The structure and intermolecular forces of DNA condensates
#MMPMID26883635
Yoo J
; Aksimentiev A
Nucleic Acids Res
2016[Mar]; 44
(5
): 2036-46
PMID26883635
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Spontaneous assembly of DNA molecules into compact structures is ubiquitous in
biological systems. Experiment has shown that polycations can turn electrostatic
self-repulsion of DNA into attraction, yet the physical mechanism of DNA
condensation has remained elusive. Here, we report the results of atomistic
molecular dynamics simulations that elucidated the microscopic structure of dense
DNA assemblies and the physics of interactions that makes such assemblies
possible. Reproducing the setup of the DNA condensation experiments, we measured
the internal pressure of DNA arrays as a function of the DNA-DNA distance,
showing a quantitative agreement between the results of our simulations and the
experimental data. Analysis of the MD trajectories determined the DNA-DNA force
in a DNA condensate to be pairwise, the DNA condensation to be driven by
electrostatics of polycations and not hydration, and the concentration of
bridging cations, not adsorbed cations, to determine the magnitude and the sign
of the DNA-DNA force. Finally, our simulations quantitatively characterized the
orientational correlations of DNA in DNA arrays as well as diffusive motion of
DNA and cations.
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