Non-equilibrium Conformation of a DNA Segment Outside a Capsid and its Effect on the DNA Packaging Rate

DNA is packaged into a nanometer-sized capsid by a motor protein, where the internal pressure is so high that DNA segment inside the capsid (trans segment) is almost jammed. Recent experiments showed that the trans segment was in non-equilibrium states, which substantially retarded the packaging process. However, the conformation of a cis segment (i.e. DNA outside the capsid) and its effect on packaging rate have attracted little attention, partly because of limits of experiments. In this study, we illustrate that the conformation of cis segment is a major determinant for packaging rate, contrary to previous expectations. The conformation of cis segment is also significantly away from its equilibrium due to tension propagation along the chain. We perform LD simulations of polymer packaging and mimic the recent experiment: the motor protein is stalled and restarted repeatedly, which allows the polymer to have equilibrium conformations during packaging. By analyzing the effect of cis and trans segment separately, we find that the conformational relaxation of the cis segment (strongly tensed) substantially accelerates packaging process and effects of trans segment are marginal under strong motor forces.