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Keywords: pattern search
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2005) 33 (3): 477–478.
Published: 01 June 2005
... © 2005 The Biochemical Society 2005 catalytic RNA database analysis hammerhead ribozyme pattern search tertiary interaction The hammerhead ribozyme is a small catalytic RNA motif found in a variety of subviral pathogens, including viral satellite RNAs and some viroids. It is also found...
Abstract
The hammerhead ribozyme is the smallest naturally occurring RNA endonuclease. It is found in subviral plant pathogens and transcripts of satellite DNA from a limited number of organisms. We have performed a database search for novel examples of this catalytic RNA, taking into consideration the recently defined structural requirements for an efficient cleavage under physiological magnesium ion concentrations. In this search, we find, apart from the known examples, several hundreds of motifs in organisms of all kingdoms of life. In a first set of experiments, we analysed hammerhead ribozymes from Arabidopsis thaliana . We found that these sequences are tissue-specifically expressed and that they undergo self-cleavage in planta . Furthermore, their activity under physiological magnesium ion concentrations depends on functional loop–loop interactions, as shown by the lack of activity of appropriate mutants.