Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging

Abstract

In many viruses molecular motors forcibly pack single DNA molecules to near-crystalline density into ~50-100 nm prohead shells^{1, 2}. Unexpectedly, we found that packaging frequently stalls in conditions that induce net attractive DNA-DNA interactions³. Here, we present findings suggesting that this stalling occurs because the DNA undergoes a nonequilibrium jamming transition analogous to that observed in many soft-matter systems, such as colloidal and granular systems^4-8. Experiments in which conditions are changed during packaging to switch DNA-DNA interactions between purely repulsive and net attractive reveal strongly history-dependent dynamics. An abrupt deceleration is usually observed before stalling, indicating that a transition in DNA conformation causes an abrupt increase in resistance. Our findings suggest that the concept of jamming can be extended to a single polymer molecule. However, compared with macroscopic samples of colloidal particles⁵ we find that single DNA molecules jam over a much larger range of densities. We attribute this difference to the nanoscale system size, consistent with theoretical predictions for jamming of attractive athermal particles.^{9, 10}.

Fig. 1. Viral DNA packaging exhibits history-dependent dynamics

(A) Prohead-motor complexes are attached to one trapped microsphere and DNA is attached to a second trapped microsphere. Packaging is initiated by bringing the two microspheres into proximity, whereupon the motor translocates the DNA. (B-D) Typical measurements of complexes that were initiated in the repulsive DNA-DNA interaction condition (blue lines) and allowed to proceed to ~20% (B), ~48% (C), or ~66% filling (D) prior to moving the complexes to the net attractive condition (red lines). (E) Standard deviation in length of DNA packaged vs. time for complexes measured in the repulsive condition (blue), net attractive condition (red), and after packaging ~20% (magenta), ~48% (green), or ~66% (grey) in the repulsive condition prior to moving them to the net attractive condition. Error bars indicate standard errors in the means calculated by applying the bootstrap method to the ensemble of datasets recorded on different complexes. (F) Typical measurements of complexes that were exposed to the net attractive condition (red) at low filling and subsequently moved to the repulsive condition (blue).

Fig. 2. Deceleration and stalling events

(a) Typical measurements showing abrupt decelerations and stalling of DNA translocation measured in the continuously net attractive condition (red), not observed in the continuously repulsive condition (blue). (b) Examples of velocity changes calculated in a 1 s window during deceleration events. (c) Maximum decelerations before 80% filling calculated in a 10 s window for the repulsive (bottom/blue) and net attractive condition (top/red). (d) Histogram of filling levels at which complexes exhibited deceleration events (top) and stalling events (bottom) when packaging in the continuously net attractive condition. (e) Probability, p, of a deceleration event vs. filling (dashed line) and probability of a stalling event vs. filling (solid line), calculated as the number of complexes that exhibit an event in each filling range divided by the number, N, that package to or through that range before stalling. Error bars indicate standard errors in the means, calculated as the standard deviation of the binomial distribution $\sqrt{p(1-p)/N}$. (f) Mean motor velocity vs. filling for all sections of packaging before a deceleration event (including complexes that did not exhibit a deceleration event) (dashed line). Mean velocity vs. filling for all sections of packaging after a deceleration event (solid line). Error bars indicate standard errors in the means, computed as standard deviation divided by square root of the number of complexes.

Fig. 3. Rescue of stalled complexes

Typical measurements in which complexes that stalled in the net attractive condition (red) were rapidly moved back to the repulsive condition (blue) causing translocation to restart. Inset: Zoomed-in plot showing one example where a stalled complex suddenly restarted (dashed lines indicate period when the complex was moved).