Supporting Information for DNA Origami and G- Quadruplex Hybrid Complexes Induce Size- Control of Single- Walled Carbon

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1 Supporting Information for DNA Origami and G- Quadruplex Hybrid Complexes Induce Size- Control of Single- Walled Carbon Nanotubes via Biological Activation Hiroshi Atsumi 1,2 and Angela M. Belcher 1,2,3* 1 The David H. Koch Institute for Integrative Cancer Research, 2 Department of Biological Engineering, and 3 Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. *e- mail: belcher@mit.edu Table of Contents 1. Photographs and UV- Vis spectrum of G- DNA- SWNTs (Fig. S1) 2. Luminol oxidation assay (Fig. S2) 3. Raman spectra of G- DNA- SWNTs after random cutting (Fig. S3) 4. D/G ratio, PL spectra, and AFM of ng- DNA- SWNTs (Fig. S4) 5. Raman spectra of ng- DNA- SWNTs (Fig. S5) 6. The agarose gel separation of the DNA origami monomer (Fig. S6) 7. The predictions of DNA origami perturbations (Fig. S7) 8. Assembly of SWNTs on DNA origami monomer templates (Fig. S8). 9. Assembly of SWNTs on the short rectangular- shaped DNA origami templates (Fig. S9). 10. Assembly of SWNTs on the long rectangular- shaped DNA origami monomer templates (Fig. S10). 11. Assembly of SWNTs on the 1- D origami polymer templates (Fig. S11). 12. Raman spectra of B- DNA- SWNTs after origami polymer- cutting and origami monomer- cutting (Fig. S12) 13. AFM image of B- DNA- SWNTs before SWNT- cutting (Fig. S13) 14. SWNT- cutting of B- DNA- SWNTs with cross- shaped DNA origami (Fig. S14) 15. SWNT- cutting of B- DNA- SWNTs with 1- D origami polymer (Fig. S15) 16. SWNT- cutting of B- DNA- SWNTs with short rectangular- shaped DNA origami (Fig. S16) 17. SWNT- cutting of B- DNA- SWNTs with long rectangular- shaped DNA origami (Fig. S17) 18. Peaks, averages with standard errors, and standard deviations with uncertainties of SWNT- length after SWNT- cutting (Table S1) 1

2 1. Figure S1 Photographs and UV- Vis spectra of G- DNA- SWNTs. (a) Photographs of pristine SWNTs in water (left), G- DNA- SWNTs in water (middle), and pristine SWNTs (right) in 1% sodium dodecyl sulfate (SDS). All photographs were taken after sonication. (b) Absorbance spectra of pristine SWNTs in 1% SDS (black) and G- DNA- SWNTs (red). 2

3 2. Figure S2 Biological activation of hydrogen peroxide by G- quadruplex hemin complex on SWNTs. (a) A schematic of the oxidation of luminol through the G- quadruplex hemin complex on a SWNT. (b) A time course of luminol chemiluminescence at 426 nm after the addition of hydrogen peroxide to an equal amount of hemin (5 µm). Black, hemin; red, G- DNA- SWNT with hemin; blue, ng- DNA- SWNT with hemin; green, without hemin. The arrow shows the time at which hydrogen peroxide was added. 3

4 3. Figure S3 Raman spectra for G- DNA- SWNTs (black) in the presence of hemin (green), hydrogen peroxide (light blue), and both (red). 4

5 4. Figure S4 ng- DNA- SWNTs with hemin and hydrogen peroxide. (a) A schematic of ng- DNA- SWNTs with hemin and hydrogen peroxide. (b) The D/G ratio from Raman spectra for ng- DNA- SWNTs (black) in the presence of hemin (green), hydrogen peroxide (light blue), and both (red). (c) PL spectra of ng- DNA- SWNTs (black) in the presence of hemin (green), hydrogen peroxide (light blue), and both (red) using 5

6 532 nm laser excitation. The spectra are normalized to the intensity of G- DNA- SWNTs at 1007 nm. (d) AFM images for ng- DNA- SWNTs before (left) and after (right) the addition of both hemin and hydrogen peroxide. Scale bars: 1 µm. (e) The distribution of SWNT- lengths based on AFM images in the absence (black) and presence (red) of both hemin and hydrogen peroxide. 6

7 5. Figure S5 Raman spectra for ng- DNA- SWNTs (black) in the presence of hemin (green), hydrogen peroxide (light blue), and both (red). 7

8 6. stained unstained M DNA DNA origami origami 3k 2k 1.5k 1k Figure S6 The agarose gel separation for the DNA origami monomer functionalized with hemin and streptavidin. A 1% agarose gel for purification of the DNA origami monomer functionalized with hemin and streptavidin. The gel was stained with SYBR Safe (ThermoFisher Scientific, #S33102). The desired unstained band (red box) was excised and eluted by using a Quantum Prep Freeze N Squeeze DNA gel extraction spin column. The product from the stained band did not extend to one- dimension efficiently, likely because dye intercalation unwinds the DNA structures and produces structural stress. M indicates 1 kbp markers. 8

9 7. Figure S7 The predictions of DNA origami perturbations. (a) (i) schematic of cross- shaped DNA origami. (ii)- (viii) predictions of cross- shaped DNA origami perturbations using CanDo ( dna- origami.org/) with ((ii)- (iv)) and without ((v)- (vii)) the twist corrections; top (ii) and (v), bottom (iii) and (vi), and side (iv) and (viii) views. (b) (i) schematic of short rectangular- shaped DNA origami. (ii)- (iv) predictions of short rectangular- shaped DNA origami perturbations using CanDo with the twist corrections; top (ii), bottom (iii), and side (iv) views. (c) (i) schematic of long rectangular- shaped DNA origami. (ii)- (iv) predictions of long rectangular- shaped DNA origami perturbations using CanDo with the twist corrections; top (ii), bottom (iii), and side (iv) views. With increasing root- mean- square error, the color changes from blue (0.2 nm) to red (1.6 nm). For SWNT- cutting to a pre- determined length, we used DNA origami as a size platform. The platform needs to 1) be flat, 2) bind to SWNTs, and 3) catalyze SWNT- cutting. First, we designed a flat DNA origami monomer so that the DNA origami monomer can extend in one dimension with linker- DNAs. Although DNA origami designed originally using a helical twist of bases/turn induced rupture of the DNA origami, a design based on a helical twist of 10.4 bases/turn dramatically improved its flatness.1 Second, biotin- modified staple strands were designed to attach streptavidin to the DNA origami. Streptavidin is attached to the biotinylated sites on the DNA origami, which helps B- DNA- SWNTs to bind to the DNA origami (Fig. 3f). Third, in order to cut SWNTs on the DNA origami, we 9

10 designed two G- quadruplex staple strands to be embedded in the top corners of the DNA origami (See Fig. 3a). See also DNA table in detail. 10

11 8. (a) 10 nm 11

12 (b) Figure S8 Assembly of SWNTs on DNA origami monomer templates. Yellow boxes indicate SWNT- binding DNA origami monomers. Scale bars: (a) 1 μm; (b) 200 nm. 12

13 9. Fig. S9 Assembly of SWNTs on the short rectangular- shaped DNA origami templates. Scale bars: 200 nm. 13

14 10. Fig. S10 Assembly of SWNTs on the long rectangular- shaped DNA origami monomer templates. Scale bars: 200 nm. 14

15 11. Fig. S11 Assembly of SWNTs on the 1- D origami polymer templates. Scale bars: 200 nm. 15

16 12. Figure S12 Raman spectra for B- DNA- SWNT (black) after 1- D origami polymer- cutting (blue), and origami monomer- cutting (pink). 16

17 13. 5 nm Figure S13 AFM image of B- DNA- SWNTs before SWNT- cutting. The AFM image of B- DNA- SWNTs show direct evidence for the change in length, compared with those after SWNT- cutting with DNA origami platforms (Fig. 4d). Scale bar: 1 µm. 17

18 14. Figure S14 SWNT- cutting of B- DNA- SWNTs with cross- shaped DNA origami. Scale bar: 1 µm. 18

19 14. 5 nm Figure S14 SWNT- cutting of B- DNA- SWNTs with 1- D origami polymer. Scale bar: 1 µm. 19

20 15. Figure S15 SWNT- cutting images of B- DNA- SWNTs with short rectangular- shaped DNA origami. (a) AFM images, (b) TEM images, (c) The comparison of the histograms of SWNT- lengths estimated by AFM and TEM. Scale bars: a, 1 µm; b, 500 nm. 20

21 16. Figure S16 SWNT- cutting of B- DNA- SWNTs with long rectangular- shaped DNA origami. Scale bars: 1 µm. 21

22 17. Table S1. The peaks, averages with standard errors, and standard deviations with the uncertainties of SWNT- lengths before and after SWNT- cutting. Peaks for each distribution were estimated by curve fitting. Peak (nm) Average ± Standard Error (nm) Standard Deviation ± Uncertainty (nm) B-DNA-SWNT ± ± 10 Random cutting ± 5 89 ± 4 Monomer cutting ± 6 97 ± 4 87 nm cutting ± 4 66 ± nm cutting ± ± 5 Polymer cutting 91 and ± 3 54 ± 2 Note that the statistical parameters of different origami template may be not comparable (monomer cutting and polymer cutting are comparable) because of a difficulty of synthesizing equal amount of DNA origami template, which provides different cutting efficiency. The curve fitting was performed with the following equation. Y=A/sqrt(2*pi)*w*x)*exp(- (ln(x/x c ))^2/(2*w^2)), where x c is a average and w is a shape parameter. In Figure 4d(vi), the R- square value of the fitting- curve (solid red) integrated with the two Gaussian components (dot cyan) is Reference 1. Woo, S.; Rothemund, P. W. K. Programmable Molecular Recognition Based on the Geometry of DNA Nanostructures. Nat. Chem. 2011, 3,