Supporting Information Table S1. Oligonucleotide sequences used in this work Oligo DNA A B C D CpG-A CpG-B CpG-C CpG-D Sequence 5 ACA TTC CTA AGT CTG AAA CAT TAC AGC TTG CTA CAC GAG AAG AGC CGC CAT AGT A - 3 5 - TAT CAC CAG GCA GTT GAC AGT GTA GCA AGC TGT AAT AGA TGC GAG GGT CCA ATA C 3 5 - TCA ACT GCC TGG TGA TAA AAC GAC ACT ACG TGG GAA TCT ACT ATG GCG GCT CTT C - 3 5 - TTC AGA CTT AGG AAT GTG CTT CCC ACG TAG TGT CGT TTG TAT TGG ACC CTC GCA T - 3 5 TCC ATG ACG TTC CTG ACG TTT TTT T ACA TTC CTA AGT CTG AAA CAT TAC AGC TTG CTA CAC GAG AAG AGC CGC CAT AGT A 3 5 - TCC ATG ACG TTC CTG ACG TTT TTT T TAT CAC CAG GCA GTT GAC AGT GTA GCA AGC TGT AAT AGA TGC GAG GGT CCA ATA C 3 5 - TCC ATG ACG TTC CTG ACG TTT TTT T TCA ACT GCC TGG TGA TAA AAC GAC ACT ACG TGG GAA TCT ACT ATG GCG GCT CTT C - 3 5 - TCC ATG ACG TTC CTG ACG TTT TTT T TTC AGA CTT AGG AAT GTG CTT CCC ACG TAG TGT CGT TTG TAT TGG ACC CTC GCA T - 3 1
Figure S1. Scheme for preparing DNA tetrahedron structures in this work. 2
Figure S2. DNA structures used in this work. (a), schematic presentation of single strand CpG DNA (SS), and tetrahedrons with 0 to 4 (0, I, II, III, IV) CpG sidechains. (b), electrophoresis analysis of these DNA structures. Each DNA structure was run on 2% agarose gel at 100 V for 30 min. Lane M, DNA Marker DL2,000. Figure S3. Melting curves of nanocages. Partially complementary duplex (strand A + B), tetrahedron and tetra-cpgs were respectively mixed with 0.5 SYBR green I, and stepwise heated with a Bio-Rad real-time RCR thermocycler (from 40 to 90 ). Their fluorescent intensities were read every 1 change. 3
Figure S4. Fluorescence studies of nanocages. Firstly, Cy3 and Cy5 were respectively labeled on each end of strand A. Partially complementary duplex (strand A+B), tetrahedron, and tetra-cpgs containing dual-labeled strand A (marked with * ) were analyzed with fluorescence spectra (excitation 530 nm). On the other hand, Cy3 and Cy5 were separately labeled on strand A and strand B (or CpG-B). Tetrahedron and tetra-cpgs containing two labeled strands (marked with ** ) were then analyzed with fluorescence spectra. 4
Figure S5. Studies of nanocages with atomic force microscopy (AFM). Solutions of nanocages (50 nm) were dried on mica surface. Contact scanning mode was employed. 5
Figure S6. FRET studies of nanocages within RAW 264.7 cells. Scale bar: 10 μm. ROI: region of interest. 6
Figure S7. Comparison of TNF-α releasing from RAW264.7 cells stimulated by tetra-cpg(i) and tetra-cpg(iv) of different CpG concentration. Error bars represent standard deviation (SD) of at least three independent measurements. * P<0.05 significantly different from CpG ODN. # P<0.05 significantly different from tetra-cpg(i) of same CpG concentration. 7
Figure S8. ELISA results of TNF-α detection. (a), Calibration curve attained by testing of TNF-α standard; (b) and (c), Colorimetric absorbance results from ELISA detection of TNF-α in treated samples. All samples including standard were 5-fold diluted in order to fit the dynamic range of ELISA. Error bars represent standard deviation (SD) of at least three independent measurements. 8
Figure S9. Raw data of IL-6 detection. (a), Calibration curve attained by testing of IL-6 standard; (b), Colorimetric absorbance results from ELISA detection of IL-6 in treated samples. Error bars represent standard deviation (SD) of at least three independent measurements. Figure S10. Raw data of IL-12 detection. (a), Calibration curve attained by testing of IL-12 standard; (b), Colorimetric absorbance results from ELISA detection of IL-12 in treated samples. Error bars represent standard deviation (SD) of at least three independent measurements. 9
Table S2. Raw data collection from ELISA detection of cytokines in treated samples. Each cell contains three values from parallel experiments. Sample Abs TNF-α IL-6 IL-12 CpG-ODN (10 nm) 0.0835 0.0820 0.0840 CpG-ODN (20 nm) 0.0843 0.0872 0.0863 CpG-ODN (40 nm) 0.0897 0.0981 0.0954 CpG-ODN (80 nm) 0.0958 0.0977 0.0983 0.0886 0.0815 0.0810 0.0527 0.0588 0.0539 CpG (80 nm) + lipofectin 0.1185 0.1127 0.1037 Tetrahedron (20 nm) 0.0855 0.0915 0.0890 0.0827 0.0925 0.0878 0.0542 0.0573 0.0528 Tetra-CpG(I) (10 nm CpG) 0.2165 0.2347 0.2041 10
Tetra-CpG (I) 0.2431 0.1219 0.2030 (20 nm CpG) 0.2508 0.1275 0.1950 0.2679 0.1162 0.2124 Tetra-CpG(I) (40 nm CpG) 0.2982 0.309 0.2881 Tetra-CpG(II) 0.3536 0.1230 0.2265 (40 nm CpG) 0.3316 0.1302 0.2462 0.3103 0.1267 0.2065 Tetra-CpG(III) 0.3784 0.1412 0.2535 (60 nm CpG) 0.4310 0.1508 0.2765 0.4026 0.1322 0.2302 Tetra-CpG(IV) (10 nm CpG) Tetra-CpG(IV) (20 nm CpG) Tetra-CpG(IV) (40 nm CpG) 0.319 0.3175 0.305 0.3611 0.3713 0.3514 0.3918 0.4260 0.4083 Tetra-CpG(IV) 0.4633 0.1478 0.2704 (80 nm CpG) 0.4332 0.1546 0.2885 0.4295 0.1512 0.2523 11