Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density

Qian Wang, Christopher G. Myers, Bernard Pettitt

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

We consider the consequences of assuming that DNA inside of phages can be approximated as a strongly nonlinear persistence length polymer. Recent cryo-EM experiments find a hole in the density map of P-SSP7 phage, located in the DNA segment filling the portal channel of the phage. We use experimentally derived structural constraints with coarse-grained simulation techniques to consider contrasting model interpretations of reconstructed density in the portal channel. The coarse-grained DNA models used are designed to capture the effects of torsional strain and electrostatic environment. Our simulation results are consistent with the interpretation that the vacancy or hole in the experimental density map is due to DNA strain leading to strand separation. We further demonstrate that a moderate negative twisting strain is able to account for the strand separation. This effect of nonlinear persistence length may be important in other aspects of phage DNA packing.

Original languageEnglish (US)
Pages (from-to)4937-4943
Number of pages7
JournalJournal of Physical Chemistry B
Volume119
Issue number15
DOIs
StatePublished - Apr 16 2015

Fingerprint

genome
Bacteriophages
DNA
deoxyribonucleic acid
Genes
Defects
defects
strands
twisting
Vacancies
Electrostatics
Polymers
simulation
electrostatics
polymers
Experiments

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density. / Wang, Qian; Myers, Christopher G.; Pettitt, Bernard.

In: Journal of Physical Chemistry B, Vol. 119, No. 15, 16.04.2015, p. 4937-4943.

Research output: Contribution to journalArticle

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