title: Opening of nucleic-acid double strands by helicases: active versus passive opening.
abstract: Helicase proteins move along double-stranded nucleic-acid molecules and unwind the double helix. This paper presents a theoretical study of the coupling between helicase translocation and duplex unwinding. Two different cases-active and passive opening-are usually distinguished. In active opening, the helicase directly destabilizes the double-stranded nucleic acid (dsNA) to promote opening. Passive opening implies that the helicase binds ssNA available when a thermal fluctuation partially opens the dsNA. We formulate a discrete model for helicase motion. An interaction potential describes how the helicase affects duplex unwinding when near a junction between single-stranded and double-stranded NA. Different choices of the potential correspond to the cases of active and passive opening. An optimal choice of interaction potential leads to a helicase which can unwind NA as rapidly as it translocates on single strands.
authors.affiliation: Department of Applied Mathematics, University of Colorado at Boulder, 526 UCB, Boulder, Colorado 80309, USA.
authors.forename: M D
authors.initials: MD
authors.lastname: Betterton
authors.forename: Frank
authors.initials: F
authors.lastname: Jülicher
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004265:DNA Helicases / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D020409:Molecular Motor Proteins / Q000737:chemistry*; D009038:Motion; D009690:Nucleic Acid Conformation; D011485:Protein Binding
chemical_list: D020409:Molecular Motor Proteins; D004247:DNA; D004265:DNA Helicases