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Simulating a burnt-bridges DNA motor with a coarse-grained DNA model

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Abstract

We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a ‘burnt-bridges’ DNA motor consisting of a single-stranded cargo that steps processively along a track of single-stranded stators. We demonstrate that the model is able to simulate such a system, and investigate the sensitivity of the stepping process to the spatial separation of stators, finding that an increased distance can suppress successful steps due to the build up of unfavourable tension. The mechanism of suppression suggests that varying the distance between stators could be used as a method for improving signal-to-noise ratios for motors that are required to make a decision at a junction of stators.

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Acknowledgments

We would like to thank Shelley Wickham, Jonathan Bath, Alex Lucas and Andrew Turberfield for helpful discussions. The authors also acknowledge financial support from the Engineering and Physical Sciences Research Council, University College (Oxford), and from the Oxford Supercomputing Centre for computer time. P. Š. is grateful for the award of a Scatcherd European Scholarship.

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Correspondence to Petr Šulc.

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Šulc, P., Ouldridge, T.E., Romano, F. et al. Simulating a burnt-bridges DNA motor with a coarse-grained DNA model. Nat Comput 13, 535–547 (2014). https://doi.org/10.1007/s11047-013-9391-8

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