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Patrick J. O'Brien, Ph.D. - Publications

Affiliations: 
2000 Stanford University, Palo Alto, CA 
Area:
ribozymes
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41 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
2023 McNally JR, Ames AM, Admiraal SJ, O'Brien PJ. Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity. Nucleic Acids Research. 51: 796-805. PMID 36625284 DOI: 10.1093/nar/gkac1263  0.384
2021 Jurkiw TJ, Tumbale PP, Schellenberg MJ, Cunningham-Rundles C, Williams RS, O'Brien PJ. LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency. Nucleic Acids Research. PMID 33444456 DOI: 10.1093/nar/gkaa1297  0.337
2020 Baldwin MR, Admiraal SJ, O'Brien PJ. Transient kinetic analysis of oxidative dealkylation by the direct reversal DNA repair enzyme AlkB. The Journal of Biological Chemistry. PMID 32284330 DOI: 10.1074/jbc.RA120.013517  0.393
2019 Thelen AZ, O'Brien PJ. Recognition of 1,-ethenoguanine by alkyladenine DNA glycosylase is restricted by a conserved active site residue. The Journal of Biological Chemistry. PMID 31882538 DOI: 10.1074/jbc.RA119.011459  0.337
2019 Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS. Two-tiered enforcement of high-fidelity DNA ligation. Nature Communications. 10: 5431. PMID 31780661 DOI: 10.1038/s41467-019-13478-7  0.371
2019 Admiraal SJ, Eyler DE, Baldwin MR, Brines EM, Lohans CT, Schofield CJ, O'Brien PJ. Expansion of base excision repair compensates for a lack of DNA repair by oxidative dealkylation in budding yeast. The Journal of Biological Chemistry. PMID 31320474 DOI: 10.1074/Jbc.Ra119.009813  0.338
2018 Taylor EL, Kesavan PM, Wolfe AE, O'Brien PJ. Distinguishing Specific and Nonspecific Complexes of Alkyladenine DNA Glycosylase. Biochemistry. PMID 29940097 DOI: 10.1021/acs.biochem.8b00531  0.381
2017 McNally JR, O'Brien PJ. Kinetic Analyses of Single-Strand Break Repair by Human DNA Ligase III Isoforms Reveals Biochemical Differences from DNA Ligase I. The Journal of Biological Chemistry. PMID 28751376 DOI: 10.1074/jbc.M117.804625  0.363
2017 Hendershot JM, O'Brien PJ. Search for DNA Damage by Human Alkyladenine DNA Glycosylase Involves Early Intercalation by an Aromatic Residue. The Journal of Biological Chemistry. PMID 28747435 DOI: 10.1074/jbc.M117.782813  0.426
2017 Hendershot JM, O'Brien PJ. Transient Kinetic Methods for Mechanistic Characterization of DNA Binding and Nucleotide Flipping. Methods in Enzymology. 592: 377-415. PMID 28668128 DOI: 10.1016/bs.mie.2017.04.003  0.424
2017 Admiraal SJ, O'Brien PJ. Reactivity and Cross-Linking of 5'-Terminal Abasic Sites Within DNA. Chemical Research in Toxicology. PMID 28485930 DOI: 10.1021/acs.chemrestox.7b00057  0.381
2015 Zhang Y, O'Brien PJ. Repair of Alkylation Damage in Eukaryotic Chromatin Depends on Searching Ability of Alkyladenine DNA Glycosylase. Acs Chemical Biology. PMID 26317160 DOI: 10.1021/acschembio.5b00409  0.402
2015 Admiraal SJ, O'Brien PJ. Base excision repair enzymes protect abasic sites in duplex DNA from interstrand cross-links. Biochemistry. 54: 1849-57. PMID 25679877 DOI: 10.1021/bi501491z  0.439
2015 Taylor EL, O'Brien PJ. Kinetic mechanism for the flipping and excision of 1,N(6)-ethenoadenine by AlkA. Biochemistry. 54: 898-908. PMID 25537480 DOI: 10.1021/bi501356x  0.431
2015 Hedglin M, Zhang Y, O'Brien PJ. Probing the DNA structural requirements for facilitated diffusion. Biochemistry. 54: 557-66. PMID 25495964 DOI: 10.1021/Bi5013707  0.713
2014 Hendershot JM, O'Brien PJ. Critical role of DNA intercalation in enzyme-catalyzed nucleotide flipping. Nucleic Acids Research. 42: 12681-90. PMID 25324304 DOI: 10.1093/nar/gku919  0.373
2013 Hedglin M, Zhang Y, O'Brien PJ. Isolating contributions from intersegmental transfer to DNA searching by alkyladenine DNA glycosylase. The Journal of Biological Chemistry. 288: 24550-9. PMID 23839988 DOI: 10.1074/Jbc.M113.477018  0.727
2013 Admiraal SJ, O'Brien PJ. DNA-N-glycosylases process novel O-glycosidic sites in DNA. Biochemistry. 52: 4066-74. PMID 23688261 DOI: 10.1021/bi400218j  0.372
2011 Taylor MR, Conrad JA, Wahl D, O'Brien PJ. Kinetic mechanism of human DNA ligase I reveals magnesium-dependent changes in the rate-limiting step that compromise ligation efficiency. The Journal of Biological Chemistry. 286: 23054-62. PMID 21561855 DOI: 10.1074/Jbc.M111.248831  0.432
2011 Zhao B, O'Brien PJ. Kinetic mechanism for the excision of hypoxanthine by Escherichia coli AlkA and evidence for binding to DNA ends. Biochemistry. 50: 4350-9. PMID 21491902 DOI: 10.1021/bi200232c  0.346
2011 Nikolova EN, Kim E, Wise AA, O'Brien PJ, Andricioaei I, Al-Hashimi HM. Transient Hoogsteen base pairs in canonical duplex DNA. Nature. 470: 498-502. PMID 21270796 DOI: 10.1038/Nature09775  0.319
2011 Hendershot JM, Wolfe AE, O'Brien PJ. Substitution of active site tyrosines with tryptophan alters the free energy for nucleotide flipping by human alkyladenine DNA glycosylase. Biochemistry. 50: 1864-74. PMID 21244040 DOI: 10.1021/bi101856a  0.362
2010 Admiraal SJ, O'Brien PJ. N-glycosyl bond formation catalyzed by human alkyladenine DNA glycosylase. Biochemistry. 49: 9024-6. PMID 20873830 DOI: 10.1021/bi101380d  0.357
2010 Baldwin MR, O'Brien PJ. Nonspecific DNA binding and coordination of the first two steps of base excision repair. Biochemistry. 49: 7879-91. PMID 20701268 DOI: 10.1021/bi100889r  0.336
2010 Hedglin M, O'Brien PJ. Hopping enables a DNA repair glycosylase to search both strands and bypass a bound protein. Acs Chemical Biology. 5: 427-36. PMID 20201599 DOI: 10.1021/Cb1000185  0.725
2008 Hedglin M, O'Brien PJ. Human alkyladenine DNA glycosylase employs a processive search for DNA damage. Biochemistry. 47: 11434-45. PMID 18839966 DOI: 10.1021/Bi801046Y  0.727
2008 O'Brien PJ, Lassila JK, Fenn TD, Zalatan JG, Herschlag D. Arginine coordination in enzymatic phosphoryl transfer: evaluation of the effect of Arg166 mutations in Escherichia coli alkaline phosphatase. Biochemistry. 47: 7663-72. PMID 18627128 DOI: 10.1021/Bi800545N  0.732
2007 Zalatan JG, Catrina I, Mitchell R, Grzyska PK, O'brien PJ, Herschlag D, Hengge AC. Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis. Journal of the American Chemical Society. 129: 9789-98. PMID 17630738 DOI: 10.1021/Ja072196+  0.732
2007 Catrina I, O'Brien PJ, Purcell J, Nikolic-Hughes I, Zalatan JG, Hengge AC, Herschlag D. Probing the origin of the compromised catalysis of E. coli alkaline phosphatase in its promiscuous sulfatase reaction. Journal of the American Chemical Society. 129: 5760-5. PMID 17411045 DOI: 10.1021/Ja069111+  0.726
2006 O'Brien PJ. Catalytic promiscuity and the divergent evolution of DNA repair enzymes. Chemical Reviews. 106: 720-52. PMID 16464022 DOI: 10.1021/cr040481v  0.382
2005 Nikolic-Hughes I, O'brien PJ, Herschlag D. Alkaline phosphatase catalysis is ultrasensitive to charge sequestered between the active site zinc ions. Journal of the American Chemical Society. 127: 9314-5. PMID 15984827 DOI: 10.1021/Ja051603J  0.613
2004 Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T. Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature. 432: 473-8. PMID 15565146 DOI: 10.1038/Nature03082  0.475
2004 O'Brien PJ, Ellenberger T. The Escherichia coli 3-methyladenine DNA glycosylase AlkA has a remarkably versatile active site. The Journal of Biological Chemistry. 279: 26876-84. PMID 15126496 DOI: 10.1074/Jbc.M403860200  0.516
2004 O'Brien PJ, Ellenberger T. Dissecting the broad substrate specificity of human 3-methyladenine-DNA glycosylase. The Journal of Biological Chemistry. 279: 9750-7. PMID 14688248 DOI: 10.1074/Jbc.M312232200  0.448
2003 O'Brien PJ, Ellenberger T. Human alkyladenine DNA glycosylase uses acid-base catalysis for selective excision of damaged purines. Biochemistry. 42: 12418-29. PMID 14567703 DOI: 10.1021/Bi035177V  0.513
2002 O'Brien PJ, Herschlag D. Alkaline Phosphatase Revisited:  Hydrolysis of Alkyl Phosphates (†). Biochemistry. 41: 3207-3225. PMID 28212002 DOI: 10.1021/bi012166y  0.572
2002 Cheng H, Nikolic-Hughes I, Wang JH, Deng H, O'Brien PJ, Wu L, Zhang ZY, Herschlag D, Callender R. Environmental effects on phosphoryl group bonding probed by vibrational spectroscopy: implications for understanding phosphoryl transfer and enzymatic catalysis. Journal of the American Chemical Society. 124: 11295-306. PMID 12236744 DOI: 10.1021/Ja026481Z  0.512
2002 O'Brien PJ, Herschlag D. Alkaline phosphatase revisited: hydrolysis of alkyl phosphates. Biochemistry. 41: 3207-25. PMID 11863460 DOI: 10.1021/Bi012166Y  0.609
2001 O'Brien PJ, Herschlag D. Functional interrelationships in the alkaline phosphatase superfamily: phosphodiesterase activity of Escherichia coli alkaline phosphatase. Biochemistry. 40: 5691-9. PMID 11341834 DOI: 10.1021/Bi0028892  0.594
1999 O'Brien PJ, Herschlag D. Catalytic promiscuity and the evolution of new enzymatic activities. Chemistry & Biology. 6: R91-R105. PMID 10099128 DOI: 10.1016/S1074-5521(99)80033-7  0.568
1999 O'Brien PJ, Herschlag D. Does the active site arginine change the nature of the transition state for alkaline phosphatase-catalyzed phosphoryl transfer? [[11] Journal of the American Chemical Society. 121: 11022-11023. DOI: 10.1021/Ja9932582  0.588
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