Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS

Abstract

Chemical probing experiments have transformed RNA structure analysis, enabling highthroughput measurement of base-pairing in living cells. Dimethyl sulfate (DMS) is one of the most widely used structure probing reagents and has played a prominent role in enabling next-generation single-molecule probing analyses. However, DMS has traditionally only been able to probe adenine and cytosine nucleobases. We previously showed that, using appropriate conditions, DMS can also be used to interrogate basepairing of uracil and guanines in vitro at reduced accuracy. However, DMS remained unable to informatively probe guanines in cells.