The effect of two antipodal fluorine-induced sugar puckers on the conformation and stability of the Dickerson-Drew dodecamer duplex [d(CGCGAATTCGCG)]2

Nucleic Acids Research

Volumn 26, Issue 9, 1998, Pages 2237-2244

  Ikeda, Hisafumi ^a   Fernandez, Raul ^a   Wilk, Andrzej ^b   Barchi Jr , Joseph J ^a   Huang, Xiaolin ^a   Marquez, Victor E ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; FLUORINE; OLIGODEOXYNUCLEOTIDE; THYMIDINE;

ARTICLE; BASE PAIRING; CONFORMATIONAL TRANSITION; DNA CONFORMATION; DNA DEGRADATION; DNA SEQUENCE; DNA STRUCTURE; GENETIC STABILITY; PRIORITY JOURNAL;

DNA; FLUORINE; HEAT; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; OLIGODEOXYRIBONUCLEOTIDES; THYMIDINE;

EID: 0032078424     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/26.9.2237     Document Type: Article

References (52)

1. Young, M.A., Ravishanker, G., Beveridge, D.L. and Berman, H.M. (1995) Biophys. J. 68, 2454-2468 (and references therein).
2. Chang, K.-Y. and Varani, G. (1997) Nature Struct. Biol. (NMR Suppl.) 4, 854-858.
3. Franklin, R.E., Goslin, R.G. (1953) Acta Cryst. 6, 673-677.
4. Berman, H.M. (1997) Biopolymers 44, 23-44.
5. Wahl, M.C. and Sundaralingam, M. (1997) Biopolymers 44, 45-63.
6. Clark, G.R., Brown, D.G., Sanderson, M.R., Chwalinski, T., Neidle, S., Veal, J.M., Jones, R.L. et al. (1990) Nucleic Acids Res. 18, 5521-5528.
7. McCall, M., Brown, T., Hunter, W.N. and Kennard, O. (1986) Nature 322, 661-664.
8. Aboul-ela, F., Varani, G., Walker, G.T. and Tinoco, I., Jr (1988) Nucleic Acids Res. 16, 3559-3572.
9. Tan, S., Hunziker, Y., Sargent, D.F. and Richmond, T.J. (1996) Nature 381, 127-134.
10. Geiger, J. H., Hahn, S., Lee, S. and Sigler, P. B. (1996) Science 272, 830-836.
11. Jacobomolina, A., Ding, J. P., Nanni, R.G., Clark, A.D., Lu, X.D., Tantillo, C., Williams, R.L., Kamer, G., Ferris, A.L., Clark, P., Hizi, A., Hughes, S.H. and Arnold, E. (1993) Proc. Natl. Acad. Sci. USA 90, 6320-6324.
12. Kim, J.L., Nikolov, D.B. and Burley, S.K. (1993) Nature 365, 520-527.
13. Kim, J.L., and Burley, S.K. (1994) Nature Struct. Biol. 1, 638-653.
14. Kim, Y., Geiger, J.H., Han, S. and Sigler, P.B. (1993) Nature 365, 512-520.
15. Fairall, L., Martin, S. and Rhodes, D. (1989) EMBO J. 8, 1809-1817.
16. Ivanov, V.I., Minchenkova, L.E., Burckhardt, G., Birch-Hirschfeld, E., Frizsche, H. and Zimmer, C. (1996) Biophys. J. 71, 3344-3349.
17. Flatters, D., Young, M., Beveridge, D.L. and Lavery, R. (1997) J. Biomol. Struct. Dyn. 14, 757-765.
18. Hakoshima, T., Omori, H., Tomita, K., Miki, H. and Ikehara, M. (1981) Nucleic Acids Res. 9, 711-729.
19. Marck, C., Lesyng, B. and Saenger, W. (1982) J. Mol. Struct. 82, 77-94.
20. Suck, D., Saenger, W., Main, P., Germain, G. and De Clercq, J. (1974) Biochim. Biophys. Acta 361, 257-265.
21. Catlin, J.C. and Guschlbauer, W. (1975) Biopolymers 14, 51-72.
22. Cushley, R.J., Codington, J.F. and Fox, J.J. (1968) Can. J. Chem. 46, 1131-1140.
23. Gushlbauer, W. and Janikowski, K. (1980) Nucleic Acids Res. 8, 1421-1433.
24. Marquez, V.E., Lim, B.B., Barchi, J.J.,Jr, Nicklaus, M.C. (1993) Conformational studies and anti-HIV activity of mono- and difluorodideoxy nucleosides in Chu, C.K. and Baker, D.C. (eds), Nucleosides and Nucleotides as Antitumor and Antiviral Agents, Plenum Press, New York, pp 265-284.
25. Barchi, J.J.,Jr, Jeong, L.S., Siddiqui, M.A. and Marquez, V.E. (1997) J. Biochem. Biosphys. Meth. 34, 11-29.
26. Fazakerley, G.V., Uesugi, S., Izumi, A., Ikehara, M. and Guschlbauer, W. (1985) FEBS Lett. 182, 365-369.
27. Kawasaki, A.M., Casper, M.D., Freier, S.M., Lesnik, E.A., Zounes, M.C. Cummins, L.L., Gonzalez, C. and Cook, P.D. (1993) J. Med. Chem. 36, 831-841.
28. Monia, B.P., Lesnik, E.A., Gonzalez, C., Lima, W.F., McGee, D., Guinoso C.J., Kawasaki, A.M., Cook, P.D. and Freier, S.M. (1993) J. Biol. Chem. 268, 14514-14522.
29. Williams, D.M., Benseler, F. and Eckstein, F. (1991) Biochemistry 30, 4001-4009.
30. Kois, P., Tocik, Z., Spassova, M., Ren, W.-Y., Rosenberg, I., Farras-Soler, J. and Watanabe, K.A. (1993) Nucleosides Nucleotides 12, 1093-1109.
31. Drew, H.R., Wing, R.M., Takano, T., Broka, C., Tanaka, S., Itakura, K. and Dickerson, R.E. (1981) Proc. Natl. Acad. Sci. USA 78, 2179-2183.
32. Vorbruggen, H. and Bennua, B. (1978) Tetrahedron Lett. 15, 1339-1342.
33. Codington, J.F., Doerr, I.L. and Fox, J.J. (1964) J. Org. Chem. 29, 558-564.
34. Tann, C.H., Brodfuehrer, P.R., Brundidge, S.P., Sapino, C.,Jr and Howell, H.G. (1985) J. Org. Chem. 50, 3644-3647.
35. Borer, P.N. (1975) In Fasman, G.D. (ed.) Handbook of Biochemistry and Molecular Biology: Nucleic Acids 3rd ed., Vol. I, CRC Press, Cleveland, OH, p 589.
36. Marky, L.A. and Breslauer, K.J. (1987) Biopolymers 26, 1601-1620.
37. Albergo-De Prisco, D., Marky, L.A., Breslauer, K.J. and Turner, D.H. (1981) Biochemistry 20, 1409-1413.
38. Petersheim, M. and Turner, D.H. (1983) Biochemistry 22, 256-263.
39. Howell, H.G., Brodfueher, P.R., Brundidge, S.P., Benigni, D.A. and Sapino, C.,Jr (1988) J. Org. Chem. 53, 85-88.
40. Watanabe, K.A., Su, T.-L., Klein, R.S., Chu, C.K., Matsuda, A., Chun, M.W., Lopez, C. and Fox, J.J. (1983) J. Med. Chem. 26, 152-156.
41. Watanabe, K.A, Reichman, U., Hirota, K., Lopez, C. and Fox, J.J. (1979) J. Med. Chem. 22, 21-24.
42. Herdewijn, P., Van Aerschot, A. and Kerremans, L. (1989) Nucleosides Nucleotides 8, 65-96.
43. Rao, A.V.R., Gurjar, M.K. and Lalitha, S.V.S. (1994) J. Chem. Soc. Chem. Commun. 1255-1256.
44. McGee, D.P.C., VaughnSettle, A., Vargeese, C. and Zhai, Y.S. (1996) J. Org. Chem. 61, 781-785.
45. Howell, H.G., Brodfuehrer, P.R. and Sapino, C.,Jr (1985) J. Org. Chem. 50, 2597-2598.
46. Kopka, M.L., Fratini, A.V., Drew, H.R. and Dickerson, R.E. (1983) J. Mol. Biol. 163, 129-146.
47. Cantor, C.R., Warshaw, M.M. and Shapiro, H. (1970) Biopolymers 9, 1059-1077.
48. Borer, P.N., Pappalardo, L., Kerwood, D.J. and Pelczer, I. (1997) Adv. Biophys. Chem. 6, 173-216.
49. Thibaudeau, C., Plavec, J., Garg, N., Papchikhin, A. and Chattopadhyaya, J. (1994) J. Am. Chem. Soc. 116, 4038-4043.
50. Plavec, J., Thibaudeau, C. and Chattopadhyaya, J. (1997) Pure Appl. Chem. 68, 2137-2144.
51. Watt, T.A., Tong, C., Arnold, A.P. and Collins, J.G. (1996) Biochem. Mol. Biol. Int. 38, 383-391.
52. Berger, I., Ikeda, H., Marquez, V.E. and Egli, M. (1998) Nucleic Acids Res. in press.