Abstract
This chapter describes methods for the successful two-dimensional modeling of a small catalytic RNA. Our laboratory has used these methods to model and name the hairpin ribozyme family based on secondary structure predicted from computer modeling and mutagenesis (see Chapter 19) (1,2,3). The methodology has two basic components: postulation and testing of the model.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Hampel, A. and Tritz, R. (1989) RNA catalytic properties of the minimum (−)sTRSV sequence. Biochemistry 28, 4929–4933.
Hampel, A., Tritz, R., Hicks, M., and Cruz, P. (1990) Hairpin catalytic RNA model evidence for helices and sequence requirement for substrate RNA. Nucleic Acids Res. 18, 299–304.
Anderson, P., Monforte, J., Tritz, R., Nesbitt, S., Hearst, J., and Hampel, A. (1994) Mutagenesis of the hairpin ribozyme. Nucleic Acids Res. 22, 1096–1100.
De Young, M. B., Siwkowski, A., Lian, Y., and Hampel, A. (1995) Catalytic properties of hairpin ribozymes derived from chicory yellow mottle virus and arabis mosaic virus satellite RNAs. Biochemistry 34, 785–791.
Rubino, L., Tousignant, M., Steger, G., and Kaper, J. (1990) Nucleotide sequence and structural analysis of two satellite RNAs associated with chicory yellow mottle virus. J. Gen. Virol. 71, 1897–1903.
Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403–410.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1997 Humana Press Inc.
About this protocol
Cite this protocol
Siwkowski, A., DeYoung, M.B., Anderson, P., Hampel, A. (1997). Mutagenesis and Modeling of the Hairpin Ribozyme Family. In: Turner, P.C. (eds) Ribozyme Protocols. Methods in Molecular Biology™, vol 74. Humana Press. https://doi.org/10.1385/0-89603-389-9:357
Download citation
DOI: https://doi.org/10.1385/0-89603-389-9:357
Publisher Name: Humana Press
Print ISBN: 978-0-89603-389-4
Online ISBN: 978-1-59259-560-0
eBook Packages: Springer Protocols