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 bindingConformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion
Hohlbein J, Aigrain L, Craggs T, Bermek O, Potapova O, Shoolizadeh P, Grindley N, Joyce C, Kapanidis A. Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion. Nature Communications 2013, 4: 2131. PMID: 23831915, PMCID: PMC3715850, DOI: 10.1038/ncomms3131.Peer-Reviewed Original ResearchConceptsClosed conformationDNA polymerase IIncorrect nucleotidesPolymerase ITernary complexSingle-molecule FRETActive site side chainsNucleotide selectionMutator phenotypeFidelity checkpointPrimary checkpointPhosphoryl transferFidelity mutantsConformational changesConformational landscapeDNA polymeraseNucleotide insertionConformational transitionDNA synthesisFRET valuesNucleotidesFree energy landscapeReduced affinityCheckpointConformation
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
2007
Conformational Changes during Normal and Error-Prone Incorporation of Nucleotides by a Y-Family DNA Polymerase Detected by 2-Aminopurine Fluorescence †
DeLucia A, Grindley N, Joyce C. Conformational Changes during Normal and Error-Prone Incorporation of Nucleotides by a Y-Family DNA Polymerase Detected by 2-Aminopurine Fluorescence †. Biochemistry 2007, 46: 10790-10803. PMID: 17725324, DOI: 10.1021/bi7006756.Peer-Reviewed Original Research2-AminopurineArchaeal ProteinsBase Pair MismatchBase SequenceDeoxyribonucleotidesDNA Polymerase betaDNA Polymerase IDNA RepairDNA ReplicationDNA-Directed DNA PolymeraseFluorescent DyesFrameshift MutationModels, MolecularMolecular Sequence DataMutagenesis, InsertionalNucleic Acid ConformationSpectrometry, FluorescenceSubstrate SpecificitySulfolobusTemplates, Genetic
2005
DNA Polymerase Catalysis in the Absence of Watson−Crick Hydrogen Bonds: Analysis by Single-Turnover Kinetics †
Potapova O, Chan C, DeLucia A, Helquist S, Kool E, Grindley N, Joyce C. DNA Polymerase Catalysis in the Absence of Watson−Crick Hydrogen Bonds: Analysis by Single-Turnover Kinetics †. Biochemistry 2005, 45: 890-898. PMID: 16411765, PMCID: PMC2567902, DOI: 10.1021/bi051792i.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 ResearchInteraction of DNA Polymerase I (Klenow Fragment) with the Single-Stranded Template beyond the Site of Synthesis †
Turner R, Grindley N, Joyce C. Interaction of DNA Polymerase I (Klenow Fragment) with the Single-Stranded Template beyond the Site of Synthesis †. Biochemistry 2003, 42: 2373-2385. PMID: 12600204, DOI: 10.1021/bi026566c.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
Contacts between the 5′ Nuclease of DNA Polymerase I and Its DNA Substrate*
Xu Y, Potapova O, Leschziner A, Grindley N, Joyce C. Contacts between the 5′ Nuclease of DNA Polymerase I and Its DNA Substrate*. Journal Of Biological Chemistry 2001, 276: 30167-30177. PMID: 11349126, DOI: 10.1074/jbc.m100985200.Peer-Reviewed Original ResearchMeSH KeywordsArginineBase SequenceBinding SitesCircular DichroismDNADNA Polymerase IDNA RepairEscherichia coliKineticsLysineModels, ChemicalModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedMutationOrganophosphorus CompoundsPhosphatesProtein BindingProtein Structure, TertiarySubstrate SpecificityTemperatureTime FactorsConceptsDNA substratesDNA polymerase INuclease domainCleavage siteBasic residuesPolymerase IDuplex DNANuclease cleavagePhosphate ethylation interferenceDNA-binding regionActive site regionDNA replicationOne-half turnBacteriophage T5Eukaryotic nucleasesSubstrate bindingAbasic DNAEthylation interferenceDuplex portionHelical archNucleaseSite regionEscherichia coliMethylphosphonate substitutionsPrimer strand
2000
Coordination between the Polymerase and 5′-Nuclease Components of DNA Polymerase I of Escherichia coli *
Xu Y, Grindley N, Joyce C. Coordination between the Polymerase and 5′-Nuclease Components of DNA Polymerase I of Escherichia coli *. Journal Of Biological Chemistry 2000, 275: 20949-20955. PMID: 10806216, DOI: 10.1074/jbc.m909135199.Peer-Reviewed Original Research
1998
How E. coli DNA polymerase I (klenow fragment) distinguishes between deoxy- and dideoxynucleotides11Edited by A. R Fersht
Astatke M, Grindley N, Joyce C. How E. coli DNA polymerase I (klenow fragment) distinguishes between deoxy- and dideoxynucleotides11Edited by A. R Fersht. Journal Of Molecular Biology 1998, 278: 147-165. PMID: 9571040, DOI: 10.1006/jmbi.1998.1672.Peer-Reviewed Original ResearchConceptsMutant derivativesWild-type Klenow fragmentKlenow fragmentTernary complexAmino acid residuesE. coli DNA polymerase IIncorporation of dNTPsDNA polymerase IDNTP ternary complexPolymerase IAcid residuesPhosphoryl transferState kinetic parametersConformational changesNatural substratePositions 762DNA polymeraseEnzyme DNAKlenow fragment DNA polymeraseDNTPsIncoming dNTPDNTPSide chain resultsRibose moietyDideoxynucleotidesA single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides
Astatke M, Ng K, Grindley N, Joyce C. A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 3402-3407. PMID: 9520378, PMCID: PMC19848, DOI: 10.1073/pnas.95.7.3402.Peer-Reviewed Original Research
1997
Biochemical and mutational studies of the 5′-3′ exonuclease of DNA polymerase I of Escherichia coli11Edited by A. R. Fersht
Xu Y, Derbyshire V, Ng K, Sun X, Grindley N, Joyce C. Biochemical and mutational studies of the 5′-3′ exonuclease of DNA polymerase I of Escherichia coli11Edited by A. R. Fersht. Journal Of Molecular Biology 1997, 268: 284-302. PMID: 9159471, DOI: 10.1006/jmbi.1997.0967.Peer-Reviewed Original Research
1995
Deoxynucleoside Triphosphate and Pyrophosphate Binding Sites in the Catalytically Competent Ternary Complex for the Polymerase Reaction Catalyzed by DNA Polymerase I (Klenow Fragment) (∗)
Astatke M, Grindley N, Joyce C. Deoxynucleoside Triphosphate and Pyrophosphate Binding Sites in the Catalytically Competent Ternary Complex for the Polymerase Reaction Catalyzed by DNA Polymerase I (Klenow Fragment) (∗). Journal Of Biological Chemistry 1995, 270: 1945-1954. PMID: 7829532, DOI: 10.1074/jbc.270.4.1945.Peer-Reviewed Original ResearchAmino Acid SequenceBacteriaBase SequenceBinding SitesConserved SequenceDeoxyribonucleotidesDiphosphatesDNA Polymerase IDNA PrimersKineticsMacromolecular SubstancesModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedOligodeoxyribonucleotidesPoint MutationPolymerase Chain ReactionProtein Structure, SecondarySaccharomyces cerevisiaeSequence Homology, Amino Acid
1992
Reactions at the polymerase active site that contribute to the fidelity of Escherichia coli DNA polymerase I (Klenow fragment).
Joyce C, Sun X, Grindley N. Reactions at the polymerase active site that contribute to the fidelity of Escherichia coli DNA polymerase I (Klenow fragment). Journal Of Biological Chemistry 1992, 267: 24485-24500. PMID: 1447195, DOI: 10.1016/s0021-9258(18)35792-2.Peer-Reviewed Original ResearchSide chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli.
Polesky A, Dahlberg M, Benkovic S, Grindley N, Joyce C. Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli. Journal Of Biological Chemistry 1992, 267: 8417-8428. PMID: 1569092, DOI: 10.1016/s0021-9258(18)42461-1.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
Identification 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