Three-dimensional director-field predictions of viral DNA packing arrangements

Abstract

In this work we develop a discrete director-field model for coarse-grained description of packing arrangements of DNA within bacteriophage virus heads. This computational lattice model allows us to explore the complex energy landscape of fully three-dimensional configurations of packaged DNA. By minimizing the system’s free energy by means of the simulated annealing and the conjugate gradient methods, we make predictions about favorable packing conformations. In particular we show that the planar-wrapped inverse spool conformation is stable everywhere inside a virus except in a central core region, where the DNA tends to buckle out of the spooling plane.