Improved parameters for the prediction of RNA hairpin stability

Biochemistry

Volumn 36, Issue 16, 1997, Pages 4844-4851

  Serra, Martin J ^a   Barnes, Thomas W ^a   Betschart, Kelly ^a   Gutierrez, Mathew J ^a   Sprouse, Kimberly J ^a   Riley, Cheryl K ^a   Stewart, Lora ^a   Temel, Ryan E ^a  

^a ALLEGHENY COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RNA;

ARTICLE; BASE PAIRING; PRIORITY JOURNAL; PROTEIN STABILITY; RNA PURIFICATION; RNA SEQUENCE; RNA STRUCTURE; RNA SYNTHESIS; THERMODYNAMICS;

MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; RNA; THERMODYNAMICS;

EID: 0030890755     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi962608j     Document Type: Article

References (34)

1. Borer, P. N., Lin, Y., Wang, S., Roggenbuck, M. W., Gott, J. M., Uhlenbeck, O. C., & Pelczer, I. (1995) Biochemistry 34, 6488-6503.
2. Borer, P. N. (1975) in Handbook of Biochemistry and Molecular Biology: Nucleic Acids (Fasman, C. D., Ed.) 3rd ed., Vol. 1, p 589, CRC Press, Cleveland, OH.
3. Coutts, S. M., Gangloff, J., & Dirheimer, G. (1974) Biochemistry 13, 3938-3948.
4. Ehresmann, C., Baudin, F., Mougel, M., Romby, P., Ebel, J., & Ehresmann, B. (1987) Nucleic Acids Res. 15, 9109-9127.
5. Fountain, M. A., Serra, M. J., Krugh, T. R., & Turner, D. H. (1996) Biochemistry 35, 6539-6548.
6. Freier, S. M., Burger, B. J., Alkema, D., Neilson, T., & Turner, D. H. (1983) Biochemistry 22, 6198-6206.
7. Gutell, R. R. (1993) Nucleic Acids Res. 21, 3051-3054.
8. Gutell, R. R., Gray, M. W., & Schnare, M. N. (1993) Nucleic Acids Res. 21, 3055-3074.
9. Haasnoot, C. A. G., de Bruin, S. H., Hilbers, C. W., van der Marel, G. A., & van Boom, J. H. (1985) J. Biosci. 8, 767-780.
10. Heus, H. A., & Pardi, A. (1991) Science 253, 191-194.
11. Huang, S., Wang, Y.-X., & Draper, D. E. (1996) J. Mol. Bio. 258, 308-321.
12. Jaeger, J. A., Turner, D. H., & Zuker, M. (1990) Methods Enzymol. 183, 281-306.
13. Jaeger, J. A., SantaLucia, J., Jr., & Tinoco, I., Jr. (1993) Annu. Rev. Biochem. 62, 255-287.
14. Lazinski, D., Grzadienska, E., & Das, A. (1989) Cell 59, 207-218.
15. Marino, J. P., Gregorian, R. S., Jr. Csankovski, G., & Crothers, D. M. (1995) Science 268, 1448-1454.
16. Martinez, H. M. (1990) Methods Enzymol. 183, 306-317.
17. Murphy, F. L., Wang, Y., Griffith, J. D., & Ceck, T. R. (1994) Science 265, 1709-1712.
18. Parker, R. (1989) in Methods in Enzymology (Dahlberg, J. E., & Abelson, J. N., Eds.) Vol. 180, p 510, Academic Press, San Diego, CA.
19. Petersheim, M., & Turner, D. H. (1983) Biochemistry 22, 256-263.
20. Pley, H. W., Flaherty, K. M., & McKay, D. B. (1994) Nature 372, 68-74.
21. Reisner, D., Maass, G., Thiebe, R., Philippsen, P., & Zachau, H. G. (1973) Eur. J. Biochem. 36, 76-88.
22. Richards, E. G. (1975) in Handbook of Biochemistry and Molecular Biology: Nucleic Acids (Fasman, C. D., Ed.) 3rd ed., Vol. 1, p 197, CRC Press, Cleveland, OH.
23. Robertus, J. D., Ladner, J. E., Finch, J. T., Rhodes, D., Brown, R. D., Clark, B. F. C., & Klug, A. (1974) Nature (London) 250, 546-551.
24. Scott, W. G., Finch, J. T., & Klug, A. (1995) Cell 81, 991-1002.
25. Serra, M. J., & Turner, D. H. (1995) Methods Enzymol. 259, 242-261.
26. Serra, M. J., Lyttle, M. H., Axenson, T. J., Schadl, C. A., & Turner, D. H. (1993) Nucleic Acids Res. 21, 3845-3849.
27. Serra, M. J., Axenson, T. J., & Turner, D. H. (1994) Biochemistry 33, 14289-14296.
28. Sussman, J. L., Holbrook, S. R., Warrent, R. W., Church, G. M., & Kim, S.-H. (1978) Nature 288, 607-630.
29. Usman, N., Ogilvie, K. K., Jiang, M. Y., & Cedergren, R. L. (1987) J. Am. Chem. Soc. 109, 7845-7854.
30. Woese, C. R., & Pace, N. R. (1993) in The RNA World (Gesteland, R. F., & Atkins, J. F., Eds.) pp 91-117, Cold Spring Harbor Laboratory Press, Plainview, NY.
31. Woo, N. H., Roe, B. A., & Rich, A. (1980) Nature 286, 346-351.
32. Wu, H. N., & Uhlenbeck, O. C. (1987) Biochemistry 26, 8221-8227.
33. Wu, T., Ogilvie, K. K., & Pon, R. T. (1989) Nucleic Acids Res. 17, 3501-3517.
34. Zuker, M. (1989) Science 244, 48-52.