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Phage‐like packing structures with mean field sequence dependence
Author(s) -
Myers Christopher G.,
Pettitt B. Montgomery
Publication year - 2017
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24727
Subject(s) - persistence length , polymer , elasticity (physics) , dna , electrostatics , chain (unit) , bending , materials science , sequence (biology) , atomic packing factor , statistical physics , physics , crystallography , chemistry , composite material , quantum mechanics , biochemistry
Packing of double‐stranded DNA in phages must overcome both electrostatic repulsions and the problem of persistence length. We consider coarse‐grained models with the ability to kink and with randomly generated disorder. We show that the introduction of kinking into configurations of the DNA polymer packaged within spherical confinement results in significant reductions of the overall energies and pressures. We use a kink model which has the ability to deform every 24 bp, close to the average length predicted from phage sequence. The introduction of such persistence length defects even with highly random packing models increases the local nematic ordering of the packed DNA polymer segments. Such local ordering allowed by kinking not only reduces the total bending energy of confined DNA due to nonlinear elasticity but also reduces the electrostatic component of the energy and pressure. We show that a broad ensemble of polymer configurations is consistent with the structural data. © 2016 Wiley Periodicals, Inc.