Regensburg 2019 – scientific programme

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CPP: Fachverband Chemische Physik und Polymerphysik

CPP 17: Poster Session I

CPP 17.41: Poster

Monday, April 1, 2019, 17:30–19:30, Poster B1

Modelling DNA-strand displacement reactions in the presence of base-pair mismatches — •Patrick Irmisch and Ralf Seidel — Molecular Biophysics group, Peter Debye Institute for Soft Matter Physics, University of Leipzig, 04103 Leipzig, Germany

Toehold-mediated strand displacement is the most abundantly used method to achieve dynamic switching in DNA-based nanotechnology. A single-stranded 'invader' strand binds to the 'toehold' overhang of a target strand and replaces a target-bound 'incumbent' strand. Hereby, complementarity of the invader to the single-stranded toehold provides the energetic bias of the reaction.

The aim of this work is to obtain a quantitative description of the kinetics of strand displacement reactions in the presence of mismatches using simple biophysical modelling. This would allow for predicting strand-displacement rates when setting up strand-displacement reaction networks. We model the strand-displacement rate as the mean-first-passage time of a random walk within a simplified 1D energy landscape. In case of single invader mismatches, our model successfully describes the displacement kinetics as function of the mismatch position and the toehold length using a minimal set of parameters. Most importantly, our model is able to predict the kinetics of strand displacement reactions in presence of multiple invader mismatches as well as incumbent mismatches. Comparisons with experimental data confirm the model prediction and thus the general applicability of our approach.