This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.104.052738v1 88/6/3912    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Spakowitz, A. J. Articles by Wang, Z.-G. Search for Related Content PubMed PubMed Citation Articles by Spakowitz, A. J. Articles by Wang, Z.-G.

DNA Packaging in Bacteriophage: Is Twist Important?

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125

Correspondence: Address reprint requests to Andrew James Spakowitz, E-mail: ajspakow{at}nature.berkeley.edu; or Zhen-Gang Wang, E-mail: zgw{at}cheme.caltech.edu.

We study the packaging of DNA into a bacteriophage capsid using computer simulation, specifically focusing on the potential impact of twist on the final packaged conformation. We perform two dynamic simulations of packaging a polymer chain into a spherical confinement: one where the chain end is rotated as it is fed, and one where the chain is fed without end rotation. The final packaged conformation exhibits distinct differences in these two cases: the packaged conformation from feeding with rotation exhibits a spool-like character that is consistent with experimental and previous theoretical work, whereas feeding without rotation results in a folded conformation inconsistent with a spool conformation. The chain segment density shows a layered structure, which is more pronounced for packaging with rotation. However, in both cases, the conformation is marked by frequent jumps of the polymer chain from layer to layer, potentially influencing the ability to disentangle during subsequent ejection. Ejection simulations with and without Brownian forces show that Brownian forces are necessary to achieve complete ejection of the polymer chain in the absence of external forces.

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]

				Z. Li, J. Wu, and Z.-G. Wang Osmotic Pressure and Packaging Structure of Caged DNA Biophys. J., February 1, 2008; 94(3): 737 - 746. [Abstract] [Full Text] [PDF]

				A. Evilevitch, L. T. Fang, A. M. Yoffe, M. Castelnovo, D. C. Rau, V. A. Parsegian, W. M. Gelbart, and C. M. Knobler Effects of Salt Concentrations and Bending Energy on the Extent of Ejection of Phage Genomes Biophys. J., February 1, 2008; 94(3): 1110 - 1120. [Abstract] [Full Text] [PDF]

				J. P. Rickgauer, D. N. Fuller, S. Grimes, P. J. Jardine, D. L. Anderson, and D. E. Smith Portal Motor Velocity and Internal Force Resisting Viral DNA Packaging in Bacteriophage {phi}29 Biophys. J., January 1, 2008; 94(1): 159 - 167. [Abstract] [Full Text] [PDF]

				C. R. Locker, S. D. Fuller, and S. C. Harvey DNA Organization and Thermodynamics during Viral Packing Biophys. J., October 15, 2007; 93(8): 2861 - 2869. [Abstract] [Full Text] [PDF]

				D. N. Fuller, J. P. Rickgauer, P. J. Jardine, S. Grimes, D. L. Anderson, and D. E. Smith From the Cover: Ionic effects on viral DNA packaging and portal motor function in bacteriophage {varphi}29 PNAS, July 3, 2007; 104(27): 11245 - 11250. [Abstract] [Full Text] [PDF]

				C. Forrey and M. Muthukumar Langevin Dynamics Simulations of Genome Packing in Bacteriophage Biophys. J., July 1, 2006; 91(1): 25 - 41. [Abstract] [Full Text] [PDF]