Microrheology of DNA hydrogels

Abstract

A key objective in DNA-based material science is understanding and precisely controlling the mechanical properties of DNA hydrogels. We perform microrheology measurements using diffusing wave spectroscopy (DWS) to investigate the viscoelastic behavior of a hydrogel made of Y-shaped DNA (Y-DNA) nanostars over a wide range of frequencies and temperatures. We observe a clear liquid-to-gel transition across the melting temperature region for which the Y-DNA bind to each other. Our measurements reveal a cross-over between the elastic [Formula: see text] and loss modulus [Formula: see text] around the melting temperature [Formula: see text] of the DNA building blocks, which coincides with the systems percolation transition. This transition can be easily shifted in temperature by changing the DNA bond length between the Y shapes. Using bulk rheology as well, we further show that, by reducing the flexibility between the Y-DNA bonds, we can go from a semiflexible transient network to a more energy-driven hydrogel with higher elasticity while keeping the microstructure the same. This level of control in mechanical properties will facilitate the design of more sensitive molecular sensing tools and controlled release systems.

Keywords: DNA nanotechnology; hydrogels; microrheology; self-assembly; semiflexible polymers.

Fig. 1.

Design and characterization of the DNA hydrogel building blocks. (A) Schematic of the ssDNA S_i used. Each oligo strand consists of four functional parts: the sticky end, the free joint, segment I, and segment II. Segments I and II are part of the ds core DNA; sticky ends are for cross-linking the Y shapes to a network. (B) Cartoon of T and T′ DNA connected via hybridization of complementary sticky ends. (C) Melting (cooling) and heating (hybridization) curves of T and T′ DNA in Tris-EDTA buffer containing 150 mM NaCl measured using ultraviolet-visible (UV-vis) spectrometer. (D) From left to right are photographs of DNA hydrogels without free joint, with free joint, and with only one component. All three samples are made of [Y-shaped DNA] = 500 $\mathrm{\mu }$M. For clarity, the left and center gels were colored with the SYBR Safe DNA Gel Stain from Invitrogen. The sample maintains its original shape at a timescale of several minutes.

Fig. 2.

(A) Schematic illustration of the DWS setup. A 685-nm diode laser beam impinges on the sample, and the diffusely scattered light is collected by the photodiode on the other side of the sample. Tracer particles are uniformly embedded inside the sample. (B) Temperature-dependent ICF curves measured for the 500 $\mathrm{\mu }$M DNA hydrogel containing 1 (vol/vol %) 600-nm-large sterically stabilized PS tracer particles. The ICF curves were measured starting from 50 ^○C (orange lines) in 1 ^○C steps, cooling down to 20 ^○C (blue lines). The photographs show the sample cuvette showing the samples’ liquid state at 50 ^○C and the gel state at 20 ^○C.

Fig. 3.

(A) Schematic phase diagram of the Y-shaped DNA. The arrow indicates the concentration and temperature range of the ICF measurements shown in Fig. 2. The red area represents the two-phase region, and $T_c$ is the critical point. (B) Illustration of the hybridization range for the sticky ends of the two different Y shapes. The graded area signifies the range over which a fraction of base pairs is formed. (C) MSD extracted from the ICF curves in Fig. 2. The color of the lines gradually changes from orange to blue, standing for the transition region ranging from about 45 ^○C to 20 ^○C, which is centered around the melting temperature $T_{m2}$ = 35 ^○C of the sticky ends. The calculated MSD for the same 600-nm-large PS colloids in pure water at 50 ^○C is presented by the dashed line as guide to the eye.

Fig. 4.

Temperature evolution of the complex moduli $G\prime \left(\omega \right)$ and $G^{″}\left(\omega \right)$ as a function of frequency extracted from the MSDs in Fig. 3. (A) The elastic moduli $G\prime \left(\omega \right)$ measured in a cooling ramp. At temperatures above $T_{m2}$, $G\prime$ drops down at a frequency below $10^2\sim 10^4$rad/s, showing close to zero elasticity; below $T_{m2}$, only the onset of the decay in the ICF could be monitored. Hence, the low-frequency region is plotted as a dashed line using extrapolations. (B) The viscous modulus $G^{″}\left(\omega \right)$ in cooling (upper) ramp. (C) Comparison of $G\prime \left(\omega \right)$ and $G^{″}\left(\omega \right)$ at temperatures of 20 ^○C, 35 ^○C, and 50 ^○C, representing typical behavior at temperatures below, around, and above $T_m$, respectively. At 20 ^○C, $G^{″}$ is higher than $G\prime$ at frequencies below the cross-over frequency $\sim 10^4$ rad/s; at 35 ^○C, $G\prime$ and $G^{″}$ are overlapping over almost the entire frequency range. At 50 ^○C, $G^{″}$ is higher than $G\prime$ over the whole measurable frequency range, showing no cross-over point at all.