ArticleAnalytical biochemistry2014
Determination of relative rate constants for in vitro RNA processing reactions by internal competition.
Article in Analytical biochemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 7 citations in OpenAlex.
- The contribution of the C5 protein subunit ofRNA (New York, N.Y.) · 2017Article
- Mapping specificity landscapes of RNA-protein interactions by high throughput sequencing.Methods (San Diego, Calif.) · 2017Article
- Optimization of high-throughput sequencing kinetics for determining enzymatic rate constants of thousands of RNA substrates.Analytical biochemistry · 2016Article
- Measuring specificity in multi-substrate/product systems as a tool to investigate selectivity in vivo.Biochimica et biophysica acta · 2016Review
- Determination of hepatitis delta virus ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics.Analytical biochemistry · 2015Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Studies of RNA recognition and catalysis typically involve measurement of rate constants for reactions of individual RNA sequence variants by fitting changes in substrate or product concentration to exponential or linear functions. A complementary approach is determination of relative rate constants by internal competition, which involves quantifying the time-dependent changes in substrate or product ratios in reactions containing multiple substrates. Here, we review approaches for determining relative rate constants by analysis of both substrate and product ratios and illustrate their application using the in vitro processing of precursor transfer RNA (tRNA) by ribonuclease P as a model system. The presence of inactive substrate populations is a common complicating factor in analysis of reactions involving RNA substrates, and approaches for quantitative correction of observed rate constants for these effects are illustrated. These results, together with recent applications in the literature, indicate that internal competition offers an alternate method for analyzing RNA processing kinetics using standard molecular biology methods that directly quantifies substrate specificity and may be extended to a range of applications.
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Registered trials
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