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

Petr Sulc, Thomas E. Ouldridge, Flavio Romano, Jonathan P.K. Doye, Ard A. Louis

Research output: Contribution to journalArticle

16 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)535-547
Number of pages13
JournalNatural Computing
Volume13
Issue number4
DOIs
StatePublished - Jan 1 2014
Externally publishedYes

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Stators
DNA
Signal to noise ratio
Physics

Keywords

  • Coarse-grained modelling
  • DNA nanotechnology
  • DNA walkers

ASJC Scopus subject areas

  • Computer Science Applications

Cite this

Sulc, P., Ouldridge, T. E., Romano, F., Doye, J. P. K., & Louis, A. A. (2014). Simulating a burnt-bridges DNA motor with a coarse-grained DNA model. Natural Computing, 13(4), 535-547. https://doi.org/10.1007/s11047-013-9391-8

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model. / Sulc, Petr; Ouldridge, Thomas E.; Romano, Flavio; Doye, Jonathan P.K.; Louis, Ard A.

In: Natural Computing, Vol. 13, No. 4, 01.01.2014, p. 535-547.

Research output: Contribution to journalArticle

Sulc, P, Ouldridge, TE, Romano, F, Doye, JPK & Louis, AA 2014, 'Simulating a burnt-bridges DNA motor with a coarse-grained DNA model', Natural Computing, vol. 13, no. 4, pp. 535-547. https://doi.org/10.1007/s11047-013-9391-8
Sulc, Petr ; Ouldridge, Thomas E. ; Romano, Flavio ; Doye, Jonathan P.K. ; Louis, Ard A. / Simulating a burnt-bridges DNA motor with a coarse-grained DNA model. In: Natural Computing. 2014 ; Vol. 13, No. 4. pp. 535-547.
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