Modelling toehold-mediated RNA strand displacement

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

Research output: Contribution to journalArticle

19 Citations (Scopus)

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

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RNA
Nanotechnology
Temperature
Thermodynamics
Nucleic Acids

ASJC Scopus subject areas

  • Biophysics

Cite this

Sulc, P., Ouldridge, T. E., Romano, F., Doye, J. P. K., & Louis, A. A. (2015). Modelling toehold-mediated RNA strand displacement. Biophysical Journal, 108(5), 1238-1247. https://doi.org/10.1016/j.bpj.2015.01.023

Modelling toehold-mediated RNA strand displacement. / Sulc, Petr; Ouldridge, Thomas E.; Romano, Flavio; Doye, Jonathan P.K.; Louis, Ard A.

In: Biophysical Journal, Vol. 108, No. 5, 10.03.2015, p. 1238-1247.

Research output: Contribution to journalArticle

Sulc, P, Ouldridge, TE, Romano, F, Doye, JPK & Louis, AA 2015, 'Modelling toehold-mediated RNA strand displacement', Biophysical Journal, vol. 108, no. 5, pp. 1238-1247. https://doi.org/10.1016/j.bpj.2015.01.023
Sulc P, Ouldridge TE, Romano F, Doye JPK, Louis AA. Modelling toehold-mediated RNA strand displacement. Biophysical Journal. 2015 Mar 10;108(5):1238-1247. https://doi.org/10.1016/j.bpj.2015.01.023
Sulc, Petr ; Ouldridge, Thomas E. ; Romano, Flavio ; Doye, Jonathan P.K. ; Louis, Ard A. / Modelling toehold-mediated RNA strand displacement. In: Biophysical Journal. 2015 ; Vol. 108, No. 5. pp. 1238-1247.
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