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

Research paper by Nicholas Keller, Shelley Grimes, Paul J. Jardine, Douglas E. Smith

Indexed on: 03 May '16Published on: 02 May '16Published in: Nature Physics



Abstract

In many viruses, molecular motors forcibly pack single DNA molecules to near-crystalline density into ~50–100 nm prohead shells1, 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 systems4, 5, 6, 7, 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 particles9, 10.

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