## 2 Materials and Methods
### 3 Synthesis of gold nanoparticles (AuNPs)  
AuNPs were synthesized based on a method adapted from the standard citrate reduction procedures [36]. First, all glassware was cleaned with aqua regia and then rinsed with DI water. After the glassware was dried completely, 500 mL of 1 mM hydrogen tetrachlorourate (III) trihydrate in DI water was prepared in a round-bottom flask and heated to a vigorous boil with stirring. Then, 50 mL of 38.8 mM sodium citrate tribasic dihydrate in DI water was added to the gold solution flask and the reaction was allowed to proceed for 15 min. The solution turned from yellow to clear, to black, to purple, and finally to deep red. Lastly, the solution was cooled down to room temperature. Synthesized AuNPs were characterized by transmission  
Figure 1: Schematic illustrations of DNA-based hydrogel formation. (**a–d**) Various types of crosslinkers: (**a**) Y-shaped DNA tile, (**b**) X-shaped DNA tile, (**c**) DNA–carbon nanotube (CNT) conjugate, and (**d**) DNA–gold nanoparticle (AuNP) conjugate. (**e**) Spacers of different lengths: Ss, Sm, and SI (short (33 nt), medium (44 nt), and long (55 nt), respectively). (**f**) Pure DNA hydrogel constructed by combining Y-shaped or X-shaped DNA tiles with spacers. (**g.h**) DNA hydrogel composites: (**g**) DNA–CNT hydrogel and (**h**) DNA–AuNP hydrogel. electron microscopy (TEM). The concentration of AuNPs was estimated with a UV-Vis spectrophotometer and calculated using the Beer-Lambert equation, \(A=\varepsilon bC\)[37]. **Construction of DNA tiles and spacers. ** To construct Y-shaped DNA tiles, 10 uL of 10 mM Y1, Y2, and Y3 precursor strands for the building blocks was added to a folding buffer solution (20 mM Tris-HCl (pH 7.5) and 100 mM NaCl) to obtain a final concentration of 1 mM for each strand. Then, the mixture went through a heat-annealing process where it was heated to 95 \({}^{\circ}\)C for 5 min and then cooled to room temperature over 30 min. Similarly, the X-shaped DNA tiles were assembled by mixing 8 uL of 10 mM precursor strands X1, X2, X3, and X4 in the folding buffer solution to obtain a final concentration of 1 mM for each strand. The mixture went through the same heat-annealing process as described above. To construct spacers, 15 uL of the two 10 mM precursor strands for the spacers was mixed in the folding buffer (to obtain a final concentration of 1.5 mM for each strand). The mixture then went through the same heat-annealing process described above for DNA tiles. Spacers were also made to different concentrations to pair with different types of crosslinkers. All pH values of the buffers were measured with a standard pH meter (Mettler Toledo SevenEasyTM, Columbus, USA). **DNA-assisted solubilization of CNTs and DNA-CNT conjugate formation. ** We constructed DNA-CNT conjugates by wrapping CNTs with DNA based on a previously reported method [38]. Briefly, 120 uL HEPES (final concentration 50 mM, pH 7.6), 1.2 mg CNTs, and 15 uL of 10 mM DNA strand C1 were mixed together. The mixture was sonicated in an ice-water bath for 30 min using a 100-W bath sonicator. Then, 15 uL of 10 mM DNA strand C2 was added. The solution was incubated at room temperature overnight and then stored at 4 \({}^{\circ}\)C.  
**DNA-AuNP conjugates. ** DNA-decorated AuNPs were synthesized with a previously reported method [39]. First, 16 uL of DNA stock solution of sequence G (100 uM in 5 mM HEPES buffer, pH 7.4) was added to 1.6 mL AuNP solution (10 nM). The solution was mixed by brief vortexing. Then, 32 uL of 500 mM citrate-HCl buffer, pH 3 (final 10 mM), was added to the AuNP solution (1 uL of buffer per 50 uL of AuNP solution). The solution once again went through vortex mixing and was incubated at room temperature for 3 min. Then, the pH of the AuNP solution was adjusted back to neutral by adding 96 uL of 500 mM HEPES buffer (pH 7.6, 3 uL of buffer per 50 uL of AuNP solution). The solution was then incubated for 5 to 10 min at room temperature. The DNA-AuNP mixture was centrifuged at 13,300 rpm for 6 min, and the supernatant was removed and discarded.