title: Sequence-dependent base pair stepping dynamics in XPD helicase unwinding.
abstract: Helicases couple the chemical energy of ATP hydrolysis to directional translocation along nucleic acids and transient duplex separation. Understanding helicase mechanism requires that the basic physicochemical process of base pair separation be understood. This necessitates monitoring helicase activity directly, at high spatio-temporal resolution. Using optical tweezers with single base pair (bp) resolution, we analyzed DNA unwinding by XPD helicase, a Superfamily 2 (SF2) DNA helicase involved in DNA repair and transcription initiation. We show that monomeric XPD unwinds duplex DNA in 1-bp steps, yet exhibits frequent backsteps and undergoes conformational transitions manifested in 5-bp backward and forward steps. Quantifying the sequence dependence of XPD stepping dynamics with near base pair resolution, we provide the strongest and most direct evidence thus far that forward, single-base pair stepping of a helicase utilizes the spontaneous opening of the duplex. The proposed unwinding mechanism may be a universal feature of DNA helicases that move along DNA phosphodiester backbones. DOI:http://dx.doi.org/10.7554/eLife.00334.001.
authors.affiliation: Center for Biophysics and Computational Biology , University of Illinois at Urbana-Champaign , Urbana , United States.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Qi
authors.forename: Robert A
authors.initials: RA
authors.lastname: Pugh
authors.forename: Maria
authors.initials: M
authors.lastname: Spies
authors.forename: Yann R
authors.initials: YR
authors.lastname: Chemla
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D019843:Archaeal Proteins / Q000737:chemistry / Q000378:metabolism*; D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004260:DNA Repair; D004261:DNA Replication; D006868:Hydrolysis; D007700:Kinetics; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D052898:Optical Tweezers; D012313:RNA / Q000096:biosynthesis; D013269:Stochastic Processes; D061785:Transcription Initiation, Genetic; D051759:Xeroderma Pigmentosum Group D Protein / Q000737:chemistry / Q000378:metabolism*
chemical_list: D019843:Archaeal Proteins; D012313:RNA; D000255:Adenosine Triphosphate; D004247:DNA; D051759:Xeroderma Pigmentosum Group D Protein
keywords: DNA repair; None; Xeroderma pigmentosum group D helicase; helicase; molecular motor; optical tweezers; single molecule