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

Mounir Fizari1, Nicholas Keller1, Paul J Jardine2

  • 1Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA.

Nucleic Acids Research
|July 14, 2023
PubMed

Insights

Viral DNA ejection is governed by DNA-DNA friction and clogging, not packaging friction. Optical tweezers reveal low initial velocity and dynamic pausing during DNA exit from phage phi29 capsids.

Area of Science:

  • Biophysics
  • Molecular Virology
  • Nanotechnology

Background:

  • Viruses eject DNA through nanochannels, driven by internal genome pressure.
  • The precise nature of friction limiting DNA exit velocity remains poorly understood.

Purpose of the Study:

  • To investigate the friction forces controlling DNA exit dynamics from viral capsids.
  • To probe the molecular mobility of confined DNA using advanced biophysical techniques.

Main Methods:

  • Utilized optical tweezers to measure the DNA exit velocity from phage phi29 capsids.
  • Applied variable forces to analyze the relationship between force and DNA mobility.
  • Observed and characterized stochastic pausing and dynamic heterogeneity during ejection.

Main Results:

  • Measured extremely low initial DNA exit velocities.
  • Identified DNA-DNA sliding friction as the primary determinant of initial velocity, aligning with nanoscale friction models.
  • Observed significant stochastic pausing and dynamic heterogeneity, suggesting a 'clogging' phenomenon.

Conclusions:

  • DNA-DNA friction and clogging critically control viral DNA exit dynamics.
  • This friction does not appear to significantly impede the DNA packaging process.
  • The findings provide insights into nanoscale friction and molecular transport in biological systems.

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