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James Stivers

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Publications

TOP 3
Joseph D Schonhoft; John G Kosowicz; James T Stivers
DNA translocation by human uracil DNA glycosylase: role of DNA phosphate charge.
Joseph D Schonhoft; James T Stivers
DNA translocation by human uracil DNA glycosylase: the case of single-stranded DNA and clustered uracils.
Amy F Weil; Yan Zhou; Devlina Ghosh; Moira A McMahon; Lauren Seiple; Robert Siliciano; Adam M Spivak; James T Stivers
Uracil DNA glycosylase initiates degradation of HIV-1 cDNA containing misincorporated dUTP and prevents viral integration.

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All Publications

2013: Joseph D Schonhoft; John G Kosowicz; James T Stivers
DNA translocation by human uracil DNA glycosylase: role of DNA phosphate charge.
Biochemistry 2013;52(15):2526-35.
2013: Joseph D Schonhoft; James T Stivers
DNA translocation by human uracil DNA glycosylase: the case of single-stranded DNA and clustered uracils.
Biochemistry 2013;52(15):2536-44.
2013: Amy F Weil; Yan Zhou; Devlina Ghosh; Moira A McMahon; Lauren Seiple; Robert Siliciano; Adam M Spivak; James T Stivers
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 2013;110(6):E448-57.
2012: Christopher S Nabel; Li Shen; James T Stivers; Yu Ye; Yi Zhang; Hana L Goldschmidt; Huijue Jia; Rahul M Kohli
AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation.
Nature chemical biology 2012;8(9):751-8.
2012: Yu Ye; Yan Sun; Jianqing Xu; Gregory D Bowman; Joshua I Friedman; Jeffrey J Gray; Jeffrey N McKnight; Mary R Stahley; James T Stivers
Enzymatic excision of uracil residues in nucleosomes depends on the local DNA structure and dynamics.
Biochemistry 2012;51(30):6028-38.
2012: Lok Hang Mak; David J Mann; Claire Scott; Katherine A Scott; James T Stivers; Gillian F Whyte; Oscar Ces; Jessica Knott; Yu Ye; Rüdiger Woscholski
Arylstibonic acids are potent and isoform-selective inhibitors of Cdc25a and Cdc25b phosphatases.
Bioorganic & medicinal chemistry 2012;20(14):4371-6.
2012: Helen Jun; James T Stivers
Diverse energetic effects of charge reversal mutations of poxvirus topoisomerase IB.
Biochemistry 2012;51(13):2940-9.
2012: Joseph D Schonhoft; James T Stivers
Timing facilitated site transfer of an enzyme on DNA.
Nature chemical biology 2012;8(2):205-10.
2011: Yan Sun; Joshua I Friedman; James T Stivers
Cosolute paramagnetic relaxation enhancements detect transient conformations of human uracil DNA glycosylase (hUNG).
Biochemistry 2011;50(49):10724-31.
2011: You Feng; Miyeong Jin; Mary R Stahley; James T Stivers; Nan Xie; Yujun Zheng
A transient kinetic analysis of PRMT1 catalysis.
Biochemistry 2011;50(32):7033-44.
2011: Carolyn B Lauzon; Peter C M van Zijl; James T Stivers
Using the water signal to detect invisible exchanging protons in the catalytic triad of a serine protease.
Journal of biomolecular NMR 2011;50(4):299-314.
2011: Breeana C Grogan; Jared B Parker; Amy F Guminski; James T Stivers
Effect of the thymidylate synthase inhibitors on dUTP and TTP pool levels and the activities of DNA repair glycosylases on uracil and 5-fluorouracil in DNA.
Biochemistry 2011;50(5):618-27.
2011: Jared B Parker; James T Stivers
Dynamics of uracil and 5-fluorouracil in DNA.
Biochemistry 2011;50(5):612-7.
2011: Joshua I Friedman; Yu Lin Jiang; Paul S Miller; James T Stivers
Unique dynamic properties of DNA duplexes containing interstrand cross-links.
Biochemistry 2011;50(5):882-90.
2010: Rahul M Kohli; Robert W Maul; Amy F Guminski; Rhonda L McClure; Kiran S Gajula; Huseyin Saribasak; Moira A McMahon; Robert Siliciano; Patricia J Gearhart; James T Stivers
Local sequence targeting in the AID/APOBEC family differentially impacts retroviral restriction and antibody diversification.
The Journal of biological chemistry 2010;285(52):40956-64.
2010: Joshua I Friedman; James T Stivers
Detection of damaged DNA bases by DNA glycosylase enzymes.
Biochemistry 2010;49(24):4957-67.
2010: Yu Ye; James T Stivers
Fluorescence-based high-throughput assay for human DNA (cytosine-5)-methyltransferase 1.
Analytical biochemistry 2010;401(1):168-72.
2010: Mary R Stahley; James T Stivers
Mechanism and specificity of DNA strand exchange catalyzed by vaccinia DNA topoisomerase type I.
Biochemistry 2010;49(13):2786-95.
2010: Joshua I Friedman; Michael McMahon; James T Stivers; Peter C M van Zijl
Indirect detection of labile solute proton spectra via the water signal using frequency-labeled exchange (FLEX) transfer.
Journal of the American Chemical Society 2010;132(6):1813-5.
2009: Rahul Kohli; Shaun R Abrams; Kiran S Gajula; Robert W Maul; Patricia J Gearhart; James T Stivers
A portable hot spot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase.
The Journal of biological chemistry 2009;284(34):22898-904.
2009: Suhman Chung; Jared B Parker; Mario Antonio Bianchet; Mario Amzel; James T Stivers
Impact of linker strain and flexibility in the design of a fragment-based inhibitor.
Nature chemical biology 2009;5(6):407-13.
2009: Joshua I Friedman; Ananya Majumdar; James T Stivers
Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage.
Nucleic acids research 2009;37(11):3493-500.
2009: Haidong Huang; James T Stivers; Marc M Greenberg
Competitive inhibition of uracil DNA glycosylase by a modified nucleotide whose triphosphate is a substrate for DNA polymerase.
Journal of the American Chemical Society 2009;131(4):1344-5.
2008: Moira A McMahon; Janet D Siliciano; Jun Lai; Jun O Liu; James T Stivers; Robert Siliciano; Rahul Kohli
The antiherpetic drug acyclovir inhibits HIV replication and selects the V75I reverse transcriptase multidrug resistance mutation.
The Journal of biological chemistry 2008;283(46):31289-93.
2008: Jared B Parker; James T Stivers
Uracil DNA glycosylase: revisiting substrate-assisted catalysis by DNA phosphate anions.
Biochemistry 2008;47(33):8614-22.
2008: Rishi H Porecha; James T Stivers
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 2008;105(31):10791-6.
2008: Hyeongnam Kim; John H Cardellina; Rhone Akee; James J Champoux; James T Stivers
Arylstibonic acids: novel inhibitors and activators of human topoisomerase IB.
Bioorganic chemistry 2008;36(4):190-7.
2008: Lauren Seiple; John H Cardellina; Rhone Akee; James T Stivers
Potent inhibition of human apurinic/apyrimidinic endonuclease 1 by arylstibonic acids.
Molecular pharmacology 2008;73(3):669-77.
2008: James T Stivers
Small molecule versus DNA repair nanomachine.
Nature chemical biology 2008;4(2):86-8.
2008: James T Stivers
Extrahelical damaged base recognition by DNA glycosylase enzymes.
Chemistry (Weinheim an der Bergstrasse, Germany) 2008;14(3):786-93.
2007: Jared B Parker; Mario Antonio Bianchet; Daniel J Krosky; Joshua I Friedman; Mario Amzel; James T Stivers
Enzymatic capture of an extrahelical thymine in the search for uracil in DNA.
Nature 2007;449(7161):433-7.
2007: Rajesh Nagarajan; James T Stivers
Unmasking Anticooperative DNA-binding interactions of vaccinia DNA topoisomerase I.
Biochemistry 2007;46(1):192-9.
2006: Chunyang Cao; Yu Lin Jiang; Daniel J Krosky; James T Stivers
The catalytic power of uracil DNA glycosylase in the opening of thymine base pairs.
Journal of the American Chemical Society 2006;128(40):13034-5.
2006: Yu Lin Jiang; Suhman Chung; Daniel J Krosky; James T Stivers
Synthesis and high-throughput evaluation of triskelion uracil libraries for inhibition of human dUTPase and UNG2.
Bioorganic & medicinal chemistry 2006;14(16):5666-72.
2006: James T Stivers; Rajesh Nagarajan
Probing enzyme phosphoester interactions by combining mutagenesis and chemical modification of phosphate ester oxygens.
Chemical reviews 2006;106(8):3443-67.
2006: Rajesh Nagarajan; James T Stivers
Major groove interactions of vaccinia Topo I provide specificity by optimally positioning the covalent phosphotyrosine linkage.
Biochemistry 2006;45(18):5775-82.
2006: Alexis Bond; Zachary Reichert; James T Stivers
Novel and specific inhibitors of a poxvirus type I topoisomerase.
Molecular pharmacology 2006;69(2):547-57.
2006: Daniel J Krosky; Mario Antonio Bianchet; Lauren Seiple; Suhman Chung; Mario Amzel; James T Stivers
Mimicking damaged DNA with a small molecule inhibitor of human UNG2.
Nucleic acids research 2006;34(20):5872-9.
2006: Lauren Seiple; Pawel Jaruga; Miral Dizdaroglu; James T Stivers
Linking uracil base excision repair and 5-fluorouracil toxicity in yeast.
Nucleic acids research 2006;34(1):140-51.
2005: Yu Lin Jiang; Daniel J Krosky; Lauren Seiple; James T Stivers
Uracil-directed ligand tethering: an efficient strategy for uracil DNA glycosylase (UNG) inhibitor development.
Journal of the American Chemical Society 2005;127(49):17412-20.
2005: Rajesh Nagarajan; Keehwan Kwon; Barbara Nawrot; Wojciech J Stec; James T Stivers
Catalytic phosphoryl interactions of topoisomerase IB.
Biochemistry 2005;44(34):11476-85.
2005: Yujun Zheng; Fatemah Mamdani; Dmitri Toptygin; Ludwig Brand; James T Stivers; Philip A Cole
Fluorescence analysis of a dynamic loop in the PCAF/GCN5 histone acetyltransferase.
Biochemistry 2005;44(31):10501-9.
2005: Daniel J Krosky; Fenhong Song; James T Stivers
The origins of high-affinity enzyme binding to an extrahelical DNA base.
Biochemistry 2005;44(16):5949-59.
2004: James T Stivers
Comment on "Uracil DNA glycosylase activity is dispensable for immunoglobulin class switch".
Science (New York, N.Y.) 2004;306(5704):2042; author reply 2042.
2004: Yu Lin Jiang; Lynda M McDowell; Barbara Poliks; Daniel R Studelska; Chunyang Cao; Gregory S Potter; Jacob Schaefer; Fenhong Song; James T Stivers
Recognition of an unnatural difluorophenyl nucleotide by uracil DNA glycosylase.
Biochemistry 2004;43(49):15429-38.
2004: Chunyang Cao; Yu Lin Jiang; James T Stivers; Fenhong Song
Dynamic opening of DNA during the enzymatic search for a damaged base.
Nature structural & molecular biology 2004;11(12):1230-6.
2004: Keehwan Kwon; Rajesh Nagarajan; James T Stivers
Ribonuclease activity of vaccinia DNA topoisomerase IB: kinetic and high-throughput inhibition studies using a robust continuous fluorescence assay.
Biochemistry 2004;43(47):14994-5004.
2004: Yu Lin Jiang; Chunyang Cao; James T Stivers; Fenhong Song; Yoshi Ichikawa
The merits of bipartite transition-state mimics for inhibition of uracil DNA glycosylase.
Bioorganic chemistry 2004;32(4):244-62.
2004: Daniel J Krosky; Frederick P Schwarz; James T Stivers
Linear free energy correlations for enzymatic base flipping: how do damaged base pairs facilitate specific recognition?
Biochemistry 2004;43(14):4188-95.
2004: James T Stivers
Site-specific DNA damage recognition by enzyme-induced base flipping.
Progress in nucleic acid research and molecular biology 2004;77():37-65.
2003: Chunyang Cao; Keehwan Kwon; Yu Lin Jiang; Alexander C Drohat; James T Stivers
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 2003;278(48):48012-20.
2003: Mario Antonio Bianchet; Lauren Seiple; Yu Lin Jiang; Yoshitaka Ichikawa; Mario Amzel; James T Stivers
Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase.
Biochemistry 2003;42(43):12455-60.
2003: James T Stivers; Yu Lin Jiang
A mechanistic perspective on the chemistry of DNA repair glycosylases.
Chemical reviews 2003;103(7):2729-59.
2003: Keehwan Kwon; Chunyang Cao; James T Stivers
A novel zinc snap motif conveys structural stability to 3-methyladenine DNA glycosylase I.
The Journal of biological chemistry 2003;278(21):19442-6.
2003: Keehwan Kwon; Yu Lin Jiang; James T Stivers
Rational engineering of a DNA glycosylase specific for an unnatural cytosine:pyrene base pair.
Chemistry & biology 2003;10(4):351-9.
2003: Yu Lin Jiang; Yoshitaka Ichikawa; Fenhong Song; James T Stivers
Powering DNA repair through substrate electrostatic interactions.
Biochemistry 2003;42(7):1922-9.
2002: Yu Lin Jiang; James T Stivers; Fenhong Song
Base-flipping mutations of uracil DNA glycosylase: substrate rescue using a pyrene nucleotide wedge.
Biochemistry 2002;41(37):11248-54.
2002: Yu Lin Jiang; James T Stivers
Mutational analysis of the base-flipping mechanism of uracil DNA glycosylase.
Biochemistry 2002;41(37):11236-47.
2002: Alexander C Drohat; Keehwan Kwon; Daniel J Krosky; James T Stivers
3-Methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member.
Nature structural biology 2002;9(9):659-64.
2002: Yu Lin Jiang; Yoshitaka Ichikawa; James T Stivers
Inhibition of uracil DNA glycosylase by an oxacarbenium ion mimic.
Biochemistry 2002;41(22):7116-24.
2002: Yu Lin Jiang; Alexander C Drohat; Yoshitaka Ichikawa; James T Stivers
Probing the limits of electrostatic catalysis by uracil DNA glycosylase using transition state mimicry and mutagenesis.
The Journal of biological chemistry 2002;277(18):15385-92.
2002: Keehwan Kwon; Yu Lin Jiang; Fenhong Song; James T Stivers
19F NMR studies of vaccinia type IB topoisomerase. Conformational dynamics of the bound DNA substrate.
The Journal of biological chemistry 2002;277(1):353-8.
2002: Keehwan Kwon; James T Stivers
Fluorescence spectroscopy studies of vaccinia type IB DNA topoisomerase. Closing of the enzyme clamp is faster than DNA cleavage.
The Journal of biological chemistry 2002;277(1):345-52.
2001: James T Stivers; Alexander C Drohat
Uracil DNA glycosylase: insights from a master catalyst.
Archives of biochemistry and biophysics 2001;396(1):1-9.
2001: Yu Lin Jiang; Keehwan Kwon; James T Stivers
Turning On uracil-DNA glycosylase using a pyrene nucleotide switch.
The Journal of biological chemistry 2001;276(45):42347-54.
2001: Yu Lin Jiang; James T Stivers
Reconstructing the substrate for uracil DNA glycosylase: tracking the transmission of binding energy in catalysis.
Biochemistry 2001;40(25):7710-9.
2001: Edward L Rachofsky; Eleanore Seibert; James T Stivers; Roman Osman; J B Alexander Ross
Conformation and dynamics of abasic sites in DNA investigated by time-resolved fluorescence of 2-aminopurine.
Biochemistry 2001;40(4):957-67.
2000: R M Werner; James T Stivers
Kinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase: evidence for an oxocarbenium ion-uracil anion intermediate.
Biochemistry 2000;39(46):14054-64.
2000: Jian Dong; Alexander C Drohat; James T Stivers; Krzysztof W Pankiewicz; Paul R Carey
Raman spectroscopy of uracil DNA glycosylase-DNA complexes: insights into DNA damage recognition and catalysis.
Biochemistry 2000;39(43):13241-50.
2000: R M Werner; Yu Lin Jiang; R G Gordley; G J Jagadeesh; Jane E Ladner; Gaoyi Xiao; Maria Tordova; Gary L Gilliland; James T Stivers
Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase.
Biochemistry 2000;39(41):12585-94.
2000: Alexander C Drohat; James T Stivers
Escherichia coli uracil DNA glycosylase: NMR characterization of the short hydrogen bond from His187 to uracil O2.
Biochemistry 2000;39(39):11865-75.
2000: K A Lacourciere; James T Stivers; John P Marino
Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy.
Biochemistry 2000;39(19):5630-41.
2000: James T Stivers; G J Jagadeesh; Barbara Nawrot; Wojciech J Stec; Stewart Shuman
Stereochemical outcome and kinetic effects of Rp- and Sp-phosphorothioate substitutions at the cleavage site of vaccinia type I DNA topoisomerase.
Biochemistry 2000;39(18):5561-72.
1999: Robert M Czerwinski; Thomas K Harris; William H Johnson; Patricia M Legler; James T Stivers; Albert S Mildvan; Christian P Whitman
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 1999;38(38):12358-66.
1999: Thomas K Harris; Robert M Czerwinski; William H Johnson; Patricia M Legler; C Abeygunawardana; Michael A Massiah; James T Stivers; Christian P Whitman; Albert S Mildvan
Kinetic, stereochemical, and structural effects of mutations of the active site arginine residues in 4-oxalocrotonate tautomerase.
Biochemistry 1999;38(38):12343-57.
1999: Alexander C Drohat; Gaoyi Xiao; Maria Tordova; J Jagadeesh; Krzysztof W Pankiewicz; K A Watanabe; Gary L Gilliland; James T Stivers
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 1999;38(37):11876-86.
1999: Alexander C Drohat; J Jagadeesh; E Ferguson; James T Stivers
Role of electrophilic and general base catalysis in the mechanism of Escherichia coli uracil DNA glycosylase.
Biochemistry 1999;38(37):11866-75.
1999: Gaoyi Xiao; Maria Tordova; J Jagadeesh; Alexander C Drohat; James T Stivers; Gary L Gilliland
Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited.
Proteins 1999;35(1):13-24.
1999: James T Stivers; Krzysztof W Pankiewicz; K A Watanabe
Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase.
Biochemistry 1999;38(3):952-63.
1998: James T Stivers
2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects.
Nucleic acids research 1998;26(16):3837-44.
1997: James T Stivers; Thomas K Harris; Albert S Mildvan
Vaccinia DNA topoisomerase I: evidence supporting a free rotation mechanism for DNA supercoil relaxation.
Biochemistry 1997;36(17):5212-22.
1996: James T Stivers; C Abeygunawardana; Albert S Mildvan
15N NMR relaxation studies of free and inhibitor-bound 4-oxalocrotonate tautomerase: backbone dynamics and entropy changes of an enzyme upon inhibitor binding.
Biochemistry 1996;35(50):16036-47.
1996: James T Stivers; C Abeygunawardana; Christian P Whitman; Albert S Mildvan
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 1996;5(4):729-41.
1996: JoAnn Sekiguchi; James T Stivers; A S Mildvan; Stewart Shuman
Mechanism of inhibition of vaccinia DNA topoisomerase by novobiocin and coumermycin.
The Journal of biological chemistry 1996;271(4):2313-22.
1996: James T Stivers; C Abeygunawardana; Albert S Mildvan; G Hajipour; Christian P Whitman
4-Oxalocrotonate tautomerase: pH dependence of catalysis and pKa values of active site residues.
Biochemistry 1996;35(3):814-23.
1996: James T Stivers; C Abeygunawardana; Albert S Mildvan; G Hajipour; Christian P Whitman; L H Chen
Catalytic role of the amino-terminal proline in 4-oxalocrotonate tautomerase: affinity labeling and heteronuclear NMR studies.
Biochemistry 1996;35(3):803-13.
1994: James T Stivers; Stewart Shuman; Albert S Mildvan
Vaccinia DNA topoisomerase I: kinetic evidence for general acid-base catalysis and a conformational step.
Biochemistry 1994;33(51):15449-58.
1994: James T Stivers; Stewart Shuman; Albert S Mildvan
Vaccinia DNA topoisomerase I: single-turnover and steady-state kinetic analysis of the DNA strand cleavage and ligation reactions.
Biochemistry 1994;33(1):327-39.
1993: James T Stivers; M W Washabaugh
Catalysis of acetoin formation by brewers' yeast pyruvate decarboxylase isozymes.
Biochemistry 1993;32(49):13472-82.