Computational and Mathematical Methods in Medicine
Volume 9 (2008), Issue 3-4, Pages 303-316
doi:10.1080/17486700802167801
Original Article

DNA Knotting in Spooling Like Conformations in Bacteriophages

J. Arsuaga1,2 and Y. Diao3

1Department of Mathematics, San Francisco State University, San Francisco, CA, USA
2Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, MN, USA
3Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC, USA

Received 13 February 2008; Accepted 3 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.

Abstract

A number of idealized models have been proposed to explain the long range organization of the DNA in bacteriophages. However, none of these models can account for the distributions of complex knots found when examining DNA extracted from bacteriophage P4 capsids. Furthermore, these models do not consider possible chirality biases in the arrangement of the DNA molecule inside the capsid. In this paper, we address these two issues by proposing a randomized version of one of the most popular models: the coaxially spooled model. We present analytical and numerical results for the properties of the random polygons (knots) generated using this model. We show that such model can easily generate complex knotted conformations and although it accounts for some chirality of the organization of the DNA molecules inside bacteriophage capsids does not fully explain the experimental data.