A Model for Viral Genome Packing

A method is developed to simulate the process of double‐stranded (ds) DNA packing in viral capsids. The dsDNA is modeled as a discrete single‐stranded homopolymer with an all‐elastic potential that is parameterized only by the experimentally measured rise per base pair (bp) and the persistence length of free dsDNA in physiological conditions. No properties from experiments on packaged viral DNA are used in the model, and thus the model does not presuppose any energies or conformations in the viral capsid. While the elastic DNA model is general and may be successfully applied to a wide range of coarse graining (up to about 20bp per monomer), a resolution of 6bp per monomer is chosen for the viral packing problem. The model is simple enough at this resolution to simulate the entire packaging process of viruses as large as bacteriophage λ (with a genome length of 48,502bp). The packing protocol developed here allows for multiple simulations of independent packing events, and the results show that there is substantial variability in the conformational space sampled in individual packing simulations. Packing forces are computed for a model φ29 bacteriophage system, and the force dependence on the amount of genome packaged is similar in functional form to experimentally determined forces, though the magnitude is about 40% lower. These results show that a simple elastic model of dsDNA with no explicit electrostatic interactions and no a priori knowledge of the packaged structure or energy is capable of capturing the main features of genome packaging in viruses. This implies that the final packed structure is largely determined by the elastic properties of the confined nucleic acid chain.