Mechanical response of a simple DNA nanostar hydrogel: symptoms of disorder and glassy emergence of solidity

Abstract

DNA self-assembly is a well-understood nanotechnology to obtain extremely ordered structures from the nanometer to up to the hundred of microns scale. By contrast, DNA hydrogels rely on the disordered assembly of DNA building blocks to reach macroscopic volumes. However, in order to hold the promise of DNA bulk materials, the sequence designer needs a systematic understanding of how macroscopic properties emerge from disorder. Here, we show a method to study systematically the mechanical response of a simple DNA nanostar hydrogel. This method mobilises bulk rheology, dynamic light scattering microrheology, mechanical modeling, as well as thermodynamic calculation and DNA sequence alteration. At low temperatures, we demonstrate a systematic deviation from Maxwell behaviour that is symptomatic of disordered materials. At temperatures much higher than the percolation of the DNA network, we characterise a surprising solid behaviour that we attribute to a glass transition. Our results show the importance of disorder in DNA materials. Furthermore, the method we showcase in this article can be widely applied to more complex DNA materials.

Figures (4)

• Figure 1: (a) Theoretical phase diagram of DNA nanostars Y16SE6. The cyan and orange lines are the concentration dependence of the melting temperatures of the nanostars without sticky ends $T_\mathrm{NS}$, respectively the duplex of sticky ends $T_\mathrm{SE}$. The black dot is experimentally determined gel concentration at coexistence. The gray dashed line is a guide for the eye. Orange and purple arrows show concentration and the respective temperature ranges of DLS microrheology and bulk rheology measurements. (b) Snapshot of the configuration of the three isolated DNA strands at high temperature from oxDNA simulations. (c) Same for an isolated nanostar at intermediate temperature. (d) Same for a gel at the statepoint shown as an empty square in (a).
• Figure 2: Bulk rheology of Y16SE6 at 1 at temperatures below $T_\mathrm{SE}$. (a) Loss factor (b) storage modulus, (c) loss modulus function of the frequency. Solid lines are fits of the fractional Maxwell model (fMM). (d-f) Time-temperature superposition of the previous. Black dashed lines show the behavior of the fMM for $\alpha=0.98$ and $\beta=0.05$, top diagram in (f). Black dotted lines show the behaviour of the non fractional Maxwell model, bottom diagram in (f). Insets of (d) and (e) present the temperature dependence of the fMM fit parameters, respectively the crossover characteristic timescale and the characteristic elasticity. Black dashed lines show respectively Arrhenius fit of activation energy 241/ and modulus prediction from nanostar concentration.
• Figure 3: DLS microrheology in Y16SE0 vs. Y16SE6 at 1 for temperatures above $T_\mathrm{SE}$. (a) Compliance of nanostars without sticky ends. Solid lines are Newtonian fits. (b) Compliance of nanostars with sticky ends. Solid lines are Jeffreys model fits. (c,d,e) Temperature dependence of the parameters of Jeffreys fits of Y16SE6: (c) elasticity modulus $G_\mathrm{M}$, (d) viscosity $\eta_M$ and (e) characteristic time $\tau=\eta_\mathrm{M}/G_\mathrm{M}$. Gray area indicates the fluid temperature range where $\tan\delta>1$ at all times. Dotted black line on (e) is an Arrhenius law of same activation energy as in the inset of Fig. \ref{['fig:tts']}(d).
• Figure 4: Effect of sequence design and concentration on the onset of solidity. (a) For Y16SE6 at 1, the loss tangent from DLS microrheology function of delay time for several temperatures. Orange circles highlight the minimum at each temperature. Below the dashed line, the behavior is solid-like. (b) For several designs, the value of the minimum of $\tan\delta$ at temperature $T$ function of the probability of SE-SE bond at the same temperature. (c) Same as (b) but function of the volume occupied by freely rotating doublets at the same temperature. The vertical dotted line is at $\phi_{2,\mathrm{rot}}=0.58$. Empty symbols are for temperatures where doublets are not the majority clusters.