Thermodynamics of RNA-RNA duplexes with 2- or 4-thiouridines: Implications for antisense design and targeting a group I intron

Biochemistry

Volumn 38, Issue 50, 1999, Pages 16655-16662

  Testa, Stephen M ^c   Disney, Matthew D ^a   Turner, Douglas H ^a   Kierzek, Ryszard ^b  

^a UNIVERSITY OF ROCHESTER   (United States)

^b INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^c UNIVERSITY OF KENTUCKY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; RNA; THIOURIDINE; URIDINE;

ARTICLE; BASE PAIRING; INTRON; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; NONHUMAN; PNEUMOCYSTIS CARINII; PRIORITY JOURNAL; RNA RNA HYBRIDIZATION;

ANIMALS; BASE PAIRING; BINDING SITES; EXONS; INTRONS; MICE; MOLECULAR MIMICRY; NUCLEIC ACID HETERODUPLEXES; PNEUMOCYSTIS; RNA PRECURSORS; RNA, ANTISENSE; RNA, CATALYTIC; RNA, RIBOSOMAL; THERMODYNAMICS; THIOURIDINE;

PNEUMOCYSTIS CARINII; PROTOZOA;

EID: 0033554848     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi991187d     Document Type: Article

References (54)

1. Herschlag, D. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 6921-6925.
2. Roberts, R. W., and Crothers, D. M. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 9397-9401.
3. Woolf, T. M., Melton, D. A., and Jennings, C. G. B. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 7205-7309.
4. Testa, S. M., Haidaris, C. G., Gigliotti, F., and Turner, D. H. (1997) Biochemistry 36, 15303-15314.
5. Freier, S. M., Kierzek, R., Caruthers, M. H., Neilson, T., and Turner, D. H. (1986) Biochemistry 25, 3209-3213.
6. Allawi, H. T., and SantaLucia, J., Jr. (1997) Biochemistry 36, 10581-10594.
7. Crick, F. H. (1966) J. Mol. Biol. 19, 548-555.
8. Baczynskyj, L., Bieman, K., and Hall, R. H. (1968) Science 159, 1481-1483.
9. Ajitkumar, P., and Cherayil, J. D. (1988) Microb. Rev. 52, 103-113.
10. Donohue, J. (1969) J. Mol. Biol. 45, 231-235.
11. Agris, P. F., Sierzputowska-Gracz, H., Smith, W. S., Malkiewicz, A., Sochacka, E., and Nawrot, B. (1992) J. Am. Chem. Soc. 114, 2652-2656.
12. Smith, W. S., Sierzputowska-Gracz, H., Sochacka, E., Malkiewicz, A., and Agris, P. F. (1992) J. Am. Chem. Soc. 114, 7989-7997.
13. Kumar, R. K., and Davis, D. R. (1997) Nucleic Acids Res. 25, 1272-1280.
14. Ashraf, S. S., Sochacka, E., Cain, R., Guenter, R., Malkiewicz, A. J., and Agris, P. F. (1999) RNA 5, 188-194.
15. Sekiya, T., Takeishi, K., and Ukita, T. (1969) Biochim. Biophys. Acta 182, 411-426.
16. Testa, S. M., Gryaznov, S. M., and Turner, D. H. (1998) Biochemistry 37, 9379-9385.
17. Pyle, A. M., Moran, S., Strobel, S. A., Chapman, T., Turner, D. H., and Cech, T. R. (1994) Biochemistry 33, 13856-13863.
18. Knitt, D. S., Narlikar, G. J., and Herschlag, D. (1994) Biochemistry 33, 13864-13879.
19. Damberger, S. H., and Gutell, R. R. (1994) Nucleic Acids Res. 22, 3508-3510.
20. Strobel, S. A., and Cech, T. R. (1995) Science 267, 675-679.
21. Testa, S. M., Gryaznov, S. M., and Turner, D. H. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 2734-2739.
22. Vorbruggen, H., and Strehlke, P. (1973) Chem. Ber. 106, 3039-3061.
23. Markiewicz, W. T., Biala, E., and Kierzek, R. (1984) Bull. Acad. Polon. Sci., Ser. Chim. 32, 433-451.
24. Kierzek, R., Caruthers, M. H., Longfellow, C. E., Swinton, D., Turner, D. H., and Freier, S. M. (1986) Biochemistry 25, 7840-7846.
25. Kumar, R. K., and Davis, D. R. (1995) J. Org. Chem. 60, 7726-7727.
26. Beaucage, S. L., and Caruthers, M. H. (1981) Tetrahedron Lett. 22, 1859-1863.
27. McBride, L. J., and Caruthers, M. H. (1983) Tetrahedron Lett. 24, 245-249.
28. Usman, N., Ogilvie, K. K., Jiang, M.-Y., and Cedergren, R. J. (1987) J. Am. Chem. Soc. 109, 7845-7854.
29. Wincott, F., DiRenzo, A., Shaffer, C., Grimm, S., Tracz, D., Workman, C., Sweedler, D., Gonzalez, C., Scaringe, S., and Usman, N. (1995) Nucleic Acids Res. 23, 2677-2684.
30. Chou, S.-H., Flynn, P., and Reid, B. (1989) Biochemistry 28, 2422-2435.
31. Fox, J. J., Praag, D. V., Wempen, I., Doerr, I. L., Cheong, L., Knoll, J. E., Eidinoff, M. L., Bendich, A., and Brown, G. B. (1959) J. Am. Chem. Soc. 81, 178-187.
32. Longfellow, C. E., Kierzek, R., and Turner, D. H. (1990) Biochemistry 29, 278-285.
33. McDowell, J. A., and Turner, D. H. (1996) Biochemistry 35, 14077-14089.
34. Borer, P. N., Dengler, B., Tinoco, I., Jr., and Uhlenbeck, O. C. (1974) J. Mol. Biol. 86, 843-853.
35. Freier, S. M., Petersheim, M., Hickey, D. R., and Turner, D. H. (1984) J. Biomol. Struct. Dyn. 1, 1229-1242.
36. Xia, T., SantaLucia, J., Jr., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., and Turner, D. H. (1998) Biochemistry 37, 14719-14735.
37. Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (1999) J. Mol. Biol. 288, 911-940.
38. Dahm, S. C., and Uhlenbeck, O. C. (1991) Biochemistry 30, 9464-9469.
39. Christian, E. L., and Yarus, M. (1993) Biochemistry 32, 4475-4480.
40. Piccirilli, J. A., Vyle, J. S., Caruthers, M. H., and Cech, T. R. (1993) Nature 361, 85-88.
41. Inoue, T., Sullivan, F. X., and Cech, T. R. (1985) Cell 43, 431-437.
42. Barfod, E. T., and Cech, T. R. (1989) Mol. Cell. Biol. 9, 3657-3666.
43. Woodson, S. A., and Cech, T. R. (1991) Biochemistry 30, 2042-2050.
44. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York.
45. Vormbrock, R., Morawietz, R., and Gassen, H. G. (1974) Biochim. Biophys. Acta 340, 348-358.
46. Mazumdar, S. K., Saenger, W., and Sheit, K. H. (1974) J. Mol. Biol. 85, 213-219.
47. Waring, R. B., Towner, P., Minter, S. J., and Davies, R. W. (1986) Nature 321, 133-139.
48. Green, R., Szostak, J. W., Benner, S. A., Rich, A., and Usman, N. (1991) Nucleic Acids Res. 19, 4161-4166.
49. Strobel, S. A., and Cech, T. R. (1996) Biochemistry 35, 1201-1211.
50. Strobel, S. A., and Ortoleva-Donnelly, L. (1999) Chem. Biol. 6, 153-165.
51. Wu, M., and Turner, D. H. (1996) Biochemistry 25, 9677-9689.
52. SantaLucia, J., Jr., Kierzek, R., and Turner, D. H. (1991) J. Am. Chem. Soc. 113, 4313-4322.
53. SantaLucia, J., Jr., Kierzek, R., and Turner, D. H. (1991) Biochemistry 30, 8242-8251.
54. Xia, T., McDowell, J. A., and Turner, D. H. (1997) Biochemistry 36, 12485-12497.