2013
Conformational 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
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
2003
An error‐prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a ‘steric gate’ residue for discrimination against ribonucleotides
DeLucia A, Grindley N, Joyce C. An error‐prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a ‘steric gate’ residue for discrimination against ribonucleotides. Nucleic Acids Research 2003, 31: 4129-4137. PMID: 12853630, PMCID: PMC165950, DOI: 10.1093/nar/gkg417.Peer-Reviewed Original Research
2002
Cryptic 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
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 ResearchMeSH KeywordsDNA Transposable ElementsExodeoxyribonuclease VExodeoxyribonucleasesMolecular Sequence DataMutagenesis, InsertionalMycobacterium smegmatisSequence Analysis, DNATransposasesConceptsDNA sequencingTarget DNAEntire operonInsertion mutantsGene clusterGenetic toolsNucleotide sequenceSequence specificityUnique sequencesMolecular biologyTransposition reactionNovel transposonTransposonSequencingComprehensive collectionDNAArsenal of toolsSequenceOperonGenomicsMutantsCosmidsMutagenesisKbBiology