Role of DNA-DNA sliding friction and nonequilibrium dynamics in viral genome ejection and packaging

Mounir Fizari, Nicholas Keller, Paul J. Jardine, Douglas E. Smith

Research output: Contribution to journalArticlepeer-review


Many viruses eject their DNA via a nanochannel in the viral shell, driven by internal forces arising from the high-density genome packing. The speed of DNA exit is controlled by friction forces that limit the molecular mobility, but the nature of this friction is unknown. We introduce a method to probe the mobility of the tightly confined DNA by measuring DNA exit from phage phi29 capsids with optical tweezers. We measure extremely low initial exit velocity, a regime of exponentially increasing velocity, stochastic pausing that dominates the kinetics and large dynamic heterogeneity. Measurements with variable applied force provide evidence that the initial velocity is controlled by DNA-DNA sliding friction, consistent with a Frenkel-Kontorova model for nanoscale friction. We confirm several aspects of the ejection dynamics predicted by theoretical models. Features of the pausing suggest that it is connected to the phenomenon of 'clogging' in soft matter systems. Our results provide evidence that DNA-DNA friction and clogging control the DNA exit dynamics, but that this friction does not significantly affect DNA packaging.

Original languageEnglish (US)
Pages (from-to)8060-8069
Number of pages10
JournalNucleic acids research
Issue number15
StatePublished - Aug 25 2023

Bibliographical note

Funding Information:
National Science Foundation [1716219]; National Institutes of Health [T32 GM008326 to M.F.]. Funding for open access charge: National Science Foundation [1716219].

Publisher Copyright:
© 2023 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.

PubMed: MeSH publication types

  • Journal Article
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, N.I.H., Extramural


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