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(a) Comparison of density ring separation in cryo-EM asymmetric reconstruction of the P22 phage (top portion, grey) versus time-averaged density distributions over 100 ns simulation of unconnected segments (bottom portion, blue). (b) Same at lower contour levels.
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(a) Time-averaged density distribution over 100 ns simulation of a non-periodic cubic box at same density (same particle number, same available volume) as our model simulation of phage P22. (b) Close-up view of select densities near phage head within the cryo-EM asymmetric reconstruction of the P22 phage. 13
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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.
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