Elucidation of the mechanism of single-stranded DNA interaction with methylene blue: A spectroscopic approach

Journal of Photochemistry and Photobiology A: Chemistry

Volumn 218, Issue 1, 2011, Pages 26-32

  Ortiz, Mayreli ^a   Fragoso, Alex ^a   Ortiz, Pedro J ^b   O'Sullivan, Ciara K ^a,c  

^a UNIVERSITAT ROVIRA I VIRGILI   (Spain)

^b UNIVERSITY OF HAVANA   (Cuba)

^c INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

DNA; Electrostatic interactions; Fluorescence; Methylene blue; Stern Volmer plot

Indexed keywords

EID: 79551516900     PISSN: 10106030     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jphotochem.2010.11.020     Document Type: Article

References (54)

1. C.F. Yang, P.J. Jackson, Z. Xi, and I.H. Goldberg Recognition of bulged DNA by a neocarzinostatin product via an induced fit mechanism Bioorg. Med. Chem. 10 2002 1329 1335
2. H. Junicke, J.R. Hart, J. Kisko, O. Glebov, and J.R. Barton A rhodium(III) complex for high-affinity DNA base-pair mismatch recognition Proc. Natl. Acad. Sci. 100 2003 3737 3742
3. L.Z. Zhang, and G.Q. Tang The binding properties of photosensitizer methylene blue to herring sperm DNA: a spectroscopic study J. Photochem. Photobiol. B 74 2004 119 125
4. J. Rengelshausen, J. Burhenne, M. Fröhlich, Y. Tayrouz, S.K. Singh, K. Riedel, O. Müller, T. Hoppe-Tichy, W.E. Haefeli, G. Mikus, and I. Walter-Sack Evaluation of pharmacokinetic interaction between cetirizine and ritonavir, an HIV-1 protease inhibitor, in healthy male volunteers Eur. J. Clin. Pharmacol. 74 2004 709 715
5. E.C. Long, and J.K. Barton On demonstrating DNA intercalation Acc. Chem. Res. 23 1990 271 273
6. B.S. Fujimoto, J.B. Clendenning, J.J. Delrow, P.J. Heath, M. Schurr, and Fluorescence Photobleaching studies of methylene blue binding to DNA J. Phys. Chem. 98 1994 6633 6643
7. E. Tuti, and B. Norden Sequence-specific interactions of methylene blue with polynucleotides and DNA: a spectroscopic study J. Am. Chem. Soc. 116 1994 7548 7556
8. B. Armitage Photocleavage of nucleic acids Chem. Rev. 98 1998 1171 1200
9. D. Li, Y. Yan, A. Wieckowska, and I. Willner Amplified electrochemical detection of DNA through the aggregation of Au nanoparticles on electrodes and the incorporation of methylene blue into the DNA-crosslinked structure Chem. Comm. 2007 3544 3546
10. S.F. Baranovskii, P.A. Bolotin, M.P. Evstigneev, and D.N. Chernyshev Complexation of heterocyclic ligands with DNA in aqueous solution J. Appl. Spectrosc. 75 2008 251 260
11. T.J. Bride, 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. 89 1992 6866 6870
12. M. Pádula, and S. Boiteux Mutations induced by methylene blue plus light in single-stranded M13mp2 J. Med. Biol. Res. 32 1999 1063 1071
13. 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
14. D. Gabrielli, E. Belisle, D. Severino, A.J. Kowaltowski, M.S. Baptista, and Binding aggregation and photochemical properties of methylene blue in mitochondrial suspensions Photochem. Photobiol. 79 2004 227 232
15. Y. Ni, D. Lin, and S. Kokot Synchronous fluorescence and UV-vis spectroscopic studies of interactions between the tetracycline antibiotic, aluminium ions and DNA with the aid of the methylene blue dye probe Anal. Chim. Acta 606 2008 19 25
16. R. Rohs, and H. Sklenar Blue binding to DNA with alternating AT base sequence: minor groove binding is favored over intercalation J. Biomol. Struct. Dyn. 21 2004 699 711
17. R. Rohs, H. Sklenar, R. Lavery, and B. Röder Methylene blue binding to DNA with alternating GC base sequence: a modeling study J. Am. Chem. Soc. 122 2000 2860 2866
18. R.M. Anson, D.L. Croteau, R.H. Strerum, C. Filburn, R. Parsell, and V.A. Bohr Homogenous repair of singlet oxygen-induced DNA damage in differentially transcribed regions and strands of human mitochondrial DNA Nucleic Acids Res. 26 1998 662 668
19. H.Ch. DeFedericis, H.B. Patrzyc, M.J. Rajecki, E.E. Budzinski, H. Iijima, J.B. Dawidzik, and M.S. Evans Singlet oxygen-induced DNA damage Radiat. Res. 165 2006 445 451
20. S.N. Kassam, and A.J. Rainbow Deficient base excision repair of oxidative DNA damage induced Biochem. Biophys. Res. Commun. 359 2007 1004 1009
21. 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 yhe backbone structure of a 25-base DNA strand Proc. Natl. Acad. Sci. 97 2000 12442 12445
22. Y. Zheng, J.R. Wagner, and L. Sanche Singlet oxygen-induced DNA damage Phys. Rev. Lett. 96 2006 208101 208104
23. S. Nishimura 8-Hydroxyguanine: from its discovery in 1983 to the present status Proc. Jpn. Acad. Ser. B 82 2006 127 141
24. W. Yang, M. Ozsoz, D.B. Hibbert, and J.J. Gooding Evidence for the direct interaction between methylene blue and guanine bases using DNA-modified carbon paste electrodes Electroanalysis 14 2002 1299 1302
25. E. Farjami, L. Clima, K.V. Gothelf, and E.E. Ferapontova DNA interactions with a methylene blue redox indictor depend on the DNA length and are sequence specific Analyst 135 2010 1443 1448
26. D. Pau, X. Zuo, Y. Wan, L. Wang, J. Zhang, S. Song, and C. Fan Electrochemical interrogation of interctions between surface-confined DNA and methylene blue Sensors 7 2007 2671 2680
27. O.Y.F. Henry, J.L. Acero Sánchez, D. Latta, and C.K. O'Sullivan Electrochemical quantification of DNA amplicons via the detection of non-hybridised guanine bases on low-density electrode arrays Biosens. Bioelectron. 24 2009 2064 2070
28. Z. Hu, and C.L. Tong Synchronous fluorescence determination of DNA based on the interaction between methylene blue and DNA Anal. Chim. Acta 587 2007 187 193
29. H. Ihmels, and D. Otto Intercalation of organic dye molecules into double-stranded DNA: general principles and recent developments Top. Curr. Chem. 258 2005 161 204
30. J. Shen, T. Yu, J. Xie, and Y. Jiang Photoluminescence of CdTe nanocrystals modulated by methylene blue and DNA. A label-free luminescent signaling nanohybrid platform Phys. Chem. Chem. Phys. 11 2009 5062 5069
31. H. Reza, S. Nafiseh, and P. Afsaneh DNA-binding studies of daunorubicin in the presence of methylene blue by spectroscopy and voltammetry techniques Chin. J. Chem. 27 2009 1055 1060
32. Y. Wang, and A. Zhou Spectroscopic studies on the binding of methylene blue with DNA by means of cyclodextrin supramolecular systems J. Photochem. Photobiol. A: Chem. 190 2007 121 127
33. S. Hongxia, X. Junfeng, Z. Yazhou, X. Guangshi, X. Lianghua, and T. Talin Spectroscopic studies of the interaction between methylene blue and G-quadruplex Chin. Sci. Bull. 51 2006 1687 1692
34. G.N. Parkinson, P.H. Lee, and S. Neidle Crystal structure of parallel quqdruplexes from human telomeric DNA Nature 417 2002 876 880
35. 4 Bioorg. Med. Chem. Lett. 20 2010 4689 4692
36. F. Rose, V. Gabelica, H. Poncelet, and E. DePauw Tetramolecular G-quadruplexes formation pathways studied by electrospray mass spectrometry Nucleic Acids Res. 38 2010 5217 5225
37. P. Sket, and J. Plavee Tetramolecular DNA quadruplexes in solution: insights into structural diversity and cation movement J. Am. Chem. Soc. 132 2010 12724 12732
38. M.H. Li, Q. Luo, X.G. Xue, and Z.S. Li Toward a full structural characterization of G-quadruplex DNA in aqueus solution: molecular dynamic simulation of four G-quadruplex molecules J. Mol. Struct.: Theochem. 952 2010 96 102
39. A.T. Phan, and D.J. Patel Two-repeat human tolomeric d(TAGGGTTGGGT) sequences forms interconverting parallel and antiparallel G-quadruplexes in solutions: distinct topologies, thermodinamics properties and folding/unfolding kinetics J. Am. Chem. Soc. 125 2003 15021 15027
40. S. Burge, G.N. Parkinson, P. Hazel, A.K. Todel, and S. Neidle Quadruplex DNA: sequence, topology and structure Nucleic Acids Res. 34 2006 5402 5411
41. J.L. Huppert Four-stranded nucleic acid: structure, function and targeting of G-quadruplexes Chem. Soc. Rev. 37 2008 1375 1393
42. Y. Quin, and L.H. Hurley Structures folding patters, and function of intramolecular DNA G-quadruplexes found in enkaryotic promoter regions Biochimie 90 2008 1149 1171
43. K. Bergmann, and C.T. O'Conski A spectroscopic study of methylene blue monomer, dimer and complexes with montmorillonite J. Phys. Chem. 67 1963 2169 2177
44. W. Kohn, L. Sham, and L. Sham Self-consistent equations including exchange and correlation effects Phys. Rev. 140 1965 A1133 A1138
45. P.J. Stephan, F.J. Devlin, C.F. Chavalowski, and M.J. Frisch Theoretical and experimental study of the conformational, structural analysis and vibrational spectra of 1,2-bis(1,2,4-triazole-1-yl)ethane J. Phys. Chem. 98 1994 11623 11630
46. 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 03, Revision C.02 2003 Gaussian Inc. Pittsburgh, PA
47. S. Mitra, R. Das, and S.J. Mukherjee Proton transfer in inclusion complexes of cyclodextrins: role of water and highly polar nonaqueous media J. Phys. Chem. B 102 1998 3730 3737
48. B. Valeur Molecular Fluorescence: Principles and Applications 2001 Wiley-VCH Heidelberg Chapter 4
49. H.R. Park, J.J. Seo, S.C. Chin, H.S. Lee, and K.M. Bark Fluorescence quenching of norfloxacin by divalent transition metal cations Bull. Kor. Chem. Soc. 28 2007 1573 1578
50. K.S. Shashidhara, and S.M. Gaikwad Fluorescence quenching and time-resolved fluorescence studies of α-mannosidase from Aspergillus fischeri (NCIM 508) J. Fluoresc. 17 2007 599 605
51. P. Atkins, and J. de Paula Physical Chemistry 8th Edition 2006 Oxford University Press New York Chapter 9
52. P. Ross, and S. Subramanian Thermodynamics of protein association reactions: forces contributing to stability Biochemistry 20 1981 3096 3102
53. A.G. Volkov, S. Paula, and D.W. Deamer Two mechanisms of permeation of small neutral molecules and hydrated ions across phospholipid bilayers Bioelectrochem. Bionerg. 42 1997 153 160
54. A.C. Hengge, and W.W. Cleland Phosphoryl-transfer reactions of phosphodiesters: characterization of transition states by heavy-atom isotope effects J. Am. Chem. Soc. 113 1991 5835 5841