Restricted mobility and jamming of densely packed DNA exiting a viral capsid

We probe the dynamics of single charged polymer molecules (DNA) under tight 3D confinement inside phage phi29 capsids by using optical tweezers to pull them out through portal nanochannels. At DNA packing densities higher than ~0.3 g/ml, we observe a sharp decrease in exit velocity, highly heterogenous dynamics, and long pauses. These findings are consistent with decreased molecular mobility and transient non-equilibrium jamming of polymer chain segments. Addition of Mg 2+ ions, which electrostatically screen DNA, decrease exit velocity and increase pause durations, consistent with decreased self-repulsion and increased self-friction between strands. Preliminary measurements with varying applied and internal forces suggest that, contrary to prior hypothesis, exit velocity may not be linearly proportional to driving force as expected for a process governed only by simple viscous friction.