2013
High-resolution optical tweezers for single-molecule manipulation.
Zhang X, Ma L, Zhang Y. High-resolution optical tweezers for single-molecule manipulation. The Yale Journal Of Biology And Medicine 2013, 86: 367-83. PMID: 24058311, PMCID: PMC3767221.Peer-Reviewed Original ResearchConceptsHigh-resolution optical tweezersOptical tweezersComplex multi-scale dynamicsATP-dependent chromatinDynamics of biomacromoleculesSingle-molecule manipulationSingle-molecule levelMolecular motorsTweezersChromatin structureSNARE complexProtein foldingCoil proteinsBiomacromoleculesMulti-scale dynamicsConformational fluctuationsTranslocation propertiesTiny forceUnprecedented resolutionDirectional movementMicron distancesComplexesFoldingRevolutionary toolUnique advantages
2012
Single Reconstituted Neuronal SNARE Complexes Zipper in Three Distinct Stages
Gao Y, Zorman S, Gundersen G, Xi Z, Ma L, Sirinakis G, Rothman JE, Zhang Y. Single Reconstituted Neuronal SNARE Complexes Zipper in Three Distinct Stages. Science 2012, 337: 1340-1343. PMID: 22903523, PMCID: PMC3677750, DOI: 10.1126/science.1224492.Peer-Reviewed Original ResearchSingle-molecule observation of helix staggering, sliding, and coiled coil misfolding
Xi Z, Gao Y, Sirinakis G, Guo H, Zhang Y. Single-molecule observation of helix staggering, sliding, and coiled coil misfolding. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 5711-5716. PMID: 22451899, PMCID: PMC3326506, DOI: 10.1073/pnas.1116784109.Peer-Reviewed Original ResearchChapter 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
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
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 Research