2012
Chapter One DNA Translocation of ATP-Dependent Chromatin Remodeling Factors Revealed by High-Resolution Optical Tweezers
Zhang Y, Sirinakis G, Gundersen G, Xi Z, Gao Y. Chapter One DNA Translocation of ATP-Dependent Chromatin Remodeling Factors Revealed by High-Resolution Optical Tweezers. Methods In Enzymology 2012, 513: 3-28. PMID: 22929763, DOI: 10.1016/b978-0-12-391938-0.00001-x.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAdenosine TriphosphateBase SequenceBinding SitesChromatin Assembly and DisassemblyDNADNA HelicasesElectrophoresis, Polyacrylamide GelEscherichia coliMicroscopy, Atomic ForceMolecular Sequence DataNucleic Acid ConformationNucleosomesOptical TweezersPlasmidsTandem Repeat SequencesConceptsChromatin remodelingChromatin structureDNA translocationATP-dependent chromatin remodeling factorsATP-dependent chromatin remodelingATP-dependent chromatinChromatin remodeling factorsDNA moleculesOptical tweezersHigh-resolution optical tweezersSingle-molecule assaysRemodeler ATPasesDNA translocasesRemodeling factorsSingle DNA moleculesDNA substratesSingle-molecule levelATP hydrolysisBiological functionsBare DNASingle-molecule experimentsMolecular mechanismsDetailed protocolTranslocationMolecular motors
2011
The RSC chromatin remodelling ATPase translocates DNA with high force and small step size
Sirinakis G, Clapier CR, Gao Y, Viswanathan R, Cairns BR, Zhang Y. The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. The EMBO Journal 2011, 30: 2364-2372. PMID: 21552204, PMCID: PMC3116276, DOI: 10.1038/emboj.2011.141.Peer-Reviewed Original ResearchConceptsATP-dependent chromatinHigh-resolution optical tweezersDNA-histone interactionsBp/sDNA translocation processRSC chromatinATPase domainTranslocase systemDiverse functionsATP hydrolysisBare DNATranslocation processBiophysical knowledgeDNAChromatinNucleosomesMechanical forcesBPForce generationRemodellersTranslocaseProcessivityTranslocationATPaseOptical tweezers
2010
Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA
Xi Z, Zhang Y, Hegde RS, Shakked Z, Crothers DM. Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA. Nucleic Acids Research 2010, 38: 3827-3833. PMID: 20185566, PMCID: PMC2887970, DOI: 10.1093/nar/gkq114.Peer-Reviewed Original Research
2006
Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping
Zhang Y, McEwen AE, Crothers DM, Levene SD. Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping. PLOS ONE 2006, 1: e136. PMID: 17205140, PMCID: PMC1762422, DOI: 10.1371/journal.pone.0000136.Peer-Reviewed Original ResearchConceptsGene regulationNucleoprotein complexesNon-specific DNA-binding proteinE. coli lac repressorWild-type E. coli strainDNA-binding proteinsSmall DNA loopsSame DNA moleculeGene repressionDNA loopingDNA loopsOperator sitesOperator affinityDNA rigidityLac repressorE. coli strainsProtein conformationDNA persistence lengthDNA moleculesRepressor concentrationRepressionColi strainsDNARegulationVivo
2005
Statistical-Mechanical Theory of DNA Looping
Zhang Y, McEwen AE, Crothers DM, Levene SD. Statistical-Mechanical Theory of DNA Looping. Biophysical Journal 2005, 90: 1903-1912. PMID: 16361335, PMCID: PMC1386771, DOI: 10.1529/biophysj.105.070490.Peer-Reviewed Original ResearchConceptsMechanical theoryRigorous analytical theoryStatistical mechanical theoryMechanics of DNARigorous theoryAnalytical theoryGeometric propertiesAccount protein flexibilityTopological constraintsTheoryDNA cyclizationTerms of amplitudeLoop topologyStrong couplingProtein geometryMultiple classesTheoretical similaritiesDependenceMechanicsLoop closureGeometryTopologyDNA length dependenceWritheLoop
2004
Predicting indirect readout effects in protein–DNA interactions
Zhang Y, Xi Z, Hegde RS, Shakked Z, Crothers DM. Predicting indirect readout effects in protein–DNA interactions. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 8337-8341. PMID: 15148366, PMCID: PMC420395, DOI: 10.1073/pnas.0402319101.Peer-Reviewed Original Research
2003
High-throughput approach for detection of DNA bending and flexibility based on cyclization
Zhang Y, Crothers DM. High-throughput approach for detection of DNA bending and flexibility based on cyclization. Proceedings Of The National Academy Of Sciences Of The United States Of America 2003, 100: 3161-3166. PMID: 12629220, PMCID: PMC152263, DOI: 10.1073/pnas.0530189100.Peer-Reviewed Original ResearchStatistical Mechanics of Sequence-Dependent Circular DNA and Its Application For DNA Cyclization
Zhang Y, Crothers DM. Statistical Mechanics of Sequence-Dependent Circular DNA and Its Application For DNA Cyclization. Biophysical Journal 2003, 84: 136-153. PMID: 12524271, PMCID: PMC1302599, DOI: 10.1016/s0006-3495(03)74838-3.Peer-Reviewed Original ResearchConceptsStatistical mechanicsAccurate analytic expressionsInhomogeneous DNAMonte Carlo simulationsAnalytic expressionsPartition functionHarmonic approximationEffect of curvatureCarlo simulationsEquilibrium configurationsLinear formThermal fluctuationsThermodynamic quantitiesSequence-dependent DNA bendingDNA cyclizationMinimum energy configurationIterative searchNew theoryMechanicsJ factorEnergy configurationTheoryCurvatureSimulationsApproximation