title: Modelling toehold-mediated RNA strand displacement.
abstract: We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5' end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds.
authors.affiliation: Center for Studies in Physics and Biology, Rockefeller University, New York, New York; Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, United Kingdom. Electronic address: petr.sulc@rockefeller.edu.
authors.forename: Petr
authors.initials: P
authors.lastname: Šulc
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, United Kingdom; Department of Mathematics, Imperial College, London, United Kingdom.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Ouldridge
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom.
authors.forename: Flavio
authors.initials: F
authors.lastname: Romano
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom.
authors.forename: Jonathan P K
authors.initials: JP
authors.lastname: Doye
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, United Kingdom.
authors.forename: Ard A
authors.initials: AA
authors.lastname: Louis
mesh_terms: D001483:Base Sequence; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA