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WWW RNA resources: NDB the nucleic acid database. The RNA World at IMB Jena, links to lots of useful RNA web sites.The RNA Page by Michael Zuker, thermodynamics and RNA folding.San Francisco Bay Area RNA Club, links to multiple RNA labs. RNA Secondary Structures , including Group I intron and some rRNA database.Thomas Cech laboratory, hear from the Nobel Prize winner. J. Doudna Lab, X-ray crystallography on RNA. J. Szostak Lab, in vitro and in vivo selection of RNA.
Reference: 1. Methods in Molecular Biology Volume 74, Ribozyme protocols, edited by Philip Turner, Humana Press, 1997. 2. Antisense Oligodeoxynucleotides and Antisense RNA, edited by Benjamin Weiss, CRC press, 1997. 3. Molecular Biology of the Cell, 3rd edition, B Alberts et al, Garland Publishing, 1994. 4. Baidya, N., & Uhlenbeck, O.C. (1996) Biochemistry. 36, 1108-1114. 5. Tuschl, T. et al Science
1994 Nov 4;266(5186):785-9 6. Birikh, K.R., Heaton, P.A., & Eckstein, F. (1997) European Journal of Biochemistry. 245, 1-16. 7. Cate, J.H. and Doudna, J.A. (1996) "A sparse matrix approach to crystallizing ribozymes and RNA motifs". In Ribozyme Protocols, Methods in Molecular Biology series, P. Turner, Editor. vol. 74, pp 379-86, Humana Press:Totowa, NJ. 8. Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Kundrot, C.E., Cech, T.R., and Doudna, J.A. (1996) "Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing". Science 273: 1678-1685. 9. Cate, J.H. and Doudna, J.A. (1996) "Metal binding sites in the major groove of a large ribozyme domain". Structure 4: 1221-29. 10. Doherty, E.A. and Doudna, J.A. (1997) "The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core". Biochemistry 36: 3159-69. 11. Fedor, M.J., & Uhlenbeck, O.C. (1992) Biochemistry. 31, 12042-12054. 12. Haseloff, J. & Gerlach, W.L. (1988) Nature 334: 585-59124. 13. D.H. Mathews, J. Sabina, M. Zuker & D.H. Turner, Expanded Sequence Dependence of Thermodynamic Parameters Provides Robust Prediction of RNA Secondary Structure J. Mol. Biol. 288, 911-940 (1999) 14. Ole Matzura and Anders Wennborg, RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows", Computer Applications in the Biosciences (CABIOS), Vol. 12 no. 3 1996, 247-249 15. Ohkawa, J., Koguma, T., Kohda, T., & Taira, K.(1995) Journal of Biochemistry. 118, 251-258. 16. Pley, H.W., Flaherty, K.M., & McKay, D.B. (1994) Nature. 372, 68-74. 17. Rossi, J. (1997) Ciba. Found. Symp. 209, 195-206. 18. Sarver, N., et al, Science 247, 1222-1225. 19. Scott, W.G., Finch , J.T. & Klug A.(1995) Cell 81: 991-1002 20. Scott, W.G., Murray, J.B.,Arnold, J.R.P., Stoddard, B.L. and Klug, A.(1996) Science 274:2065-2069 21. Sioud, M., Opstad, A., Zhao, J.Q., Levitz, R., Benham, C. & Drlica, K. (1994) Nucleic Acids Res 22: 5571-5575 22. Tanner, M. A. and Cech, T. R. Joining the Two Domains of a Group I Ribozyme to Form the Catalytic Core.Science 275, 847-849, 1997. 23. Werner, M. & Uhlenbeck, O.C. (1995) Nucleic Acids Research 23: 2092-2096 24. Zhou, C., Bahner, I.C., Larson, G.P., Zaia, J.A. Rossi, J.J., & Kohn, E.B. (1994) Gene.149, 33-39. 25. M. Zuker, D.H. Mathews & D.H. Turner, Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide in RNA Biochemistry and Biotechnology, J. Barciszewski & B.F.C. Clark, eds., NATO ASI Series, Kluwer Academic Publishers, (1999)
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