Modelling toehold-mediated RNA strand displacement

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

Research output: Contribution to journalArticlepeer-review

24 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1238-1247
Number of pages10
JournalBiophysical journal
Volume108
Issue number5
DOIs
StatePublished - Mar 10 2015
Externally publishedYes

ASJC Scopus subject areas

  • Biophysics

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