RNase R (source code)
= RNase R
{c}
\b[RNase R] is a bacterial <exoribonuclease> that degrades <RNA> from the3′ end toward the5′ end. It hydrolyzes successive <phosphodiester bonds> rather than requiring an internal cut at each step. Its ability to digest structured RNA distinguishes it from enzymes restricted mainly to accessible single-stranded regions.<How RNase R Degrades Structured RNA: Role of the Helicase Activity and the S1 Domain by Sk Tofajjen Hossain and others>[Abstract:3′ exoribonuclease and structured-RNA degradation]{ref}
The direction matters. For a sufficiently accessible linear RNA whose final three nucleotides are written5′–…GCA–3′, degradation encounters the terminal A before the preceding C. This notation illustrates direction, not a claim that an isolated three-nucleotide fragment is an efficient substrate. An intact <circular RNA> has no free end for this entry route; a strand break creates ends and changes the substrate's topology.
A2016 mechanistic study compared designed single-stranded and duplex RNA substrates with altered enzyme variants. It examined the <S1 RNA-binding domain>, intrinsic <RNA helicase> activity, ATP binding and conformational changes measured through tryptophan <fluorescence>. Those comparisons separated RNA binding, strand separation and phosphodiester cleavage rather than treating disappearance of an RNA band as a complete mechanistic explanation.<How RNase R Degrades Structured RNA: Role of the Helicase Activity and the S1 Domain by Sk Tofajjen Hossain and others>[Abstract and Figures1–3: designed substrates, binding assays and conformational observations]{ref}
Substrate structure and end accessibility therefore matter when interpreting resistance to digestion. Surviving RNA is an observation under the chosen reaction conditions; by itself it does not establish the exact structure or topology of every surviving molecule.
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