A chemo-genetic approach for the study of nucleobase participation in nucleolytic ribozymes
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David M.J. Lilley
Abstract
A novel chemo-genetic approach for the analysis of general acid-base catalysis by nucleobases in ribozymes is reviewed. This involves substitution of a C-nucleoside with imidazole in place of a natural nucleobase. The Varkud satellite ribozyme in which the nucleobase at the critical 756 position has been replaced by imidazole is active in both cleavage and ligation reactions. Similarly, a modified hairpin ribozyme with the nucleobase at position 8 substituted by imidazole is active in cleavage and ligation reactions. Although the rates are lower than those of the natural ribozymes, they are significantly greater than other variants at these positions. The dependence of the hairpin ribozyme reaction rates on pH has been studied. Both cleavage and ligation reactions display a bell-shaped pH dependence, consistent with general acid-base catalysis involving the nucleotide at position 8.
©2007 by Walter de Gruyter Berlin New York
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Articles in the same Issue
- 25 years of catalytic RNA: looking younger than ever!
- On the occasion of the 25th anniversary of the discovery of catalytic RNA
- An overview of the RNA world – for now
- Group II introns: structure, folding and splicing mechanism
- Expression of protein-coding genes embedded in ribosomal DNA
- Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs
- The spliceosome: a ribozyme at heart?
- A chemo-genetic approach for the study of nucleobase participation in nucleolytic ribozymes
- Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme
- A 2′-methyl or 2′-methylene group at G+1 in precursor tRNA interferes with Mg2+ binding at the enzyme-substrate interface in E-S complexes of E. coli RNase P
- Morphing the minimal and full-length hammerhead ribozymes: implications for the cleavage mechanism
- Idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof
- RNA self-processing towards changed topology and sequence oligomerization
- Plasminogen-dependent internalization of soluble melanotransferrin involves the low-density lipoprotein receptor-related protein and annexin II
- Could the effect of modeled microgravity on osteogenic differentiation of human mesenchymal stem cells be reversed by regulation of signaling pathways?
