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

The Journal of Physical Chemistry. B
Qian WangB Montgomery Pettitt

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.

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Citations

Mar 5, 2016·The Journal of Physical Chemistry Letters·Qian Wang, B Montgomery Pettitt
Jun 14, 2017·Nucleic Acids Research·Qian WangB Montgomery Pettitt
Feb 20, 2020·Physical Review. E·Cecilia Bores, B Montgomery Pettitt
Mar 30, 2017·Journal of Computational Chemistry·Christopher G Myers, B Montgomery Pettitt
Nov 6, 2020·The Journal of Physical Chemistry. B·Cecilia BoresB Montgomery Pettitt
Sep 30, 2021·Nature Communications·Jonathan M FoggLynn Zechiedrich

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