2019
Duplication of an Insertion Sequence During Transpositional Recombination
Weinert T, Schaus N, Grindley N. Duplication of an Insertion Sequence During Transpositional Recombination. 2019, 365-377. DOI: 10.4324/9780429050329-29.Peer-Reviewed Original Research
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
2012
Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end
Bai H, Kath J, Zörgiebel F, Sun M, Ghosh P, Hatfull G, Grindley N, Marko J. Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 16546-16551. PMID: 23011800, PMCID: PMC3478594, DOI: 10.1073/pnas.1203118109.Peer-Reviewed Original ResearchRemote Control of DNA-Acting Enzymes by Molecular Boundary Conditions
Bai H, Kath J, Zorgebiel F, Grindley N, Marko J. Remote Control of DNA-Acting Enzymes by Molecular Boundary Conditions. Biophysical Journal 2012, 102: 70a. DOI: 10.1016/j.bpj.2011.11.412.Peer-Reviewed Original Research
2011
Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase
Bai H, Sun M, Ghosh P, Hatfull GF, Grindley ND, Marko JF. Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 7419-7424. PMID: 21502527, PMCID: PMC3088605, DOI: 10.1073/pnas.1018436108.Peer-Reviewed Original ResearchNovel Conformational States in Mutator DNA Polymerases Observed Using Single-Molecule FRET
Hohlbein J, Joyce C, Shoolizadeh P, Evans G, Potapova O, Bermek O, Duchillumigusin D, Grindley N, Kapanidis A. Novel Conformational States in Mutator DNA Polymerases Observed Using Single-Molecule FRET. Biophysical Journal 2011, 100: 240a-241a. DOI: 10.1016/j.bpj.2010.12.1532.Peer-Reviewed Original Research
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 ResearchSeparating Static and Dynamic Heterogeneity in Single-Molecule FRET Experiments with Burst Variance Analysis (BVA)
Torella J, Santoso Y, Holden S, Hohlbein J, Joyce C, Potapova O, Grindley N, Kapanidis A. Separating Static and Dynamic Heterogeneity in Single-Molecule FRET Experiments with Burst Variance Analysis (BVA). Biophysical Journal 2010, 98: 591a. DOI: 10.1016/j.bpj.2009.12.3213.Peer-Reviewed Original ResearchConformational Changes in DNA Polymerase I Revealed by Single-Molecule FRET
Santoso Y, Joyce C, Potapova O, Le Reste L, Hohlbein J, Torella J, Grindley N, Kapanidis A. Conformational Changes in DNA Polymerase I Revealed by Single-Molecule FRET. Biophysical Journal 2010, 98: 436a-437a. DOI: 10.1016/j.bpj.2009.12.2370.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 structureSingle-molecule Study of Site-specific DNA Recombination by γδ Resolvase
Sun M, Bai H, Grindley N, Marko J. Single-molecule Study of Site-specific DNA Recombination by γδ Resolvase. Biophysical Journal 2009, 96: 59a. DOI: 10.1016/j.bpj.2008.12.204.Peer-Reviewed Original Research
2008
Chemical shift mapping of γδ resolvase dimer and activated tetramer: Mechanistic implications for DNA strand exchange
Gehman J, Cocco M, Grindley N. Chemical shift mapping of γδ resolvase dimer and activated tetramer: Mechanistic implications for DNA strand exchange. Biochimica Et Biophysica Acta 2008, 1784: 2086-2092. PMID: 18840551, DOI: 10.1016/j.bbapap.2008.08.023.Peer-Reviewed Original ResearchConceptsDNA strand exchangeStrand exchangeChemical shift mappingWild-type dimerNMR chemical shift assignmentsChemical shift assignmentsDNA recombinaseResolvase dimersX-ray diffraction modelSequence regionsSubunit interfaceTetrameric stateProtomer-protomer interactionsGammadelta resolvaseShift mappingShift assignmentsMechanistic hypothesesStructural variationsResiduesFingers-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, GeneticThe Movement of Tn 3 ‐Like Elements: Transposition and Cointegrate Resolution
Grindley N. The Movement of Tn 3 ‐Like Elements: Transposition and Cointegrate Resolution. 2007, 272-302. DOI: 10.1128/9781555817954.ch14.Peer-Reviewed Original Research
2006
Implications of structures of synaptic tetramers of γδ resolvase for the mechanism of recombination
Kamtekar S, Ho RS, Cocco MJ, Li W, Wenwieser SV, Boocock MR, Grindley ND, Steitz TA. Implications of structures of synaptic tetramers of γδ resolvase for the mechanism of recombination. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 10642-10647. PMID: 16807292, PMCID: PMC1483221, DOI: 10.1073/pnas.0604062103.Peer-Reviewed Original ResearchThe 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 ResearchMechanisms 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
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