Supporting Information

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1 Supporting Information Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: I. Recognizing mixed G-quadruplex in human telomeres Qianfan Yang, Junfeng Xiang, Shu Yang, Qiuju Zhou, Qian Li, Yalin Tang*, and Guangzhi Xu Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry for Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences (ICCAS). Beijing, , P. R. China Tel: Fax: Tangyl@iccas.ac.cn Graduate University of Chinese Academy of Sciences, Beijing, , P. R. China Contents: S (a) Materials and Sample Preparation S (b) - Spectral Measurement S (c) PAGE Experiment S (d) - Identification of Cyanine Dye ETC S (e) - Identification of the Structure of G-quadruplex DNA Samples by Measuring CD Spectra S (f) - The Absorption Spectra of ETC in PBS (K + ) and PBS (Na + ) S (g) - Stability Experiment of ETC J-aggregates in PBS (K + ) and PBS (Na + ) S (h) - Fluorescence Spectra of MTC Monomer and J-aggregates S (i) - The Absorption and Fluorescence Spectra of ETC with DNAs S (j) - The PAGE of A24 stained by ETC in PBS (Na + ) S (k) - The CD Spectra of ETCwith DNAs Reference S1

2 S (a) Materials and Sample Preparation The cyanine dye (ETC) was synthesized according to Hamer 1 and Fichen s 2 methods, and the purity was proved by MS and NMR [as shown in Section S(c)]. Calf thymus DNA were purchased from Sigma-Aldrich and used without further purification. All oligonucleotides (listed in Table S1) were purchased from Invitrogen (Beijing, China), purified by PAGE (purity 98%) and used without further purification. Analytical grade methanol, KH 2 PO 4, K 2 HPO 4, NaH 2 PO 4, Na 2 HPO 4 and EDTA were purchased from Beijing Chem. Co. Ultrapure water prepared by Mili-Q Gradient ultrapure water system (Millipore) was used throughout the experiments. The stock solution of ETC was prepared by dissolving ETC in methanol. The stock solution of CT was prepared by dissolving calf thymus DNA directly into 10 nm PBS (K + ). The stock solutions of single strand S24 and S17, and G-quadruplex A24 and M24 were prepared by dissolving oligonucleotides directly into buffer solutions in terms of Table S1. The stock solutions of double strand were prepared by heating the two complementary oligonucleotides (D24 and D17) or the self-complementary oligonucleotide (D26) at 85 for 15 min in 10 nm PBS (K + ) followed by a slow cooling to room temperature. All DNA samples had been stored for more than 24h at 4 and then identified by the CD spectra. The measured sample was prepared by mixing a quantity of ETC solution with DNA solution and then being diluted by corresponding buffer solution. The sample solutions were kept in darkness overnight at 4 before measurement in order to realize the full complexation. S2

3 Table S1. DNA samples preparation Expected Conformations Abb. Sequences Buffer Solution Mixed G4 in human telomeres * M24 [5 -(TTAGGG) 4-3 ] Calf thymus DNA CT Random sequence Double strand DNAs Single strand DNAs D24 [5 -(TTAGGG) 4-3 ] / [5 -(CCCTAA) 4-3 ] D17 [5 -CCAGTTCGTAGTAACCC-3 ] / [5 -GGGTTACTACGAACTGG-3 ] D26 [5 -CAATCGGATCGAATTCGATCCGATTG-3 ] S24 [5 -(CCCTAA) 4-3 ] S17 [5 -CCAGTTCGTAGTAACCC-3 ] 10 mm PBS (K + ) with 10 mm EDTA ph 7.04 Anti-parallel G4 A24 3, 4 [5 -(TTAGGG) 4-3 ] 10 mm PBS (Na + ) with 10 mm EDTA ph 7.04 *. 3, 5-7 Mixture of several different quadruplex forms S3

4 S (b) - Spectral Measurement Absorption, fluorescence and CD spectra were taken on a UV-1601PC spectrophotometer, a Hitachi F-4500 spectrophotometer and a JASCO J-815 spectrophotometer, respectively, in 10 mm quartz cells at room temperature. Xenon arc lamp was used in the excitation light source in fluorescence measurement. The excitation wavelength was 530 nm. Both excitation and emission slits were 5 nm and the scan speed was 240 nm / min. S4

5 S (c) PAGE Experiment The PAGE was conducted in 1X TBE (Tris base-boric acid-edta) buffer solution with 20% native gels. Electrophoresis gels were carried out at 100V for 2h at room temperature. Then the gels were incubated in 1X SYBR Gold and 20 μm ETC PBS (K + ) solution for 30 min, respectively, rinsed with ultrapure water, and then photographed in GE Typhoon Trio. The excitation wavelength was 532 nm. Fluorescence images were recorded under the emission filters of 526 nm (for SYBR Gold) and 610 nm (for ETC), respectively. S5

6 S (d) - Identification of Cyanine Dye ETC The structure and purification of cyanine dye ETC were identified by MS-ESI, elemental analysis, NMR and absorption spectroscopy. a) MS-ESI From the mass spectrum, the measured molecular weight of ETC is 679, which is consistent with the calculated value, 680. b) Elemental Analysis ETC molecular formula: C 39 H 47 N 3 O 6 S 4 3H 2 O Table S2. Elemental analysis of cyanine dye ETC Element N C H S Calculated Value (%) Experimental Value (%) c) NMR spectrum Chart S1. The numbering scheme of molecular structure of ETC S6

7 Figure S1. The 1 H-NMR spectrum of cyanine dye ETC in DMSO-d 6 Table S3. The full assignments of the proton peaks of ETC Proton Proton 1 H peak Proton Proton 1 H peak number kind number kind 1 Aromatic , d 13 Aromatic 7.663, t 2 Aromatic 7.788, t 14 Aromatic 7.788, t 3 Aromatic 7.663, t 15 Aromatic , d 4 Aromatic , d 16 Secondary 4.97, s 5 Aromatic , d 17 Secondary -- * 6 Aromatic , d 18 Secondary , m 7 Tertiary 6.653, s 19 Secondary 4.97, s 8 Secondary , m 20 Secondary -- * 9 Tertiary 6.653, s 21 Secondary , m 10 Aromatic , d 22 Secondary , q 11 Aromatic , d 23 Primary 1.17, t 12 Aromatic , d 24 Primary 1.374, t S7

8 * The peaks of these secondary protons are covered by the peak of the solvent DMSO-d 6 d) UV/Vis spectra and absorption coefficient calculation Figure S2. The absorption spectra of ETC monomer in methanol. Insert gives the curve of the absorbance at 573 nm against the concentration of ETC monomer. Based on lambert-beer's law, the molar absorption coefficient of ETC monomer is M ε 1cm,573nm = mol L cm. S8

9 S (e) - Identification of the Structure of G-quadruplex DNA Samples by Measuring CD Spectra Figure S3. The CD spectra of 4 μm M24 and A24 From the CD spectra, we can see clearly that different DNA samples with different conformation present distinct CD spectral feature. The exact structure of M24 is still unsure, but it is generally accepted M24 is a mixture of several different quadruplex forms 3, 5-7. As shown in Figure S3, we can see that M24 shows a more complicated CD spectrum, containing two positive signals at 269 nm and 284 nm, respectively, and a negative one at 238 nm. A24 has the same nucleotide sequence as that of M24 but is prepared in different buffer solutions. In PBS (Na + ), the CD spectrum of A24 exhibits two positive signals at 295 nm and 246 nm, respectively, and a negative one at nm, indicating an antiparallel quadruplex structure 3. NMR experiment also indicate that oligonucleotides [5 -(TTAGGG) 4-3 ] can form anti-parallel G-quadruplex in sodium solution 4. S9

10 S (f) - The Absorption Spectra of ETC in PBS (K + ) and PBS (Na + ) Figure S4. The absorption spectra of 4 μm ETC in PBS (K + ) and PBS (Na + ) S10

11 S (g) - Stability Experiment of ETC J-aggregates in PBS (K + ) and PBS (Na + ) Figure S5. The changes of 4 μm ETC J-aggregates absorbance (at 659 nm) against temperature in PBS (K + ) and PBS (Na + ), respectively. S11

12 S (h) - Fluorescence Spectra of MTC Monomer and J-aggregates Figure S6. The fluorescence spectra of ETC monomer (in methanol) and J-aggregates [in both PBS (K + ) and PBS (Na + )] S12

13 S (i) - The Absorption and Fluorescence Spectra of ETC with DNAs Figure S7. The changes of 4 μm ETC J-aggregates absorbance against the ratio of [DNA]/[ETC]. Figure S8. The changes of 4 μm ETC monomer fluorescence intensity against the ratio of [DNA]/[ETC]. S13

14 S (i) - The PAGE of A24 Stained by ETC in PBS (Na + ) Figure S9. Electrophoresis images of A24: 2 μm DNAs stained by conventional staining agent SYBR Gold (lanes 1) and 10 μm DNAs by ETC in PBS (Na + ) (lanes 2), respectively. S14

15 S (j) - The CD Spectra of ETC in the Presence of DNAs Figure S10. The CD spectra of 4 μm ETC J-aggregates (dash line) and 4 μm ETC J-aggregates with 12 μm M24 (solid line) Figure S11. The CD spectra of 4 μm ETC J-aggregates (dash line) and 4 μm ETC J-aggregates with 2 μm A24 (solid line) Figure S12. The CD spectra of ETC (4 μm) J-aggregates (dash line) and ETC (4 μm) J-aggregates with (a) double strand and (b) single strand DNAs. S15

16 Reference 1. F. M. Hamer, The Chemistry of Heterocyclic Compounds, Interscience, New York, G. E. Ficken, The Chemistry of Synthetic Dyes, Academic Press, New York, I. N. Rujan, J. C. Meleney and P. H. Bolton, Nucleic Acids Res., 2005, 33, J. X. Dai, M. Carver, C. Punchihewa, R. A. Jones and D. Z. Yang, Nucleic Acids Res., 2007, 35, C. Granotier, G. Pennarun, L. Riou, F. Hoffschir, L. R. Gauthier, A. De Cian, D. Gomez, E. Mandine, J. F. Riou, J. L. Mergny, P. Mailliet, B. Dutrillaux and F. D. Boussin, Nucleic Acids Res., 2005, 33, J. Li, J. J. Correia, L. Wang, J. O. Trent and J. B. Chaires, Nucleic Acids Res., 2005, 33, A. T. Phan, K. N. Luu and D. J. Patel, Nucleic Acids Res., 2006, 34, S16