Abstract
The photophysical properties of an intercalating unsymmetrical monomethine cyanine dye and single-stranded DNA homopolymers show strong association for poly(dA) and poly(dG), but not for poly(dC) and poly(dT), as determined by several spectroscopic techniques and molecular dynamics calculations. While poly(dA) and poly(dG) appear to bind the dye as a monomer (with dramatic increase in fluorescence), poly(dC) and poly(dT) bind only very weakly, and seem to promote dye aggregation. Only in the case of poly(dA) there seems to be a unique, well defined form of intercalation, that molecular dynamics calculations suggest involve the quinoline ring between two bases, in an arrangement that should favor π-stacking; consistently with this, the decay of the fluorescence shows a single exponential, the absorption spectrum shows a shift in the dye maximum, the fluorescence is strong, and the induced circular dichroism follows a simple pattern.
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G. Cosa, K.-S. Focsaneanu, J. R. N. McLean and J. C. Scaiano, Direct Determination of Single-to-Double Stranded DNA Ratio in Solution Applying Time-Resolved Fluorescence Measurements of Dye-DNA Complexes, Chem. Commun, 2000, 689–690.
G. Cosa, A. L. Vinette, J. R. N. McLean and J. C. Scaiano, Novel DNA Damage Detection Technique Applying Time-Resolved Fluorescence Measurements, Anal. Chem., 2002, 74, 6163–6169.
J. Nygren, N. Svanvik and M. Kubista, The Interactions between the Fluorescent Dye Thiazole Orange and DNA, Biopolymers, 1998, 46, 39–51.
L. Mikelsons and J. C. Scaiano, Can. Chem. News, 2004 (October), 18–19.
G. Cosa, K.-S. Focsaneanu, J. R. N. McLean, J. P. McNamee and J. C. Scaiano, Photophysical Properties of Fluorescent DNA-Dyes Bound to Single- and Double-Stranded DNA in Aqueous Buffered Solution, Photochem. Photobiol., 2001, 73, 585–599.
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, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. 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. G. Johnson, W. Chen, M. W. Wong, C. Gonzalez and J. A. Pople, Gaussian 03, Gaussian, Inc., Pittsburgh, 2003.
D. A. Case, T. A. Darden, T. E. Cheatham, III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, K. M. Merz, B. Wang, D. A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J. W. Caldwell, W. S. Ross and P. A. Kollman, (2004), Amber 8, University of California, San Francisco.
J. Wang, P. Cieplak and P. A. Kollman, How Well Does a Restrained Electrostatic Potential (Resp) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules?, J. Comput. Chem., 2000, 21, 1049–1074.
J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, Developing and Testing of a General Amber Force Field, J. Comput. Chem., 2004, 25, 1157–1174.
W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey and K. M. L., Comparison of Simple Potential Functions for Simulating Liquid Water, J. Chem. Phys., 1983, 79, 926–935.
R. W. Pastor, B. R. Brooks and A. Szabo, An Analysis of the Accuracy of Langevin and Molecular Dynamics Algorithms, Mol. Phys., 1988, 65, 1409–1419.
S. Miyamoto and P. A. Kollman, An Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models, J. Comput. Chem., 1992, 13, 952–962.
T. Y. Ogul’chansky, M. Y. Losytskyy, V. B. Kovalska, V. M. Yashchuk and S. M. Yarmoluk, Interactions of Cyanine Dyes with Nucleic Acids. XXIV. Aggregation of Monomethine Cyanine Dyes in Presence of DNA and Its Manifestation in Absorption and Fluorescence Spectra, Spectrochim. Acta, Part A, 2001, 57, 1525–1532.
J. Saltiel, Perdeuteriostilbene. The Role of Phantom States in the Cis–Trans Photoisomerization of Stilbenes, J. Am. Chem. Soc., 1967, 89, 1036–1037.
N. Berova, K. Nakanishi and R. W. Woody, Circular Dichroism: Principles and Applications, 2nd edn, Wiley-VCH, New York, 2000.
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† Electronic supplementary information (ESI) available: Computational details, Fig. S1–S6; movies of the dynamic simulation of Fig. S1–S4. See http://dx.doi.org/10.1039/b508720a
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Mikelsons, L., Carra, C., Shaw, M. et al. Experimental and theoretical study of the interaction of single-stranded DNA homopolymers and a monomethine cyanine dye: nature of specific binding. Photochem Photobiol Sci 4, 798–802 (2005). https://doi.org/10.1039/b508720a
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DOI: https://doi.org/10.1039/b508720a