title: Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint.
abstract: Hammerhead ribozyme is a versatile tool for down-regulation of gene expression in vivo. Owing to its small size and high activity, it is used as a model for RNA structure-function relationship studies. In the present paper we describe a new extended hammerhead ribozyme HH-2 with a tertiary stabilizing motif constructed on the basis of the tetraloop receptor sequence. This ribozyme is very active in living cells, but shows low activity in vitro. To understand it, we analysed tertiary structure models of substrate-ribozyme complexes. We calculated six unique catalytic core geometry parameters as distances and angles between particular atoms that we call the ribozyme fingerprint. A flanking sequence and tertiary motif change the geometry of the general base, general acid, nucleophile and leaving group. We found almost complete correlation between these parameters and the decrease of target gene expression in the cells. The tertiary structure model calculations allow us to predict ribozyme intracellular activity. Our approach could be widely adapted to characterize catalytic properties of other RNAs.
authors: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
authors: Marta Magdalena
authors: MM
authors: Gabryelska
authors: Eliza
authors: E
authors: Wyszko
authors: Maciej
authors: M
authors: Szymański
authors: Mariusz
authors: M
authors: Popenda
authors: Jan
authors: J
authors: Barciszewski
mesh_terms: D000818:Animals; D020134:Catalytic Domain; D006367:HeLa Cells; D006801:Humans; D055029:Inverted Repeat Sequences; D007527:Isoenzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D012754:Sharks / Q000378:metabolism; D013329:Structure-Activity Relationship; D014162:Transfection
chemical_list: D007527:Isoenzymes; D016337:RNA, Catalytic; C427204:hammerhead ribozyme