Trajectory Retracing of the Packaging and Ejection Processes of Coaxially Spooled DNA.

Abstract

The coaxial spool structure of DNA has been regarded as an equilibrium conformation inside of a viral capsid. It has also been accepted that the DNA conformation inside the viral capsid should correlate strongly with the ejection of DNA out of the viral capsid. However, how the coaxial spool structure of DNA would affect the ejection kinetics remains elusive at the molecular level. In this study, we perform extensive Langevin dynamics simulations for a single polymer chain packaged within a small confinement to mimic the packaging and ejection processes of viral DNA and investigate the effects of its conformation on the ejection kinetics. We show that when the polymer chain within a small rectangular confinement is coaxially spooled, its ejection kinetics is facilitated significantly due to the trajectory retracing. We tune the conformation of the polymer chain inside the confinement by changing both the chain rigidity and the aspect ratio (γ) of the confinement. As either the aspect ratio (γ) decreases or the rigidity increases, the chain packaged inside the confinement is more likely to have a coaxial spool structure. And the polymer chain of the coaxial spool structure ejects quickly than chains of other conformations. We find that the coaxial spool structure enables the single chain to follow the reverse pathway of the packaging during ejection without significant structural rearrangement, thus enhancing the ejection kinetics.