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. 1997 May 15;25(10):1890–1896. doi: 10.1093/nar/25.10.1890

Coralyne has a preference for intercalation between TA.T triples in intramolecular DNA triple helices.

A A Moraru-Allen 1, S Cassidy 1, J L Asensio Alvarez 1, K R Fox 1, T Brown 1, A N Lane 1
PMCID: PMC146695  PMID: 9115354

Abstract

Intercalating ligands may improve both the stability and sequence specificity of triple helices. Numerous intercalating drugs have been described, including coralyne, which preferentially binds triple helices, though its sequence specificity has been reported to be low [Lee,J.S., Latimer,L.J.P. and Hampel,K.J. (1993) Biochemistry , 32, 5591-5597]. In order to analyse the sequence preferences of coralyne we have used a combination of DNase I footprinting, UV melting, UV-visible spectrophotometry, circular dichroism and NMR spectroscopy to examine defined intermolecular triplexes and intramolecular triplexes linked either by hexaethylene glycol chains or by octandiol chains. DNase I footprinting demonstrated that coralyne has a moderate preference for triplexes over duplexes, but a substantial preference for TA.T triplets compared with CG. C+triplets. The drug was found to have essentially no effect on the melting temperatures of duplexes of the kind d(A)n.d(T)n or d(GA)n.d(TC)n. In contrast, it increased the T m for triplexes of the kind d(T)nd(A)n.dTn, but had little effect on the stability of d(TC)nd(GA).d(CT)n at either low or high pH. On binding to DNA triplexes, there is a large change in the absorption spectrum of coralyne and also a substantial fluorescence quenching that can be attributed to intercalation. The changes in the optical spectra have been used for direct titration with DNA. For triplexes d(T)6d(A)6.d(T)6, the Kd at 298 K was 0.5-0.8 microM. In contrast, the affinity for d(TC) nd(GA)n.d(CT)n triplexes was 6- to 10-fold lower and was characterized by smaller changes in the absorption and CD spectra. This indicates a preference for intercalation between TAT triples over CG.C+/TA.T triples. NMR studies confirmed interaction by intercalation. However, a single, secondary binding was observed at high concentrations of ligand to the triplex d(AGAAGA-L-TCTTCT-L-TCTTCT), presumably owing to the relatively low difference in affinity between the TA.T site and the competing, neighbouring sites.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Brown T., Brown D. J. Purification of synthetic DNA. Methods Enzymol. 1992;211:20–35. doi: 10.1016/0076-6879(92)11004-3. [DOI] [PubMed] [Google Scholar]
  2. Cassidy S. A., Strekowski L., Fox K. R. DNA sequence specificity of a naphthylquinoline triple helix-binding ligand. Nucleic Acids Res. 1996 Nov 1;24(21):4133–4138. doi: 10.1093/nar/24.21.4133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cassidy S. A., Strekowski L., Wilson W. D., Fox K. R. Effect of a triplex-binding ligand on parallel and antiparallel DNA triple helices using short unmodified and acridine-linked oligonucleotides. Biochemistry. 1994 Dec 27;33(51):15338–15347. doi: 10.1021/bi00255a015. [DOI] [PubMed] [Google Scholar]
  4. Chandler S. P., Strekowski L., Wilson W. D., Fox K. R. Footprinting studies on ligands which stabilize DNA triplexes: effects on stringency within a parallel triple helix. Biochemistry. 1995 May 30;34(21):7234–7242. doi: 10.1021/bi00021a039. [DOI] [PubMed] [Google Scholar]
  5. Ebel S., Lane A. N., Brown T. Very stable mismatch duplexes: structural and thermodynamic studies on tandem G.A mismatches in DNA. Biochemistry. 1992 Dec 8;31(48):12083–12086. doi: 10.1021/bi00163a017. [DOI] [PubMed] [Google Scholar]
  6. Feigon J., Koshlap K. M., Smith F. W. 1H NMR spectroscopy of DNA triplexes and quadruplexes. Methods Enzymol. 1995;261:225–255. doi: 10.1016/s0076-6879(95)61012-x. [DOI] [PubMed] [Google Scholar]
  7. Lane A., Martin S. R., Ebel S., Brown T. Solution conformation of a deoxynucleotide containing tandem G.A mismatched base pairs and 3'-overhanging ends in d(GTGAACTT)2. Biochemistry. 1992 Dec 8;31(48):12087–12095. doi: 10.1021/bi00163a018. [DOI] [PubMed] [Google Scholar]
  8. Latimer L. J., Payton N., Forsyth G., Lee J. S. The binding of analogues of coralyne and related heterocyclics to DNA triplexes. Biochem Cell Biol. 1995 Jan-Feb;73(1-2):11–18. doi: 10.1139/o95-002. [DOI] [PubMed] [Google Scholar]
  9. Lee J. S., Latimer L. J., Hampel K. J. Coralyne binds tightly to both T.A.T- and C.G.C(+)-containing DNA triplexes. Biochemistry. 1993 Jun 1;32(21):5591–5597. doi: 10.1021/bi00072a014. [DOI] [PubMed] [Google Scholar]
  10. Mergny J. L., Duval-Valentin G., Nguyen C. H., Perrouault L., Faucon B., Rougée M., Montenay-Garestier T., Bisagni E., Hélène C. Triple helix-specific ligands. Science. 1992 Jun 19;256(5064):1681–1684. doi: 10.1126/science.256.5064.1681. [DOI] [PubMed] [Google Scholar]
  11. Pilch D. S., Waring M. J., Sun J. S., Rougée M., Nguyen C. H., Bisagni E., Garestier T., Hélène C. Characterization of a triple helix-specific ligand. BePI (3-methoxy-7H-8-methyl-11- [(3'-amino)propylamino]-benzo[e]pyrido[4,3-b]indole) intercalates into both double-helical and triple-helical DNA. J Mol Biol. 1993 Aug 5;232(3):926–946. doi: 10.1006/jmbi.1993.1440. [DOI] [PubMed] [Google Scholar]
  12. Piotto M., Saudek V., Sklenár V. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J Biomol NMR. 1992 Nov;2(6):661–665. doi: 10.1007/BF02192855. [DOI] [PubMed] [Google Scholar]
  13. Stonehouse T. J., Fox K. R. 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. 1994 Aug 2;1218(3):322–330. doi: 10.1016/0167-4781(94)90184-8. [DOI] [PubMed] [Google Scholar]
  14. Trauger J. W., Baird E. E., Dervan P. B. Recognition of DNA by designed ligands at subnanomolar concentrations. Nature. 1996 Aug 8;382(6591):559–561. doi: 10.1038/382559a0. [DOI] [PubMed] [Google Scholar]
  15. Wilson W. D., Tanious F. A., Mizan S., Yao S., Kiselyov A. S., Zon G., Strekowski L. DNA triple-helix specific intercalators as antigene enhancers: unfused aromatic cations. Biochemistry. 1993 Oct 12;32(40):10614–10621. doi: 10.1021/bi00091a011. [DOI] [PubMed] [Google Scholar]

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