On the Role of Flexibility in Linker-Mediated DNA Hydrogels

TL;DR

This study investigates how linker flexibility affects the phase behavior and rheological properties of DNA hydrogels formed by nanostars, revealing that flexible linkers lead to different gelation dynamics and structures.

Contribution

It introduces the use of flexible, non-binding bases in DNA linkers to control the phase behavior and elasticity of DNA nanostar hydrogels, supported by experimental and computational analysis.

Findings

Flexible linkers induce cluster fluid behavior with lower viscosity.

Rigid linkers promote classical gelation.

Simulation suggests distinct nanostar-linker topologies.

Abstract

Three-dimensional DNA networks, composed of tri- or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we use linker-mediated gels, where the sticky ends of two trivalent nanostars are connected through the complementary sticky ends of a linear DNA duplex. We can design this connection to be either rigid or flexible by introducing flexible, non-binding bases. The additional flexiblity provided by these non-binding bases influences the effective elasticity of the percolating gel formed at low temperatures. Here we show that by choosing the right length of the linear duplex and non-binding flexible joints, we obtain a completely different phase behaviour to that observed for rigid linkers. In particular, we use dynamic light scattering as microrheological tool to monitor the self-assembly of DNA nanostars with linear linkers as a function of temperature. While we observe classical gelation when using rigid linkers, the presence of flexible joints leads to a cluster fluid with reduced viscosity. Using both the oxDNA model and a coarse-grained simulation to investigate the nanostar-linker topology, we hypothesise on the possible structure formed by the DNA clusters.