Method identifies differences between refolded and native RNA

Studies of RNA structure often involve denaturing, purifying, and refolding the RNA. But the structures adopted after such manipulations may not accurately reflect the original structure the molecule had in a cell. Using a strategy called SHAPE-MaP, which uses acylation of the 2′-hydroxyl group to determine the conformational flexibility of individual nucleotides in an RNA sequence, Kevin Weeks and Elizabeth Dethoff of the University of North Carolina at Chapel Hill found that RNA from a dengue virus adopts different structures when it has been denatured and refolded than it does straight out of the virus. The refolded RNA was more highly structured and tended to adopt a single conformation, whereas the native RNA was more flexible and adopted multiple conformations (Biochemistry 2019, DOI: 10.1021/acs.biochem.8b01219). “Natural RNAs are likely to be more dynamic than those in many common biochemical experiments,” Weeks says. However, he also notes, the SHAPE-MaP experiment can be used to identify those RNA regions for which the refolded structure is a good proxy for the native version. Hashim Al-Hashimi, an expert on RNA structure at Duke University, says, “This study very nicely highlights the dynamic nature of RNA and the folly of ever assuming that RNAs—especially large and complex ones—fold into a single structure.”