DNA Organization and Thermodynamics During Viral Packaging

¹ Georgia Institute of Technology
² University of Oxford

^* To whom correspondence should be addressed. E-mail: steve.harvey{at}biology.gatech.edu.

Submitted on August 9, 2006
Revised on October 5, 2006
Accepted on 17 May 2007

	Abstract

An elastic DNA molecular mechanics model is used to compare DNA structures and packing thermodynamics in two bacteriophage systems, T7 and 29. A discrete packing protocol allows for multiple molecular dynamics simulations of the entire packing event. In T7 the DNA is coaxially spooled around the cylindrical core protein, while the 29 system, which lacks a core protein, organizes the DNA concentrically, but not coaxially. Two dimensional pro jections of the packed structures from T7 simulations are consistent with cryo-electron (cryoEM) micrographs of T7 phage DNA. The functional form of the force required to package the 29 DNA is similar to forces determined experimentally, although the total free energy change is only 40% of the experimental value. Since electrostatics are not included in the simulations, this suggests that electrostatic repulsions are responsible for about 60% of the free energy required for packaging. The entropic penalty from DNA confinement has not been computed in previous studies, but it is often assumed to make a negligible contribution to the total work done in packing the DNA. Conformational entropy can be measured in our approach, and it accounts for 70%-80% of the total work done in packing the elastic model DNA in both phages. For 29, this corresponds to an entropic penalty of about 35% of the total work observed experimentally.

Key Words: Coarse-grain model, DNA elasticity, DNA structure, Molecular modeling, Viral packing, Virus structure

This article has been cited by other articles:

				A. S. Petrov and S. C. Harvey Packaging Double-Helical DNA into Viral Capsids: Structures, Forces, and Energetics Biophys. J., July 15, 2008; 95(2): 497 - 502. [Abstract] [Full Text] [PDF]

				G. C. Rollins, A. S. Petrov, and S. C. Harvey The Role of DNA Twist in the Packaging of Viral Genomes Biophys. J., March 1, 2008; 94(5): L38 - L40. [Abstract] [Full Text] [PDF]