Nucleic Acids Research, 2001, Vol. 29, No. 24 5115-5120
© 2001 Oxford University Press
An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5'- and 3'-termini
1Department of Molecular Biophysics and Biochemistry and 2Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
The Neurospora Varkud Satellite (VS) RNA is capable of promoting a reversible self-cleavage reaction important for its replication pathway. In vivo the VS RNA performs a cis-cleavage reaction to generate monomeric length transcripts that are subsequently ligated to produce circular VS RNA. The predominant form of VS RNA observed in vivo is the closed circular form, though minimal VS ribozyme self-cleavage constructs lack detectable ligation activity. MFOLD analysis of the entire VS RNA sequence revealed an extended region 5' and 3' of the minimal self-cleaving region that could anneal to form a complementary helix, which we have termed helix 7. In full-length VS RNA, this helix appears to span over 40 bp of sequence and brings the 5'- and 3'-ends of the RNA into proximity for the ligation reaction. Here we report a variant of the VS ribozyme with an extended 5'- and 3'-terminus capable of forming a truncated helix 7 that promotes the ligation reaction in vitro. Through mutation and selection of this RNA we have identified a ribozyme containing two point mutations in the truncated helix 7 that ligates with >70% efficiency. These results show that an additional helical element absent in current VS ribozyme constructs is likely to be important for the ligation activity of VS RNA.
* To whom correspondence should be addressed at: Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, 260 Whitney Avenue, New Haven, CT 06520-8114, USA. Tel: +1 203 432 9772; Fax: +1 203 432 5767; Email: scott.strobel{at}yale.eduPresent address:Sean P. Ryder, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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