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arXiv · 1411.3239

Modelling toehold-mediated RNA strand displacement

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

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Petr Šulc, Thomas E. Ouldridge, Flavio Romano, Jonathan P. K. Doye, Ard A. Louis. 2014-11-12. Modelling toehold-mediated RNA strand displacement. https://doi.org/10.1016/j.bpj.2015.01.023

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