James T. Stivers - Publications

Johns Hopkins University, Baltimore, MD 

73 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Cravens SL, Stivers JT. Comparative Effects of Ions, Molecular Crowding, and Bulk DNA on the Damage Search Mechanisms of hOGG1 and hUNG. Biochemistry. PMID 27571472 DOI: 10.1021/Acs.Biochem.6B00482  1
2015 Cravens SL, Schonhoft JD, Rowland MM, Rodriguez AA, Anderson BG, Stivers JT. Molecular crowding enhances facilitated diffusion of two human DNA glycosylases. Nucleic Acids Research. 43: 4087-97. PMID 25845592 DOI: 10.1016/J.Bpj.2014.11.450  1
2014 Cravens SL, Hobson M, Stivers JT. Electrostatic properties of complexes along a DNA glycosylase damage search pathway. Biochemistry. 53: 7680-92. PMID 25408964 DOI: 10.1021/Bi501011M  1
2014 Gajula KS, Huwe PJ, Mo CY, Crawford DJ, Stivers JT, Radhakrishnan R, Kohli RM. High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase. Nucleic Acids Research. 42: 9964-75. PMID 25064858 DOI: 10.1093/Nar/Gku689  1
2014 Rowland MM, Schonhoft JD, McKibbin PL, David SS, Stivers JT. Microscopic mechanism of DNA damage searching by hOGG1. Nucleic Acids Research. 42: 9295-303. PMID 25016526 DOI: 10.1093/Nar/Gku621  1
2014 Seamon KJ, Hansen EC, Kadina AP, Kashemirov BA, McKenna CE, Bumpus NN, Stivers JT. Small molecule inhibition of SAMHD1 dNTPase by tetramer destabilization. Journal of the American Chemical Society. 136: 9822-5. PMID 24983818 DOI: 10.1021/Ja5035717  1
2014 Hansen EC, Seamon KJ, Cravens SL, Stivers JT. GTP activator and dNTP substrates of HIV-1 restriction factor SAMHD1 generate a long-lived activated state. Proceedings of the National Academy of Sciences of the United States of America. 111: E1843-51. PMID 24753578 DOI: 10.1073/Pnas.1401706111  1
2013 Weil AF, Ghosh D, Zhou Y, Seiple L, McMahon MA, Spivak AM, Siliciano RF, Stivers JT. Uracil DNA glycosylase initiates degradation of HIV-1 cDNA containing misincorporated dUTP and prevents viral integration. Proceedings of the National Academy of Sciences of the United States of America. 110: E448-57. PMID 23341616 DOI: 10.1073/Pnas.1219702110  1
2012 Ye Y, Stahley MR, Xu J, Friedman JI, Sun Y, McKnight JN, Gray JJ, Bowman GD, Stivers JT. Enzymatic excision of uracil residues in nucleosomes depends on the local DNA structure and dynamics. Biochemistry. 51: 6028-38. PMID 22784353 DOI: 10.1021/Bi3006412  1
2012 Nabel CS, Jia H, Ye Y, Shen L, Goldschmidt HL, Stivers JT, Zhang Y, Kohli RM. AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nature Chemical Biology. 8: 751-8. PMID 22772155 DOI: 10.1038/Nchembio.1042  1
2012 Mak LH, Knott J, Scott KA, Scott C, Whyte GF, Ye Y, Mann DJ, Ces O, Stivers J, Woscholski R. Arylstibonic acids are potent and isoform-selective inhibitors of Cdc25a and Cdc25b phosphatases. Bioorganic & Medicinal Chemistry. 20: 4371-6. PMID 22705189 DOI: 10.1016/J.Bmc.2012.05.040  1
2012 Jun H, Stivers JT. Diverse energetic effects of charge reversal mutations of poxvirus topoisomerase IB. Biochemistry. 51: 2940-9. PMID 22417571 DOI: 10.1021/Bi3001903  1
2011 Lauzon CB, van Zijl P, Stivers JT. Using the water signal to detect invisible exchanging protons in the catalytic triad of a serine protease. Journal of Biomolecular Nmr. 50: 299-314. PMID 21809183 DOI: 10.1007/S10858-011-9527-Z  1
2011 Feng Y, Xie N, Jin M, Stahley MR, Stivers JT, Zheng YG. A transient kinetic analysis of PRMT1 catalysis. Biochemistry. 50: 7033-44. PMID 21736313 DOI: 10.1021/Bi200456U  1
2011 Friedman JI, Jiang YL, Miller PS, Stivers JT. Unique dynamic properties of DNA duplexes containing interstrand cross-links. Biochemistry. 50: 882-90. PMID 21174443 DOI: 10.1021/Bi101813H  1
2010 Kohli RM, Maul RW, Guminski AF, McClure RL, Gajula KS, Saribasak H, McMahon MA, Siliciano RF, Gearhart PJ, Stivers JT. Local sequence targeting in the AID/APOBEC family differentially impacts retroviral restriction and antibody diversification. The Journal of Biological Chemistry. 285: 40956-64. PMID 20929867 DOI: 10.1074/Jbc.M110.177402  1
2010 Stahley MR, Stivers JT. Mechanism and specificity of DNA strand exchange catalyzed by vaccinia DNA topoisomerase type I. Biochemistry. 49: 2786-95. PMID 20187656 DOI: 10.1021/Bi902204V  1
2009 Kohli RM, Abrams SR, Gajula KS, Maul RW, Gearhart PJ, Stivers JT. A portable hot spot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase. The Journal of Biological Chemistry. 284: 22898-904. PMID 19561087 DOI: 10.1074/Jbc.M109.025536  1
2009 Chung S, Parker JB, Bianchet M, Amzel LM, Stivers JT. Impact of linker strain and flexibility in the design of a fragment-based inhibitor. Nature Chemical Biology. 5: 407-13. PMID 19396178 DOI: 10.1038/Nchembio.163  1
2009 Huang H, Stivers JT, Greenberg MM. Competitive inhibition of uracil DNA glycosylase by a modified nucleotide whose triphosphate is a substrate for DNA polymerase. Journal of the American Chemical Society. 131: 1344-5. PMID 19173657 DOI: 10.1021/Ja807705Z  1
2008 McMahon MA, Siliciano JD, Lai J, Liu JO, Stivers JT, Siliciano RF, Kohli RM. The antiherpetic drug acyclovir inhibits HIV replication and selects the V75I reverse transcriptase multidrug resistance mutation. The Journal of Biological Chemistry. 283: 31289-93. PMID 18818198 DOI: 10.1074/Jbc.C800188200  1
2008 Porecha RH, Stivers JT. Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils. Proceedings of the National Academy of Sciences of the United States of America. 105: 10791-6. PMID 18669665 DOI: 10.1073/Pnas.0801612105  1
2008 Kim H, Cardellina JH, Akee R, Champoux JJ, Stivers JT. Arylstibonic acids: novel inhibitors and activators of human topoisomerase IB. Bioorganic Chemistry. 36: 190-7. PMID 18508107 DOI: 10.1016/J.Bioorg.2008.04.001  1
2008 Seiple LA, Cardellina JH, Akee R, Stivers JT. Potent inhibition of human apurinic/apyrimidinic endonuclease 1 by arylstibonic acids. Molecular Pharmacology. 73: 669-77. PMID 18042731 DOI: 10.1124/Mol.107.042622  1
2007 Parker JB, Bianchet MA, Krosky DJ, Friedman JI, Amzel LM, Stivers JT. Enzymatic capture of an extrahelical thymine in the search for uracil in DNA. Nature. 449: 433-7. PMID 17704764 DOI: 10.1038/Nature06131  1
2006 Krosky DJ, Bianchet MA, Seiple L, Chung S, Amzel LM, Stivers JT. Mimicking damaged DNA with a small molecule inhibitor of human UNG2. Nucleic Acids Research. 34: 5872-9. PMID 17062624 DOI: 10.1093/Nar/Gkl747  1
2006 Cao C, Jiang YL, Krosky DJ, Stivers JT. The catalytic power of uracil DNA glycosylase in the opening of thymine base pairs. Journal of the American Chemical Society. 128: 13034-5. PMID 17017766 DOI: 10.1021/Ja062978N  1
2006 Jiang YL, Chung S, Krosky DJ, Stivers JT. Synthesis and high-throughput evaluation of triskelion uracil libraries for inhibition of human dUTPase and UNG2. Bioorganic & Medicinal Chemistry. 14: 5666-72. PMID 16678429 DOI: 10.1016/J.Bmc.2006.04.022  1
2006 Seiple L, Jaruga P, Dizdaroglu M, Stivers JT. Linking uracil base excision repair and 5-fluorouracil toxicity in yeast. Nucleic Acids Research. 34: 140-51. PMID 16407331 DOI: 10.1093/Nar/Gkj430  0.48
2006 Stivers JT, Kuchta RD. Introduction: DNA damage and repair Chemical Reviews. 106: 213-214. DOI: 10.1021/Cr0404949  1
2005 Jiang YL, Krosky DJ, Seiple L, Stivers JT. Uracil-directed ligand tethering: an efficient strategy for uracil DNA glycosylase (UNG) inhibitor development. Journal of the American Chemical Society. 127: 17412-20. PMID 16332091 DOI: 10.1021/Ja055846N  1
2005 Nagarajan R, Kwon K, Nawrot B, Stec WJ, Stivers JT. Catalytic phosphoryl interactions of topoisomerase IB. Biochemistry. 44: 11476-85. PMID 16114884 DOI: 10.1021/Bi050796K  0.36
2005 Zheng Y, Mamdani F, Toptygin D, Brand L, Stivers JT, Cole PA. Fluorescence analysis of a dynamic loop in the PCAF/GCN5 histone acetyltransferase. Biochemistry. 44: 10501-9. PMID 16060659 DOI: 10.1021/Bi050776I  1
2005 Krosky DJ, Song F, Stivers JT. The origins of high-affinity enzyme binding to an extrahelical DNA base. Biochemistry. 44: 5949-59. PMID 15835884 DOI: 10.1021/Bi050084U  1
2004 Jiang YL, McDowell LM, Poliks B, Studelska DR, Cao C, Potter GS, Schaefer J, Song F, Stivers JT. Recognition of an unnatural difluorophenyl nucleotide by uracil DNA glycosylase. Biochemistry. 43: 15429-38. PMID 15581354 DOI: 10.1021/Bi0483864  0.48
2004 Cao C, Jiang YL, Stivers JT, Song F. Dynamic opening of DNA during the enzymatic search for a damaged base. Nature Structural & Molecular Biology. 11: 1230-6. PMID 15558051 DOI: 10.1038/Nsmb864  0.48
2004 Kwon K, Nagarajan R, Stivers JT. Ribonuclease activity of vaccinia DNA topoisomerase IB: kinetic and high-throughput inhibition studies using a robust continuous fluorescence assay. Biochemistry. 43: 14994-5004. PMID 15554707 DOI: 10.1021/Bi048801S  0.36
2004 Jiang YL, Cao C, Stivers JT, Song F, Ichikawa Y. The merits of bipartite transition-state mimics for inhibition of uracil DNA glycosylase. Bioorganic Chemistry. 32: 244-62. PMID 15210339 DOI: 10.1016/J.Bioorg.2004.03.001  0.48
2004 Krosky DJ, Schwarz FP, Stivers JT. Linear free energy correlations for enzymatic base flipping: how do damaged base pairs facilitate specific recognition? Biochemistry. 43: 4188-95. PMID 15065862 DOI: 10.1021/Bi036303Y  1
2003 Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel LM, Stivers JT. Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase. Biochemistry. 42: 12455-60. PMID 14580190 DOI: 10.1021/Bi035372+  1
2003 Cao C, Kwon K, Jiang YL, Drohat AC, Stivers JT. Solution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3-methyladenine DNA glycosylase I. The Journal of Biological Chemistry. 278: 48012-20. PMID 13129925 DOI: 10.1074/Jbc.M307500200  1
2003 Stivers JT, Jiang YL. A mechanistic perspective on the chemistry of DNA repair glycosylases. Chemical Reviews. 103: 2729-59. PMID 12848584 DOI: 10.1021/Cr010219B  0.48
2003 Kwon K, Jiang YL, Stivers JT. Rational engineering of a DNA glycosylase specific for an unnatural cytosine:pyrene base pair. Chemistry & Biology. 10: 351-9. PMID 12725863 DOI: 10.1016/S1074-5521(03)00077-2  0.48
2003 Kwon K, Cao C, Stivers JT. A novel zinc snap motif conveys structural stability to 3-methyladenine DNA glycosylase I. The Journal of Biological Chemistry. 278: 19442-6. PMID 12654914 DOI: 10.1074/Jbc.M300934200  0.36
2003 Jiang YL, Ichikawa Y, Song F, Stivers JT. Powering DNA repair through substrate electrostatic interactions. Biochemistry. 42: 1922-9. PMID 12590578 DOI: 10.1021/Bi027014X  0.48
2002 Jiang YL, Stivers JT, Song F. Base-flipping mutations of uracil DNA glycosylase: substrate rescue using a pyrene nucleotide wedge. Biochemistry. 41: 11248-54. PMID 12220190 DOI: 10.1021/Bi026227J  0.48
2002 Jiang YL, Stivers JT. Mutational analysis of the base-flipping mechanism of uracil DNA glycosylase. Biochemistry. 41: 11236-47. PMID 12220189 DOI: 10.1021/Bi026226R  0.48
2002 Drohat AC, Kwon K, Krosky DJ, Stivers JT. 3-Methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member. Nature Structural Biology. 9: 659-64. PMID 12161745 DOI: 10.1038/Nsb829  1
2002 Jiang YL, Ichikawa Y, Stivers JT. Inhibition of uracil DNA glycosylase by an oxacarbenium ion mimic. Biochemistry. 41: 7116-24. PMID 12033946 DOI: 10.1021/Bi025694Y  0.48
2002 Jiang YL, Drohat AC, Ichikawa Y, Stivers JT. Probing the limits of electrostatic catalysis by uracil DNA glycosylase using transition state mimicry and mutagenesis. The Journal of Biological Chemistry. 277: 15385-92. PMID 11859082 DOI: 10.1074/Jbc.M200634200  1
2002 Kwon K, Jiang YL, Song F, Stivers JT. 19F NMR studies of vaccinia type IB topoisomerase. Conformational dynamics of the bound DNA substrate. The Journal of Biological Chemistry. 277: 353-8. PMID 11689573 DOI: 10.1074/Jbc.M109450200  0.48
2002 Kwon K, Stivers JT. Fluorescence spectroscopy studies of vaccinia type IB DNA topoisomerase. Closing of the enzyme clamp is faster than DNA cleavage. The Journal of Biological Chemistry. 277: 345-52. PMID 11689572 DOI: 10.1074/Jbc.M109449200  1
2001 Stivers JT, Drohat AC. Uracil DNA glycosylase: insights from a master catalyst. Archives of Biochemistry and Biophysics. 396: 1-9. PMID 11716455 DOI: 10.1006/Abbi.2001.2605  1
2001 Rachofsky EL, Seibert E, Stivers JT, Osman R, Ross JB. Conformation and dynamics of abasic sites in DNA investigated by time-resolved fluorescence of 2-aminopurine. Biochemistry. 40: 957-67. PMID 11170417 DOI: 10.1021/Bi001665G  1
2000 Werner RM, Stivers JT. Kinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase: Evidence for an oxocarbenium ion - Uracil anion intermediate Biochemistry. 39: 14054-14064. PMID 11087352 DOI: 10.1021/Bi0018178  1
2000 Dong J, Drohat AC, Stivers JT, Pankiewicz KW, Carey PR. Raman spectroscopy of uracil DNA glycosylase-DNA complexes: Insights into DNA damage recognition and catalysis Biochemistry. 39: 13241-13250. PMID 11052677 DOI: 10.1021/Bi001437M  1
2000 Werner RM, Jiang YL, Gordley RG, Jagadeesh GJ, Ladner JE, Xiao G, Tordova M, Gilliland GL, Stivers JT. Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase Biochemistry. 39: 12585-12594. PMID 11027138 DOI: 10.1021/bi001532v  1
2000 Drohat AC, Stivers JT. Escherichia coli uracil DNA glycosylase: NMR characterization of the short hydrogen bond from His187 to uracil O2. Biochemistry. 39: 11865-75. PMID 11009598 DOI: 10.1021/Bi000922E  1
2000 Lacourciere KA, Stivers JT, Marino JP. Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy. Biochemistry. 39: 5630-41. PMID 10801313 DOI: 10.1021/Bi992932P  1
2000 Drohat AC, Stivers JT. NMR evidence for an unusually low N1 pK(a) for uracil bound to uracil DNA glycosylase: Implications for catalysis [20] Journal of the American Chemical Society. 122: 1840-1841. DOI: 10.1021/Ja993254X  1
1999 Drohat AC, Xiao G, Tordova M, Jagadeesh J, Pankiewicz KW, Watanabe KA, Gilliland GL, Stivers JT. Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187. Biochemistry. 38: 11876-86. PMID 10508390 DOI: 10.1021/Bi9910880  1
1999 Drohat AC, Jagadeesh J, Ferguson E, Stivers JT. Role of electrophilic and general base catalysis in the mechanism of Escherichia coli uracil DNA glycosylase. Biochemistry. 38: 11866-75. PMID 10508389 DOI: 10.1021/Bi9910878  1
1999 Czerwinski RM, Harris TK, Johnson WH, Legler PM, Stivers JT, Mildvan AS, Whitman CP. Effects of mutations of the active site arginine residues in 4-oxalocrotonate tautomerase on the pKa values of active site residues and on the pH dependence of catalysis. Biochemistry. 38: 12358-66. PMID 10493803 DOI: 10.1021/Bi9911177  1
1999 Harris TK, Czerwinski RM, Johnson WH, Legler PM, Abeygunawardana C, Massiah MA, Stivers JT, Whitman CP, Mildvan AS. Kinetic, stereochemical, and structural effects of mutations of the active site arginine residues in 4-oxalocrotonate tautomerase. Biochemistry. 38: 12343-57. PMID 10493802 DOI: 10.1021/Bi991116E  1
1999 Xiao G, Tordova M, Jagadeesh J, Drohat AC, Stivers JT, Gilliland GL. Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited. Proteins. 35: 13-24. PMID 10090282 DOI: 10.1002/(Sici)1097-0134(19990401)35:1<13::Aid-Prot2>3.0.Co;2-2  1
1997 Stivers JT, Harris TK, Mildvan AS. Vaccinia DNA topoisomerase I: evidence supporting a free rotation mechanism for DNA supercoil relaxation. Biochemistry. 36: 5212-22. PMID 9136883 DOI: 10.1021/Bi962880T  1
1996 Stivers JT, Abeygunawardana C, Mildvan AS. 15N NMR relaxation studies of free and inhibitor-bound 4-oxalocrotonate tautomerase: backbone dynamics and entropy changes of an enzyme upon inhibitor binding. Biochemistry. 35: 16036-47. PMID 8973173 DOI: 10.1021/Bi961834Q  1
1996 Stivers JT, Abeygunawardana C, Whitman CP, Mildvan AS. 4-Oxalocrotonate tautomerase, a 41-kDa homohexamer: backbone and side-chain resonance assignments, solution secondary structure, and location of active site residues by heteronuclear NMR spectroscopy. Protein Science : a Publication of the Protein Society. 5: 729-41. PMID 8845763 DOI: 10.1002/Pro.5560050418  1
1996 Sekiguchi J, Stivers JT, Mildvan AS, Shuman S. Mechanism of inhibition of vaccinia DNA topoisomerase by novobiocin and coumermycin. The Journal of Biological Chemistry. 271: 2313-22. PMID 8567695 DOI: 10.1074/Jbc.271.4.2313  1
1996 Stivers JT, Abeygunawardana C, Mildvan AS, Hajipour G, Whitman CP. 4-Oxalocrotonate tautomerase: pH dependence of catalysis and pKa values of active site residues. Biochemistry. 35: 814-23. PMID 8547261 DOI: 10.1021/Bi9510789  1
1996 Stivers JT, Abeygunawardana C, Mildvan AS, Hajipour G, Whitman CP, Chen LH. Catalytic role of the amino-terminal proline in 4-oxalocrotonate tautomerase: affinity labeling and heteronuclear NMR studies. Biochemistry. 35: 803-13. PMID 8547260 DOI: 10.1021/Bi951077G  1
1994 Stivers JT, Shuman S, Mildvan AS. Vaccinia DNA topoisomerase I: single-turnover and steady-state kinetic analysis of the DNA strand cleavage and ligation reactions. Biochemistry. 33: 327-39. PMID 8286354 DOI: 10.1021/Bi00167A043  1
1994 Stivers JT, Shuman S, Mildvan AS. Vaccinia DNA topoisomerase I: kinetic evidence for general acid-base catalysis and a conformational step. Biochemistry. 33: 15449-58. PMID 7803409 DOI: 10.1021/Bi00255A027  1
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