ArticleBiophysical journal2017
A Molecular View of the Dynamics of dsDNA Packing Inside Viral Capsids in the Presence of Ions.
Article in Biophysical journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 25 citations in OpenAlex.
- Role of viral protein ratio in the structure and separation of empty and full adeno-associated virus capsids: A molecular dynamics study.Molecular therapy. Advances · 2026Article
- Viral infection collapses intracytoplasmic membrane integrity and autotrophic metabolism in ammonia-oxidizingISME communications · 2026Article
- Phage reprogramming ofmBio · 2025Article
- Mutagenesis and functional analysis of the varicella-zoster virus portal protein.Journal of virology · 2024Article
- Article
- Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy.Journal of the American Chemical Society · 2021Article
- Molecular dynamics of the viral life cycle: progress and prospects.Current opinion in virology · 2021Review
- Ion-dependent DNA configuration in bacteriophage capsids.Biophysical journal · 2021Article
- Bottom-Up Coarse-Grained Modeling of DNA.Frontiers in molecular biosciences · 2021Review
- Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor.Biophysical journal · 2020Article
- Pattern preferences of DNA nucleotide motifs by polyamines putrescine2+, spermidine3+ and spermine4.Nucleic acids research · 2019Article
- A multiscale analysis of DNA phase separation: from atomistic to mesoscale level.Nucleic acids research · 2019Article
- Influence of Microscopic Interactions on the Flexible Mechanical Properties of Viral DNA.Biophysical journal · 2018Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome packing in viruses and prokaryotes relies on positively charged ions to reduce electrostatic repulsions, and induce attractions that can facilitate DNA condensation. Here we present molecular dynamics simulations spanning several microseconds of dsDNA packing inside nanometer-sized viral capsids. We use a detailed molecular model of DNA that accounts for molecular structure, basepairing, and explicit counterions. The size and shape of the capsids studied here are based on the 30-nanometer-diameter gene transfer agents of bacterium Rhodobacter capsulatus that transfer random 4.5-kbp (1.5 μm) DNA segments between bacterial cells. Multivalent cations such as spermidine and magnesium induce attraction between packaged DNA sites that can lead to DNA condensation. At high concentrations of spermidine, this condensation significantly increases the shear stresses on the packaged DNA while also reducing the pressure inside the capsid. These effects result in an increase in the packing velocity and the total amount of DNA that can be packaged inside the nanometer-sized capsids. In the simulation results presented here, high concentrations of spermidine
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