 RNA helicase

An RNA helicase is a protein activity that separates paired RNA strands or opens local RNA secondary structure. Strand separation concerns noncovalent pairing; it is different from cutting the phosphodiester bonds in the RNA backbone. The way a helicase couples nucleotide binding, energy use and structural change depends on the protein, so an unwinding observation does not alone specify its mechanism.^[ref]

For an inventory example, consider a duplex formed by two 12-nucleotide RNA strands. Separation without cleavage leaves two 12-nucleotide strands and 24 nucleotides in total. Cleavage would instead change the lengths of covalent chains. A falling duplex signal could therefore reflect unwinding, degradation or both unless the measurement distinguishes these outcomes.

A 2016 study of RNase R made that separation experimentally: designed RNA substrates and an altered nuclease-deficient protein were used to examine strand separation independently of normal RNA degradation. ATP-binding assays and fluorescence measurements supplied different evidence about binding and conformational change.^[ref]

This example also cautions against using “ATP-dependent” as shorthand for a complete mechanism. ATP binding and ATP hydrolysis are distinct events. Demonstrating one does not establish the other, and observing loss of paired RNA does not establish that the RNA backbone remained intact.