Oxford Theoretical Physics

Condensed Matter Theory: Soft and Biological Matter

Julia Yeomans
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EJECTION OF DNA FROM VIRAL CAPSIDS

Bacteriophages comprise DNA, the genome, packaged inside a rigid container, the phage capsid. In order to reproduce itself a bacteriophage must inject a cell with its DNA. A simple way of doing this used by many viruses, for example λ-phage and Φ29, is to exploit the enormous pressure built up because of the strong confinement of the DNA within the capsid. In the λ-phage, for example, a genome of length 16 microns is packed into a spherical capsid with diameter 58 nm leading to a pressure of tens of atmospheres.

We are investigating the ejection by treating the DNA as a model polymer that is driven from the capsid by the energetic and entropic penalty of close confinement. Simulations are allowing us to study the interplay between equilibrium thermodynamics and non equilibrium effects due to the crowding and tangling of the confined DNA. Current work is focussing on the role of knotting on the ejection process, and on whether chemical chaperones outside the capsid can facilitate ejection.

Left: molecular motor, which packs the DNA; ejection is driven by pressure
Right: turnip yellow mosaic virus
Packing and ejection rates showing clear pauses due to crowding at the exit

Recent Publications:

1. Polymer packaging and ejection in viral capsids: Shape matters, Phys. Rev. Lett. 96, 208102 (2006) [arxiv]

2. Ejection Dynamics of Polymeric Chains from Viral Capsids: Effect of Solvent Quality, Biophys. J. 94, 4159 (2008)

Last updated: 26th May 2008