Effect of bridging units on photophysical and DNA binding properties of a few cyclophanes

Photochemistry and Photobiology

Volumn 86, Issue 2, 2010, Pages 282-289

  Neelakandan, Prakash P ^a   Sanju, Krishnankutty S ^a   Ramaiah, Danaboyina ^a  

^a REGIONAL RESEARCH LABORATORY CSIR   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLOPHANE 1; CYCLOPHANE 2; DNA; ETHER DERIVATIVE; INTERCALATING AGENT; PIPERIDINE DERIVATIVE; SOLVENT;

ARTICLE; BINDING SITE; CHEMISTRY; METABOLISM; SPECTROSCOPY; STATIC ELECTRICITY; SYNTHESIS;

BINDING SITES; DNA; ETHERS, CYCLIC; INTERCALATING AGENTS; PIPERIDINES; SOLVENTS; SPECTRUM ANALYSIS; STATIC ELECTRICITY;

EID: 77649244482     PISSN: 00318655     EISSN: 17511097     Source Type: Journal    
DOI: 10.1111/j.1751-1097.2009.00660.x     Document Type: Article

References (57)

1. Neidle, S. N. M. J. Waring (eds 1993) Molecular Aspects of Anticancer Drug-DNA Interactions, Vol. 2. The Macmillan Press, Ltd., London.
2. Nardo, L., M. Bondani A. Andreoni (2008) DNA-ligand binding mode discrimination by characterizing fluorescence resonance energy transfer through lifetime measurements with picosecond resolution. Photochem. Photobiol. 84, 101 110.
3. Adams, R. L. P., R. H. Burdon, A. M. Campbell, D. P. Leader R. M. S. Smellie (1981) The Biochemistry of Nucleic Acids, 9th edn. Chapman and Hall, New York.
4. Harrison, S. C. R. T. Saeur (1994) Protein-nucleic acid interactions. Curr. Opin. Struct. Biol. 4, 1 64.
5. Cadet, J., J.-L. Ravanat, G. R. Martinez, M. H. G. Medeiros P. D. Mascio (2006) Singlet oxygen oxidation of isolated and cellular DNA: Product formation and mechanistic insights. Photochem. Photobiol. 82, 1219 1225. (Pubitemid 44702000)
6. Dervan, P. B. (2001) Molecular recognition of DNA by small molecules. Bioorg. Med. Chem. 9, 2215 2235.
7. Tan, W. B., A. Bhambhani, M. R. Duff, A. Rodger C. V. Kumar (2006) Spectroscopic identification of binding modes of anthracene probes and DNA sequence recognition. Photochem. Photobiol. 82, 20 30.
8. Nielsen, P. E. (1991) Sequence-selective DNA recognition by synthetic ligands. Bioconjug. Chem. 2, 1 12.
9. Ihmels, H., K. Faulhaber, D. Vedaldi, F. Dall'Acqua G. Viola (2005) Intercalation of organic dye molecules into double-stranded DNA. Part 2: The annelated quinolizinium ion as a structural motif in DNA intercalators. Photochem. Photobiol. 81, 1107 1115.
10. Kuruvilla, E., P. C. Nandajan, G. B. Schuster D. Ramaiah (2008) Acridine-viologen dyads: Selective recognition of single-strand DNA through fluorescence enhancement. Org. Lett. 10, 4295 4298.
11. Kohler, B. (2007) DNA photodynamics. Introduction. Photochem. Photobiol. 83, 592 594.
12. Lewis, F. D. (2005) DNA molecular photonics. Photochem. Photobiol. 81, 65 72.
13. Schuster, G. B. (2000) Long-range charge transfer in DNA: Transient structural distortions control the distance dependence. Acc. Chem. Res. 33, 253 260.
14. Cosa, G., K.-S. Focsaneanu, J. R. N. McLean, J. P. McNamee J. C. Scaiano (2001) Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution. Photochem. Photobiol. 73, 585 599.
15. Wang, Q., M. Raytchev T. Fiebig (2007) Ultrafast energy delocalization and electron transfer dynamics in 2-aminopurine-containing trinucleotides. Photochem. Photobiol. 83, 637 641.
16. Diederich, F. B. Felber (2002) Supramolecular chemistry of dendrimers with functional cores. Proc. Natl Acad. Sci. USA, 99, 4778 4781.
17. Schneider, H.-J. A. K. Yatsimirsky (2008) Selectivity in supramolecular host-guest complexes. Chem. Soc. Rev. 37, 263 277.
18. Nguyen, B. T. E. V. Anslyn (2006) Indicator-displacement assays. Coord. Chem. Rev. 250, 3118 3127.
19. Bartholomew, G. P. G. C. Bazan (2001) Bichromophoric paracyclophanes: Models for interchromophore delocalization. Acc. Chem. Res. 34, 30 39.
20. Saha, S. J. F. Stoddart (2007) Photo-driven molecular devices. Chem. Soc. Rev. 36, 77 92.
21. Masuko, T., H. Nagaoka, M. Miyake, K. Metori, Y. Kizawa, K. Kashiwagi, K. Igarashi T. Kusama (2007) Cyclophane and acyclic cyclophane: Novel channel blockers of N-methyl-d-aspartate receptor. Neurochem. Int. 50, 443 449. (Pubitemid 46097175)
22. Camacho, D. H., E. V. Salo, J. W. Ziller Z. Guan (2004) Cyclophane-based highly active late-transition-metal catalysts for ethylene polymerization. Angew. Chem. Int. Ed. Engl. 43, 1821 1825.
23. Flood, A. H., Y. Liu J. F. Stoddart (2004) From cyclophanes to molecular machines. In Modern Cyclophane Chemistry (Edited by R. Gleiter H. Hopf pp. 485 518. Wiley-VCH, Weinheim.
24. Seel, C. F. Vogtle (1992) Molecules with large cavities in supramolecular chemistry. Angew. Chem. Int. Ed. Engl. 31, 528 549.
25. Meyer, E. A., R. K. Castellano F. Diederich (2003) Interactions with aromatic rings in chemical and biological recognition. Angew. Chem. Int. Ed. Engl. 42, 1210 1250.
26. Inouye, M., K. Fujimoto, M. Furusyo H. Nakazumi (1999) Molecular recognition abilities of a new class of water-soluble cyclophanes capable of encompassing a neutral cavity. J. Am. Chem. Soc. 121, 1452 1458.
27. Hennig, A., H. Bakirci W. M. Nau (2003) Label-free continuous enzyme assays with macrocycle-fluorescent dye complexes. Nat. Methods, 4, 629 632.
28. Jourdan, M., J. Garcia, J. Lhomme, M.-P. Teulade-Fichou, J.-P. Vigneron J.-M. Lehn (1999) Threading bis-intercalation of a macrocyclic bisacridine at abasic sites in DNA: Nuclear magnetic resonance and molecular modeling study. Biochemistry 38, 14205 14213.
29. Fernandez-Saiz, M., H.-J. Schneider, J. Sartorius W. D. Wilson (1996) A cationic cyclophane that forms a base-pair open complex with RNA duplexes. J. Am. Chem. Soc. 118, 4739 4745.
30. Neelakandan, P. P. D. Ramaiah (2008) DNA-assisted long-lived excimer formation in a cyclophane. Angew. Chem. Int. Ed. Engl. 47, 8407 8411.
31. Neelakandan, P. P., M. Hariharan D. Ramaiah (2006) A supramolecular ON-OFF-ON fluorescence assay for selective recognition of GTP. J. Am. Chem. Soc. 128, 11334 11335.
32. Neelakandan, P. P., M. Hariharan D. Ramaiah (2005) Synthesis of a novel cyclic donor-acceptor conjugate for selective recognition of ATP. Org. Lett. 7, 5765 5768.
33. Sajimon, M. C., D. Ramaiah, C. H. Suresh, W. Adam, F. D. Lewis M. V. George (2007) Photochromic dibenzobarrlenes: Long-lived triplet biradical intermediates. J. Am. Chem. Soc. 129, 9439 9445.
34. Jyothish, K., M. Hariharan D. Ramaiah (2007) Chiral supramolecular assemblies of a squaraine dye in solution and thin films: Concentration-, temperature-, and solvent-induced chirality inversion. Chem. Eur. J. 13, 5944 5951.
35. Takenaka, S., T. Ihara M. Takagi (1990) Bis-9-acridinyl derivative containing a viologen linker chain: Electrochemically active intercalator for reversible labeling of DNA. J. Chem. Soc., Chem. Commun. 1485 1487.
36. Baguley, B. C. E.-M. Falkenhaug (1978) The interaction of ethidium with synthetic double stranded polynucleotides at low ionic strength. Nucleic Acids Res. 5, 161 171.
37. Duff, M. R., W. B. Tan, A. Bhambhani, B. S. Perrin Jr., J. Thota, A. Rodger C. V. Kumar (2006) Contributions of hydroxyethyl groups to the DNA binding affinities of anthracene probes. J. Phys. Chem. B 110, 20693 20701. (Pubitemid 44797503)
38. Kuruvilla, E., J. Joseph D. Ramaiah (2005) Novel bifunctional acridine-acridinium conjugates: Synthesis and study of their chromophore-selective electron-transfer and DNA-binding properties. J. Phys. Chem. B 109, 21997 22002.
39. McMasters, S. L. A. Kelly (2007) Sequence-dependent interactions of cationic naphthalimides and polynucleotides. Photochem. Photobiol. 83, 889 896.
40. Joseph, J., N. V. Eldho D. Ramaiah (2003) Design of photoactivated DNA oxidizing agents: Synthesis and study of photophysical properties and DNA interactions of novel viologen-linked acridines. Chem. Eur. J. 9, 5926 5935.
41. Joseph, J., N. V. Eldho D. Ramaiah (2003) Control of electron-transfer and DNA binding properties by the tolyl spacer group in viologen linked acridines. J. Phys. Chem. B 107, 4444 4450.
42. Gong, Y.-K., T. Miyamoto, K. Nakashima S. Hashimoto (2000) Photoinduced electron transfer from 3-(9-anthracene)propyltrimethyl ammonium bromide and pyrene to methyl viologen on the surface of polystyrene latex particles. J. Phys. Chem. B 104, 5772 5778.
43. Zhu, H. F. D. Lewis (2007) Pyrene excimer fluorescence as a probe for parallel G-quadruplex formation. Bioconjug. Chem. 18, 1213 1217.
44. Bouas-Laurent, H., A. Castellan, J.-P. Desvergne R. Lapouyade (2001) Photodimerization of anthracenes in fluid solutions: (Part 2) Mechanistic aspects of the photocycloaddition and of the photochemical and thermal cleavage. Chem. Soc. Rev. 30, 248 263.
45. Minato, S., T. Osa, M. Morita, A. Nakamura, H. Ikeda, F. Toda A. Ueno (1991) Intramolecular excimer formation and molecular recognition of modified cyclodextrins appended by two naphthalene rings. Photochem. Photobiol. 54, 593 597.
46. Garbett, N. C., P. A. Ragazzon J. B. Chaires (2007) Circular dichroism to determine binding mode and affinity of ligand-DNA interactions. Nat. Protoc. 2, 3166 3172.
47. Ihmels, H., K. Faulhaber, C. Sturm, G. Bringmann, K. Messer, N. Gabellini, D. Vedaldi G. Viola (2001) Acridizinium salts as a novel class of DNA-binding and site-selective DNA-photodamaging chromophores. Photochem. Photobiol. 74, 505 511.
48. Ardhammar, M., B. Nordén T. Kurucsev (2000) DNA-drug interactions. In Circular Dichroism. Principles and Applications (Edited by N. Berova, K. Nakanishi R. W. Woody pp. 741 796. Wiley-VCH, New York.
49. Nordén, B. T. Kurucsev (1994) Analysing DNA complexes by circular and linear dichroism. J. Mol. Recognit. 7, 141 156.
50. Satyanarayana, S., J. C. Dabrowiak J. B. Chaires (1993) Tris(phenanthroline)ruthenium(II) enantiomer interactions with DNA: Mode and specificity of binding. Biochemistry 32, 2573 2584.
51. Kapicak, L. E. J. Gabbay (1975) Topography of nucleic acid helixes in solutions. XXXIII. Effect of aromatic cations on the tertiary structures of deoxyribonucleic acid. J. Am. Chem. Soc. 97, 403 408.
52. Joseph, J., E. Kuruvilla, A. T. Achuthan, D. Ramaiah G. B. Schuster (2004) Tuning of intercalation and electron-transfer processes between DNA and acridinium derivatives through steric effects. Bioconjug. Chem. 15, 1230 1235.
53. Patel, D. J. L. Cannel (1976) Nuclear magnetic resonance studies of the helix-coil transition of poly (dA-dT) in aqueous solution. Proc. Natl Acad. Sci. USA 73, 674 678.
54. Kumar, C. V., E. H. A. Punzalan W. B. Ten (2000) Adenine-thymine base pair recognition by an anthryl probe from the DNA minor groove. Tetrahedron 56, 7027 7040.
55. Jisha, V. S., K. T. Arun, M. Hariharan D. Ramaiah (2006) Site-selective binding and dual mode recognition of serum albumin by a squaraine dye. J. Am. Chem. Soc. 128, 6024 6025.
56. Lhiaubet-Vallet, V., Z. Sarabia, F. Bosca M. A. Miranda (2004) Human serum albumin-mediated stereodifferentiation in the triplet state behavior of (S)- and (R)-carprofen. J. Am. Chem. Soc. 126, 9538 9539.
57. Kaanumalle, L. S., C. L. D. Gibb, B. C. Gibb V. Ramamurthy (2005) A hydrophobic nanocapsule controls the photophysics of aromatic molecules by suppressing their favored solution pathways. J. Am. Chem. Soc. 127, 3674 3675.