Computational and Mathematical Methods in Medicine
Volume 9 (2008), Issue 3-4, Pages 317-325
Original Article

Computer Simulations of DNA Packing inside Bacteriophages: Elasticity, Electrostatics and Entropy

SUPA, School of Physics, University of Edinburgh, Edinburgh, UK

Received 22 January 2008; Accepted 2 April 2008

Copyright © 2008 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


There is now a considerable literature on computer simulations of DNA packaging inside bacteriophage capsids. While most studies have reached a semiquantitative or qualitative agreement with single molecule packaging and ejection studies, several quantitative answers are to date still lacking, needing either more accurate measurements or more realistic or difficult simulations. Here, I briefly review the outstanding questions in this field and report some new numerical results on DNA packaging inside the phi29 phage, modelled either as a capped sphero-cylinder or as a sphere with the same internal volume. These simulations include electrostatics and a realistic genome length, and contribute to seriously questioning the inverse spool model, which arises from a purely continuum mechanics view of the problem, and is still commonly adopted to describe the shape of the packaged genome.