Biopolym. Cell. 2013; 29(6):515-520.
Molecular Biophysics
Thermodynamic analysis of DNA complexes with methylene blue, ethidium bromide and Hoechst 33258
1Vardevanyan P. O., 1Antonyan A. P., 1Hambardzumyan L. A., 1Shahinyan M. A., 2Karapetian A. T.
  1. Yerevan State University
    1 Alex Manoogian, Yerevan, Republic of Armenia, 0025
  2. Yerevan State University Architecture and Construction
    105 Teryan Str., Yerevan, Republic of Armenia, 0009

Abstract

Aim. To investigate the thermodynamic characteristics of complexes of calf thymus double-stranded DNA with methylene blue (MB), ethidium bromide (EtBr) and Hoechst 33258 (H33258). Methods. The binding of MB with double-stranded DNA was observed by UV-melting method. Results. Several types of MB binding to DNA-intercalating, semi-intercalating and electrostatic with DNA phosphate backbone, have been revealed at low concentrations of Na+ (2 mM). At high concentrations of cations and low ratios of rb = [ligand]/[DNA] ( 0.05), the molecules of ligand semi-intercalate into the space between adjacent bases. At higher concentrations of ligand the main mode becomes electrostatic binding of MB to DNA phosphate groups. Conclusions. The comparison of thermodynamic characteristics of DNA-MB complexes with those of EtBr and H33258 indicates that there is more than one mode of binding ligands to DNA: besides nonspecific, external electrostatic binding with phosphate groups, intercalation and semi-intercalation modes of interaction coexist.
Keywords: UV-spectrophotometry of DNA melting, methylene blue, intercalation, semi-intercalation

References

[1] Hurley L. H. Secondary DNA structures as molecular targets for cancer therapeutics Biochem. Soc. Trans 2001 29, Pt 6 P. 692–696.
[2] Hurley L. H. DNA and its associated processes as targets for cancer therapy Nat. Rev. Cancer 2002 2, N 3:188–200.
[3] Hossain M., Giri P., Kumar G. S. DNA intercalation by quinacrine and methylene blue: a comparative binding and thermodynamic characterization study DNA Cell Biol 2008 27, N 2 P. 81–90.
[4] Denison L., Haigh A., D'Cunha G., Martin R. F. DNA ligands as radioprotectors: molecular studies with Hoechst 33342 and Hoechst 33258 Int. J. Radiat. Biol 1992 61, N 1:69–81.
[5] van Iperen H. P., Beijersbergen van Henegouwen G. M. Clinical and mechanistic aspects of photopheresis J. Photochem. Photobiol. B: Biology 1997 39, N 2:99–109.
[6] Osashi M., Oki T. Overview Oncologic, Endocrine & Metabolic: Oncologic, Endocrine & Metabolic: Ellipticine and related anticancer agents Expert. Opin. Therp. Patents 1996 6, N 12.:1285–1294.
[7] Bartulewicz D., Markowska A., Wolczynski S., Dabrowska M., Rozanski A. Molecular modeling, synthesis and antitumor activity of carbocyclic analogues of netropsin and distamycin – new carriers of alkylating elements Acta Biochim. Pol 2000 47, N 1:23–35.
[8] Vardevanyan P. O., Antonyan A. P., Parsadanyan M. A., Pirumyan K. V., Muradyan A. M., Karapetyan A. T. Influence of ionic strength of Hoechst 33258 binding with DNA J. Biomol. Struct. Dyn 2008 25, N 6:641–646.
[9] Bugs M. R., Cornelio M. L. Analysis of the ethidium bromide bound to DNA by photoacoustic and FTIR spectroscopy Photochem. Photobiol 2001 74, N 4:512–520.
[10] Vardevanyan P. O., Antonyan A. P., Parsadanyan M. A., Davtyan H. G., Karapetyan A. T. The binding of ethidium bromide with DNA: Interaction with singleand double-stranded structures Exp. Mol. Med 2003 35, N 6:527–533.
[11] Vardevanyan P. O., Antonyan A. P., Parsadanyan M. A., Davtyan H. G., Boyajyan Z. R., Karapetian A. T. Complex-formation of ethidium bromide with poly [d(A-T)]-poly[d(A-T)] J. Biomol. Struct. Dyn 2005 22, N 4:465–470.
[12] Brana M. F., Cacho M., Gradillas A., de Pascual-Teresan B., Ramos A. Interacalators as anticancer drugs Curr. Pharm. Des 2001 7, N 17:1745–1780.
[13] Martinez R., Chacon-Garcia L. The search of DNA-intercalators as antitumoral drugs: what if worked and what did not work Curr. Med. Chem 2005 12, N 2:127–151.
[14] Zhang Z., Yang Y., Liu F., Qian X., Xu Q. Study on the interaction between 4-(2-diethylamino-ethylamino)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-carbonitrile and DNA by molecular spectra Int. J. Biol. Macromol 2006 38, N 1:59–64.
[15] Wheate N. J., Brodie C. R., Collins G. J., Kemp S., AldrichWright J. R. DNA intercalators in cancer therapy: organic and inorganic drugs and their spectroscopic tools of analysis Mini Rev. Med. Chem 2007 7, N 6:627–648.
[16] Hendry L. B., Mahesh V. B., Bransome E. D. Jr., Ewing D. E. Small molecule intercalation with double stranded DNA: implications for normal gene regulation and for predicting the biological efficacy and genotoxicity of drugs and other chemicals Mutat. Res 2007 623, N 1–2:53–71.
[17] Ghosh R., Bhowmik S., Bagchi A., Das.D., Ghosh S. Chemotherapeutic potential of 9-phenyl acridine: biophysical studies on its binding to DNA Eur. Biophys. J 2010 39, N 8:1243– 1249.
[18] Strekowski L., Wilson B. Noncovalent interactions with DNA: an overview Mutat. Res 2007 623, N 1–2:3–13.
[19] Ismail M. A., Rodger P. M., Rodger A. Drug self-assembly on DNA: sequence effects with trans-bis-(4-N-methylpyridiniumyl)diphenyl porphyrin and Hoechst 33258 J. Biomol. Struct. Dyn 2000 17, Suppl. 1:335–348.
[20] Rohs R., Sklenar H. Methylene blue binding to DNA with alternating AT base sequence: minor groove binding is favored over intercalation J. Biomol. Struct. Dyn 2004 21, N 5:699–711.
[21] Vardevanyan P. O., Antonyan A. P., Manukyan G. A., Karapetyan A. T. Study of ethidium bromide interaction peculiarities with DNA Exp. Mol. Med 2001 33, N 4:205–208.
[22] Wadkins R. M., Jares-Erijman E. A., Klement R., Rudiger A., Jovin T. M. Actinomycin D binding to sigle-stranded DNA: sequence specificity and hemi-intercalation model from fluorescence and 1H NMR spectroscopy J. Mol. Biol 1996 262, N 1 P. 53–68.
[23] Veselkov A. N., Dimant L. N., Bolotin P. A., Baranovskii S. F., Parkes Ch., Devis D. Investigation of ethidium bromide interaction with deoxitetraribonucleozidetriphosphate 5'-d(GCGC) by 1N MMR spectroscopy method Mol. Biol. (Mosk.) 1995 29, N 2:326–338.
[24] Karapetian A. T., Mehrabian N. M., Terzikian G. A., Vardevanian P. O., Antonian A. P., Borisova O. F., Frank-Kamenetskii M. D. Theoretical treatment of melting of complexes of DNA with ligands having several types of binding sites on helical and single-stranded DNA J. Biomol. Struct. Dyn 1996 14, N 2 P. 275–283.
[25] Karapetian A. T., Terzikian G. A., Megrabyan N. M., Arutyunyan S. G., Vardevanian P. O. Theory of cooperative transitions in DNA complexes with multimodal ligands Mol. Biol. (Mosk.) 1995 29, N 4:841–847.
[26] Karapetian A. T., Vardevanian P. O., Terzikian G. A., Frank-Kamenetskii M. D. Theory of helix-coil transition on DNA-ligand complexes: the effect of two types of interaction of ligand on the parameters of transition J. Biomol. Struct. Dyn 1990 8, N 1 P. 123–130.
[27] Karapetyan A. T., Vardevanyan P. O., Frank-Kamenetskii M. D. The effect of [Na+] ions concentration on the enthalpy of DNA helix-coil transition Biopolym. Cell 1989 5, N 5:31–37.
[28] Vardevanyan P. O., Antonyan A. P., Parsadanyan M. A., Shahinyan M. A., Hambardzumyan L. A. Mechanisms for binding between methylene blue and DNA J. Appl. Spectrosc 2013 80, N 4:595–599.
[29] Nafisi S., Saboury A. A., Keramat N., Neault J.-F., Tajmir-Riahi H.-A. Stability and structural features of DNA intercalation with ethidiume bromide, acridine orange and methylene blue J. Mol. Struct 2007 827, N 1–3:35–43.
[30] Tong C., Hu Z., Wu J. Interaction between methylene blue and calf thymus deoxyribonucleic acid by spectroscopic technologies J. Fluoresc 2010 20, N 1:261–267.
[31] Lane A. N., Jenkins T. C. Thermodynamics of nucleic acids and their interactions with ligands Q. Rev. Biophys 2000 33, N 3 P. 255–306.
[32] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[33] Cantor CR, Schimmel PR. Biophysical Chemistry: Part I: The Conformation of Biological Macromolecules (Their Biophysical Chemistry; PT. 1) 1980 365 p..
[34] Chaires J. B. Energetics of drug-DNA interactions Biopolymers 1997 44, N 3:201–215.
[35] Monaco R. R. A novel major groove binding site in B form DNA for ethidium cation J. Biomol. Struct. Dyn 2007 25, N 2 P. 119–125.