Ion-Specific Modulation of the Conformation and Compactness of DNA Oligo-Catenanes

TL;DR

This paper studies how different ions affect the shape and structure of linked DNA rings using computer simulations.

Contribution

It reveals how ion type and DNA length influence the conformation and compactness of DNA catenanes.

Findings

Catenated DNA minicircles become more anisotropic and oblate compared to noncatenated ones.

Divalent ions cause nonmonotonic structural changes in short DNA minicircles but only contraction in longer ones.

In-plane stretching in catenanes reduces steric hindrance and spreads out charges.

Abstract

The scope of the work presented here is the computational
investigation
of the effects of counterion valency, on the ensuing pairwise effective
interactions between topologically interlinked DNA ring molecules
within the dilute solution regime. Atomistic molecular dynamics (MD)
simulations were performed for double stranded DNA [2]-catenanes in
low to moderate ionic strength solutions of monovalent sodium and
divalent counterions calcium and magnesium solutions. Upon catenation,
stiff DNA minicircles obtain more anisotropic, more aspherical and
slightly more oblate shapes, compared to their noncatenated conformations.
In-plane ring stretching is observed in the catenated structures,
which facilitates the spreading out of charges and reduces steric
hindrance. Prominent effects of the ion type on the separation of
the center-of-masses of the individual minicircles, as well as their
preferred relative orientations have been established. An interesting
interplay arises upon increasing ionic strength of divalent counterions,
depending on the contour length of the individual DNA minicircle constituents:
short DNA minicircles give rise to a nonmonotonic behavior that comprises
sequential elongation and contraction regimes of the catenane, but
longer minicircles give rise only to contracted catenane conformations.

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