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
2006
The Properties of Steric Gate Mutants Reveal Different Constraints within the Active Sites of Y-family and A-family DNA Polymerases*
DeLucia A, Chaudhuri S, Potapova O, Grindley N, Joyce C. The Properties of Steric Gate Mutants Reveal Different Constraints within the Active Sites of Y-family and A-family DNA Polymerases*. Journal Of Biological Chemistry 2006, 281: 27286-27291. PMID: 16831866, DOI: 10.1074/jbc.m604393200.Peer-Reviewed Original Research
2004
The Left End of IS2: a Compromise between Transpositional Activity and an Essential Promoter Function That Regulates the Transposition Pathway
Lewis L, Cylin E, Lee H, Saby R, Wong W, Grindley N. The Left End of IS2: a Compromise between Transpositional Activity and an Essential Promoter Function That Regulates the Transposition Pathway. Journal Of Bacteriology 2004, 186: 858-865. PMID: 14729714, PMCID: PMC321474, DOI: 10.1128/jb.186.3.858-865.2004.Peer-Reviewed Original ResearchBase SequenceDNA Transposable ElementsDNA, CircularMolecular Sequence DataPromoter Regions, GeneticTransposases
2002
The Mutational Specificity of the Dbh Lesion Bypass Polymerase and Its Implications*
Potapova O, Grindley N, Joyce C. The Mutational Specificity of the Dbh Lesion Bypass Polymerase and Its Implications*. Journal Of Biological Chemistry 2002, 277: 28157-28166. PMID: 12023283, DOI: 10.1074/jbc.m202607200.Peer-Reviewed Original ResearchCryptic plasmids of Mycobacterium avium: Tn552 to the rescue
Kirby C, Waring A, Griffin T, Falkinham J, Grindley N, Derbyshire K. Cryptic plasmids of Mycobacterium avium: Tn552 to the rescue. Molecular Microbiology 2002, 43: 173-186. PMID: 11849545, DOI: 10.1046/j.1365-2958.2002.02729.x.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBlotting, SouthernDNA Transposable ElementsDNA, BacterialDNA, CircularMolecular Sequence DataMutagenesis, InsertionalMycobacterium aviumMycobacterium bovisMycobacterium smegmatisPlasmidsReplication OriginRestriction MappingSequence Analysis, DNASequence Homology, Nucleic AcidConceptsEssential genetic toolsCryptic plasmidGenetic toolsOpportunistic pathogen Mycobacterium aviumGenetic exploitationTransposon insertionConjugative relaxaseTransposition systemSelectable markerExtrachromosomal DNAGenetic analysisHost rangePlasmid genesPlasmid originBacterial speciesPlasmid establishmentCircular DNAPlasmidMycobacterium smegmatisGenesMycobacterial plasmidsDNAReplicationMycobacterium aviumRescue
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 strandIn Vitro Transposition System for Efficient Generation of Random Mutants of Campylobacter jejuni
Colegio O, Griffin T, Grindley N, Galán J. In Vitro Transposition System for Efficient Generation of Random Mutants of Campylobacter jejuni. Journal Of Bacteriology 2001, 183: 2384-2388. PMID: 11244083, PMCID: PMC95150, DOI: 10.1128/jb.183.7.2384-2388.2001.Peer-Reviewed Original Research
2000
Identification of Genes Encoding Exported Mycobacterium tuberculosis Proteins Using a Tn552′phoA In Vitro Transposition System
Braunstein M, Griffin T, Kriakov J, Friedman S, Grindley N, Jacobs W. Identification of Genes Encoding Exported Mycobacterium tuberculosis Proteins Using a Tn552′phoA In Vitro Transposition System. Journal Of Bacteriology 2000, 182: 2732-2740. PMID: 10781540, PMCID: PMC101980, DOI: 10.1128/jb.182.10.2732-2740.2000.Peer-Reviewed Original ResearchMeSH KeywordsAlkaline PhosphataseAmino Acid SequenceArtificial Gene FusionBacterial ProteinsBiological TransportCosmidsCyclin-Dependent KinasesDNA Transposable ElementsDNA, BacterialGenes, BacterialGenomic LibraryMolecular Sequence DataMutagenesis, InsertionalMycobacterium tuberculosisPlasmidsReplication OriginConceptsProtective immunityM. tuberculosisMycobacterium tuberculosis pathogenesisImmune responseTuberculosis pathogenesisMycobacterium tuberculosis proteinsM. tuberculosis databaseTuberculosisTuberculosis databasePathogenesisTuberculosis proteinsImmunityEnvelope-associated proteinsM. smegmatisProteinPeptides
1999
In vitro transposition of Tn552: A tool for DNA sequencing and mutagenesis
Griffin T, Leschziner A, Grindley N, Parsons L, DeVost J, Derbyshire K. In vitro transposition of Tn552: A tool for DNA sequencing and mutagenesis. Nucleic Acids Research 1999, 27: 3859-3865. PMID: 10481025, PMCID: PMC148649, DOI: 10.1093/nar/27.19.3859.Peer-Reviewed Original ResearchConceptsDNA sequencingTarget DNAEntire operonInsertion mutantsGene clusterGenetic toolsNucleotide sequenceSequence specificityUnique sequencesMolecular biologyTransposition reactionNovel transposonTransposonSequencingComprehensive collectionDNAArsenal of toolsSequenceOperonGenomicsMutantsCosmidsMutagenesisKbBiology
1998
Architecture of the γδ Resolvase Synaptosome Oriented Heterodimers Identify Interactions Essential for Synapsis and Recombination
Murley L, Grindley N. Architecture of the γδ Resolvase Synaptosome Oriented Heterodimers Identify Interactions Essential for Synapsis and Recombination. Cell 1998, 95: 553-562. PMID: 9827807, DOI: 10.1016/s0092-8674(00)81622-0.Peer-Reviewed Original ResearchTn552 transposase catalyzes concerted strand transfer in vitro
Leschziner A, Griffin T, Grindley N. Tn552 transposase catalyzes concerted strand transfer in vitro. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 7345-7350. PMID: 9636151, PMCID: PMC22612, DOI: 10.1073/pnas.95.13.7345.Peer-Reviewed Original ResearchHow 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
1997
Two abundant intramolecular transposition products, resulting from reactions initiated at a single end, suggest that IS2 transposes by an unconventional pathway
Lewis L, Grindley N. Two abundant intramolecular transposition products, resulting from reactions initiated at a single end, suggest that IS2 transposes by an unconventional pathway. Molecular Microbiology 1997, 25: 517-529. PMID: 9302014, DOI: 10.1046/j.1365-2958.1997.4871848.x.Peer-Reviewed Original ResearchBacterial ProteinsBase SequenceBinding SitesCloning, MolecularDNA NucleotidyltransferasesDNA PrimersDNA Transposable ElementsDNA, BacterialDNA, CircularEscherichia coliEscherichia coli ProteinsMicroscopy, ElectronModels, GeneticMolecular Sequence DataNucleic Acid ConformationPolymerase Chain ReactionRecombinant Fusion ProteinsTransposasesBiochemical 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
Catalytic residues of gamma delta resolvase act in cis.
Boocock M, Zhu X, Grindley N. Catalytic residues of gamma delta resolvase act in cis. The EMBO Journal 1995, 14: 5129-5140. PMID: 7588641, PMCID: PMC394616, DOI: 10.1002/j.1460-2075.1995.tb00195.x.Peer-Reviewed Original ResearchBase SequenceBinding SitesCrossing Over, GeneticDNA NucleotidyltransferasesDNA Topoisomerases, Type IDNA Transposable ElementsGenetic Complementation TestModels, GeneticModels, MolecularMolecular Sequence DataPlasmidsRecombination, GeneticStructure-Activity RelationshipSubstrate SpecificityTransposasesA functional analysis of the inverted repeat of the gamma delta transposable element.
May E, Grindley N. A functional analysis of the inverted repeat of the gamma delta transposable element. Journal Of Molecular Biology 1995, 247: 578-87. PMID: 7723015, DOI: 10.1006/jmbi.1995.0164.Peer-Reviewed Original ResearchConceptsIntegration host factorInverted repeatsBase pairsTransposable elementsTransposase bindingGroove contactsIHF siteReduced transposition activityTerminal inverted repeatsMinor groove contactsBase pair regionGamma delta transposaseBase pair stretchSusceptible to mutationsTransposon gamma deltaTn3 familyTransposition activityPoint mutantsTarget plasmidTransposition defectBinding regionMutationsBinding sitesBinding contactsHost factorsA functional analysis of the inverted repeat of the γδ transposable element
May E, Grindley N. A functional analysis of the inverted repeat of the γδ transposable element. Journal Of Molecular Biology 1995, 247: 578-587. DOI: 10.1016/s0022-2836(05)80139-1.Peer-Reviewed Original ResearchThe tyrosine‐6 hydroxyl of γδ resolvase is not required for the DNA cleavage and rejoining reactions
Leschziner A, Boocock M, Grindley N. The tyrosine‐6 hydroxyl of γδ resolvase is not required for the DNA cleavage and rejoining reactions. Molecular Microbiology 1995, 15: 865-870. PMID: 7596288, DOI: 10.1111/j.1365-2958.1995.tb02356.x.Peer-Reviewed Original ResearchDeoxynucleoside 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
1993
Analysis of a Nucleoprotein Complex: the Synaptosome of γδ Resolvase
Grindley N. Analysis of a Nucleoprotein Complex: the Synaptosome of γδ Resolvase. Science 1993, 262: 738-740. PMID: 8235593, DOI: 10.1126/science.8235593.Peer-Reviewed Original Research