ArticleJournal of structural biology2011
Role of DNA-DNA interactions on the structure and thermodynamics of bacteriophages Lambda and P4.
Article in Journal of structural biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 27 citations in OpenAlex.
- Condensed Supramolecular Helices: The Twisted Sisters of DNA.Angewandte Chemie (International ed. in English) · 2022Article
- Ion-dependent DNA configuration in bacteriophage capsids.Biophysical journal · 2021Article
- Effects of Model Shape, Volume, and Softness of the Capsid for DNA Packaging of phi29.The journal of physical chemistry. B · 2020Article
- Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor.Biophysical journal · 2020Article
- Phage-like packing structures with mean field sequence dependence.Journal of computational chemistry · 2017Article
- Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging.Nature physics · 2016Article
- Shapes of minimal-energy DNA ropes condensed in confinement.Scientific reports · 2016Article
- Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density.The journal of physical chemistry. B · 2015Article
- Repulsive DNA-DNA interactions accelerate viral DNA packaging in phage Phi29.Physical review letters · 2014Article
- Reply to the comment by S. Harvey on "entropy, energy, and bending of DNA in viral capsids".Biophysical journal · 2014Article
- Discovery of a new motion mechanism of biomotors similar to the earth revolving around the sun without rotation.Virology · 2013Review
- Entropy, energy, and bending of DNA in viral capsids.Biophysical journal · 2013Article
- Effects of pulling forces, osmotic pressure, condensing agents and viscosity on the thermodynamics and kinetics of DNA ejection from bacteriophages to bacterial cells: a computational study.Journal of physics. Condensed matter : an Institute of Physics journal · 2013Article
- Communication: Origin of the contributions to DNA structure in phages.The Journal of chemical physics · 2013Article
- Dualities in the analysis of phage DNA packaging motors.Bacteriophage · 2012Article
- Nucleic acid packaging in viruses.Current opinion in structural biology · 2012Review
- Common mechanisms of DNA translocation motors in bacteria and viruses using one-way revolution mechanism without rotation.Biotechnology advancesReview
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Electrostatic interactions play an important role in both packaging of DNA inside bacteriophages and its release into bacterial cells. While at physiological conditions DNA strands repel each other, the presence of polyvalent cations such as spermine and spermidine in solutions leads to the formation of DNA condensates. In this study, we discuss packaging of DNA into bacteriophages P4 and Lambda under repulsive and attractive conditions using a coarse-grained model of DNA and capsids. Packaging under repulsive conditions leads to the appearance of the coaxial spooling conformations; DNA occupies all available space inside the capsid. Under the attractive potential both packed systems reveal toroidal conformations, leaving the central part of the capsids empty. We also present a detailed thermodynamic analysis of packaging and show that the forces required to pack the genomes in the presence of polyamines are significantly lower than those observed under repulsive conditions. The analysis reveals that in both the repulsive and attractive regimes the entropic penalty of DNA confinement has a significant non-negligible contribution into the total energy of packaging. Additionally we report the results of simulations of DNA condensation inside partially packed Lambda. We found that at low densities DNA behaves as free unconfined polymer and condenses into the toroidal structures; at higher densities rearrangement of the genome into toroids becomes hindered, and condensation results in the formation of non-equilibrium structures. In all cases packaging in a specific conformation occurs as a result of interplay between bending stresses experienced by the confined polymer and interactions between the strands.
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