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
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
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
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 moietyDideoxynucleotides
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
1985
Genetic mapping and DNA sequence analysis of mutations in the polA gene of Escherichia coli
Joyce C, Fujii D, Laks H, Hughes C, Grindley N. Genetic mapping and DNA sequence analysis of mutations in the polA gene of Escherichia coli. Journal Of Molecular Biology 1985, 186: 283-293. PMID: 3910840, DOI: 10.1016/0022-2836(85)90105-6.Peer-Reviewed Original ResearchConceptsDNA sequence analysisDNA polymerase IThree-dimensional structurePolymerase ISequence analysisPolA geneSingle-subunit enzymeEscherichia coliEnzyme-DNA interactionsGenetic mappingDeletion mutantsSubunit enzymeMutant formsPrimary sequenceMutational changesBacteriophage lambdaExcellent modelPolA mutantsPolA mutationEnzymatic behaviorMutantsMutationsGenesDNAColi
1983
Construction of a plasmid that overproduces the large proteolytic fragment (Klenow fragment) of DNA polymerase I of Escherichia coli.
Joyce C, Grindley N. Construction of a plasmid that overproduces the large proteolytic fragment (Klenow fragment) of DNA polymerase I of Escherichia coli. Proceedings Of The National Academy Of Sciences Of The United States Of America 1983, 80: 1830-1834. PMID: 6340110, PMCID: PMC393703, DOI: 10.1073/pnas.80.7.1830.Peer-Reviewed Original ResearchConceptsDNA polymerase IOverproducing strainPolymerase IGene fusion techniquesLarge proteolytic fragmentCellular proteinsLac promoterGene fragmentsProtein structurePhage lambdaLeftward promoterEscherichia coliCarboxyl terminalPolymerase fragmentProteolytic fragmentsKlenow fragmentPromoterPlasmidPurification procedureFragmentsOverproductionExpressionI. MoreoverMechanistic studiesCloning
1982
Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I.
Joyce C, Kelley W, Grindley N. Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I. Journal Of Biological Chemistry 1982, 257: 1958-1964. PMID: 6276402, DOI: 10.1016/s0021-9258(19)68132-9.Peer-Reviewed Original ResearchConceptsDNA polymerase IPolymerase INucleotide sequencePolA geneKilobase pair regionProtein chemical dataAmino acid sequenceWild-type alleleResidues 342Sequence comparisonDNA polymerase I.Polymerase moleculesDNA sequencesResidue 323Acid sequencePair regionPolA1 mutationPolymerase I.Primary structureBase pairsType alleleMild proteolysisGenesActive fragmentSequence
1980
THE PRIMARY STRUCTURE OF DNA POLYMERASE I OF E. COLI11This work was supported by Health and Research Services Foundation grant V-34 (to NDFG), NIH grant GM24688 (to WSK) and ACS Faculty Research Award 198 (to WSK).
Joyce C, Kelley W, Brown W, Grindley N. THE PRIMARY STRUCTURE OF DNA POLYMERASE I OF E. COLI11This work was supported by Health and Research Services Foundation grant V-34 (to NDFG), NIH grant GM24688 (to WSK) and ACS Faculty Research Award 198 (to WSK). 1980, 589-596. DOI: 10.1016/b978-0-12-048850-6.50054-5.Peer-Reviewed Original ResearchDNA polymerase IPolymerase IE. coli polA geneAmino acid sequenceHalf-cystine residuesProteolytic cleavage sitesResidues 342Sequence comparisonDNA polymerase I.DNA sequencesResidue 323Acid sequencePolymerase I.PolA geneNative enzymeCleavage siteAmino acidsSequenceGenesProteinMutationsAllelesEnzymeResiduesTrp
1976
polA6, a mutation affecting the DNA binding capacity of DNA polymerase I
Kelly W, Grindley N. polA6, a mutation affecting the DNA binding capacity of DNA polymerase I. Nucleic Acids Research 1976, 3: 2971-2984. PMID: 12497, PMCID: PMC343145, DOI: 10.1093/nar/3.11.2971.Peer-Reviewed Original ResearchMapping of thepolA locus ofEscherichia coli K12: Orientation of the amino- and carboxy-termini of the cistron
Kelley W, Grindley N. Mapping of thepolA locus ofEscherichia coli K12: Orientation of the amino- and carboxy-termini of the cistron. Molecular Genetics And Genomics 1976, 147: 307-314. PMID: 787765, DOI: 10.1007/bf00582882.Peer-Reviewed Original Research