RNase R

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.^[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.^[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.