A Molecular View of the Dynamics of dsDNA Packing Inside Viral Capsids in the Presence of Ions.

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 o

SUBMITTER: Cordoba A 

PROVIDER: S-EPMC5389966 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature