Abstract
While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.
Highlights
Behavior of dsDNA in the biological milieu is seldom mimicked by its properties in dilute solutions[1, 2]
Recently it became feasible to set up a realistic all-atom molecular dynamics (MD) simulation, with properly parameterized and tested molecular potentials that could be applied to a larger set of DNA molecules[41,42,43], describing a condensed DNA array in the presence of counterions and salt, characterized by a single packing geometry, but as yet with only partial characterization of the DNA countercharge and solvent ordering
We investigated the couplings between different kinds of interactions and order in the high density DNA mesophases, as well as phase transitions between them, by carrying out a number of multiscale simulations of large systems containing an array of 16 DNA molecules
Summary
Behavior of (double-stranded) dsDNA in the biological milieu is seldom mimicked by its properties in dilute solutions[1, 2]. Recently it became feasible to set up a realistic all-atom MD simulation, with properly parameterized and tested molecular potentials that could be applied to a larger set of DNA molecules[41,42,43], describing a condensed DNA array in the presence of counterions and salt, characterized by a single packing geometry, but as yet with only partial characterization of the DNA countercharge and solvent ordering In this respect, the full characterization of concentrated DNA solutions at different densities, including the mono- and multivalent counterions, salt and explicit molecular solvent together with ordering transitions between the density dependent mesophases at atomic resolution is still to a large extent missing
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