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

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• 作者：Petr ?ulc (1)
  Thomas E. Ouldridge (1)
  Flavio Romano (2)
  Jonathan P. K. Doye (2)
  Ard A. Louis (1)
  
• 关键词：DNA nanotechnology ; DNA walkers ; Coarse ; grained modelling
• 刊名：Natural Computing
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：13
• 期：4
• 页码：535-547
• 全文大小：1,351 KB
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• 作者单位：Petr ?ulc (1)
  Thomas E. Ouldridge (1)
  Flavio Romano (2)
  Jonathan P. K. Doye (2)
  Ard A. Louis (1)
  
  1. Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford, OX1 3NP, UK
  2. Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
  
• ISSN：1572-9796

文摘

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.