ArticleRNA (New York, N.Y.)2004
Cross-linking experiments reveal the presence of novel structural features between a hepatitis delta virus ribozyme and its substrate.
Article in RNA (New York, N.Y.), 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Characterization of the trans Watson-Crick GU base pair located in the catalytic core of the antigenomic HDV ribozyme.PloS one · 2012Article
- Developing three-dimensional models of putative-folding intermediates of the HDV ribozyme.Structure (London, England : 1993) · 2010Article
- Modulating RNA structure and catalysis: lessons from small cleaving ribozymes.Cellular and molecular life sciences : CMLS · 2009Review
- Monitoring of an RNA multistep folding pathway by isothermal titration calorimetry.Biophysical journal · 2009Article
- Potassium ions modulate a G-quadruplex-ribozyme's activity.RNA (New York, N.Y.) · 2008Article
- A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme.Nucleic acids research · 2007Article
- Examination of the folding pathway of the antigenomic hepatitis delta virus ribozyme reveals key interactions of the L3 loop.RNA (New York, N.Y.) · 2007Article
- Cation-specific structural accommodation within a catalytic RNA.Biochemistry · 2006Article
- Antigenomic delta ribozyme variants with mutations in the catalytic core obtained by the in vitro selection method.Nucleic acids research · 2006Article
- Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence.Nucleic acids research · 2006Article
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2 authors.
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Abstract
The kinetic pathway of a trans-acting delta ribozyme includes an essential structural rearrangement involving the P1 stem, a stem that is formed between the substrate and the ribozyme. We performed cross-linking experiments to determine the substrate position within the catalytic center of an antigenomic, trans-acting, delta ribozyme. Substrates that included a 4-thiouridine either in position -1, +4, or +8 (i.e., adjacent to the cleavage site, or located either in the middle of or at the 3'-end of the P1 stem, respectively) were synthesized and shown to be efficiently cleaved. Examination of the cross-linking conditions, the use of various mutated ribozymes, as well as the probing and characterization of the resulting ribozyme-substrate complexes, revealed several new features of the molecular mechanism: (1) the close proximity of several bases between nucleotides of the substrate and ribozyme; (2) the active ribozyme-substrate complex folds in a manner that docks the middle of the P1 stem on the P3 stem, while concomitantly the scissile phosphate is in close proximity to the catalytic cytosine; and, (3) some complexes appear to be compatible with being active intermediates along the folding pathway, while others seem to correspond to misfolded structures. To provide a model representation of these data, a three-dimensional structure of the delta ribozyme was developed using several RNA bioinformatic software packages.
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