegradation of DNA and nucleotides to nucleosides and free bases
    Hanna Kruszewska
    National Institute of Public Health, 30 34 Chelmska, 00725, Warszawa, Poland
    Farmaco 59:13-20. 2004
    ..The mode of degradation of DNA nucleotides depended on the type of nucleotide and its concentration, but nucleic bases or their derivatives were always formed at the end of the reaction process...
  35. ncbi Evaluating the contributions of desolvation and base-stacking during translesion DNA synthesis
    Xuemei Zhang
    Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
    Org Biomol Chem 2:1703-11. 2004
    ..This result indicates that indolyl-2'-deoxyriboside triphosphate acts as an indiscriminate chain terminator of DNA synthesis that may have unique therapeutic applications...
  36. ncbi Synthesis and recognition by DNA polymerases of a reactive nucleoside for DNA diversification
    S Pochet
    Institut Pasteur, Unité de Chimie Organique URA CNRS 2128, Paris Cedex, France
    Nucleosides Nucleotides Nucleic Acids 22:1665-7. 2003
    ..The mutagenic properties was evaluated by PCR. The potential of this new monomer for DNA diversification is illustrated by the reactivity of the nucleobase towards various aldehydes...
  37. ncbi Tight binding of deoxyribonucleotide triphosphates to human thymidine kinase 2 expressed in Escherichia coli. Purification and partial characterization of its dimeric and tetrameric forms
    João Filipe Barroso
    Department of Biochemistry and Molecular Biology, University of Bergen, Jonas Lies vei 91, N 5009 Bergen, Norway
    Biochemistry 42:15158-69. 2003
    ..The calculated relative nonbonded interaction energies are in agreement with the biochemical data and show that the inhibitor complexes have lower stabilization energies (higher affinity) than the substrates...
  38. ncbi Biosynthesis reaction mechanism and kinetics of deoxynucleoside triphosphates, dATP and dGTP
    Jie Bao
    Biochemical Engineering Program, University of California, One Shields Ave, Davis, CA 95616, USA
    Biotechnol Bioeng 89:485-91. 2005
    ..There is a significant advantage of using enzymatic biosyntheses of dATP and dGTP as compared to the chemical method that has been in commercial use...
  39. ncbi LC-MS/MS identification and yeast polymerase eta bypass of a novel gamma-irradiation-induced intrastrand cross-link lesion G[8-5]C
    Chunang Gu
    Environmental Toxicology Graduate Program, University of California, Riverside, California 92521 0403, USA
    Biochemistry 43:6745-50. 2004
    ..The above results support that the oxidative cross-link lesion, if not repaired, can be mutagenic...
  40. ncbi Involvement of the "linker" region between the exonuclease and polymerization domains of phi29 DNA polymerase in DNA and TP binding
    Verónica Truniger
    Instituto de Biología Molecular Eladio Viñuela CSIC, Centro de Biologia Molecular Severo Ochoa CSIC UAM, Universidad Autonoma, Canto Blanco, 28049 Madrid, Spain
    Gene 348:89-99. 2005
    ..These results allow us to propose that this interdomain region of phi29 DNA polymerase is playing an important role for substrate binding including both DNA and TP...
  41. pmc Relationship between 3'-azido-3'-deoxythymidine resistance and primer unblocking activity in foscarnet-resistant mutants of human immunodeficiency virus type 1 reverse transcriptase
    Peter R Meyer
    Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Florida 33101, USA
    J Virol 77:6127-37. 2003
    ....
  42. ncbi Initiation of repair of A/G mismatches is modulated by sequence context
    Ana M Sanchez
    Sealy Center for Molecular Science, University of Texas Medical Branch, Galveston, TX 77555 1071, USA
    DNA Repair (Amst) 2:863-78. 2003
    ..These data established that the relative syn/anti conformation did not correlate with the excision efficiency, as well as there being a lack of correlation between kinetics and thermal stability of these DNAs...
  43. ncbi Role of base stacking and sequence context in the inhibition of yeast DNA polymerase eta by pyrene nucleotide
    Hanshin Hwang
    Department of Chemistry, Washington University, St Louis, Missouri 63130, USA
    Biochemistry 43:14612-23. 2004
    ..Thus, pyrene nucleotide represents a novel class of nucleotide-based chain-terminating DNA synthesis inhibitors whose base portion consists of a hydrophobic, non-hydrogen bonding, base-pair mimic...
  44. ncbi Phase I and pharmacodynamic study of Triapine, a novel ribonucleotide reductase inhibitor, in patients with advanced leukemia
    Francis J Giles
    Department of Leukemia, M D Anderson Cancer Center, University of Texas, Box 428, Houston, TX 77030, USA
    Leuk Res 27:1077-83. 2003
    ..Based on these clinical, pharmacokinetic, and pharmacodynamic data, Triapine warrants further study in patients with hematologic malignancies...
  45. ncbi Excess dNTPs minimize RNA hydrolysis during reverse transcription
    Gary F Gerard
    Invitrogen, Frederick, MD, USA
    Biotechniques 33:984, 986, 988 passim. 2002
  46. ncbi Deoxyribonucleotide pool imbalance stimulates deletions in HeLa cell mitochondrial DNA
    Shiwei Song
    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregeon 97331 7305, USA
    J Biol Chem 278:43893-6. 2003
    ..Our finding of dTTP and dGTP elevations and dATP depletion in mitochondrial dNTP pools are consistent with a mutagenic mechanism involving T-G mispairing followed by a next-nucleotide effect involving T insertion opposite A...
  47. ncbi Base selectivity is impaired by mutants that perturb hydrogen bonding networks in the RB69 DNA polymerase active site
    Guangwei Yang
    Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, New Haven, Connecticut 06520, USA
    Biochemistry 44:3338-46. 2005
    ..We have interpreted our results within the context of the crystal structure of the RB69 pol ternary complex [Franklin, M. C., et al. (2001) Cell 105, 657-667]...
  48. ncbi Effects of nucleotides on N-acetyl-d-glucosamine 2-epimerases (renin-binding proteins): comparative biochemical studies
    S Takahashi
    Department of Bioengineering, Akita Research Institute of Food and Brewing ARIF, 4 26 Sanuki, Arayamachi Akita 010 1623, Japan
    J Biochem 130:815-21. 2001
    ..These results indicate that mammalian RnBPs have GlcNAc 2-epimerase activity and that nucleotides are essential for formation of the catalytic domain of the enzyme...
  49. ncbi Identification of nucleotides with identical fluorescent labels based on fluorescence polarization in surfactant solutions
    Y Yan
    Department of Chemistry and Biochemistry, University of South Carolina, Columbia 29208, USA
    Anal Chem 73:4508-13. 2001
    ..A blind test of 40 samples showed no errors in classification based on polarization. The reproducibility obtained during this study demonstrates that the four dye-labeled nucleotides can be discriminated with more than 99.8% confidence...
  50. pmc Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta
    Yanli Wang
    Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York, USA
    Biophys J 92:3063-70. 2007
    ....
  51. pmc Distinct energetics and closing pathways for DNA polymerase beta with 8-oxoG template and different incoming nucleotides
    Yanli Wang
    Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
    BMC Struct Biol 7:7. 2007
    ....
  52. ncbi 8-oxo-guanine bypass by human DNA polymerases in the presence of auxiliary proteins
    Giovanni Maga
    Institute of Molecular Genetics IGM CNR, via Abbiategrasso 207, I 27100 Pavia, Italy
    Nature 447:606-8. 2007
    ....
  53. ncbi Surface-initiated enzymatic polymerization of DNA
    Dominic C Chow
    Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
    Langmuir 23:11712-7. 2007
    ..TdTase-mediated SIEP can also be used to grow spatially defined three-dimensional DNA structures by soft lithography and is a new tool for bioinspired fabrication at the micro- and nanoscale...
  54. ncbi Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase: a 5'-slippage mechanism
    Pingna Xu
    Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York City, New York 10003, USA
    Biochemistry 47:2701-9. 2008
    ..In addition, the dATP can be misincorporated opposite the adduct. The 5'-slippage pattern may be generally facilitated in cases where the base 3' to the lesion is the same as the adducted base...
  55. ncbi Nuclear magnetic resonance investigation of primer--template models: formation of a pyrimidine bulge upon misincorporation
    Lai Man Chi
    Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
    Biochemistry 47:4469-76. 2008
    ..Although misalignment also occurs when the newly formed terminal base pair is an A.T base pair or a T.A base pair, both misaligned and mismatched conformers coexist, which can lead to deletion and substitution mutations, respectively...
  56. ncbi Translesion synthesis past platinum DNA adducts by human DNA polymerase mu
    Jody M Havener
    Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599 7260, USA
    Biochemistry 42:1777-88. 2003
    ..This reaction appears to be facilitated by the presence of a downstream "acceptor" and a gap large enough to provide undamaged template DNA for elongation past the adduct, although gapped DNA is clearly not required for bypass...
  57. ncbi Enzymatic synthesis of oligodeoxyribonucleotides of defined sequence
    S Gillam
    J Biol Chem 253:2532-9. 1978
    ..The effects of added polyamines and some organic solvents on the reaction are described. Spermidine or dimethylsulfoxide in the incubation medium tend to favor the addition of several residues of deoxyribonucleotide to the primer...
  58. ncbi Dynamics of DNA polymerase III holoenzyme of Escherichia coli in replication of a multiprimed template
    M E O'Donnell
    J Biol Chem 260:12875-83. 1985
    ..Based on these findings, schemes can be considered for holoenzyme action at the replication fork of a duplex chromosome...
  59. ncbi Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity
    Martin Welin
    Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, Biomedical Center, S 751 24 Uppsala, Sweden
    J Mol Biol 366:1615-23. 2007
    ..The structure of Mm-dAK provides a starting point for making new anti bacterial agents against pathogenic bacteria...
  60. ncbi Significance of nucleobase shape complementarity and hydrogen bonding in the formation and stability of the closed polymerase-DNA complex
    L Dzantiev
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    Biochemistry 40:3215-21. 2001
    ..Finally, a stable closed complex is not formed in the presence of a ddNTP or rNTP. These results are discussed in relation to the steric exclusion model for the nucleotide insertion...
  61. pmc Mitochondrial deoxynucleotide pool sizes in mouse liver and evidence for a transport mechanism for thymidine monophosphate
    Paola Ferraro
    Departments of Biology and Biomedical Sciences, University of Padua, I 35131 Padua, Italy
    Proc Natl Acad Sci U S A 103:18586-91. 2006
    ..At nM external dTMP the nucleotide is concentrated 100-fold inside the mt matrix. Export of thymidine phosphates was much slower and possibly occurred at the level of dTDP...
  62. ncbi [Association between high activity of DNA polymerase iota and the development of human uveal melanoma]
    L V Gening
    Genetika 42:98-103. 2006
    ..The Pol t activity was observed in seven out of eight malignant tumors, while it was absent in the normal uveal tract cells of the same patients. These findings serve as an additional confirmation of the Pol t oncogenic potential...
  63. ncbi Benzo[a]pyrene-7,8-quinone-3'-mononucleotide adduct standards for 32P postlabeling analyses: detection of benzo[a]pyrene-7,8-quinone-calf thymus DNA adducts
    Narayanan Balu
    Environmental Carcinogenesis Division, Office of Research and Development, U S Environmental Protection Agency, Research Triangle Park, NC 27711, USA
    Anal Biochem 355:213-23. 2006
    ....
  64. pmc Kinetics of error generation in homologous B-family DNA polymerases
    Matthew Hogg
    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
    Nucleic Acids Res 34:2528-35. 2006
    ..These results show that there are kinetic differences between the two enzymes but they are not large enough to preclude structural assumptions for T4 DNA polymerase based on the known structure of the RB69 DNA polymerase...
  65. pmc Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies
    Ling Zhang
    Department of Chemistry, New York University, New York, NY, USA
    Nucleic Acids Res 34:3326-37. 2006
    ..2006), PLoS Biol., 4, e11). However, N2-dG adducts, which can reside on the minor groove side, appear to cause less hindrance when in this position...
  66. ncbi Activation of deoxycytidine kinase by deoxyadenosine: implications in deoxyadenosine-mediated cytotoxicity
    Gergely Keszler
    Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, P O Box 260, H 1444 Budapest, Hungary
    Arch Biochem Biophys 436:69-77. 2005
    ..inborn deficiency of adenosine deaminase is characterised by accumulation of excess amounts of cytotoxic deoxyadenine nucleotides in lymphocytes...
  67. ncbi Activation energy of single-stranded DNA moving through cross-linked polyacrylamide gels at 300 V/cm. Effect of temperature on sequencing rate in high-electric-field capillary gel electrophoresis
    H Lu
    Department of Chemistry, University of Alberta, Edmonton, Canada
    J Chromatogr A 680:503-10. 1994
    ..5 J/mol per base. This transition in the activation energy presumably reflects a change in conformation of the DNA fragments; small fragments exist in a random coil configuration and larger fragments migrate in an elongated configuration...
  68. ncbi Expanding the borononucleotide family: synthesis of borono-analogues of dCMP, dGMP and dAMP
    Anthony R Martin
    Institut des Biomolecules Max Mousseron, UMR 5247 CNRS Université Montpellier 1, Place Eugene Bataillon, 34095 Montpellier, France
    Org Biomol Chem 7:4369-77. 2009
    ....
  69. ncbi Differential regulation of transcription preinitiation complex assembly by activator and repressor homeo domain proteins
    F B Johnson
    Department of Biochemistry, Stanford University, California 94305
    Genes Dev 6:2177-89. 1992
    ..Implications for the mechanism of transcription complex assembly and turnover and its regulation are discussed, including a new role for ATP in turnover...
  70. ncbi The effect of deoxyadenosine plus deoxycoformycin on replicative and repair synthesis of DNA in human lymphoblasts and isolated nuclei
    S S Matsumoto
    Department of Pediatrics, University of California, San Diego, La Jolla 92093
    J Biol Chem 263:7153-8. 1988
    ..In addition, dATP may interfere with some steps of semiconservative DNA synthesis, but not the repair synthesis of DNA...
  71. pmc Novel inhibition of archaeal family-D DNA polymerase by uracil
    Tomas T Richardson
    Institute for Cell and Molecular Biosciences ICaMB, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
    Nucleic Acids Res 41:4207-18. 2013
    ....
  72. ncbi [Tenofovir: pharmacology and interactions]
    Jose Ramon Azanza
    Servicio de Farmacologia Clinica, Clinica Universitaria de Navarra, Facultad de Medicina Universidad de Navarra, Pamplona, Espana
    Enferm Infecc Microbiol Clin 26:2-6. 2008
    ..The absence of interactions with other non-antiretroviral agents has been reported...
  73. pmc An efficiently extended class of unnatural base pairs
    Aaron M Leconte
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    J Am Chem Soc 128:6780-1. 2006
    ..Screening, when complemented by further kinetic analysis, can improve the understanding of the determinants of efficient extension as well as identify viable hetero base pairs...
  74. ncbi The molecular mechanism of multidrug resistance by the Q151M human immunodeficiency virus type 1 reverse transcriptase and its suppression using alpha-boranophosphate nucleotide analogues
    Jerome Deval
    Centre National de la Recherche Scientifique and Universités d Aix Marseille I et II, UMR 6098, Architecture et Fonction des Macromolecules Biologiques, ESIL case 925, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
    J Biol Chem 277:42097-104. 2002
    ..These results highlight the general capacity of such analogues to circumvent multidrug resistance when RT-mediated nucleotide resistance originates from the selective decrease of the catalytic rate constant k(pol)...
  75. pmc Altered order of substrate binding by DNA polymerase X from African Swine Fever virus
    Sandeep Kumar
    Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
    Biochemistry 47:7875-87. 2008
    ..Together, our results suggest that Pol X prefers an ordered sequential mechanism with Mg (2+).dNTP as the first substrate...
  76. pmc dNTP-dependent conformational transitions in the fingers subdomain of Klentaq1 DNA polymerase: insights into the role of the "nucleotide-binding" state
    Paul J Rothwell
    Chair for Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraβe 1, 40225 Dusseldorf, Germany
    J Biol Chem 288:13575-91. 2013
    ..Conformational selection plays a key role in the polymerase cycle...
  77. ncbi New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target
    Roberta Costi
    Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza Universita di Roma, P le Aldo Moro 5, I 00185 Roma, Italy
    J Med Chem 56:7431-41. 2013
    ..In addition, because of the observed dual localization of the phenyl substituent, these studies open the possibility of rationally designing more potent compounds. ..
  78. pmc Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase
    Christina M Zimanyi
    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Structure 20:1374-83. 2012
    ....
  79. ncbi Mechanism of electron transfer processes photoinduced by lumazine
    M Paula Denofrio
    Instituto de Investigaciones Fisicoquimicas Teoricas y Aplicadas INIFTA, Departamento de Quimica, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CCT La Plata CONICET Casilla de Correo 16, Sucursal 4, 1900, La Plata, Argentina
    Photochem Photobiol Sci 11:409-17. 2012
    ..Finally dAMP˙(+) participates in subsequent reactions to yield products...
  80. pmc Involvement of residues of the 29 terminal protein intermediate and priming domains in the formation of a stable and functional heterodimer with the replicative DNA polymerase
    Alicia del Prado
    Instituto de Biología Molecular Eladio Viñuela CSIC, Centro de Biologia Molecular Severo Ochoa CSIC UAM, c Nicolas Cabrera 1, Universidad Autonoma, Cantoblanco, 28049 Madrid, Spain
    Nucleic Acids Res 40:3886-97. 2012
    ....
  81. ncbi Recognition of nucleotide analogs containing the 7,8-dihydro-8-oxo structure by the human MTH1 protein
    Hiroyuki Kamiya
    Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita ku, Sapporo 060 0812
    J Biochem 140:843-9. 2006
    ..These results clarify the effects of the 2-amino group and the two-ring system of the purine base on the recognition by the human MTH1 protein...
  82. ncbi A simple in vitro RNA editing assay for chloroplast transcripts using fluorescent dideoxynucleotides: distinct types of sequence elements required for editing of ndh transcripts
    Tadamasa Sasaki
    Graduate School of Natural Sciences, Nagoya City University, Yamanohata, Mizuho, Nagoya 467 8501, Japan
    Plant J 47:802-10. 2006
    ..These results suggest that distinct editing mechanisms are present in chloroplasts...
  83. pmc Determinants of vaccinia virus early gene transcription termination
    Sarah Piacente
    Department of Microbiology and Immunology, SUNY School of Medicine and Biomedical Sciences, Buffalo, NY, 14214 3200, USA
    Virology 376:211-24. 2008
    ..These observations demonstrate that NPH I is a component of the elongating RNA polymerase, which is catalytically active during transcription elongation...
  84. ncbi In vitro supplementation with dAMP/dGMP leads to partial restoration of mtDNA levels in mitochondrial depletion syndromes
    Stefanie Bulst
    Department of Neurology, Friedrich Baur Institute, Ludwig Maximilians University of Munich, Germany
    Hum Mol Genet 18:1590-9. 2009
    ..No adverse effect on mtDNA copy number was observed on high-dose supplementation in vitro. Further studies are needed to determine possible therapeutic implications of dAMP/dGMP supplementation for DGUOK deficiency in vivo...
  85. ncbi Visualization of RecA filaments and DNA by fluorescence microscopy
    Taro Nishinaka
    Yashima Super structured Helix Project, ERATO, Japan Science and Technology Agency, 101 Creation Core Nagoya, 2266 22 Anagahora, Nagoya 463 0003, Japan
    J Biochem 141:147-56. 2007
    ..We showed that the RecA-DNA filament disassembled in the direction from 5' to 3' of ssDNA as dATP hydrolysis proceeded...
  86. ncbi Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP
    E Hohenester
    Department of Crystallography, Birkbeck College, University of London, UK
    J Mol Biol 269:570-8. 1997
    ....
  87. pmc Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved
    M Shahgholi
    Sequenom Inc, 3595 John Hopkins Court, San Diego, CA 92121, USA
    Nucleic Acids Res 29:E91. 2001
    ..During automatic data acquisition it is difficult to routinely detect heterozygous A/T mutations, which requires resolving a mass difference of 9 Da, unless a sugar is added during crystallization...
  88. ncbi Base sequence dependence of in vitro translesional DNA replication past a bulky lesion catalyzed by the exo- Klenow fragment of Pol I
    P Zhuang
    Chemistry Department, New York University, 31 Washington Place, New York, New York 10003-5180, USA
    Biochemistry 40:6660-9. 2001
    ..The latter depend on the base Y and on the base preferentially inserted opposite the adduct. Thus, downstream template sequences as well as the bases flanking G* influence DNA translesion synthesis...
  89. ncbi Release and aggregation of cytochrome c and alpha-synuclein are inhibited by the antiparkinsonian drugs, talipexole and pramipexole
    J Kakimura
    Department of Neurobiology, Kyoto Pharmaceutical University, Misasagi, Kyoto 607-8412, Yamashina, Japan
    Eur J Pharmacol 417:59-67. 2001
    ..These results suggest that talipexole and pramipexole may have protective effects against the neurodegeneration, which is induced by intracellular accumulation of cytochrome c and alpha-synuclein...
  90. ncbi Mass spectrometry of cis-diamminedichloroplatinum(II) adducts with the dinucleosidemonophosphates d(ApG), d(GpG) and d(TpC) in an ion trap
    Timo Hagemeister
    Humboldt University Berlin, Department of Chemistry, Brook Taylor Strasse 2, 12489 Berlin, Germany
    J Mass Spectrom 37:731-47. 2002
    ..Fragmentation of these ions was also performed, mainly resulting in fragmentation of the bases. The study confirmed the remarkable stability of the platinum-guanine bond compared with other nucleobases...
  91. pmc Isolation and characterization of DNA-dependent RNA polymerase III from Leishmania mexicana and inhibition by purine analogs
    L L Nolan
    Division of Public Health, Morrill Science Center, University of Massachusetts, Amherst 01003 0081
    Antimicrob Agents Chemother 31:1734-8. 1987
    ..Formycin A triphosphate was found to be a noncompetitive inhibitor of RNA polymerase III, and cordycepin triphosphate was found to be inhibitory, although the exact mode of inhibition was not determined...
  92. ncbi The active site of the rolling circle replication protein Rep75 is involved in site-specific nuclease, ligase and nucleotidyl transferase activities
    S Marsin
    Institut de Genetique et Microbiologie, Bat 409, CNRS UMR 8621, Universite Paris Sud, 91405 Orsay Cedex, France
    Mol Microbiol 33:537-45. 1999
    ..Finally, we show that NC is inhibited by ATP or dATP at concentrations that promote NTT. We propose a model in which the NTT activity of Rep75 plays a role in the regulation of pGT5 replication in vivo...
  93. ncbi Maintenance of ATP favours apoptosis over necrosis triggered by benzamide riboside
    M Grusch
    Institute of Clinical Pathology, University of Vienna, Austria
    Cell Death Differ 9:169-78. 2002
    ..Thus, the monitoring and maintenance of cellular energy pools during therapeutic drug treatment may help to minimize nonspecific side effects and to improve attempted drug effects...
  94. pmc A sensitive, single-tube assay to measure the enzymatic activities of influenza RNA polymerase and other poly(A) polymerases: application to kinetic and inhibitor analysis
    L Hooker
    Department of Biology and Department of Chemistry, Roche Discovery Welwyn, 40 Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AY, UK
    Nucleic Acids Res 29:2691-8. 2001
    ..4-0.6 microM) is approximately 100-fold lower than the K(m) value for ATP (50 microM) in the case of yeast PAP...
  95. ncbi Transfer RNA-dependent translocation of misactivated amino acids to prevent errors in protein synthesis
    T K Nomanbhoy
    Skaggs Institute for Chemical Biology, Scripps Research Institute, Beckman Center, La Jolla, California 92037, USA
    Mol Cell 4:519-28. 1999
    ..These results illustrate a remarkable capacity for a specific tRNA to enhance amino acid fine structure recognition by triggering a unimolecular translocation event...
  96. ncbi DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. Effect of pyrophosphorolysis and metal ions
    S Tabor
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
    J Biol Chem 265:8322-8. 1990
    ....
  97. ncbi Enzyme activities of leukemic cells and biochemical changes induced by deoxycoformycin in vitro--lack of correlation with clinical response
    A D Ho
    Department of Internal Medicine V, University of Heidelberg, Federal Republic of Germany
    Leuk Res 13:269-78. 1989
    ..Our results show that neither measurement of these enzymes nor studies of these biochemical sequelae of ADA inhibition in vitro predicts clinical responsiveness to DCF therapy...
  98. ncbi Binding of deoxyadenylate and deoxycytidylate antibodies to double-stranded DNA
    Y N Vaishnav
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore
    Biochem Biophys Res Commun 154:118-23. 1988
    ..The antibodies did not react with tRNA and rRNA. These antibodies were also shown to react with supercoiled and relaxed forms of pBR322 DNA as demonstrated by gel retardation assay...
  99. pmc Functional role of vasoactive intestinal polypeptide in inhibitory motor innervation in the mouse internal anal sphincter
    K D Keef
    Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV 89557, USA
    J Physiol 591:1489-506. 2013
    ..In conclusion, this study identified an ultraslow component of inhibitory NMT in the IAS mediated by VIP. In vivo, this pathway may be activated with larger rectal distensions, leading to a more prolonged period of anal relaxation...
  100. pmc How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations
    Serdal Kirmizialtin
    Department of Chemistry and Biochemistry and Institute for Computational Engineering and Sciences ICES, The University of Texas at Austin, 1 University Station, Austin, TX 78712, USA
    Structure 20:618-27. 2012
    ....
  101. pmc Stereospecific formation of a ternary complex of (S)-α,β-fluoromethylene-dATP with DNA pol β
    Brian T Chamberlain
    Departments of Chemistry and Biology, University of Southern California, Los Angeles, CA 90089, USA
    Chembiochem 13:528-30. 2012
    ....

Research Grants10

  1. CARDIAC CONTRACTILE KINETICS
    Michael Regnier; Fiscal Year: 2009
    ..abstract_text> ..
  2. Repair of DNA Damages Induced by Ionizing Radiation
    Susan Wallace; Fiscal Year: 2009
    ..The ultimate goal is to develop strategies based on structure/function relationships that would increase the effective dose to the tumor without damaging the normal tissue. ..
  3. 9th International Workshop on "Radiation Damage to DNA"
    Susan Wallace; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  4. Molecular Models of Adenosine Signaling and Asthma
    Michael Blackburn; Fiscal Year: 2008
    ..These studies will lead to a better understanding of adenosine's impact on the severity of chronic lung diseases such as asthma and COPD, which will help guide the development of novel therapies for their treatment. ..
  5. Phase I Clinical Trials of Anti-Cancer Agents
    Francis Giles; Fiscal Year: 2007
    ..abstract_text> ..
  6. Engineering DNA nicking endonucleases
    Shuang yong Xu; Fiscal Year: 2006
    ..Under Phase II funding, this isothermal amplification method (NEMDA) will be optimized and the sensitivity will be improved. Finally, we will investigate the potential of NEMDA for detections of pathogens and its use in bio-prospecting. ..
  7. A Genetic System Able to Screen for Active DNA Demethylation
    Shuang yong Xu; Fiscal Year: 2006
    ..In addition, knowledge of the mechanism of demethylation could be crucial in converting fully differentiated adult stem cells into totipotent stem cells. [unreadable] [unreadable] [unreadable]..
  8. A universal DNA endonuclease
    Shuang yong Xu; Fiscal Year: 2005
    ..For isothermal applications of the universal nuclease at 50oC-70oC, the nuclease domain will be derived from thermophilic endonucleases. ..
  9. Cloning and Engineering of Nicking enzymes
    Shuang yong Xu; Fiscal Year: 2004
    ..abstract_text> ..
  10. ADENOSINE SIGNALING AND LUNG INFLAMMATION
    Michael Blackburn; Fiscal Year: 2001
    ..4. Evaluate acute and long-term changes of airway function in ADA deficient mice as well as ADA deficient mice exposed to environmental challenges. ..