In Vitro Selection of Second Site Revertants Analysis of the Hairpin Ribozyme Active Site

Journal of Biological Chemistry

Volumn 278, Issue 52, 2003, Pages 52783-52791

  Sargueil, Bruno ^a   Hampel, Ken J ^b   Lambert, Dominic ^b   Burke, John M ^b  

^a CNRS   (France)

^b UNIVERSITY OF VERMONT COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; ENZYMES; GENETIC ENGINEERING; MUTAGENESIS; RNA;

NUCLEOBASES;

BIOCHEMISTRY;

CYTOSINE; GUANINE; HAIRPIN RIBOZYME; RIBOZYME; UNCLASSIFIED DRUG; URACIL;

AMINO ACID SUBSTITUTION; ARTICLE; CATALYSIS; CATTLE; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME STRUCTURE; ENZYME SUBSTRATE; IN VITRO STUDY; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; RNA ANALYSIS; SENSITIVITY AND SPECIFICITY; STRUCTURE ANALYSIS;

BASE SEQUENCE; BINDING SITES; BIOCHEMISTRY; CATALYSIS; DNA; GENETIC TECHNIQUES; HYDROGEN BONDING; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; RNA; RNA, CATALYTIC; TIME FACTORS;

BOS TAURUS;

EID: 0347993061     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.M306703200     Document Type: Article

References (48)

1. Buzayan, J. M., Hampel, A., and Bruening, G. (1986) Nucleic Acids Res. 14, 9729-9743
2. Hampel, A., and Tritz, R. (1989) Biochemistry 28, 4929-4933
3. Butcher, S. E., Allain, F. H., and Feigon, J. (1999) Nat. Struct. Biol. 6, 212-216
4. Rupert, P. B., and Ferre-D'Amare, A. R. (2001) Nature 410, 780-786
5. Fedor, M. J. (2000) J. Mol. Biol. 297, 269-291
6. Walter, F., Murchie, A. I., Thomson, J. B., and Lilley, D. M. (1998) Biochemistry 37, 14195-14203
7. Walter, N. G., Hampel, K. J., Brown, K. M., and Burke, J. M. (1998) EMBO J. 17, 2378-2391
8. Sargueil, B., McKenna, J., and Burke, J. M. (2000) J. Biol. Chem. 275, 32157-32166
9. Esteban, J. A., Banerjee, A. R., and Burke, J. M. (1997) J. Biol. Chem. 272, 13629-13639
10. Esteban, J. A., Walter, N. G., Kotzorek, G., Heckman, J. E., and Burke, J. M. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 6091-6096
11. Cai, Z., and Tinoco, I., Jr. (1996) Biochemistry 35, 6026-6036
12. Hampel, K. J., and Burke, J. M. (2001) Biochemistry 40, 3723-3729
13. Komatsu, Y., Kumagai, I., and Ohtsuka, E. (1999) Nucleic Acids Res. 27, 4314-4323
14. Walter, N. G., Chan, P. A., Hampel, K. J., Millar, D. P., and Burke, J. M. (2001) Biochemistry 40, 2580-2587
15. Pinard, R., Lambert, D., Walter, N. G., Heckman, J. E., Major, F., and Burke, J. M. (1999) Biochemistry 38, 16035-16039
16. Earnshaw, D. J., Masquida, B., Muller, S., Sigurdsson, S. T., Eckstein, F., Westhof, E., and Gait, M. J. (1997) J. Mol. Biol. 274, 197-212
17. Hampel, A., and Cowan, J. A. (1997) Chem. Biol. 4, 513-517
18. Nesbitt, S., Hegg, L. A., and Fedor, M. J. (1997) Chem. Biol. 4, 619-630
19. Young, K. J., Gill, F., and Grasby, J. A. (1997) Nucleic Acids Res. 25, 3760-3766
20. Murray, J. B., Seyhan, A. A., Walter, N. G., Burke, J. M., and Scott, W. G. (1998) Chem. Biol. 5, 587-595
21. Rupert, P. B., Massey, A. P., Sigurdsson, S. T., and Ferre-D'Amare, A. R. (2002) Science 298, 1421-1424
22. Wilson, T. J., and Lilley, D. M. (2002) RNA (N. Y.) 8, 587-600
23. Lebruska, L. L., Kuzmine, II, and Fedor, M. J. (2002) Chem. Biol. 9, 465-473
24. Pinard, R., Hampel, K. J., Heckman, J. E., Lambert, D., Chan, P. A., Major, F., and Burke, J. M. (2001) EMBO J. 20, 6434-6442
25. Wilson, T. J., Zhao, Z. Y., Maxwell, K., Kontogiannis, L., and Lilley, D. M. (2001) Biochemistry 40, 2291-2302
26. Milligan, J. F., and Uhlenbeck, O. C. (1989) Methods Enzymol. 180, 51-62
27. Walter, N. G., Burke, J. M., and Millar, D. P. (1999) Nat. Struct. Biol. 6, 544-549
28. Sargueil, B., Pecchia, D. B., and Burke, J. M. (1995) Biochemistry 34, 7739-7748
29. Fedor, M. J., and Uhlenbeck, O. C. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 1668-1672
30. Pyle, A. M., and Green, J. B. (1994) Biochemistry 33, 2716-2725
31. Berzal-Herranz, A., Joseph, S., and Burke, J. M. (1992) Genes Dev. 6, 129-134
32. Major, F., Turcotte, M., Gautheret, D., Lapalme, G., Fillion, E., and Cedergren, R. (1991) Science 253, 1255-1260
33. Major, F., and Griffey, R. (2001) Curr. Opin. Struct. Biol. 11, 282-286
34. Pearlman, D., Case, D., Caldwell, J., Ross, W., and Cheatman, T. (1995) Computer Physics Communications, Vol. 91, pp. 1-41, University of California, San Francisco
35. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946-950
36. Anderson, P., Monforte, J., Tritz, R., Nesbitt, S., Hearst, J., and Hampel, A. (1994) Nucleic Acids Res. 22, 1096-1100
37. Berzal-Herranz, A., Joseph, S., Chowrira, B. M., Butcher, S. E., and Burke, J. M. (1993) EMBO J. 12, 2567-2573
38. Shippy, R., Siwkowski, A., and Hampel, A. (1998) Biochemistry 37, 564-570
39. Sargueil, B., and Burke, J. M. (1997) Methods Mol. Biol. 74, 289-300
40. Joseph, S., and Burke, J. M. (1993) J. Biol. Chem. 268, 24515-24518
41. Green, R., Ellington, A. D., Bartel, D. P., and Szostak, J. W. (1991) Methods Companion Methods Enzymol. 2, 75-86
42. Deleted in proof
43. Butcher, S. E., Heckman, J. E., and Burke, J. M. (1995) J. Biol. Chem. 270, 29648-29651
44. Walter, N. G., and Burke, J. M. (1997) RNA (N. Y.) 3, 392-404
45. Butcher, S. E., and Burke, J. M. (1994) J. Mol. Biol. 244, 52-63
46. Zhuang, X., Kim, H., Pereira, M. J., Babcock, H. P., Walter, N. G., and Chu, S. (2002) Science 296, 1473-1476
47. Ryder, S. P., and Strobel, S, A. (1999) J. Mol. Biol. 291, 295-311
48. Burke, J. M. (1994) Nucleic Acids Mol. Biol. 8, 105-118