DNA sequence specificity of triplex-binding ligands

European Journal of Biochemistry

Volumn 270, Issue 24, 2003, Pages 4982-4992

  Keppler, Melanie D ^a,c   James, Peter L ^a   Neidle, Stephen ^b   Brown, Tom ^a   Fox, Keith R ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b UNIVERSITY OF LONDON   (United Kingdom)

^c QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Anthraquinone; Molecular beacon; Naphthylquinoline; Triple helix; Triplex binding ligand

Indexed keywords

ANTHRAQUINONE DERIVATIVE; BENZO[E]PYRENE; INDOLE DERIVATIVE; NAPHTHYL GROUP; QUINOLONE DERIVATIVE;

ARTICLE; CHEMICAL STRUCTURE; DNA FOOTPRINTING; DNA SEQUENCE; FLUORESCENCE; LIGAND BINDING; MELTING POINT; MOLECULAR STABILITY; PRIORITY JOURNAL;

ANTHRAQUINONES; BASE SEQUENCE; DEOXYRIBONUCLEASE I; DNA; DOSE-RESPONSE RELATIONSHIP, DRUG; KINETICS; LIGANDS; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; QUINOLINES; SPECTROMETRY, FLUORESCENCE; TEMPERATURE;

EID: 0346249749     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1033.2003.03901.x     Document Type: Article

References (42)

1. Soyfer, V.N. & Potoman, V.N. (1996) Triple-Helical Nucleic Acids. Springer-Verlag, New York.
2. Thuong, N.T. & Hélène, C. (1993) Sequence specific recognition and modification of double helical DNA by oligonucleotides. Angew. Chem. Int. Ed. Engl. 32, 666-690.
3. Fox, K.R. (2000) Targeting DNA with triplexes. Curr. Med. Chem. 7, 17-37.
4. Neidle, S. (1997) Recent developments in triple helix regulation of gene expression. Anti-Cancer Drug Des. 12, 433-442.
5. Vasquez, K.M. & Wilson, J.H. (1998) Triplex-directed modification of genes and gene activity. Trends Biochem. Sci. 23, 4-9.
6. Chan, P.P. & Glazer, P.M. (1997) Triplex DNA: fundamental advances and potential applications for gene therapy. J. Mol. Med. 75, 267-282.
7. Lacroix, L., Arimondo, P.B., Takasugi, M., Hélène, C. & Mergny, J.L. (2000) Pyrimidine morpholino oligonucleotides form a stable triple helix in the absence of magnesium ions. Biochem. Biophys. Res. Commun. 270, 363-369.
8. Zhou-Sun, B.W., Sun, J.S., Gryaznov, S.M., Liquier, J., Garestier, T., Hélène, C. & Taillandier, E. (1997) A physico-chemical study of triple helix formation by an oligodeoxythymidylate with N3′ → P5′ phosphoramidate linkages. Nucleic Acids Res. 25, 1782-1787.
9. Cuenoud, B., Casset, F., Hüsken, D., Natt, F., Wolf, R.M., Altmann, K.H., Martin, P. & Moser, H.E. (1998) Dual recognition of double-stranded DNA by 2′-aminoethoxy-modified oligonucleotides. Angew. Chem. Int. Ed. Engl. 37, 1288-1291.
10. P): a novel thymidine analogue for generating DNA triplexes with increased stability. Nucleic Acids Res. 27, 1802-1809.
11. Sun, J.-S., François, J.-C., Montenay-Garestier, T., Saison-Behmoaras, T., Roig, V., Thuong, N.T. & Hélène, C. (1989) Sequence-specific intercalating agents: Intercalation at specific sequences on duplex DNA via major groove recognition by oligonucleotide- intercalator conjugates. Proc. Natl Acad. Sci. USA 86, 9198-9202.
12. Stonehouse, T.J. & Fox, K.R. (1994) DNase I footprinting of triple helix formation at polypurine tracts by acridine-linked oligopyrimidines: Stringency, structural changes and interaction with minor groove binding ligands. Biochim. Biophys. Acta 1218, 322-330.
13. Takasugi, M., Guendouz, A., Chassignol, M., Decout, J.L., Lhomme, J., Thuong, N.T. & Hélène, C. (1991) Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix-forming oligonucleotide. Proc. Natl Acad. Sci. USA 88, 5602-5605.
14. Darby, R.A.J. & Fox, K.R. (2002) Triple-helix-specific ligands. In: Interaction of Small Molecules with DNA and RNA: from Synthesis to Nucleic Acid Complexes (eds Demeunynck, M., Bailly, C., Wilson, W.D.) pp. 360-383, Wiley VCH, NJ.
15. Mergny, J.L., Duval-Valentin, G., Nguyen, C.H., Perrouault, L., Faucon, B., Rougée, M., Montenay-Garestier, T., Bisagni, E. & Hélène, C. (1992) Triple-helix specific ligands. Science 256, 1681-1684.
16. Marchand, C., Bailly, C., Nguyen, C.H., Bisagni, E., Garestier, T., Hélène, C. & Waring, M.J. (1996) Stabilization of triple helical DNA by a benzopyridoquinoxaline intercalator. Biochemistry 35, 5022-5032.
17. Schmitt, P., Nguyen, C.H., Sun, J.S., Grierson, D.S., Bisagni, E., Garestier, T. & Hélène, C. (2000) 13H-benzo[6-7]indolo[3,2-c] quinolines (B[6,7]IQ): optimization of their DNA triplex-specific stabilization properties. Chem. Commun. 763-764.
18. Silver, G.C., Sun, J.S., Nguyen, C.H., Boutorine, A.S., Bisagni, E. & Hélène, C. (1997) Stable triple-helical DNA complexes formed by benzopyridoindole-and benzopyridoquinoxaline-oligonucleotide conjugates. J. Am. Chem. Soc. 119, 263-268.
19. +-containing DNA triplexes. Biochemistry 32, 5591-5597.
20. Latimer, L.J.P., Payton, N., Forsyth, G. & Lee, J.S. (1995) The binding of analogues of coralyne and related heterocyclics to DNA triplexes. Biochem. Cell Biol. 73, 11-18.
21. Moraru-Allen, A.A., Cassidy, S., Alvarez, J.L.A., Fox, K.R., Brown, T. & Lane, A.N. (1997) Coralyne has a preference for intercalation between TA. T triples in intramolecular DNA triple helices. Nucleic Acids Res. 25, 1890-1896.
22. Wilson, W.D., Tanious, F.A., Mizan, S., Yao, S., Kiselyov, A.S., Zon, G. & Strekowski, L. (1993) DNA triple-helix specific intercalators as antigene enhancers. Biochemistry 32, 10614-10621.
23. Chandler, S.P., Strekowski, L., Wilson, W.D. & Fox, K.R. (1995) Footprinting studies on ligands which stabilise DNA triplexes. Biochemistry 34, 7234-7242.
24. Cassidy, S.A., Strekowski, L., Wilson, W.D. & Fox, K.R. (1994) Effect of a triplex-binding ligand on parallel and antiparallel DNA triple helices using short unmodified and acridine-linked oligonucleotides. Biochemistry 33, 15338-15347.
25. Cassidy, S.A., Strekowski, L. & Fox, K.R. (1996) DNA sequence specificity of a naphthylquinoline triple helix-binding ligand. Nucleic Acids Res. 24, 4133-4138.
26. Chaires, J.B., Ren, J., Henary, M., Zegrocka, O., Bischop, G.R. & Strekowski, L. (2003) Triplex selective 2-(2-naphthyl) quinoline compounds: origins of affinity and new design principles. J. Am. Chem. Soc. 125, 7272-7283.
27. Fox, K.R., Polucci, P., Jenkins, T.C. & Neidle, S. (1995) A molecular anchor for stabilizing triple-helical DNA. Proc. Natl Acad. Sci. USA 92, 7887-7891.
28. Keppler, M.D., Read, M.A., Perry, P.J., Trent, J.O., Jenkins, T.C., Reszka, A.P., Neidle, S. & Fox, K.R. (1999) Stabilization of DNA triple helices by a series of mono-and disubstituted amidoanthraquinones. Eur. J. Biochem. 263, 817-825.
29. Escudé, C., Sun, J.-S., Nguyen, C.H., Bisagni, E., Garestier, T. & Hélène, C. (1996) Ligand-induced formation of triple helices with antiparallel third strands containing G and T. Biochemistry 35, 5735-5740.
30. Volker, J. & Klump, H.H. (1994) Electrostatic effects in DNA triple helices. Biochemistry 33, 13502-13508.
31. Asensio, J.L., Lane, A.N., Dhesi, J., Bergvist, S. & Brown, T. (1998) The contribution of cytosine protonation to the stability of parallel DNA triple helices. J. Mol. Biol. 275, 811-822.
32. +.GC triplets. Nucleic Acids Res. 25, 4644-4649.
33. Lee, J.S., Woodsworth, M.L., Latimer, L.J.P. & Morgan, A.R. (1984) Poly (pyrimidine) poly (purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH. Nucleic Acids Res. 12, 6603-6614.
34. Darby, R.A.J., Sollogoub, M., McKeen, C., Brown, L., Risitano, A., Brown, N., Barton, C., Brown, T. & Fox, K.R. (2002) High throughput measurement of duplex, triplex and quadruplex melting curves using molecular beacons and the LightCycler. Nucleic Acids Res. 29, e39.
35. Perry, P.J., Gowan, S.M., Reszka, A.P., Polucci, P., Jenkins, T.C., Kelland, L.R. & Neidle, S. (1998) 1,4-and 2,6-disubstituted amidoanthracene-9,10-dione derivatives as inhibitors of human telomerase. J. Med. Chem. 41, 3253-3260.
36. Perry, P.J., Reszka, A.P., Wood, A.A., Read, M.A., Gowan, S.M., Dosanjh, H.S., Trent, J.O., Jenkins, T.C., Kelland, L.R. & Neidle, S. (1998) Human telomerase inhibition by regioisomeric disubstituted amidoanthacene-9,10-diones. J. Med. Chem. 41, 4873-4874.
37. Dabrowiak, J.C. & Goodisman, J. (1989) Quantitative footprinting analysis of drug-DNA interactions. In: Chemistry and Physics of DNA-Ligand Interactions (Kallenbach, N.R., ed.), pp. 143-174. Academic Press, New York.
38. +?GC and T?AT triplets. Nucleic Acids Res. 31, 5598-5606.
39. Risitano, A. & Fox, K.R. (2003) Stability of intramolecular DNA quadruplexes: comparison with DNA duplexes. Biochemistry 42, 6507-6513.
40. Roberts, R.W. & Crothers, D.M. (1996) Prediction of the stability of DNA triplexes. Proc. Natl Acad. Sci. USA 93, 4320-4325.
41. Plum, G.E. & Breslauer, K.J. (1995) Thermodynamics of an intramolecular DNA triple helix: a calorimetric and spectroscopic study of the pH and salt dependence of thermally induced structural transitions. J. Mol. Biol. 248, 679-695.
42. Wilson, W.D., Hopkins, H.P., Mizan, S., Hamilton, D.D. & Zon, G. (1994) Thermodynamics of DNA triplex formation in oligomers with and without cytosine base. J. Am. Chem. Soc. 116, 3607-3608.