Exploratory studies on azole carboxamides as nucleobase analogs: Thermal denaturation studies on oligodeoxyribonucleotide duplexes containing pyrrole-3-carboxamide

Nucleic Acids Research

Volumn 26, Issue 9, 1998, Pages 2208-2215

  Zhang, Peiming ^a   Johnson, W Travis ^b   Klewer, Douglas ^b   Paul, Natasha ^b   Hoops, Geoffrey ^b   Davisson, V J ^b   Bergstrom, Donald E ^a,b,c  

^a WALTHER CANCER INSTITUTE   (United States)

^b PURDUE UNIVERSITY   (United States)

^c PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDE; NUCLEIC ACID BASE; OLIGODEOXYRIBONUCLEOTIDE; PHOSPHORAMIDIC ACID; PROTON; PYRROLE;

ARTICLE; BASE PAIRING; BINDING AFFINITY; DNA CONFORMATION; DNA DENATURATION; HYDROGEN BOND; MOLECULAR MODEL; PRIORITY JOURNAL; ULTRAVIOLET RADIATION;

AZOLES; COMPUTER SIMULATION; DNA; HEAT; HYDROGEN BONDING; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; OLIGODEOXYRIBONUCLEOTIDES; PYRROLES; THERMODYNAMICS;

EID: 0032077532     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/26.9.2208     Document Type: Article

References (66)

1. Bergstrom, D.E., Zhang, P., Toma, P.H., Andrews, C.A. and Nichols, R. (1995) J. Am. Chem. Soc., 117, 1201-1209.
2. Loakes, D. and Brown, D.M. (1994) Nucleic Acids Res., 22, 4039-4043.
3. Aerschot, A.V., Rozenski, J., Loakes, D., Pillet, N., Schepers, G. and Herdewijn, P. (1995) Nucleic Acids Res., 23, 4363-1370.
4. Nichols, R., Andrews, P.C., Zhang, P. and Bergstrom, D.E. (1994) Nature, 369, 492-493.
5. Loakes, D., Brown, D.M., Linde, S. and Hill, F. (1995) Nucleic Acids Res., 23, 2361-2366.
6. Hoops, G.C., Zhang, P., Johnson, W.T., Paul, N., Bergstrom, D.E. and Davisson, V.J. (1997) Nucleic Acids Res., 25, 4866-4871.
7. Bergstrom, D.E., Zhang, P. and Johnson, W.T. (1997) Nucleic Acids Res., 25, 1935-1942.
8. Bergstrom, D.E., Zhang, P. and Zhou, J. (1994) J. Chem. Soc. Perkin Transactions I, 3029-3034.
9. Johnson, W.T., Zhang, P. and Bergstrom, D.E. (1997) Nucleic Acids Res., 25, 559-567.
10. Ramasamy, K., Robins, R.K. and Revankar, G.R. (1986) Tetrahedron, 42, 5869-5878.
11. Gralla, J. and Crothers, D.M. (1973) J. Mol. Biol., 78, 301-319.
12. Law, S.M., Eritja, R., Goodman, M.F. and Breslauer, K.J. (1996) Biochemistry, 35, 12329-12337.
13. Savitzky, A. and Golay, M.J.E. (1964) Anal. Chem., 36, 1627.
14. Marky, L.A. and Breslauer, K.J. (1987) Biopolymers, 26, 1601-1620.
15. Bevington, P.R. (1969) Data Reduction and Error Analysis for the Physical Sciences, McGraw-Hill Book Company, New York.
16. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Gill, P.M.W., Johnson, B.G., Robb, M.A., Cheeseman, J.R., Keith, T., Petersson, G.A., Montgomery, J.A. et al. (1995) Gaussian 94, Revision D.2, Gaussian, Inc., Pittsburgh PA.
17. Frisch, M.J., Frisch, Æ. and Foresman, J.B. (1995) Gaussian 94 User's Reference.
18. Bergstrom, D.E., Zhang, P. and Johnson, W.T. (1996) Nucleosides Nucleotides, 15, 59-68.
19. Loader, C.E. and Anderson, H.J. (1981) Can. J. Chem., 59, 2673-2676.
20. Rapoport, H. and Willson, C.D. (1961) J. Org. Chem., 26, 1102-1104.
21. Rokach, J., Hamel, P. and Kakushima, M. (1981) Tetrahedron Lett., 22, 4901-4904.
22. Cativiela, C. and Garcia, J.I. (1986) Organic Preparations Procedures Int., 18, 283-285.
23. Basha, A., Lipton, M. and Weinreb, S.M. (1977) Tetrahedron Lett., 4171-4174.
24. Wing, R., Drew, H., Takano, T., Broca, C., Itakura, K. and Dickerson, R.E. (1980) Nature, 287, 755-757.
25. Dickerson, R.E. and Drew, H.R. (1981) J. Mol. Biol., 149, 761-786.
26. Dickerson, R.E. (1990) In Sarma, R.H. and Sarma, M.H. (eds), Structure and Methods, DNA and RNA Proceeding of the Sixth Conversation in Biomolecular Stereodynamics. Adenine Press, Schenectady, NY, Vol. 3, pp. 1-38.
27. Bax, A. and Lerner, J. (1988) J. Magn. Reson., 79, 429-438.
28. Nerdal, W., Hare, D.R. and Ried, B.R. (1989) Biochemistry, 28, 10008-10021.
29. Lane, A., Jenkins, J.C., Brown, T. and Neidle. S. (1991) Biochemistry, 30, 1372-1385.
30. Moe, J.G. and Russu, I.M. (1990) Nucleic Acids Res., 18, 821-827.
31. Berveridge, D.L. and Ravishanker, G. (1994) Curr. Opin. Struct. Biol., 4, 246-255.
32. Guarnieri, F. and Mezei, M. (1996) J. Am. Chem. Soc., 118, 8493-8494.
33. Drew, H.R. and Dickerson, R.E. (1981) J. Mol. Biol., 151, 535-556.
34. Kopka, M.L., Fratini, A.V., Drew, H.R. and Dickerson, R.E. (1983) J. Mol. Biol., 163, 129-146.
35. Kubinec, M.G. and Wemmer, D.E. (1992) J. Am. Chem. Soc., 114, 8739-8740.
36. Liepinsh, E., Otting, G. and Wuthrich, K. (1992) Nucleic Acids Res., 20, 6549-6553.
37. Patel, D.J., Kozlowski, S.A., Marky, L.A., Broka, C., Rice, J.A., Itakura, K. and Breslauer, K.J. (1982) Biochemistry, 21, 428-436.
38. Patel, D.J., Kozlowski, S.A., Marky, L.A., Rice, J.A., Broka, C., Itakura, K. and Breslauer, K.J. (1982) Biochemistry, 21, 445-451.
39. Leonard, G.A., Booth, E.D. and Brown, T. (1990) Nucleic Acids Res., 18, 5617-5623.
40. Marky, L.A., Blumenfeld, K.S., Kozlowski, S. and Breslauer, K.J. (1983) Biopolymers, 22, 1247-1257.
41. Schweitzer, B.A. and Kool, E. (1995) J. Am. Chem. Soc., 117, 1864-1872.
42. Kennard, O. (1987) In Eckstein, F. and Lilley, D.M.J. (eds), Nucleic Acids and Molecular Biology. Springer-Verlag, Berlin, Vol. 1, pp. 25-52.
43. Hunter, W.N. (1992) In Lilley, D.M.J., and Dahlberg, J.E. (eds), Methods in Enzymology: DNA Structures Part A: Synthesis and Physical Analysis of DNA. Academic Press, New York, Vol. 211, pp. 221-231.
44. Parr, R.G. and Yang, W. (1989) Density-Functional Theory of Atoms and Molecules, Oxford University Press, New York.
45. Becke, A.D. (1993) J. Chem. Phys, 98, 5648-5652.
46. Becke, A.D. (1988) Phys. Rev., A38, 3098-3100.
47. Lee, C., Yang, W. and Parr, R.G. (1988) Phys. Rev., B37, 785-789.
48. Vosko, S.H., Wilk, L. and Nusair, M. (1980) Can. J. Phys., 58, 1200.
49. Wong, M.W., Frisch, M.J. and Wiberg, K.B. (1991) J. Am. Chem. Soc., 113, 4776-4782.
50. Tapia, O. and Goscinski, O. (1975) Mol. Phys., 29, 1653-1661.
51. Roberts, C., Bandaru, R. and Switzer, C. (1997) J. Am. Chem. Soc., 119, 4640-4649.
52. Florian, J. and Leszczynski, J. (1996) J. Am. Chem. Soc., 118, 3010-3017.
53. Onsager, L. (1936) J. Am. Chem. Soc., 58, 1486-1493.
54. Olson, W.K. (1982) In Neidle, S. (ed.), Topics in Nucleic Acid Structure Part 2. The Macmillan Press Ltd., London, pp. 12.
55. Hingerty, B.E., Ritchie, R.H., Ferrell, T.L. and Turner, J.E. (1985) Biopolymers, 24, 427-439.
56. Sarai, A., Mazur, J., Nussinov, R. and Jernigan, R.L. (1988) Biochemistry, 27, 8498-8502.
57. Friedman, R.A. and Honig, B. (1992) Biopolymers, 32, 145-159.
58. Kollman, P.A., Weiner, P.K. and Dearing, A. (1981) Biopolymers, 20, 2583-2621.
59. Jin, R. and Breslauer, K.J. (1988) Proc. Natl. Acad. Sci. USA, 85, 8939-8942.
60. Barawkar, D.A. and Ganesh, K.N. (1995) Nucleic Acids Res., 23, 159-164.
61. Lamm, G. and Pack, G.R. (1997) J. Phys. Chem., 101, 959-965.
62. Kyogoku, Y., Lord, R.C. and Rich, A. (1967) Proc. Natl. Acad. Sci. USA, 57, 250-257.
63. Etter, M.C. (1990) Acc. Chem. Res., 23, 120-126.
64. Etter, M.C., MacDonald, J.C. and Bernstein, J. (1990) Acta Cryst., B46, 256-262.
65. Bernstein, J., Davis, R.E., Shimoni, L. and Chang, N. (1995) Angew. Chem. Int. Ed. Engl., 34, 1555-1573.
66. Shimoni, L. and Glusker, J.P. (1995) Protein Sci., 4, 65-74.