Packaging of DNA by bacteriophage epsilon15: structure, forces, and thermodynamics.
The structure of bacteriophage epsilon15 has recently been determined by 3D reconstruction of single particle cryo-electron microscopy images. Although this study revealed that the viral genome inside the bacteriophage is on average coaxially spooled, individual DNA conformations inside the capsid could not be determined. In the current study, we present the results of 40 independent simulations of DNA packaging into epsilon15 using the previously described low-resolution model for bacteriophages. In addition to coaxially spooled conformations, we also observe a number of folded-toroidal patterns, but the density averaged over all conformations closely resembles the experimental density. Thermodynamic analysis of the simulations predicts that a force of approximately 125 pN would be required to package DNA into epsilon15. We also show that the origin of this force is predominantly due to electrostatic and entropic contributions. However, the DNA conformation is determined primarily by the need to minimize the DNA bending energy.
Petrov
Anton S
AS
School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA.
Lim-Hing
Krista
K
Harvey
Stephen C
SC
D003198:Computer Simulation; D042003:DNA Packaging; D004279:DNA, Viral / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D017902:Podoviridae / Q000737:chemistry*; D013816:Thermodynamics
D004279:DNA, Viral