Small-angle neutron scattering and Molecular Dynamics structural study of gelling DNA nanostars

TL;DR

This study combines small-angle neutron scattering and molecular dynamics simulations to analyze the structure and aggregation process of tetravalent DNA nanostars, providing insights into their gelation behavior.

Contribution

It introduces a combined experimental and computational approach to characterize DNA nanostar structures and their gelation, with a focus on form factor and temperature effects.

Findings

Numerical form factor matches experimental data closely.

Form factor remains temperature independent during gelation.

Simulations enable extraction of structure factor evolution.

Abstract

DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed by 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nano star concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor theoretically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.