Calorimetric, spectroscopic and computational investigation of DNA triplexes containing a 3′–3′ internucleoside junction

Abstract

Triple helix (triplex) formation between a 24-mer oligonucleotide double helix (duplex) and two kinds of 24-mer single strands containing a 3′–3′ phosphodiester bond was investigated by calorimetric, spectroscopic and computational techniques in order to analyze the effect of chemical modification of the third strand on the stability of DNA triplex. The duplex target is composed of two adjacent oligopurine–oligopyrimidine domains where the oligopurine sequences alternate on the two duplex strands. The third strands differ between each other from the substitution of cytosine with a thymine at the junction point. The two triplexes exhibit different CD spectra, suggesting that they have non-equivalent conformational states. Differential scanning calorimetric data show that the triplex with a cytosine–thymine junction (CT-triplex) is thermodynamically less stable than that with a cytosine–cytosine junction (CC-triplex). Molecular mechanics calculations revealed that the two triplexes have different geometries at the junction point. The thermodynamic data are successfully discussed in relation to the molecular models of the two triplexes.

References

1. V. I. Lyamichev, S. N. Mirkin and M. D. Frank-Kamenetsckii, J. Biomol. Struct. Dynam., 1985, 3, 667.
2. N. T. Thuong and C. Hélène, Angew. Chem, Int. Ed. Engl., 1993, 32, 822.
3. K. Hoogsteen, Acta Crystallogr., 1959, 12, 822.
4. R. Macaya, E. Wang, P. Schultze, V. Sklenar and J. Feigon, J. Mol. Biol., 1992, 225, 755.
5. F. B. Howard, H. T. Miles, K. Liu, J. Frazier, G. Raughunathan and V. Sasisekharan, Biochemistry, 1992, 31, 10671.
6. K. Liu, V. Sasisekharan, H. T. Miles and G. Raghunathan, Biopolymers, 1996, 39, 573.
7. S. Arnott and E. Selsing, J. Mol. Biol., 1974, 88, 509.
8. C. Hélène, Anti-Cancer Drug Des., 1991, 6, 569.
9. A. Ono, C. N. Chen and L. Kan, Biochemistry, 1991, 30, 9914.
10. B. W. Zhou, C. Marchand, U. Asseline, N. T. Thuong, J. S. Sun, T. Garestier and C. Hélène, Bioconj. Chem., 1995, 6, 516.
11. B. C. Froehler, T. Terhorst, J. P. Shaw and S. McCurdy, Biochemistry, 1992, 31, 1603.
12. Oligonucleotide Synthesis: a Practical Approach, ed. M. Gait, IRL Press, Oxford, 1984.
13. L. De Napoli, A. Messere, D. Montesarchio, A. Pepe, G. Piccialli and N. Barra, J. Org. Chem., 1997, 26, 9024.
14. C. R. Cantor, M. M. Warshaw and H. Shapiro, Biopolymers, 1970, 9, 1059.
15. G. Barone, P. Del Vecchio, D. Fessas, C. Giancola and G. Graziano, J. Therm. Anal., 1993, 38, 2779.
16. E. Freire and R. L. Biltonen, Biopolymers, 1978, 17, 463.
17. J. T. Yang, C. S. C. Wu and H. N. Martinez, Methods Enzymol., 1986, 130, 208.
18. C. Giancola, A. Buono, G. Barone, L. De Napoli, D. Montasarchio, D. Palomba and G. Piccialli, J. Therm. Anal., 1999, 38, 1177.
19. C. R. Cantor and P. R. SchimmelBiophysical Chemistry, Part III, Freeman, San Francisco, 1980, pp. 1201-1202.
20. K. J. Breslauer, in Thermodynamic Data for Biochemistry and Biotechnology, ed. H. J. Hinz, Springer, Berlin, 1986, pp. 402-427.
21. J. L. Asensio, A. N. Lane, J. Dhesi, S. Bergqvist and T. Brown, J. Mol. Biol., 1998, 275, 811.
22. G. Manzini, L. E. Xodo, D. Gasparotto, F. Quadrifoglio, G. A. van der Marel and J. H. van Boom, J. Mol. Biol., 1990, 213, 833.
23. D. M. Gray, R. L. Ratliff and M. R. Vaughan, Methods Enzymol., 1992, 211, 389.
24. V. I. Ivanov, L. E. Minchenkova, E. E. Minyat, M. D. Frank-Kamenetskii and A. K. Schyalkina, J. Mol. Biol., 1974, 87, 817.
25. V. P. Antao, D. M. Gray and R. L. Ratliff, Nucleic Acids Res., 1988, 16, 719.
26. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell and P. A. Kollman, J. Am. Chem. Soc., 1995, 117, 5179.
27. H. Klump and T. Ackermann, Biopolymers, 1971, 10, 513.