# Modelling toehold-mediated RNA strand displacement

Source: [Modelling toehold-mediated RNA strand displacement](<https://www.sota2.com/research/paper/68fa2e771e209131ce862d1a>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-24T16:55:55.064Z

Authors: Petr \\v{S}ulc, Thomas E. Ouldridge, Flavio Romano, Jonathan P. K. Doye, Ard A. Louis

Published: 2014-11-12T16:56:28.000Z

## 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.

## Recorded benchmark results

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/1411.3239>)

[PDF](<https://arxiv.org/pdf/1411.3239.pdf>)