Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding

Proceedings of the National Academy of Sciences of the United States of America

Volumn 91, Issue 20, 1994, Pages 9218-9222

  Walter, Amy E ^a   Turner, Douglas H ^a   Kim, James ^a   Lyttle, Matthew H ^b,e   Müller, Peter ^c   Mathews, David H ^a   Zuker, Michael ^d  

^a UNIVERSITY OF ROCHESTER   (United States)

^b MILLIPORE CORPORATION   (United States)

^c BOEHRINGER INGELHEIM PHARMA GMBH AND CO KG   (Germany)

^d WASHINGTON UNIVERSITY   (United States)

^e Terrapin Technologies Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; OLIGOMER; OLIGORIBONUCLEOTIDE; RIBOSOME RNA; RNA; TETRAMER; TRANSFER RNA;

ARTICLE; BASE PAIRING; BINDING AFFINITY; MODEL; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; THERMODYNAMICS;

EID: 0028000994     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.91.20.9218     Document Type: Article

References (42)

1. Watson, J. D., Hopkins, N. H., Roberts, J. W., Steitz, J. A. & Weiner, A. M. (1987) Molecular Biology of the Gene (Benjamin/Cummings, Menlo Park, CA).
2. Kim, S.-H., Suddath, F. L., Quigley, G. J., McPherson, A., Sussman, J. L., Wang, A. H. J., Seeman, N. C. & Rich, A. (1974) Science 185, 435-440.
3. 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.
4. Kim, S.-H. & Cech, T. R. (1987) Proc. Natl. Acad. Sci. USA 84, 8788-8792.
5. James, B. D., Olsen, G. J. & Pace, N. R. (1989) Methods Enzymol. 180, 227-239.
6. Gutell, R. R., Weiser, B., Woese, C. R. & Noller, H. F. (1985) Prog. Nucleic Acid Res. Mol. Biol. 32, 155-195.
7. Moazed, D., Stern, S. & Noller, H. F. (1986) J. Mol. Biol. 187, 399-416.
8. Gutell, R. R., Larsen, N. & Woese, C. R. (1994) Microbiol. Rev. 58, 10-26.
9. Michel, F. & Westhof, E. (1990) J. Mol. Biol. 216, 585-610.
10. Tinoco, I., Jr., Uhlenbeck, O. C. & Levine, M. D. (1971) Nature (London) 230, 362-367.
11. DeLisi, C. & Crothers, D. M. (1971) Proc. Natl. Acad. Sci. USA 68, 2682-2685.
12. Zuker, M. (1989) Science 244, 48-52.
13. Turner, D. H., Sugimoto, N. & Freier, S. M. (1988) Annu. Rev. Biophys. Biophys. Chem. 17, 167-192.
14. Jaeger, J. A., Turner, D. H. & Zuker, M. (1989) Proc. Natl. Acad. Sci. USA 86, 7706-7710.
15. Zuker, M., Jaeger, J. A. & Turner, D. H. (1991) Nucleic Acids Res. 19, 2707-2714.
16. Wu, T., Ogilvie, K. K. & Pon, R. T. (1989) Nucleic Acids Res. 17, 3501-3517.
17. Wang, Y. Y., Lyttle, M. H. & Borer, P. N. (1990) Nucleic Acids Res. 18, 3347-3352.
18. Kierzek, R., Caruthers, M. H., Longfellow, C. E., Swinton, D., Turner, D. H. & Freier, S. M. (1986) Biochemistry 25, 7840-7846.
19. Uhlenbeck, O. C. & Cameron, V. (1977) Nucleic Acids Res. 4, 85-98.
20. England, T. E. & Uhlenbeck, O. H. (1978) Biochemistry 17, 2069-2076.
21. Petersheim, M. & Turner, D. H. (1983) Biochemistry 22, 256-263.
22. He, L., Kierzek, R., SantaLucia, J., Jr., Walter, A. E. & Turner, D. H. (1991) Biochemistry 30, 11124-11132.
23. Peritz, A. E., Kierzek, R., Sugimoto, N. & Turner, D. H. (1991) Biochemistry 30, 6428-6436.
24. SantaLucia, J., Jr., Kierzek, R. & Turner, D. H. (1991) Biochemistry 30, 8242-8251.
25. SantaLucia, J., Jr., Kierzek, R. & Turner, D. H. (1991) J. Am. Chem. Soc. 113, 4313-4322.
26. Groebe, D. R. & Uhlenbeck, O. C. (1988) Nucleic Acids Res. 16, 11725-11735.
27. Gralla, J. & Crothers, D. M. (1973) J. Mol. Biol. 73, 497-511.
28. Riesner, D., Maass, G., Thiebe, R., Philippsen, P. & Zachau, H. G. (1973) Eur. J. Biochem. 36, 76-88.
29. Coutts, S. M., Gangloff, J. & Dirheimer, G. (1974) Biochemistry 13, 3938-3948.
30. Serra, M. J., Lyttle, M. H., Axenson, T. J., Schadt, C. A. & Turner, D. H. (1993) Nucleic Acids Res. 21, 3845-3849.
31. Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T. & Turner, D. H. (1986) Proc. Natl. Acad. Sci. USA 83, 9373-9377.
32. Gutell, R. R., Schnare, M. N. & Gray, M. W. (1990) Nucleic Acids Res. 18, 2319-2330.
33. SantaLucia, J., Jr., Kierzek, R. & Turner, D. H. (1992) Science 256, 217-219.
34. Jacobson, Y. & Stockmayer, W. H. (1950) J. Chem. Phys. 18, 1600-1606.
35. Turner, D. H., Sugimoto, N., Jaeger, J. A., Longfellow, C. E., Freier, S. M. & Kierzek, R. (1987) Cold Spring Harbor Symp. Quant. Biol. 52, 123-133.
36. Wyatt, J. R., Puglisi, J. D. & Tinoco, I., Jr. (1990) J. Mol. Biol. 214, 455-470.
37. Lu, M., Guo, Q., Marky, C. A., Seeman, N. C. & Kallenbach, N. R. (1992) J. Mol. Biol. 223, 781-789.
38. Leontis, N. B., Kwok, W. & Newman, J. S. (1991) Nucleic Acids Res. 19, 759-766.
39. Pan, T., Gutell, R. R. & Uhlenbeck, O. C. (1991) Science 254, 1361-1364.
40. Kieleczawa, J., Dunn, J. J. & Studier, F. W. (1992) Science 258, 1787-1791.
41. Ecker, D. J., Vickers, T. A., Bruice, T. W., Freier, S. M., Jenison, R. D., Manoharan, M. & Zounes, M. (1992) Science 257, 958-961.
42. Bevilacqua, P. C. & Turner, D. H. (1991) Biochemistry 30, 10632-10640.