ArticleProceedings of the National Academy of Sciences of the United States of America2014
Nonequilibrium dynamics and ultraslow relaxation of confined DNA during viral packaging.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed.
- Something old, something new? Herpesvirus genome packaging examined in light of lessons from the tailed bacteriophages.Journal of virology · 2026Review
- Dynamics of viral self-assembly, viral genome packaging, and virus-cell interactions studied by optical tweezers.European biophysics journal : EBJ · 2026Review
- Methods for Studying Motor-Driven Viral DNA Packaging in Bacteriophages phi29, Lambda, and T4 via Single DNA Molecule Manipulation and Rapid Solution Exchange.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Optical Tweezers to Study Viruses.Sub-cellular biochemistry · 2024Review
- Temperature-induced DNA density transition in phage λ capsid revealed with contrast-matching SANS.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Role of DNA-DNA sliding friction and nonequilibrium dynamics in viral genome ejection and packaging.Nucleic acids research · 2023Article
- AT-specific DNA visualization revisits the directionality of bacteriophage λ DNA ejection.Nucleic acids research · 2023Article
- Experimental study of a nanoscale translocation ratchet.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Knot formation of dsDNA pushed inside a nanochannel.Scientific reports · 2022Article
- Intravirion DNA Can Access the Space Occupied by the Bacteriophage P22 Ejection Proteins.Viruses · 2021Article
- Effects of Model Shape, Volume, and Softness of the Capsid for DNA Packaging of phi29.The journal of physical chemistry. B · 2020Article
- Function of a viral genome packaging motor from bacteriophage T4 is insensitive to DNA sequence.Nucleic acids research · 2020Article
- Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor.Biophysical journal · 2020Article
- Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif.Journal of molecular biology · 2019Article
- Slow and steady wins the race: physical limits on the rate of viral DNA packaging.Current opinion in virology · 2019Review
- Using a system's equilibrium behavior to reduce its energy dissipation in nonequilibrium processes.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Nucleotide-dependent DNA gripping and an end-clamp mechanism regulate the bacteriophage T4 viral packaging motor.Nature communications · 2018Article
- Article
- Influence of Microscopic Interactions on the Flexible Mechanical Properties of Viral DNA.Biophysical journal · 2018Article
Corrections and comments
- Commented on by
Authors and funding
5 authors.
Funding
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.