Modelling toehold-mediated RNA strand displacement

Petr Šulc; Thomas E Ouldridge; Flavio Romano; Jonathan P K Doye; Ard A Louis

doi:10.1016/j.bpj.2015.01.023

Modelling toehold-mediated RNA strand displacement

Biophys J. 2015 Mar 10;108(5):1238-47. doi: 10.1016/j.bpj.2015.01.023.

Authors

Petr Šulc¹, Thomas E Ouldridge², Flavio Romano³, Jonathan P K Doye³, Ard A Louis⁴

Affiliations

¹ 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.
² Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, United Kingdom; Department of Mathematics, Imperial College, London, United Kingdom.
³ Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom.
⁴ Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, United Kingdom.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Molecular Dynamics Simulation*
Molecular Sequence Data
Nucleic Acid Conformation
RNA / chemistry*

Substances

RNA