Communication: Origin of the contributions to DNA structure in phages

Christopher G Myers,B Montgomery Pettitt

doi:10.1063/1.4791708

Abstract

Cryo electron microscopy (cryo-EM) data of the interior of phages show ordering of the interior DNA that has been interpreted as a nearly perfectly ordered polymer. We show surface-induced correlations, excluded volume, and electrostatic forces are sufficient to predict most of the major features of the current structural data for DNA packaged within viral capsids without additional ordering due to elastic bending forces for the polymer. Current models assume highly-ordered, even spooled, hexagonally packed conformations based on interpretation of cryo-EM density maps. We show herein that the surface induced packing of short (6mer), unconnected DNA polymer segments is the only necessary ingredient in creating ringed densities consistent with experimental density maps. This implies the ensemble of possible conformations of polymeric DNA within the capsid that are consistent with cryo-EM data may be much larger than implied by traditional interpretations where such rings can only result from highly-ordered spool-like conformations. This opens the possibility of a more disordered, entropically-driven view of phage packaging thermodynamics. We also show the electrostatics of the DNA contributes a large portion of the internal hydrostatic and osmotic pressures of a phage virion, suggesting that nonlinear elastic anomalies might reduce the overall elastic bending enthalpy of more disordered conformations to have allowable free energies.

Highlights

The physical confinement of double-stranded DNA within viral capsids is a long studied problem, both theoretically and experimentally.1–7 A proper description of nucleic acids under confinement and/or elastic strain has implications for describing nucleosomal packing, transcription, and other important in vivo processes.8,9 An advantage of phage systems is that they are experimentally well-studied structurally via cryo electron microscopy,10–15 as well as thermodynamically via single-molecule motor loading force measurements16–18 and osmotic pressure ejectioninhibition experiments.19–21 Asymmetric structural density maps of phages (e.g., P22, epsilon15) have been reconstructed from cryo-electron microscopy.10,12,13 use of phages has shown potential for safe, low-cost methods of gene transfer, and vaccine delivery vectors.22 A precise, sequencedependent ability to thermodynamically control packaging and release of nucleic acids would be useful for efficacious drug development and delivery
While higher resolution structures are expected to be pivotal in elucidating detailed physical mechanisms and provide tests of proposed models,14 a proper physical interpretation of the data is required to obtain thermodynamic mechanistic insight
The cost of the symmetry assumption, is that only features possessing the imposed symmetry are accurately represented by the averaged density map, and features which do not share this symmetry, such as the packaged genome or tail machinery, will be inappropriately averaged or “smeared.”27

Summary

Introduction

The physical confinement of double-stranded DNA within viral capsids is a long studied problem, both theoretically and experimentally.1–7 A proper description of nucleic acids under confinement and/or elastic strain has implications for describing nucleosomal packing, transcription, and other important in vivo processes.8,9 An advantage of phage systems is that they are experimentally well-studied structurally via cryo electron microscopy (cryo-EM),10–15 as well as thermodynamically via single-molecule motor loading force measurements16–18 and osmotic pressure ejectioninhibition experiments.19–21 Asymmetric structural density maps of phages (e.g., P22, epsilon15) have been reconstructed from cryo-electron microscopy.10,12,13 use of phages has shown potential for safe, low-cost methods of gene transfer, and vaccine delivery vectors.22 A precise, sequencedependent ability to thermodynamically control packaging and release of nucleic acids would be useful for efficacious drug development and delivery. (Received 19 December 2012; accepted 28 January 2013; published online 19 February 2013)

Results

Conclusion