DNA packaging in bacteriophage: Is twist important?

¹ University of California, Berkeley
² California Institute of Technology

^* To whom correspondence should be addressed. E-mail: ajspakow{at}nature.berkeley.edu.

Submitted on September 9, 2004
Revised on October 30, 2004
Accepted on 16 March 2005

	Abstract

We study the packaging of DNA into a bacteriophage capsid using computer simulation, specifically focusing on the potential impact of twist on the final packaged conformation. We perform two dynamic simulations of packaging a polymer chain into a spherical confinement: one where the chain end is rotated as it is fed, and one where the chain is fed without end rotation. The final packaged conformation exhibits distinct differences in these two cases: the packaged conformation from feeding with rotation exhibits a spool-like character that is consistent with experimental and previous theoretical work, whereas feeding without rotation results in a folded conformation inconsistent with a spool conformation. The chain segment density shows a layered structure, which is more pronounced for packaging with rotation. However in both cases, the conformation is marked by frequent jumps of the polymer chain from layer to layer, potentially influencing the ability to disentangle during subsequent ejection. Ejection simulations with and without Brownian forces show that Brownian forces are necessary to achieve complete ejection of the polymer chain in the absence of external forces.

Key Words: DNA, mechanics, packaging, twist, virus

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