The effects of DNA Entanglement in Viral Capsids on the Conformational Relaxation and the DNA Ejection Rate

DNA ejects from a small viral capsid due to a large repulsion force, thus infecting the host cells. Because the DNA confined within a small viral capsid which is jammed and entangled significantly, the DNA conformation does not usually relax to equilibrium conformation during the ejection. In this work, we delineate the importance of the DNA entanglement by allowing the conformational relaxation via strand-crossings during ejection. We carry out Langevin Dynamics simulations of a single chain with 1024 monomers. The viral capsid is modeled as a cubic box with a long tail, through which the DNA is ejected. By tuning the force constant of FENE (Finitely Extensible Non-linear Elastic) model for the chain, we either allow or disallow the chain to undergo strand-crossing. We employ two types of initial configuration of the DNA; (1) ordered and (2) disordered. We find that strand-crossings help the DNA relax, not only segments of DNA near the pore but entire parts of the DNA, thus making the ejection fast despite its disordered initial conformation. When the strand-crossing is forbidden, the ejection rate becomes slow by a factor of two or more in disordered initial conformations.