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• W2110473615 endingPage "1760" @default.
• W2110473615 startingPage "1746" @default.
• W2110473615 abstract "The hepatitis delta virus (HDV) ribozyme occurs in the genomic and antigenomic strands of the HDV RNA and within mammalian transcriptomes. Previous kinetic studies suggested that a wobble pair (G*U or A(+)*C) is preferred at the cleavage site; however, the reasons for this are unclear. We conducted sequence comparisons, which indicated that while G*U is the most prevalent combination at the cleavage site, G-C occurs to a significant extent in genomic HDV isolates, and G*U, G-C, and A-U pairs are present in mammalian ribozymes. We analyzed the folding of genomic HDV ribozymes by free energy minimization and found that variants with purine-pyrimidine combinations at the cleavage site are predicted to form native structures while pyrimidine-purine combinations misfold, consistent with earlier kinetic data and sequence comparisons. To test whether the cleavage site base pair contributes to catalysis, we characterized the pH and Mg(2+)-dependence of reaction kinetics of fast-folding genomic HDV ribozymes with cleavage site base pair purine-pyrimidine combinations: G*U, A-U, G-C, and A(+)*C. Rates for these native-folding ribozymes displayed highly similar pH and Mg(2+) concentration dependencies, with the exception of the A(+)*C ribozyme, which deviated at high pH. None of the four ribozymes underwent miscleavage. These observations support the A(+)*C ribozyme as being more active with a wobble pair at the cleavage site than with no base pair at all. Overall, the data support a model in which the cleavage site base pair provides a structural role in catalysis and does not need to be a wobble pair." @default.
• W2110473615 created "2016-06-24" @default.
• W2110473615 creator A5034947573 @default.
• W2110473615 creator A5036539847 @default.
• W2110473615 creator A5053201698 @default.
• W2110473615 creator A5090853950 @default.
• W2110473615 date "2008-07-24" @default.
• W2110473615 modified "2023-09-27" @default.
• W2110473615 title "Mechanistic characterization of the HDV genomic ribozyme: The cleavage site base pair plays a structural role in facilitating catalysis" @default.
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• W2110473615 doi "https://doi.org/10.1261/rna.1140308" @default.
• W2110473615 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2525964" @default.
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