Effects of Model Shape, Volume, and Softness of the Capsid for DNA Packaging of phi29
| Autor: | Michael Woodson, Cecilia Bores, Marc C. Morais, B. Montgomery Pettitt |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Materials science
Flexibility (anatomy) Sequence dependence viruses Bacillus Phages 010402 general chemistry 01 natural sciences Article chemistry.chemical_compound Capsid DNA Packaging 0103 physical sciences Materials Chemistry medicine Physical and Theoretical Chemistry 010304 chemical physics 0104 chemical sciences Surfaces Coatings and Films medicine.anatomical_structure chemistry Density distribution Volume (thermodynamics) Chemical physics DNA Viral Nucleic Acid Conformation Capsid Proteins Elongation Dna packaging DNA |
| Zdroj: | J Phys Chem B |
| ISSN: | 1520-5207 1520-6106 |
| DOI: | 10.1021/acs.jpcb.0c07478 |
| Popis: | Double-stranded DNA is under extreme confinement when packed in phage phi29 with osmotic pressures approaching 60 atm and densities near liquid crystalline. The shape of the capsid determined from experiment is elongated. We consider the effects of the capsid shape and volume on the DNA distribution. We propose simple models for the capsid of phage phi29 to capture volume, shape, and wall flexibility, leading to an accurate DNA density profile. The effect of the packaging motor twisting the DNA on the resulting density distribution has been explored. We find packing motor induced twisting leads to a greater numbers of defects formed. The emergence of defects such as bubbles or large roll angles along the DNA shows a sequence dependence, and the resulting flexibility leads to an inhomogeneous distribution of defects occurring more often at TpA steps and AT-rich regions. In conjunction with capsid elongation, this has effects on the global DNA packing structures. |
| Databáze: | OpenAIRE |
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