Computing the elastic mechanical properties of rod-like DNA nanostructures

TL;DR

This study uses coarse-grained simulations to analyze the elastic properties of rod-like DNA nanostructures, revealing their bending and twisting behaviors and how these properties scale with structure size.

Contribution

It provides detailed estimates of elastic moduli and couplings for DNA nanostructures using long simulations and fluctuation analysis, advancing understanding of their mechanical properties.

Findings

Bending persistence lengths are larger than those of double-stranded DNA.

Persistence lengths increase non-linearly with the number of helices.

Twist-bend coupling constants are approximately zero.

Abstract

To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and twist persistence lengths, and the underlying bend and twist elastic moduli and couplings between them. Only on length scales beyond those associated with the spacings between the interhelix crossovers do the bending fluctuations behave like those of a worm-like chain. The obtained bending persistence lengths are much larger than that for double-stranded DNA and increase non-linearly with the number of helices, whereas the twist moduli increase approximately linearly. To within the numerical error in our data, the twist-bend coupling constants are of order zero. That the bending persistence lengths we obtain are generally somewhat higher than in experiment probably reflects both that the simulated origami have no assembly defects and that the oxDNA extensional modulus for double-stranded DNA is too large.