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1 DN guided crystalline organization of nanoparticles Dmytro Nykypanchuk, 1* Mathew M. Maye, 1* Daniel van der Lelie, 2 and Oleg Gang 1 1 Center for Functional Nanomaterials, 2 iology Department, rookhaven National Laboratory, Upton, NY 11973, US * These authors contributed equally to this work Supplementary Discussion Thermal behaviour of DN-nanoparticle systems before annealing: Upon heating the aggregates assembled at room temperature, system I-IV and VI (Table S1), we observed three structurally distinct regimes with SXS. First, (1) the initially disordered amorphous state at room temperature after assembly (Figure S1a), (2) a structural reorganization due to heating to premelting temperatures (T pm ) (Figure S1a), and (3) a disassembled state above the DN linkers melting temperature (T m ). In each system, we observed the shift of peak to lower q values at higher temperatures, indicating a d expansion with temperature. For example, system IV showed a q-shift of ~05-1, which corresponds to ~20% (~4.5 nm) increase in particle surface-to-surface distance. The larger interparticle distances can be attributed to the development of more uniaxial character of hybridization with annealing, as well as to the conformational changes of DN with increased temperature. 31 t T pm, SXS revealed a narrowing of peak for each system, which is an indication of improved ordering. Compared to room temperature, in systems I, II, and III we observed a 10-20% increase of scattering correlation length, ξ 2π/ q, where q is resolution corrected ( q res 015Å -1 ) FWHM of the diffraction peak. This shows that ξ is limited to only few interparticle spacings, thus still indicating essentially amorphous organization of particles. In 1

2 contrast, systems IV and VI revealed more than 50% ξ increase, to about 5d, accompanied by the emergence of higher order peaks, suggesting the presence of relatively ordered domains. 2

3 a b T=59 C System I System II T=57 C System III T=53 C T=56 C System IV System VI T=30 C T=62 C q,(å -1 ) Supplementary Figure S1. SXS patterns (a) and corresponding structure factors (b) for as-assembled systems and annealed at T pm. The experimental temperature indicated on each image. lue and yellow curves representing for room and T pm respectively. Positions of the first peaks are q I =403, q II =324, q III =273, q IV =266, and q VI =226 Å -1 at low temperature and q I =37, q II =298, q III =244, q IV =233, and q VI =199 Å -1 at T pm. 3

4 1000 Intensity, a.u q, -1 Supplementary Figure S2. Scattering intensity from system IV at 71 C (solid symbols). Solid line represent fitting using spheroidal model for particles with Gaussian size distribution. Fitted particle diameter 11.5±1.2 nm. Fitting performed with Irena 2 macros package (available at 4

5 Supplementary Table S1. The ssdn used in the study System-I TC TTC C TCC T TTT-C 6 DN Sequence (5 to 3 ) TT GG TTG G GT TTT-C 6 System-II TC TTC C TCC T TTT TTT TTT TTT TTT-C 3 H 6 TT GG TTG G GT TTT TTT TTT TTT TTT-C 3 H 6 System-III TC TTC C TCC TT CTT GTG TC GT GG TCG GTT GCT TTT TTT TTT TT-C 6 TT GG TTG G GT TTT TTT TTT TTT TTT-C 3 H 6 System-IV System-V TC TTC C TCC T TCT TGT GTC GT GG TCG GTT GCT TTT TTT TTT TT-C 6 TT GG TTG G GT TCT TGT GTC GT GG TCG GTT GCT TTT TTT TTT TT-C 6 SH-C 6 -TTT TTT TTT TTT TTT TTT TTT TTT TTT CGT TGG CTG GT GC TGT GTT CTT C CT CC TTC T SH-C 6 -TTT TTT TTT TTT TTT TTT TTT TTT TTT CGT TGG CTG GT GC TGT GTT CT TG GG TT GGT T System-VI TC TTC C TCC T TCT TGT GTC GT GG TCG GTT GCT TTT TTT TTT TT-C 6 3 -G C CG CT TCC GC C CG -5 TT GG TTG G GT TCT TGT GTC GT GG TCG GTT GCT TTT TTT TTT TT-C 6 3 -G C CG CT TCC GC C CG

6 Supplementary Table S2: Results of UV-vis melting analysis for assembled aggregates. Melting nalysis System T m ( o C) I 63.4 (±0.5) II 64.0 (±0.5) III 64.3 (±0.6) IV 63.1 (±0.3) V 62.5(±0.3) VI 66.3 (±0.5) Supplementary Table S3. Interparticle spacing d obtained from the first scattering peak of SXS data and worm-like chain model 32 idealized estimates d w, for aggregates assembled at room temperature. System d, (nm) d w, (nm) I II III IV V VI

7 SupplementaryNotes 31. Zhou, J., Gregurick, S. K., Krueger, S. & Schwarz, F. P. Conformational changes in single-strand DN as a function of temperature by SNS. iophys. J. 90, (2006). 32. Rivetti, C., Walker, C. & ustamante, C. Polymer chain statistics and conformational analysis of DN molecules with bends or sections of different flexibility. J. Mol. iol. 280, (1998). T=56 C 7