2013
Prechemistry Nucleotide Selection Checkpoints in the Reaction Pathway of DNA Polymerase I and Roles of Glu710 and Tyr766
Bermek O, Grindley N, Joyce C. Prechemistry Nucleotide Selection Checkpoints in the Reaction Pathway of DNA Polymerase I and Roles of Glu710 and Tyr766. Biochemistry 2013, 52: 6258-6274. PMID: 23937394, PMCID: PMC3770053, DOI: 10.1021/bi400837k.Peer-Reviewed Original ResearchConceptsFidelity checkpointDNA polymerase IPolymerase IHigh-fidelity DNA polymeraseMutator allelesCheckpoint functionMutator polymeraseIncorrect base pairsSelection checkpointDNA templateConformational changesSubstrate poolBase pairsDNA polymeraseComplementary nucleotidesCheckpointNoncomplementary nucleotidesTemplating baseFinger closingPolymeraseDNTPsNucleotidesCorrect incomingPathwayWeak binding
2010
Distinct Roles of the Active-site Mg2+ Ligands, Asp882 and Asp705, of DNA Polymerase I (Klenow Fragment) during the Prechemistry Conformational Transitions*
Bermek O, Grindley ND, Joyce CM. Distinct Roles of the Active-site Mg2+ Ligands, Asp882 and Asp705, of DNA Polymerase I (Klenow Fragment) during the Prechemistry Conformational Transitions*. Journal Of Biological Chemistry 2010, 286: 3755-3766. PMID: 21084297, PMCID: PMC3030377, DOI: 10.1074/jbc.m110.167593.Peer-Reviewed Original Research
2009
Conformational transitions in DNA polymerase I revealed by single-molecule FRET
Santoso Y, Joyce CM, Potapova O, Le Reste L, Hohlbein J, Torella JP, Grindley ND, Kapanidis AN. Conformational transitions in DNA polymerase I revealed by single-molecule FRET. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 107: 715-720. PMID: 20080740, PMCID: PMC2818957, DOI: 10.1073/pnas.0910909107.Peer-Reviewed Original ResearchConceptsDNA polymerase IClosed conformationPolymerase IConformational transitionSingle-molecule fluorescence resonance energy transferEarly stepsSingle-molecule FRETFluorescence resonance energy transferAvailable crystallographic structuresResonance energy transferMost DNA polymerasesComplementary ribonucleotidesChemical stepIncorrect substratesPolymerase moleculesPol DNAReaction pathwaysAcceptor fluorophoresKinetic checkpointsConformational dynamicsConformational flexibilityNucleotide additionStructural studiesDNA polymeraseCrystallographic structure
2008
Fingers-Closing and Other Rapid Conformational Changes in DNA Polymerase I (Klenow Fragment) and Their Role in Nucleotide Selectivity
Joyce CM, Potapova O, DeLucia AM, Huang X, Basu VP, Grindley ND. Fingers-Closing and Other Rapid Conformational Changes in DNA Polymerase I (Klenow Fragment) and Their Role in Nucleotide Selectivity. Biochemistry 2008, 47: 6103-6116. PMID: 18473481, DOI: 10.1021/bi7021848.Peer-Reviewed Original Research
2006
Mechanisms of Site-Specific Recombination*
Grindley ND, Whiteson KL, Rice PA. Mechanisms of Site-Specific Recombination*. Annual Review Of Biochemistry 2006, 75: 567-605. PMID: 16756503, DOI: 10.1146/annurev.biochem.73.011303.073908.Peer-Reviewed Original Research
2003
Use of 2-Aminopurine Fluorescence To Examine Conformational Changes during Nucleotide Incorporation by DNA Polymerase I (Klenow Fragment) †
Purohit V, Grindley N, Joyce C. Use of 2-Aminopurine Fluorescence To Examine Conformational Changes during Nucleotide Incorporation by DNA Polymerase I (Klenow Fragment) †. Biochemistry 2003, 42: 10200-10211. PMID: 12939148, DOI: 10.1021/bi0341206.Peer-Reviewed Original Research
2002
Discrimination against purine–pyrimidine mispairs in the polymerase active site of DNA polymerase I: A structural explanation
Minnick D, Liu L, Grindley N, Kunkel T, Joyce C. Discrimination against purine–pyrimidine mispairs in the polymerase active site of DNA polymerase I: A structural explanation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2002, 99: 1194-1199. PMID: 11830658, PMCID: PMC122166, DOI: 10.1073/pnas.032457899.Peer-Reviewed Original Research
2001
A Model for the γδ Resolvase Synaptic Complex
Sarkis G, Murley L, Leschziner A, Boocock M, Stark W, Grindley N. A Model for the γδ Resolvase Synaptic Complex. Molecular Cell 2001, 8: 623-631. PMID: 11583624, DOI: 10.1016/s1097-2765(01)00334-3.Peer-Reviewed Original Research
1995
DNA transposition: From a black box to a color monitor
Grindley N, Leschziner A. DNA transposition: From a black box to a color monitor. Cell 1995, 83: 1063-1066. PMID: 8548793, DOI: 10.1016/0092-8674(95)90132-9.Peer-Reviewed Original Research
1993
Protein‐protein interactions directing resolvase site‐specific recombination: a structure‐function analysis.
Hughes R, Rice P, Steitz T, Grindley N. Protein‐protein interactions directing resolvase site‐specific recombination: a structure‐function analysis. The EMBO Journal 1993, 12: 1447-1458. PMID: 8385604, PMCID: PMC413356, DOI: 10.1002/j.1460-2075.1993.tb05788.x.Peer-Reviewed Original Research
1991
The 3′‐5′ exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction.
Derbyshire V, Grindley N, Joyce C. The 3′‐5′ exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction. The EMBO Journal 1991, 10: 17-24. PMID: 1989882, PMCID: PMC452606, DOI: 10.1002/j.1460-2075.1991.tb07916.x.Peer-Reviewed Original ResearchConceptsActive siteMetal ionsEnzyme-bound metal ionSide chainsExonuclease reactionDivalent metal ionsAmino acid side chainsCarboxylate side chainAcid side chainsHydroxide ionMetal ligandsNucleophilic attackIonsTerminal phosphodiester bondPhosphodiester bondReactionExonuclease active siteActivity resultsKlenow fragmentDuplex DNA substratesCatalysisChainCarboxylateTerminal baseSubstrate
1990
Cooperativity mutants of the γδ resolvase identify an essential interdimer interaction
Hughes R, Hatfull G, Rice P, Steitz T, Grindley N. Cooperativity mutants of the γδ resolvase identify an essential interdimer interaction. Cell 1990, 63: 1331-1338. PMID: 2175679, DOI: 10.1016/0092-8674(90)90428-h.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsHigher-order protein-protein interactionsCooperativity mutantsSite-specific recombinaseGamma delta resolvaseMutant phenotypeResolvase mutantsNucleoprotein complexesCrystallographic tetramersResolvase dimersΓδ resolvaseResolvaseCooperative bindingMutantsDNARecombinationSide chainsRecombinaseProteinInteractionCointegrate intermediatePhenotypeRecombination reactionBindingTetramerThe crystal structure of the catalytic domain of the site-specific recombination enzyme γδ resolvase at 2.7 Å resolution
Sanderson M, Freemont P, Rice P, Goldman A, Hatfull G, Grindley N, Steitz T. The crystal structure of the catalytic domain of the site-specific recombination enzyme γδ resolvase at 2.7 Å resolution. Cell 1990, 63: 1323-1329. PMID: 2175678, DOI: 10.1016/0092-8674(90)90427-g.Peer-Reviewed Original ResearchIdentification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli.
Polesky A, Steitz T, Grindley N, Joyce C. Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli. Journal Of Biological Chemistry 1990, 265: 14579-14591. PMID: 2201688, DOI: 10.1016/s0021-9258(18)77342-0.Peer-Reviewed Original ResearchConceptsCluster of residuesIdentification of residuesSite-directed mutagenesisActive site residuesAmino acid residuesFuture mutational studiesImportant active site residuesDNA-binding propertiesActive site regionDNA polymerase IGenetic screenPosition 849Polymerase active siteMutant proteinsDNA substratesMutational studiesPolymerase IBiochemical experimentsSite residuesAcid residuesSite regionEscherichia coliPolymerase activityMutationsPolymerase reaction