DNA Knotting in Spooling Like Conformations in Bacteriophages.pdfVIP

Computational and Mathematical Methods in Medicine Vol. 9, Nos. 3–4, September–December 2008, 303–316 DNA knotting in spooling like conformations in bacteriophages J. Arsuagaa,b1* and Y. Diaoc2 aDepartment of Mathematics, San Francisco State University, San Francisco, CA, USA; bInstitute for Mathematics and Its Applications, University of Minnesota, Minneapolis, MN, USA; cDepartment of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC, USA ( Received 13 February 2008; final version received 3 April 2008 ) 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. Keywords: random polygons; random knots; bacteriophage; DNA packing; spooling model AMS Subject Classification: 57M25; 92Bxx 1. Introduction All icosahedral bacteriophages with double-stranded DNA genomes pack their chromosomes in a similar manner [13] and are believed to hold similar DNA arrangements as those found in herpes viruses [8] a