Binding branched and linear DNA structures: from isolated clusters to fully bonded gels

TL;DR

This study uses DNA self-assembly to create and analyze binary mixtures of tetravalent nanostars and bivalent chains, controlling bonding via temperature and component ratio, revealing different gelation and clustering behaviors.

Contribution

It demonstrates precise control over DNA-based particle bonding to study percolation and gel formation in a binary mixture system.

Findings

System behaves as a fully bonded network at low T

Transitions between gel, cluster fluid, and percolating states

Bonding controlled by temperature and component ratio

Abstract

The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to experimentally realize particles with well defined valence, namely tetravalent nanostars (A) and bivalent chains (B). We specifically focus on the case in which A particles can only bind to B particles, via appropriately designed sticky-end sequences. Hence AA and BB bonds are not allowed. Such a binary mixture system reproduces with DNA-based particles the physics of poly-functional condensation, with an exquisite control over the bonding process, tuned by the ratio, r, between B and A units and by the temperature, T. We report dynamic light scattering experiments in a window of Ts ranging from 10{\deg}C to 55{\deg}C and an interval of r around the percolation transition to quantify the decay of the density correlation for the different cases. At low T, when all possible bonds are formed, the system behaves as a fully bonded network, as a percolating gel and as a cluster fluid depending on the selected r.