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.
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Research Article|
April 12 2013
Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint
Marta Magdalena Gabryelska;
Marta Magdalena Gabryelska
1Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
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Eliza Wyszko;
Eliza Wyszko
1
1Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
1Correspondence may be addressed to either of these authors (email wyszkoe@ibch.poznan.pl or jbarcisz@ibch.poznan.pl).
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Maciej Szymański;
Maciej Szymański
1Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
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Mariusz Popenda;
Mariusz Popenda
1Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
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Jan Barciszewski
Jan Barciszewski
1
1Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
1Correspondence may be addressed to either of these authors (email wyszkoe@ibch.poznan.pl or jbarcisz@ibch.poznan.pl).
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Publisher: Portland Press Ltd
Received:
November 21 2012
Revision Received:
February 15 2013
Accepted:
February 19 2013
Accepted Manuscript online:
February 19 2013
Online ISSN: 1470-8728
Print ISSN: 0264-6021
© The Authors Journal compilation © 2013 Biochemical Society
2013
Biochem J (2013) 451 (3): 439–451.
Article history
Received:
November 21 2012
Revision Received:
February 15 2013
Accepted:
February 19 2013
Accepted Manuscript online:
February 19 2013
Citation
Marta Magdalena Gabryelska, Eliza Wyszko, Maciej Szymański, Mariusz Popenda, Jan Barciszewski; Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint. Biochem J 1 May 2013; 451 (3): 439–451. doi: https://doi.org/10.1042/BJ20121761
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