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Simulating a burnt-bridges DNA motor with a coarse-grained DNA modelPetr Sulc, Thomas E. Ouldridge, Flavio Romano, Jonathan P.K. Doye, and Ard A. LouisNatural Computing, 13, 535-547 (2014)AbstractWe 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 sen- sitivity of the stepping process to the spatial separa- tion of stators, finding that an increased distance can suppress successful steps due to the build up of un- favourable tension. The mechanism of suppression sug- gests that varying the distance between stators could be used as a method for improving signal-to-noise ra- tios for motors that are required to make a decision at a junction of stators.The full paper is available from Natural Computing and arXiv.org. |