title: Simultaneous, coincident optical trapping and single-molecule fluorescence.
abstract: We constructed a microscope-based instrument capable of simultaneous, spatially coincident optical trapping and single-molecule fluorescence. The capabilities of this apparatus were demonstrated by studying the force-induced strand separation of a dye-labeled, 15-base-pair region of double-stranded DNA (dsDNA), with force applied either parallel ('unzipping' mode) or perpendicular ('shearing' mode) to the long axis of the region. Mechanical transitions corresponding to DNA hybrid rupture occurred simultaneously with discontinuous changes in the fluorescence emission. The rupture force was strongly dependent on the direction of applied force, indicating the existence of distinct unbinding pathways for the two force-loading modes. From the rupture force histograms, we determined the distance to the thermodynamic transition state and the thermal off rates in the absence of load for both processes.
authors.affiliation: Department of Biological Sciences, Stanford University, Stanford, California 94305, USA.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Lang
authors.forename: Polly M
authors.initials: PM
authors.lastname: Fordyce
authors.forename: Anita M
authors.initials: AM
authors.lastname: Engh
authors.forename: Keir C
authors.initials: KC
authors.lastname: Neuman
authors.forename: Steven M
authors.initials: SM
authors.lastname: Block
mesh_terms: D004247:DNA / Q000032:analysis* / Q000737:chemistry*; D004548:Elasticity; D004867:Equipment Design; D019544:Equipment Failure Analysis; D007834:Lasers; D008846:Micromanipulation / Q000295:instrumentation* / Q000379:methods; D008856:Microscopy, Fluorescence / Q000295:instrumentation* / Q000379:methods; D018715:Microscopy, Video / Q000295:instrumentation* / Q000379:methods; D010812:Physical Stimulation / Q000295:instrumentation* / Q000379:methods; D013314:Stress, Mechanical; D018511:Systems Integration
chemical_list: D004247:DNA