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

Y. A. G. Fosado, D. Michieletto, J. Allan, C. A. Brackley, O. Henrich, D. Marenduzzo

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

LanguageEnglish
Pages9458-9470
Number of pages13
JournalSoft Matter
Volume12
Issue number47
DOIs
Publication statusPublished - 21 Dec 2016

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nucleotides
Nucleotides
Molecules
simulation
molecules
deoxyribonucleic acid
Denaturation
biopolymer denaturation
DNA
nanotechnology
Nanotechnology
rigidity
Rigidity
grooves
strands
torque
Electrostatics
Torque
Experiments
electrostatics

Cite this

Fosado, Y. A. G. ; Michieletto, D. ; Allan, J. ; Brackley, C. A. ; Henrich, O. ; Marenduzzo, D. / A single nucleotide resolution model for large-scale simulations of double stranded DNA. In: Soft Matter. 2016 ; Vol. 12, No. 47. pp. 9458-9470.
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A single nucleotide resolution model for large-scale simulations of double stranded DNA. / Fosado, Y. A. G.; Michieletto, D.; Allan, J.; Brackley, C. A.; Henrich, O.; Marenduzzo, D.

In: Soft Matter, Vol. 12, No. 47, 21.12.2016, p. 9458-9470.

Research output: Contribution to journalArticle

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