title: DNA Y structure: a versatile, multidimensional single molecule assay.
abstract: Optical trapping is a powerful single molecule technique used to study dynamic biomolecular events, especially those involving DNA and DNA-binding proteins. Current implementations usually involve only one of stretching, unzipping, or twisting DNA along one dimension. To expand the capabilities of optical trapping for more complex measurements would require a multidimensional technique that combines all of these manipulations in a single experiment. Here, we report the development and utilization of such a novel optical trapping assay based on a three-branch DNA construct, termed a "Y structure". This multidimensional assay allows precise, real-time tracking of multiple configurational changes. When the Y structure template is unzipped under both force and torque, the force and extension of all three branches can be determined simultaneously. Moreover, the assay is readily compatible with fluorescence, as demonstrated by unzipping through a fluorescently labeled, paused transcription complex. This novel assay thus allows for the visualization and precision mapping of complex interactions of biomechanical events.
authors.affiliation: Department of Physics, LASSP and ‡Howard Hughes Medical Institute, Cornell University , Ithaca, New York 14853, United States.
authors.forename: James T
authors.initials: JT
authors.lastname: Inman
authors.forename: Benjamin Y
authors.initials: BY
authors.lastname: Smith
authors.forename: Michael A
authors.initials: MA
authors.lastname: Hall
authors.forename: Robert A
authors.initials: RA
authors.lastname: Forties
authors.forename: Jing
authors.initials: J
authors.lastname: Jin
authors.forename: James P
authors.initials: JP
authors.lastname: Sethna
authors.forename: Michelle D
authors.initials: MD
authors.lastname: Wang
mesh_terms: D004247:DNA / Q000737:chemistry*; D005453:Fluorescence; D055595:Mechanical Phenomena; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D052898:Optical Tweezers
chemical_list: D004247:DNA
keywords: DNA Y structure; DNA torque; Optical tweezers; force spectroscopy; single molecule; unzipping DNA