Natural Computing

, Volume 13, Issue 4, pp 535–547 | Cite as

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

  • Petr Šulc
  • Thomas E. Ouldridge
  • Flavio Romano
  • Jonathan P. K. Doye
  • Ard A. Louis
Article

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.

Keywords

DNA nanotechnology DNA walkers Coarse-grained modelling 

Notes

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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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Petr Šulc
    • 1
  • Thomas E. Ouldridge
    • 1
  • Flavio Romano
    • 2
  • Jonathan P. K. Doye
    • 2
  • Ard A. Louis
    • 1
  1. 1.Rudolf Peierls Centre for Theoretical PhysicsUniversity of OxfordOxfordUK
  2. 2.Physical and Theoretical Chemistry Laboratory, Department of ChemistryUniversity of OxfordOxfordUK

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