title: Unzipping single DNA molecules to study nucleosome structure and dynamics.
abstract: DNA unzipping is a powerful tool to study protein-DNA interactions at the single-molecule level. In this chapter, we provide a detailed and practical guide to performing this technique with an optical trap, using nucleosome studies as an example. We detail protocols for preparing an unzipping template, constructing and calibrating the instrument, and acquiring, processing, and analyzing unzipping data. We also summarize major results from utilization of this technique for the studies of nucleosome structure, dynamics, positioning, and remodeling.
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.forename: Michelle D
authors.initials: MD
authors.lastname: Wang
mesh_terms: D001483:Base Sequence; D042002:Chromatin Assembly and Disassembly; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D006657:Histones / Q000737:chemistry / Q000235:genetics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009707:Nucleosomes / Q000737:chemistry* / Q000235:genetics; D052898:Optical Tweezers / Q000592:standards*; D010957:Plasmids / Q000737:chemistry / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods; D013314:Stress, Mechanical; D014157:Transcription Factors / Q000737:chemistry; D015003:Yeasts / Q000737:chemistry
chemical_list: D002868:Chromosomal Proteins, Non-Histone; D006657:Histones; D009707:Nucleosomes; C445179:SWI-SNF-B chromatin-remodeling complex; D014157:Transcription Factors; D004247:DNA