A versatile communication module for controlling RNA folding and catalysis

Nucleic Acids Research

Volumn 30, Issue 21, 2002, Pages 4599-4606

  Kertsburg, Alexis ^a   Soukup, Garrett A ^a  

^a CREIGHTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; NUCLEOTIDE; RIBOZYME; RNA;

ALLOSTERISM; ARTICLE; BASE PAIRING; CATALYSIS; CATALYST; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME BINDING; GENETIC ENGINEERING; HEPATITIS DELTA VIRUS; IN VITRO STUDY; MOLECULAR GENETICS; NONHUMAN; PRIORITY JOURNAL; RNA ISOLATION; RNA STRUCTURE; TETRAHYMENA;

HEPATITIS DELTA VIRUS; PROTOZOA; TETRAHYMENA;

EID: 0036849338     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf596     Document Type: Article

References (46)

1. Tang, J. and Breaker, R.R. (1997) Rational design of allosteric ribozymes. Chem. Biol., 4, 453-459.
2. Tang, J. and Breaker, R.R. (1998) Mechanism for allosteric inhibition of an ATP-sensitive ribozyme. Nucleic Acids Res., 26, 4214-4221.
3. Kuwabara, T., Warashina, M., Tanabe, T., Kenzaburo, T., Asano, S. and Taira, K. (1998) A novel allosterically trans-activated ribozyme, the maxizyme, with exceptional specificity in vitro and in vivo. Mol. Cell, 2, 617-627.
4. Robertson, M.P. and Ellington, A.D. (1999) In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat. Biotechnol., 17, 62-66.
5. Soukup, G.A. and Breaker, R.R. (1999) Engineering precision RNA molecular switches. Proc. Natl Acad. Sci. USA, 96, 3584-3589.
6. Koizumi, M., Soukup, G.A., Kerr, J.N.Q. and Breaker, R.R. (1999) Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nature Struct. Biol., 6, 1062-1071.
7. Soukup, G.A., Emilsson, G.A.M. and Breaker, R.R. (2000) Altering molecular recognition of RNA aptamers by allosteric selection. J. Mol. Biol., 298, 623-632.
8. Burke, D.H., Ozerova, N.D. and Nilsen-Hamilton, M. (2002) Allosteric hammerhead ribozyme TRAPs. Biochemistry, 41, 6588-6594.
9. Wang, D.Y., Lai, B.H., Feldman, A.R. and Sen, D. (2002) A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes. Nucleic Acids Res., 30, 1735-1742.
10. Robertson, M.P. and Ellington, A.D. (2001) In vitro selection of nucleoprotein enzymes. Nat. Biotechnol., 19, 650-655.
11. Wang, D.Y. and Sen, D. (2002) Rationally designed allosteric variants of hammerhead ribozymes responsive to the HIV-1 Tat protein. Comb. Chem. High Throughput Screen., 5, 301-312.
12. Hartig, J.S., Najifi-Shoushtari, S.H., Grune, I., Yan, A., Ellington, A.D. and Famulok, M. (2002) Protein-dependent ribozymes report molecular interactions in real time. Nat. Biotechnol., 20, 717-722.
13. Vaish, N.K., Dong, F., Andrews, L., Schweppe, R.E., Ahn, N.G., Blatt, L. and Seiwert, S.D. (2002) Monitoring post-translational modifications of proteins with allosteric ribozymes. Nat. Biotechnol., 20, 810-815.
14. Seetharaman, S., Zivarts, M., Sudarsan, N. and Breaker, R.R. (2001) Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nat. Biotechnol., 19, 336-341.
15. Wang, D.Y., Lai, B.H. and Sen, D. (2002) A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes. J. Mol. Biol. 318, 33-43.
16. Tanabe, T., Kuwabara, T., Warashina, M., Tani, K., Taira, K. and Asano, S. (2000) Oncogene inactivation in a mouse model. Nature, 406, 473-474.
17. Tanabe, T., Takata, I., Kuwabara, T., Warashina, M., Kawasaki, H., Tani, K., Ohta, S., Asano, S. and Taira, K. (2000) Maxizymes, novel allosterically controllable ribozymes, can be designed to cleave various substrates. Biomacromolecules, 1, 108-117.
18. Kuwabara, T., Tanabe, T., Warashina, M., Xiong, K.X., Tani, K., Taira, K. and Asano, S. (2001) Allosterically controllable maxizyme-mediated suppression of progression of leukemia in mice. Biomacromolecules, 2, 1220-1228.
19. Soukup, G.A. and Breaker, R.R. (2000) Allosteric nucleic acid catalysts. Curr. Opin. Struct. Biol., 10, 318-325.
20. Soukup, G.A. and Breaker, R.R. (2000) Allosteric ribozymes. In Krupp, G. and Gaur, R.K. (eds), Ribozyme Biochemistry and Biotechnology. Eaton Publishing, Natick, MA, pp. 149-170.
21. Kuwabara, T., Warashina, M. and Taira, K. (2000) Allosterically controllable ribozymes with biosensor functions. Curr. Opin. Chem. Biol., 4, 669-677.
22. Breaker, R.R. (2002) Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol., 13, 31-39.
23. Iyo, M., Kawasaki, H. and Taira, K. (2002) Allosterically controllable maxizymes for molecular gene therapy. Curr. Opin. Mol. Ther., 4, 154-165.
24. Sclavi, B., Sullivan, M., Chance, M.R., Brenowitz, M. and Woodson, S.A. (1998) RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science, 279, 1940-1943.
25. Treiber, D.K., Rook, M.S., Zarrinkar, P.P. and Williamson, J.R. (1998) Kinetic intermediates trapped by native interactions in RNA folding. Science, 279, 1943-1946.
26. Pan, J., Thirumalai, D. and Woodson, S.A. (1999) Magnesium-dependent folding of self-splicing RNA: exploring the link between cooperativity, thermodynamics and kinetics. Proc. Natl Acad. Sci. USA, 96, 6149-6154.
27. Zhuang, X., Bartley, L.E., Babcock, H.P., Russell, R., Ha, T., Herschlag, D. and Chu, S. (2000) A single-molecule study of RNA catalysis and folding. Science, 288, 2048-2051.
28. Russell, R., Zhuang, X., Babcock, H.P., Millett, I.S., Doniach, S., Chu, S. and Herschlag, D. (2002) Exploring the folding landscape of a structured RNA. Proc. Natl Acad. Sci. USA, 99, 155-160.
29. Wu, H.N., Lin, Y.J., Lin, F.P., Makino, S., Chang, M.F. and Lai, M.M (1989) Human hepatitis delta virus RNA subfragments contain an autocleavage activity. Proc. Natl Acad. Sci. USA, 86, 1831-1835.
30. Kumar, P.K.R., Suh, Y.A., Taira, K. and Nishikawa, S. (1993) Point and compensation mutations to evaluate essential stem structures of genomic HDV ribozyme. FASEB J., 7, 124-129.
31. Ferré-D'Amaré, A.R., Zhou, K. and Doudna, J.A. (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature, 395, 567-574.
32. Rosenstein, S.P. and Been, M.D. (1990) Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions. Biochemistry, 29, 8011-8016.
33. Duhamel, J., Liu, D.M., Evilia, C., Fleysh, N., Dinter-Gottlieb, G. and Lu, P. (1996) Secondary structure content of the HDV ribozyme in 95% formamide. Nucleic Acids Res., 24, 3911-3917.
34. Jenison, R.D., Gill, S.C., Pardi, A. and Polisky, B. (1994) High-resolution molecular discrimination by RNA. Science, 263, 1425-1429.
35. Zimmermann, G.R., Jenison, R.D., Wick, C.L., Simorre, J.P. and Pardi, A. (1997) Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nat. Struct. Biol., 4, 644-649.
36. Wadkins, T.S. and Been, M.D. (1997) Core-associated non-duplex sequences distinguishing the genomic and antigenomic self-cleaving RNAs of hepatitis delta virus. Nucleic Acids Res., 25, 4085-4092.
37. Serra, M.J. and Turner, D.H. (1995) Predicting thermodynamic properties of RNA. Methods Enzymol., 259, 242-261.
38. Burgstaller, P. and Famulok, M. (1994) Isolation of RNA aptamers for biological cofactors by in vitro selection. Angew Chem. Int. Ed. Engl., 33, 1084-1087.
39. Fan, P., Suri, A.K., Fiala, R., Live, D. and Patel, D.J. (1996) Molecular recognition in the FMN-RNA aptamer complex. J. Mol. Biol., 258, 480-500.
40. Sassanfar, M. and Szostak, J.W. (1993) An RNA motif that binds ATP. Nature, 364, 550-553.
41. Jiang, F., Kumar, R.A., Jones, R.A. and Patel, D.J. (1996) Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature, 382, 183-186.
42. Forster, A.C. and Symons, R.H. (1987) Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell, 49, 211-220.
43. Scott, W.G., Finch, J.T. and Klug, A. (1995) The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell, 81, 991-1002.
44. Tang, J. and Breaker, R.R. (2000) Structural diversity of self-cleaving ribozymes. Proc. Natl Acad. Sci. USA, 97, 5784-5789.
45. Cech, T.R. (1990) Self-splicing of group I introns. Annu. Rev. Biochem., 59, 543-568.
46. Golden, B.L., Gooding, A.R., Podell, E.R. and Cech, T.R. (1998) A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science, 282, 259-264.