= RNA helicase
{c}
An \b[<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.<How RNase R Degrades Structured RNA: Role of the Helicase Activity and the S1 Domain by Sk Tofajjen Hossain and others>[Abstract: intrinsic RNA helicase, ATP binding and nuclease activities distinguished]{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.<How RNase R Degrades Structured RNA: Role of the Helicase Activity and the S1 Domain by Sk Tofajjen Hossain and others>[Abstract; Figures1–2: designed duplexes, RNase R D272N and ATP-binding measurements]{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.
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