Supporting Information. Copyright Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 2006
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1 Supporting Information Copyright Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 2006
2 Formation and stability of G-quadruplex self-assembled from guanine-rich strands Jiang Zhou, Gu Yuan*, Junjun Liu, and Chang-Guo Zhan S1
3 1. The formation of Quadruplexes Oligonucleotides were directly dissolved in deionization water, and the stock concentrations were 500 µm. Then each 2.0 µl DNA solution was diluted with 20:80 (v/v) methanol-100 mm ammonium acetate to 40 µl (resulting DNA 25µM). The ESI-MS spectra were obtained in the negative-ion mode by directly infusing the oligonucleotide solutions. S2
4 S3
5 S4
6 S5
7 S6
8 Figure S1. ESI mass spectra of fifteen potential 6-nt quadruplex sequences. S, single strand; D, duplex; Q, quadruplex. S7
9 2. ESI mass spectra for the mixture of oligonucleotides with different sequences Oligonucleotides were stocked in deionization water. After froze, each 2.0 µl DNA solution were mixed, then diluted with 20:80 (v/v) methanol-100 mm ammonium acetate to 40 µl (resulting 25µM for each DNA). The ESI-MS spectra were obtained in the negative-ion mode by directly infusing the oligonucleotide solutions. S8
10 Figure S2(a). ESI mass spectra of mixture of different sequences. S, single strand; D, duplex; Q, quadruplex. Figure S2(b). ESI mass spectra of mixture of different quadruplex. S, single strand; D, duplex; Q, quadruplex. The ESI mass spectra did not reveal any peak associated with a hetero-quadruplex; only single-strand, self-association duplex, and self-association quadruplex were S9
11 observed, which indicated that each G-rich sequence preferred self-association rather than hybridized integration. 3. ESI mass spectra of binding molecules with Q(1) S10
12 Figure S3. ESI mass spectra of ImImImßDp (1) with Q(1), ranging from Q(1): binder = 1:1and 1:8. Q(1), quadruplex; binder, ImImImßDp (1). Figure S4. ESI mass spectra of Tel01(2) with Q(1), ranging from Q(1): binder = 1:1 and 1:2. Q(1), quadruplex; binder, Tel01 (2). S11
13 4. ESI mass spectra of Tel01 (2) with Q(2), Q(3) S12
14 Figure S5. ESI mass spectra of Tel01 (2) with Q(2) and Q(3), Q(n): binder = 1:1. Q(n), quadruplex; binder, Tel01 (2). 5. Computational Modeling The X-ray structure of parallel-stranded guanine tetraplex (PDB entry 244D) was selected as the template to construct the initial structures used for the molecular mechanics-poisson-boltzmann surface area (MM-PBSA) i,ii calculations. Prior to the MM-PBSA energy calculations, the structures of 15 hypothesized G-quadruplexes and 6 hetero-quadruplexes were constructed by using the LEaP module of AMBER8 program suite. iii + The restrained electrostatic potential (RESP) charges used for NH 4 ion were calculated at the HF/6-31G* level by using the Gaussian 03 program. iv Each of the structures was fully energy-minimized. After the energy-minimizations, the solute energies were evaluated without using any cutoff for all of the structures. The same structures were used in the PBSA solvation energy calculations using the PBSA S13
15 module of the AMBER8 program suite. In the PBSA calculations, the grid size used was defined as 0.5 Å and the radius of the probe atom was set to 1.4 angstrom. The charges used in the Poisson-Boltzmann (PB) calculations were read from the AMBER topology parameters. The solvent accessible surface (SAS) was obtained by using the molsurf module of the AMBER8 program suite. In addition, the entropy contributions from the translations, rotations, and vibrations to the binding free energy were calculated by performing the standard normal mode analyses on the energy-minimized structures using the nmode module of the AMBER8 program suite. The Gibbs free energy G for each structure was calculated by G = E MM + G PB + G SA TS (see the AMBER8 user manual for the details). iii The calculated free energies and the binding free energies are listed in Tables S1 and S2. Table S1. The calculated relative binding free energies (in kcal/mol) of 15 hypothesized 6-nt potential quadruplexes. Sequence G(Complex) G(Monomer) G(NH + 4 )??G 5'-AGGGGA-3' '-TGGGGT-3' '-CGGGGC-3' '-TTGGTT-3' '-TTGGGT-3' '-TCGGGT-3' '-ACCCCA-3' '-TGCCGT-3' '-TCGGCT-3' '-CCGGCC-3' '-TCGCCT-3' '-TGTGTT-3' '-TGTGGT-3' '-TGCGGT-3' S14
16 5'-TCGCGT-3' Table S2. The calculated absolute free energy changes (in kcal/mol) of the hypothesized hetero-quadruplexes. Structure a E(Total) TS G?G 5'-AGGGGA-3' Complex '-CCGGGC-3' Complex '-TGGGGT-3' Complex A1C Complex A1T Complex C1A Complex C1T Complex T1A Complex T1C Complex a A represents strand 5'-AGGGGA-3', T refers to 5'-TCGGGT-3', and C represents 5'-CCGGGC-3'. 5'-AGGGGA-3' complex consists of four 5'-AGGGGA-3' strands. 3A1C complex consists of three 5'-AGGGGA-3' strands and one 5'-CCGGGC-3' strand. Other complexes are defined in the same way. The positive free energy changes suggest that only homo-quadruplexes can exist as the hetero-quadruplexes tend to form homo-quadruplexes. References i Fadrna, E.; Spackova, N.; Stefl, R.; Koca, J.; Cheatham, T.E.; Sponer. J. Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations, Biophys. J. 2004, 87, ii Harris, D.L.; Park, J.Y.; Gruenke. L.; Waskell, L. Theoretical study of the ligand-cyp2b4 complexes: Effect of structure on binding free energies and heme spin state, Proteins 2004, 55, iii Case, D.A.; Darden, T.A.; Cheatham, III, T.E.; Simmerling, C.L.; Wang, J.; Duke, R.E.; Luo, R.; Merz, K.M.; Wang, B.; Pearlman, D.A.; Crowley, M.; Brozell, S.; Tsui, S15
17 V.; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Schafmeister, C.; Caldwell, J.W.; Ross, W.S.; Kollman, P.A. AMBER 8, University of California, San Francisco, iv Gaussian 03, Revision A.1, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, S16
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