Binding of the phenothiazinium dye methylene blue with single stranded polyriboadenylic acid

Dyes and Pigments

Volumn 92, Issue 3, 2012, Pages 1376-1383

  Hossain, Maidul ^a   Kabir, Ayesha ^a   Suresh Kumar, Gopinatha ^a  

^a INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

Author keywords

Calorimetry; Methylene blue; Phenothiazinium dye; Poly(A) binding; Self assembly; Spectroscopy

Indexed keywords

ABSORBANCES; BINDING AFFINITIES; BINDING MODES; CALORIMETRIC TECHNIQUES; CIRCULAR DICHROISM SPECTRA; DUPLEX FORMATION; DYE METHYLENE BLUE; INTERCALATIVE BINDING; ION CONCENTRATIONS; METHYLENE BLUE; NUCLEIC ACID STRUCTURE; PHENOTHIAZINIUM DYE; POLY(A) BINDING; POLYRIBOADENYLIC ACIDS; SELF-ASSEMBLED;

BINDING ENERGY; DICHROISM; NUCLEIC ACIDS; STOICHIOMETRY;

CALORIMETRY;

EID: 80054873574     PISSN: 01437208     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dyepig.2011.09.016     Document Type: Article

References (42)

1. E.M. Tuite, and J.M. Kelly Photochemical interactions of methylene blue and analogues with DNA and other biological substrates J Photochem Photobiol B Biol 21 1993 103 124 (Pubitemid 24011420)
2. E.M. Tuite, and B. Norden Sequence specific interactions of methylene blue with polynucleotides and DNA: a spectroscopic study J Am Chem Soc 116 1994 7548 7556
3. L.Z. Zhang, and G.Q. Tang The binding properties of the photosensitizer methylene blue to herring sperm DNA: a spectroscopic study J Photochem Photobiol B Biol 74 2004 119 125 (Pubitemid 38667453)
4. B.S. Fujimoto, J.B. Clendenning, J.J. Delrow, P.J. Heath, and M. Schurr Fluorescence, photo bleaching studies of methylene blue binding to DNA J Phys Chem 98 1994 6633 6643
5. M. Hossain, P. Giri, and G. Suresh Kumar DNA intercalation by quinacrine and methylene blue: a comparative binding and thermodynamic characterization study DNA Cell Biol 27 2008 81 90 (Pubitemid 351271515)
6. M. Hossain, and G. Suresh Kumar DNA intercalation of methylene blue and quinacrine: new insights into base and sequence specificity from structural and thermodynamic studies Mol BioSyst 5 2009 1311 1322
7. T.J. McBride, J.E. Schneider, R.A. Floyd, and L.A. Loeb Mutations induced by methylene blue plus light in single-stranded M13mp2 Proc Natl Acad Sci USA 89 1992 6866 6870
8. M. Pádula, and S. Boiteux Photodynamic DNA damage induced by phycocyanin and its repair in Saccharomyces cerevisiae Braz J Med Biol Res 32 1999 1063 1071 (Pubitemid 29470581)
9. D. Severino, H.C. Junqueira, M. Gugliotti, D.S. Gabrielli, and M.S. Baptista Influence of negatively charged interfaces on the ground and excited state properties of methylene blue Photochem Photobiol 77 2003 459 468
10. D. Gabrielli, E. Belisle, D. Severino, A.J. Kowaltowski, and M.S. Baptista Binding, aggregation and photochemical properties of methylene blue in mitochondrial suspensions Photochem Photobiol 79 2004 227 232
11. D.C. Malins, N.L. Polissar, G.K. Ostrander, and M.A. Vinson Single 8-oxo-guanine and 8-oxo-adenine lesions induced marked changes in the backbone structure of a 25-base DNA strand Proc Natl Acad Sci USA 97 2000 12442 12445
12. H. Sies, and C.F.M. Menck Singlet oxygen-induced DNA damage Mutat Res 275 1992 367 375
13. M. Ortiz, A. Fragoso, P.J. Ortiz, and C.K. O'Sullivan Elucidation of the mechanism of single-stranded DNA interaction with methylene blue: a spectroscopic approach J Photochem Photobiol A Chem 218 2011 26 32
14. J.B. Harford Translation-targeted therapeutics for viral diseases Gene Expr 4 1995 357 367
15. P. Giri, and G. Suresh Kumar Molecular aspects of small molecules-poly(A) interaction: an approach to RNA based drug design Curr Med Chem 16 2009 965 987
16. P. Giri, and G. Suresh Kumar Molecular recognition of poly(A) targeting by protoberberine alkaloids: in vitro biophysical studies and biological perspectives Mol BioSyst 6 2010 81 88
17. M. Wickens, P. Anderson, and R.J. Jackson Life and death in the cytoplasm: messages from the 3′ end Curr Opin Genet Dev 7 1997 220 232 (Pubitemid 27206761)
18. K. Dower, N. Kuperwasser, H. Merrikh, and M. Rosbash A synthetic A tail rescues yeast nuclear accumulation of ribozyme-terminated transcript RNA 10 2004 1888 1899 (Pubitemid 39557826)
19. W. Saenger Principles of nucleic acid structure 1984 Springer-Verlag New York
20. A.G. Petrovic, and P.L. Polavarapu Structural transitions in polyriboadenylic acid induced by the changes in pH and temperature: vibrational circular dichroism study in solution and film states J Phys Chem B 109 2005 23698 23705 (Pubitemid 43081545)
21. W.M. Scovell Structural and conformational studies of polyriboadenylic acid in neutral and acid solution Biopolymers 17 1978 969 984 (Pubitemid 8318512)
22. P. Giri, and G. Suresh Kumar Isoquinoline alkaloids and their binding with polyadenylic acid: potential basis of therapeutic action Mini-Rev Med Chem 10 2010 568 577
23. P. Giri, and G. Suresh Kumar Self-structure induction in single stranded poly(A) by small molecules: studies on DNA intercalators, partial intercalators and groove binding molecules Arch Biochem Biophys 474 2008 183 192
24. M.I. Zarudnaya, and D.M. Hovorun Structural transitions in polyadenylic acid and hypothesis on biological role of its double-stranded forms Ukr Biokhim Zh 71 1999 15 20
25. M.I. Zarudnaya, and D.M. Hovorun Hypothetical double-helical poly(A) formation in a cell and its possible biological significance IUBMB Life 48 1999 581 584 (Pubitemid 30043802)
26. C. Ciatto, M.L. D'Amico, G. Natile, F. Secco, and M. Venturini Intercalation of proflavine and a platinum derivative of proflavine into double-helical poly(A) Biophys J 77 1999 2717 2724 (Pubitemid 29519516)
27. K. Bergmann, and C.T. O'Konski A spectroscopic study of methylene blue monomer, dimer, and complexes with montmorillonite J Phys Chem 67 1963 2169 2177
28. K. Bhadra, M. Maiti, and G. Suresh Kumar Molecular recognition of DNA by small molecules: aT base pair specific intercalative binding of cytotoxic plant alkaloid palmatine Biochim Biophys Acta 1770 2007 1071 1080 (Pubitemid 46678609)
29. J.D. McGhee, and P.H. von Hippel Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice J Mol Biol 86 1974 469 489
30. R. Sinha, M.M. Islam, K. Bhadra, G. Suresh Kumar, A. Banerjee, and M. Maiti The binding of DNA intercalating and non-intercalating compounds to A-form and protonated form of poly (rC)· poly (rG): spectroscopic and viscometric study Bioorg Med Chem 14 2006 800 814 (Pubitemid 41767582)
31. P. Job Formation and stability of inorganic complexes in solution Ann Chim 9 1928 113 203
32. C.Y. Huang Determination of binding stoichiometry by the continuous variation method: the Job plot S.P. Colowick, N.O. Kaplan, Methods enzymol vol. 87 1982 Academic Press 509 525
33. P. Giri, and G. Suresh Kumar Specific binding and self-structure induction to poly(A) by the cytotoxic plant alkaloid sanguinarine Biochim Biophys Acta 1770 2007 1419 1426 (Pubitemid 47248048)
34. S. Das, and G. Suresh Kumar Molecular aspects on the interaction of phenosafranine to deoxyribonucleic acid: model for intercalative drug-DNA binding J Mol Struct 872 2008 56 63 (Pubitemid 350088011)
35. M.M. Islam, R. Sinha, and G. Suresh Kumar RNA binding small molecules: studies on t-RNA binding by cytotoxic plant alkaloids berberine, palmatine and the comparison to ethidium Biophys Chem 125 2007 508 520 (Pubitemid 46138021)
36. P. Giri, and G. Suresh Kumar Spectroscopic and calorimetric studies on the binding of the phototoxic and cytotoxic plant alkaloid sanguinarine with double helical poly(A) J Photochem Photobiol A Chem 194 2008 111 121
37. I. Haq, B.Z. Chowdhry, and T.C. Jenkins Calorimetric techniques in the study of high order DNA-drug interactions J.B. Chaires, M.J. Waring, Methods enzymol vol. 340 2001 Academic Press 109 149 (Pubitemid 32751699)
38. F. Xing, G. Song, J. Ren, J.B. Chaires, and X. Qu Molecular recognition of nucleic acids: coralyne binds strongly to poly (A) FEBS Lett 579 2005 5035 5039 (Pubitemid 41242849)
39. Mudasir, E.T. Wahyuni, D.H. Tjahjono, N. Yoshioka, and H. Inoue Spectroscopic studies on the thermodynamic and thermal denaturation of the ct-DNA binding methylene blue Spectrochim Acta A Mol Biomol Spectrosc 77 2010 528 534
40. R.C. Yadav, G. Suresh Kumar, K. Bhadra, P. Giri, R. Sinha, and S. Pal Berberine, a strong polyriboadenylic acid binding plant alkaloid: spectroscopic, viscometric, and thermodynamic study Bioorg Med Chem 13 2005 165 174 (Pubitemid 39575701)
41. O.P. Centikol, and N.V. Hud Molecular recognition of poly (A) by small ligands: an alternative method of analysis reveals nanomolar, cooperative and shape-selective binding Nucleic Acids Res 37 2009 611 621
42. M.M. Islam, A. Basu, and G. Suresh Kumar Binding of 9-O-(ω-amino) alkyl ether analogues of the plant alkaloid berberine to poly(A): insights into self-structure induction Med Chem Comm 2 2011 631 637