title: Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging.
abstract: Many viruses use molecular motors that generate large forces to package DNA to near-crystalline densities inside preformed viral proheads. Besides being a key step in viral assembly, this process is of interest as a model for understanding the physics of charged polymers under tight 3D confinement. A large number of theoretical studies have modeled DNA packaging, and the nature of the molecular dynamics and the forces resisting the tight confinement is a subject of wide debate. Here, we directly measure the packaging of single DNA molecules in bacteriophage phi29 with optical tweezers. Using a new technique in which we stall the motor and restart it after increasing waiting periods, we show that the DNA undergoes nonequilibrium conformational dynamics during packaging. We show that the relaxation time of the confined DNA is >10 min, which is longer than the time to package the viral genome and 60,000 times longer than that of the unconfined DNA in solution. Thus, the confined DNA molecule becomes kinetically constrained on the timescale of packaging, exhibiting glassy dynamics, which slows the motor, causes significant heterogeneity in packaging rates of individual viruses, and explains the frequent pausing observed in DNA translocation. These results support several recent hypotheses proposed based on polymer dynamics simulations and show that packaging cannot be fully understood by quasistatic thermodynamic models.
authors.affiliation: Departments of Physics andChemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093; and.
authors.forename: Zachary T
authors.initials: ZT
authors.lastname: Berndsen
authors.affiliation: Departments of Physics and.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Keller
authors.affiliation: Department of Diagnostic and Biological Sciences andInstitute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455.
authors.forename: Shelley
authors.initials: S
authors.lastname: Grimes
authors.affiliation: Department of Diagnostic and Biological Sciences andInstitute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Jardine
authors.affiliation: Departments of Physics and des@ucsd.edu.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Smith
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D017103:Bacillus Phages / Q000235:genetics* / Q000502:physiology*; D001412:Bacillus subtilis / Q000821:virology; D042003:DNA Packaging; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016679:Genome, Viral / Q000235:genetics; D007700:Kinetics; D008957:Models, Genetic; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D052898:Optical Tweezers; D011485:Protein Binding; D013997:Time Factors; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D019065:Virus Assembly
chemical_list: D004279:DNA, Viral; D014764:Viral Proteins; D000255:Adenosine Triphosphate
keywords: DNA condensation; soft matter; virology