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Modelling toehold-mediated RNA strand displacementPetr Sulc, Thomas E. Ouldridge, Flavio Romano, Jonathan P.K. Doye, and Ard A. LouisBiophys J. 108, 1238-1247 (2015)AbstractWe 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 diļ¬erent 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.The full paper is available from Biophysical Journal and arXiv.org. |