A single nucleotide resolution model for large-scale simulations of double stranded DNA

Fosado, Y. A. G. and Michieletto, D. and Allan, J. and Brackley, C. A. and Henrich, O. and Marenduzzo, D. (2016) A single nucleotide resolution model for large-scale simulations of double stranded DNA. Soft Matter, 12 (47). pp. 9458-9470. ISSN 1744-6848 (https://doi.org/10.1039/c6sm01859a)

[thumbnail of Fosado-etal-SM2016-A-single-nucleotide-resolution-model-for-large-scale-simulations-of-double]
Preview
 Text. Filename: Fosado_etal_SM2016_A_single_nucleotide_resolution_model_for_large_scale_simulations_of_double.pdf
Final Published Version
License: Creative Commons Attribution 3.0 logo
Download (3MB)| Preview

Abstract

The computational modelling of DNA is becoming crucial in light of new advances in DNA nano-technology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide level which retains the characteristic helical structure, while being able to simulate large molecules-up to a million base pairs-for time-scales which are relevant to physiological processes. This is made possible by an efficient and highly-parallelised implementation of the model which we discuss here. The model captures the main characteristics of DNA, such as the different persistence lengths for double and single strands, pitch, torsional rigidity and the presence of major and minor grooves. The model constitutes a starting point for the future implementation of further features, such as sequence specificity and electrostatic repulsion. We show that the behaviour of the presented model compares favourably with single molecule experiments where dsDNA is manipulated by external forces or torques. We finally present some results on the kinetics of denaturation of linear DNA and supercoiling of closed dsDNA molecules.

ORCID iDs

Fosado, Y. A. G., Michieletto, D., Allan, J. ORCID logoORCID: https://orcid.org/0000-0001-8264-3277, Brackley, C. A., Henrich, O. ORCID logoORCID: https://orcid.org/0000-0003-0384-982X and Marenduzzo, D.;
  • Item type:Article
    ID code:61492
    Dates:
    Date
    Event
    21 December 2016
    Published
    8 November 2016
    Accepted
    Subjects:Science > Physics
    Department:Faculty of Science > Physics
    Depositing user: Pure Administrator
    Date deposited:07 Aug 2017 11:01
    Last modified:11 Nov 2024 11:45
    Related URLs:
    URI:https://strathprints.strath.ac.uk/id/eprint/61492
CORE (COnnecting REpositories)