Supporting Information. Copyright Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 2006

Transcription

1 Supporting Information Copyright Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 2006

2 A New Optimum in the Structure Space of DNA Solubilizing Single-Walled Carbon Nanotubes Stephanie R. Vogel, a Manfred M. Kappes, b,c Frank Hennrich, c and Clemens Richert a * a Institut für Organische Chemie Universität Karlsruhe (TH) Karlsruhe, Germany b Institut für Physikalische Chemie Universität Karlsruhe (TH) Karlsruhe, Germany c Institut für Nanotechnologie Forschungzentrum Karlsruhe D-76021, Karlsruhe, Germany

3 - 2 - Preparation of DNA-SWCNT Suspensions. sonifier microtip 500 ml ice/water Figure S1. Cartoon of sonication set-up for preparation of DNA-SWCNT suspensions.

4 - 3 - Additional Absorption Spectra The spectra shown in Figure S2, below, are additional, representative spectra of SWCNT suspensions, prepared with individual, non-selfcomplementary DNA strands. For equivalent spectra of the mixture of oligonucleotides, see Figure 1 of the main manuscript. r _ r u 2,0 1,5 1,0 0,5 d(gt)3_i2_slpur_puffer_13 3 d(gt)5_h_slpur_puffer_09 5 d(gt)10_j_slpur_puffer_0 d(gt)20_g_sl_puffer_ d(gt)40_k_slpur_puffer_1 40 1,00 0,75 0,50 5 dsdna_slpur_puffer_ genomic wavelength [nm] a) b) wavelength [nm] 2,0 1,5 2,0 d(ac) d(ac)3_d(gt)3_i7_3_sl_puffer_ d(gt) 3 half concentrated 1,5 d(ac) d(ac)3_d(gt)3_i9_slpur_ 3 + d(gt) 3 triply concentrated 1,0 0,5 1,0 0, wavelength [nm] c) d) wavelength [nm] Figure S2. Representative absorption spectra of suspensions of SWCNTs generated through sonication in the presence of oligonucleotides a) d(gt) n, (where n is 3, 5, 10, 20 or 40) or b) genomic DNA from salmon sperm (initially fully double-stranded) at 0.74 mm nucleotide concentration, and c)/d) of d(ac) 3 + d(gt) 3 half concentrated or triply concentrated. Spectra were acquired after ultracentrifugation. The discontinuity at 800 nm is caused by a change of gratings in the spectrophotometer.

5 - 4 - Converting Absorbance Readings into Masses of Nanotubes Solubilized The amount of solubilized carbon nanotubes was determined via UV-Vis absorption spectroscopy. The at 730 nm was used for determining an approximate mass for the solubilized nanotube material, according to Lambert-Beer's law. For the calculation, an average extinction coefficient for SWCNTs from the literature of ε = 7.9 x 10 6 M -1 cm -1 was used. [1] The values thus obtained for the different preparations are compiled in Table S1, below. Table S1. Amount of SWCNT solubilized with DNA. DNA-sequence SWCNT [µg/ml] d(ac) ± 4.8 d(gt) ± 4.4 d(ac) 3 /d(gt) ± 6.4 d(ac) d(gt) d(ac) 5 /d(gt) d(ac) d(gt) d(ac) 10 /d(gt) d(ac) d(gt) d(ac) 20 /d(gt) d(ac) ± 2.8 d(gt) ± 3.2 d(ac) 40 /d(gt) ± 0.8

6 - 5 - Removal of Unbound DNA via Filtration and Resuspension of Nanotubes that are Free of Excess DNA a) b) c) Attempts to prepare stable SWNT solutions in our labs sonifier mocrotip microtip spin filter SWCNT/DNA concentrate clear gray suspension SWCNT pellet excess DNA DNA-SWCNT suspension Figure S3. Schematic of the steps employed for preparation of DNA-wrapped SWCNT suspensions freed of excess DNA. Top row: a) sonication, b) ultracentrifugation, and c) filtration followed by re-suspending concentrated material.

7 - 6 - AFM Images of Solubilized SWCNTs AFM samples were prepared by spin coating nanotube suspensions onto silicon wafers and rinsing with water and acetone. Intermittent Contact Mode [2] AFM images were taken with a Digital Instruments Multimode SPM with NSC15 silicon cantilevers (MikroMasch). The height and lengths of the measured objects were extracted from AFM pictures with the help of the Software package SIMAGIS (Smart Imaging Technologies Co.). Tube lengths were determined within a lateral resolution of nm. [2],[3] Shown below (Figures S4 and S5), are AFM images of a sample prepared with the mixture of hexamers (d(ac) 3 and d(gt) 3 ) and with sodium cholate (control). Further, the size and diameter distribution determined for the former case is given in Figure S6. Figure S4. Representative AFM image of HiPco carbon nanotube material solubilized with the mixture of DNA hexamers d(ac) 3 and d(gt) 3. The more noisy background compared to the control case (Figure S5) is presumably caused by residual buffer salts.

8 - 7 - Figure S5. Representative AFM image of HiPco carbon nanotube material solubilized in a sodium cholate solution (1% weight in D 2 O) as control. 3 Height Height [nm] Length [nm] Figure S6. Height and length distribution of solubilized HiPco-material with the mixture of DNA hexamers (d(ac) 3 and d(gt) 3 ).

9 - 8 - Thermal Denaturation of SWCNT-DNA Complexes as Determined through Absorption Changes Induced by Flocculation a) b) d(ac) 10 d(ac) 10 d(ac) 10 /d(gt) 10 d(ac) 10 d(gt) 10 d(gt) 10 d(ac) 10 /d(gt) 10 Figure S7. Photographs of cuvettes containing suspensions of SWCNT-DNA complexes obtained through sonication, ultracentrifugation and spin-filtration, a) prior to and b) after heating to 90 C for > 24h. In most cases precipitates formed at the bottom of cuvettes, in other cases (e.g. for d(gt) 10 in the case shown above) the nanotube aggregates floated on top of the solution after denaturation. d(ac) 40 d(ac)40, K3 d(gt) 40 d(gt)40, K3 d(ac) 40 + d(gt) 40 d(ac)40/d(gt)40, K Figure S8. Representative changes caused by thermal dissociation of SWCNT-DNA complexes at 90 C for 80mer DNA. Lines are fits of a monoexponential function.

10 - 9 - d(ac) 10 d(ac)10-swnt d(gt) 10 d(gt)10-swnt d(ac) 10 + d(gt) 10 d(ac)10/d(gt)10-swnt Figure S9. Absorbance changes caused by thermal dissociation of SWCNT-DNA complexes at 90 C for 20mers (data gaps are due to absence of the operator during the night). Lines are fits of a monoexponential function. d(gt) 3 d(gt)3_swnt d(ac) 3 + d(gt) 3 d(ac)3_d(gt)3_swnt Figure S10. Absorbance changes caused by thermal dissociation of SWCNT-DNA complexes at 90 C for hexamers. (Flocculation left some mobile, suspended aggregates in solution for the mixture of oligonucleotides, causing fluctuation in some late values). Lines are fits of a monoexponential function. Figures S8-10 show representative kinetics of dissociation for DNA carbon nanotube complexes. The first time-dependent measurements of UV-Vis spectra were performed manually explaining the lack of data after ten hours in Figure S9. Later kinetic measurements were facilitated by an automatic mode, a capability of the spectrometer developed during the course of this study.

11 Reproducibility of Noisy Kinetics Experiment 1 Experiment Figure S11. Absorbance changes of two thermal dissociation experiments of SWCNT-DNA complexes with the equimolar mixture of the hexameric DNA strands d(ac) 3 and d(gt) 3. In Experiment 1 and Experiment 2 two different suspensions that had been prepared following an identical procedure were heated to 90 C after sonication. Please note that while the scattering of data points is substantial in individual cases, the the time course is similar.

12 Bathochromic Shifts in Absorbance Maxima upon Heating 745 d(gt) maximum [nm] d(ac) 3 /d(gt) maximum [nm] d(gt) 5 d(ac) 5 /d(gt) d(ac) d(ac) 20 maximum [nm] d(gt) 10 d(ac) 10 /d(gt) maximum [nm] d(gt) 20 d(ac) 20 /d(gt) d(ac) 40 maximum [nm] d(gt) 40 d(ac) 40 /d(gt) Figure S12. Shifts in a representative maximum (730 nm) of nanotubes upon heating to 90 C. The first data point is that recorded at room temperature. As mentioned in the main text, heating the nanotube-dna suspension led to different bathochromic shifts in the peaks of the SWCNTs. Figure S12 shows the change in maxima for suspensions with oligonucleotides of different length for one maximum of the nanotubes. Other bands give similar results. As the results show, the shift upon heating is greater for short DNA strands than for longer ones, suggesting that heating exposes the nanotubes more readily in these cases. Further, there is a modest difference between individual sequences or mixtures of sequences.

13 Position of the SWCNT-DNA Suspensions Prepared in a Proposed Phase Diagram proposed limit 4,0x10-3 3,0x10-3 homogeneously dispersed DNA [wt%] 2,0x10-3 1,0x10-3 non-homogeneously dispersed 1,0x10-3 2,0x10-3 3,0x10-3 4,0x10-3 SWCNT [wt%] Figure S13. Data points from our current experiments with d(gt) n / d(ac) n entered in the phase diagram for suspensions of carbon nanotubes proposed recently. [4] The data points (calculated weight percent values for the SWCNT suspensions) are entered as open circles. All preparations gave homogeneously dispersed suspensions.

14 Thermal Denaturation of Hexamer Duplexes in the Absence of Nanotubes Shown below are two heating and two cooling curves for the mixture of DNA hexamers d(ac) 3 /d(gt) 3 in the absence of nanotubes, demonstrating that the formation of conventional Watson-Crick duplex occurs at low temperatures and is readily reversible (fast kinetics) Absorbance at 260 nm at 260 nm temperature [ C] Temperature ( C) Figure S14. Thermal denaturation curves for the DNA duplex formed by the mixture of hexamers d(ac) 3 /d(gt) 3 in the same D 2 O-buffer that was used to prepare the DNA-SWCNT suspensions. The oligonucleotide strand concentration was 4.5 µm, i.e. similar to the DNA concentration of the suspensions used for thermal denaturation of SWCNT-DNA complexes generated through filtration and re-suspending the concentrate. All four curves acquired are shown to demonstrate the reversibility and reproducibility. Site-Directed Deposition of SWCNTs via Selective Thermal Denaturation Samples of the SWCNT suspensions prepared with the mixture d(ac) 2 /d(gt) 2 or d(gt) 40 were heated locally to approximately 90 C by exposing parts of the surface of a glass capillary containing the suspensions to a hot metal surface for 5 min. The capillary was placed on a U-shaped heated brass block so that the contact areas were 2 mm in width. As shown in Figure S15, SWCNT material was deposited site-selectively at the boundaries between the heated zones and the remainder of the suspension. When the same experiment was performed with a suspension prepared with d(gt) 40, no visible deposition of carbon nanotubes was observed under the same conditions.

15 d(ac) 2 /d(gt) 2 d(gt) 40 a) b) c) d) e) Figure S15. Photographs documenting the exploratory experiment for site-selective thermal deposition of nanotubes from DNA-carbon nanotube suspensions. a) Glass capillaries filled with suspension prepared with the mixture d(ac) 2 /d(gt) 2 or (GT) 40. b) Side view of the experimental set-up during local heating; the brass block is located on a heating plate. c) Top view, after heating for 5 min. d) and e) Close-up views of capillary with local flocculation zones produced by short-term heating (note black particulate matter at the four boundaries between heated and 'air-cooled' zones). A ruler with cm marks was placed in the photographs a) and d).

16 References for Supporting Information [1] N.W.S. Kam, M. O Connell, J.A. Wisdom, H. Dai, Proc. Natl. Acad. Sci. USA 2005, 102, [2] Q. Zhong, D. Inniss, K. Kjoller, V. B. Elings Surf. Sci. Lett. 1993, 290, L688. [3] G.K.H. Pang, K.Z. Baba-Kishi, A. Patel, Ultramicroscopy 2000, 81, 35. [4] S. Badaire, C. Zakri, M. Maugey, A. Derré, J.N Barisci, G. Wallace, P. Poulin, Adv. Mater. 2005, 17,