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Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20081-6. doi: 10.1073/pnas.1306601110. Epub 2013 Nov 22.

Topological friction strongly affects viral DNA ejection.

Author information

1
Scottish Universities Physics Alliance, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, Scotland.

Abstract

Bacteriophages initiate infection by releasing their double-stranded DNA into the cytosol of their bacterial host. However, what controls and sets the timescales of DNA ejection? Here we provide evidence from stochastic simulations which shows that the topology and organization of DNA packed inside the capsid plays a key role in determining these properties. Even with similar osmotic pressure pushing out the DNA, we find that spatially ordered DNA spools have a much lower effective friction than disordered entangled states. Such spools are only found when the tendency of nearby DNA strands to align locally is accounted for. This topological or conformational friction also depends on DNA knot type in the packing geometry and slows down or arrests the ejection of twist knots and very complex knots. We also find that the family of (2, 2k+1) torus knots unravel gradually by simplifying their topology in a stepwise fashion. Finally, an analysis of DNA trajectories inside the capsid shows that the knots formed throughout the ejection process mirror those found in gel electrophoresis experiments for viral DNA molecules extracted from the capsids.

KEYWORDS:

DNA knotting; Monte Carlo simulations

PMID:
24272939
PMCID:
PMC3864349
DOI:
10.1073/pnas.1306601110
[Indexed for MEDLINE]
Free PMC Article

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