Abstract
We evaluate, by means of synchrotron small-angle X-ray scattering, the shape and mutual interactions of DNA tetravalent nanostars as a function of temperature in both the gas-like state and across the gel transition. To this end, we calculate the form factor from coarse-grained molecular dynamics simulations with a novel method that includes hydration effects; we approximate the radial interaction of DNA nanostars as a hard-sphere potential complemented by a repulsive and an attractive Yukawa term; and we predict the structure factors by exploiting the perturbative random phase approximation of the Percus–Yevick equation. Our approach enables us to fit all the data by selecting the particle radius and the width and amplitude of the attractive potential as free parameters. We determine the evolution of the structure factor across gelation and detect subtle changes of the effective interparticle interactions, that we associate to the temperature and concentration dependence of the particle size. Despite the approximations, the approach here adopted offers new detailed insights into the structure and interparticle interactions of this fascinating system.
Highlights
In the last decades, DNA has acquired an increasing importance in material science applications.[1]
The form factor developed for this study describes the average structure of randomly oriented DNA nanostars, which we build on the basis of their coarse grained model as obtained by molecular dynamic simulations with the OxDNA code
By taking advantage of numerical simulations, we have developed a fairly accurate model for the form factor, and we have disentangled the information concerning the interactions from the ones concerning the molecular shape
Summary
DNA has acquired an increasing importance in material science applications.[1]. The hybridization of the overhangs, occurring at a temperature T that depends on their length and sequence, leads to tip-to-tip adhesion, in turn yielding the formation of clusters and eventually of spanning networks These structures have found important applications as model systems to investigate colloidal gelation[7] (both chemical[8,9] and physical[10−12] gelation), network viscoelasticity,[13−16] liquid−liquid phase transitions,[17,18] and the dependence of the phase-behavior on the valence.[10] These particles have been used as elementary bricks in more complex architectures to give rise to solutions gelling on heating[19] or to assemble cold-swappable networks.[20]
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