Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex the recognizing mechanism

Nucleic Acids Research

Volumn 38, Issue 3, 2009, Pages 1022-1033

  Yang, Qianfan ^a,b   Xiang, Junfeng ^a   Yang, Shu ^a,b   Li, Qian ^a,b   Zhou, Qiuju ^a,b   Guan, Aijiao ^a,b   Zhang, Xiufeng ^a   Zhang, Hong ^a   Tang, Yalin ^a   Xu, Guangzhi ^a  

^a PEKING UNIVERSITY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

3,3' BIS(3 SULFOPROPYL) 4,5,4',5' DIBENZO 9 ETHYLTHIACARBOCYANINE TRIETHYLAMMONIUM SALT; CYANINE DYE; UNCLASSIFIED DRUG; 3,3' DI(3 SULFOPROPYL) 4,5,4',5' DIBENZO 9 ETHYL THIACARBOCYANINE; 3,3'-DI(3-SULFOPROPYL)-4,5,4',5'-DIBENZO-9-ETHYL-THIACARBOCYANINE; CARBOCYANINE; DNA; FLUORESCENT DYE; GUANINE QUADRUPLEX; SINGLE STRANDED DNA;

ARTICLE; BINDING KINETICS; CIRCULAR DICHROISM; DNA BINDING; DNA SEQUENCE; DNA STRUCTURE; FLUORESCENCE ANALYSIS; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; SPECTROSCOPY; STRUCTURE ANALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; NUCLEAR MAGNETIC RESONANCE; SPECTROFLUOROMETRY; SPECTROPHOTOMETRY;

CARBOCYANINES; DNA; DNA, SINGLE-STRANDED; FLUORESCENT DYES; G-QUADRUPLEXES; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY;

EID: 77950367232     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1045     Document Type: Article

References (49)

1. Blackburn, E.H. (1991) Structure and function of telomeres. Nature, 350, 569-573.
2. Sen, D. and Gilbert, W. (1988) Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature, 334, 364-366.
3. Pennisi, E. (2006) Genetics - DNA's molecular gymnastics. Science, 312, 1467-1468.
4. Fu, B.Q., Huang, J., Ren, L., Weng, X.C., Zhou, Y.Y., Du, Y.H., Wu, X.J., Zhou, X. and Yang, G.F. (2007) Cationic corrole derivatives: a new family of G-quadruplex inducing and stabilizing ligands. Chem. Commun., 3264-3266.
5. Zhou, Q., Li, L., Xiang, J., Tang, Y., Zhang, H., Yang, S., Li, Q., Yang, Q. and Xu, G. (2008) Screening potential antitumor agents from natural plant extracts by G-quadruplex recognition and NMR methods. Angew. Chem.-Int. Edit., 47, 5590-5592.
6. Zhou, Q., Li, L., Xiang, J., Sun, H. and Tang, Y. (2009) Fast screening and structural elucidation of G-quadruplex ligands from a mixture via G-quadruplex recognition and NMR methods. Biochimie, 91, 304-308.
7. Li, Q., Xiang, J., Li, X., Chen, L., Xu, X., Tang, Y., Zhou, Q., Li, L., Zhang, H., Sun, H. et al. (2009) Stabilizing parallel G-quadruplex DNA by a new class of ligands: two non-planar alkaloids through interaction in lateral grooves. Biochimie, 91, 811-819.
8. Todd, A.K., Johnston, M. and Neidle, S. (2005) Highly prevalent putative quadruplex sequence motifs in human DNA. Nucleic Acids Res., 33, 2901-2907.
9. Huppert, J.L. and Balasubramanian, S. (2005) Prevalence of quadruplexes in the human genome. Nucleic Acids Res., 33, 2908-2916.
10. Rawal, P., Kummarasetti, V.B., Ravindran, J., Kumar, N., Halder, K., Sharma, R., Mukerji, M., Das, S.K. and Chowdhury, S. (2006) Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation. Genome Res., 16, 644-655.
11. Huppert, J.L. and Balasubramanian, S. (2007) G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res., 35, 406-413.
12. Dexheimer, T.S., Fry, M. and Hurley, L.H. (2006) In Neidle, S. and Balasubramanian, S. (eds), Quadruplex Nucleic Acids. RSC Publishing, Cambridge, UK, pp. 180-207.
13. Ambrus, A., Chen, D., Dai, J., Jones, R.A. and Yang, D. (2005) Solution structure of the biologically relevant G-quadruplex element in the human c-MYC promoter. Implications for G-quadruplex stabilization. Biochemistry, 44, 2048-2058.
14. Phan, A.T., Kuryavyi, V., Gaw, H.Y. and Patel, D.J. (2005) Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter. Nat. Chem. Biol., 1, 167-173.
15. Phan, A.T., Modi, Y.S. and Patel, D.J. (2004) Propeller-type parallel-stranded g-quadruplexes in the human c-myc promoter. J. Am. Chem. Soc., 126, 8710-8716.
16. Phan, A.T., Kuryavyi, V., Burge, S., Neidle, S. and Patel, D.J. (2007) Structure of an unprecedented G-quadruplex scaffold in the human c-kit promoter. J. Am. Chem. Soc., 129, 4386-4392.
17. Dai, J., Dexheimer, T.S., Chen, D., Carver, M., Ambrus, A., Jones, R.A. and Yang, D. (2006) An intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solution. J. Am. Chem. Soc., 128, 1096-1098.
18. Williamson, J.R. (1994) G-quartet structures in telomeric DNA. Annu. Rev. Biophys. Biomolec. Struct., 23, 703-730.
19. Neidle, S. and Parkinson, G.N. (2003) The structure of telomeric DNA. Curr. Opin. Struct. Biol., 13, 275-283.
20. Luu, K.N., Phan, A.T., Kuryavyi, V., Lacroix, L. and Patel, D.J. (2006) Structure of the human telomere in K+ solution: an intramolecular (3 + 1) G-quadruplex scaffold. J. Am. Chem. Soc., 128, 9963-9970.
21. Ambrus, A., Chen, D., Dai, J., Bialis, T., Jones, R.A. and Yang, D. (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res., 34, 2723-2735.
22. Liu, Z., Frantz, J.D., Gilbert, W. and Tye, B.K. (1993) Identification and characterization of a nuclease activity specific for G4 tetrastranded DNA. Proc. Natl Acad. Sci. USA, 90, 3157-3161.
23. Schaffitzel, C., Berger, I., Postberg, J., Hanes, J., Lipps, H.J. and Pluckthun, A. (2001) In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc. Natl Acad. Sci. USA, 98, 8572-8577.
24. Siddiqui-Jain, A., Grand, C.L., Bearss, D.J. and Hurley, L.H. (2002) Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl Acad. Sci. USA, 99, 11593-11598.
25. Fang, G.W. and Cech, T.R. (1993) The beta-subunit of oxytricha telomere-binding protein promotes G-quartet formation by telomeric DNA. Cell, 74, 875-885.
26. Dash, J., Shirude, P.S. and Balasubramanian, S. (2008) G-quadruplex recognition by bis-indole carboxamides. Chem. Commun., 3055-3057.
27. Sun, H.X., Xiang, J.F., Tang, Y.L. and Xu, G.Z. (2007) Regulation and recognization of the extended G-quadruplex by rutin. Biochem. Biophys. Res. Commun., 352, 942-946.
28. Waller, Z.A.E., Shirude, P.S., Rodriguez, R. and Balasubramanian, S. (2008) Triarylpyridines: a versatile small molecule scaffold for G-quadruplex recognition. Chem. Commun., 1467-1469.
29. Zhang, Y.Z., Xiang, J.F., Tang, Y.L., Xu, G.Z. and Yang, W.P. (2006) Transition of H-and J-aggregate of a cyanine dye based on cation embedded in aggregation. Chem. Lett., 35, 1316-1317.
30. Zhang, Y., Xiang, J., Tang, Y., Xu, G. and Yan, W. (2007) Chiral transformation of achiral J-aggregates of a cyanine dye templated by human serum albumin. Chem Phys Chem, 8, 224-226.
31. Yang, Q., Xiang, J., Li, Q., Yan, W., Zhou, Q., Tang, Y. and Xu, G. (2008) Chiral transformation of cyanine dye aggregates induced by small peptides. J. Phys. Chem. B, 112, 8783-8787.
32. Yang, Q., Xiang, J., Yang, S., Zhou, Q., Li, Q., Tang, Y. and Xu, G. (2009) Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: I. Recognizing mixed G-quadruplex in human telomeres. Chem. Commun., 1103-1105.
33. Hamer, F.M. (1964) The Chemistry of Heterocyclic Compounds. Interscience, New York.
34. Ficken, G.E. (1971) The Chemistry of Synthetic Dyes. Academic Press, New York.
35. Herz, A.H. (1977) Aggregation of sensitizing dyes in solution and their adsorption onto silver halides. Adv. Colloid Interface Sci., 8, 237-298.
36. Bean, R.C., Shepherd, W.C., Kay, R.E. and Walwick, E.R. (1965) Spectral changes in a cationic dye due to interaction with macromolecules. III. Stoichiometry and mechanism of the complexing reaction1. J. Phys. Chem., 69, 4368-4379.
37. Guo, C.N., Xiang, J.F., Feng, J., Tang, Y.L., Chen, C.P. and Xu, G.Z. (2002) Effect of TiO2 colloids on the fluorescence behavior of two cyanine dyes. J. Colloid Interface Sci., 246, 401-409.
38. Gavathiotis, E., Heald, R.A., Stevens, M.F.G. and Searle, M.S. (2003) Drug recognition and stabilisation of the parallel-stranded DNA quadruplex d(TTAGGGT)(4) containing the human telomeric repeat. J. Mol. Biol., 334, 25-36.
39. Dai, J.X., Chen, D., Jones, R.A., Hurley, L.H. and Yang, D.Z. (2006) NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region. Nucleic Acids Res., 34, 5133-5144.
40. Bugaut, A. and Balasubramanian, S. (2008) A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes. Biochemistry, 47, 689-697.
41. Guedin, A., De Cian, A., Gros, J., Lacroix, L. and Mergny, J.L. (2008) Sequence effects in single-base loops for quadruplexes. Biochimie, 90, 686-696.
42. Campbell, N.H., Patel, M., Tofa, A.B., Ghosh, R., Parkinson, G.N. and Neidle, S. (2009) Selectivity in ligand recognition of G-quadruplex loops. Biochemistry, 48, 1675-1680.
43. Balagurumoorthy, P. and Brahmachari, S.K. (1994) Structure and stability of human telomeric sequence. J. Biol. Chem., 269, 21858-21869.
44. Wang, Y. and Patel, D.J. (1993) Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure, 1, 263-282.
45. Burge, S., Parkinson, G.N., Hazel, P., Todd, A.K. and Neidle, S. (2006) Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res., 34, 5402-5415.
46. Bock, L.C., Griffin, L.C., Latham, J.A., Vermaas, E.H. and Toole, J.J. (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature, 355, 564-566.
47. Schultze, P., Macaya, R.F. and Feigon, J. (1994) Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTT GGTGTGGTTGG). J. Mol. Biol., 235, 1532-1547.
48. Chen, Q., Kuntz, I.D. and Shafer, R.H. (1996) Spectroscopic recognition of guanine dimeric hairpin quadruplexes by a carbocyanine dye. Proc. Natl Acad. Sci. USA, 93, 2635-2639.
49. Chang, C.C., Kuo, I.C., Ling, I.F., Chen, C.T., Chen, H.C., Lou, P.J., Lin, J.J. and Chang, T.C. (2004) Detection of quadruplex DNA structures in human telomeres by a fluorescent carbazole derivative. Anal. Chem., 76, 4490-4494.