A high-throughput approach to profile RNA structure

Delli Ponti, Riccardo; Marti, Stefanie; Armaos, Alexandros; Tartaglia, Gian Gaetano

The structure of an RNA determines its interactions and functions (1, 2) . RNA structure can be studied using lowthroughput techniques such as nuclear magnetic resonance (NMR) and X-ray crystallography. More recent approaches have started to exploit biochemical reactions to perform high-throughput profiling of the RNA structure: Parallel Analysis of RNA Structure (PARS) distinguishes doubleand single-stranded regions using the catalytic activity of two enzymes, RNase V1 (able to cut double-stranded nucleotides) and S1 (able to cut single-stranded nucleotides) (3, 4) , while Selective 2 -Hydroxyl Acylation analyzed by Primer Extension (SHAPE) (5,6) employs highly reactive chemical probes such as 1M6, NMIA (SHAPE) and NAI-N 3 (icSHAPE) to characterize RNA backbone flexibility. Another technique based on dimethyl sulfate (DMS) (7) is often used for in vivo probing of transcriptomes (8, 9) . DMS experiments are of high quality due to the smaller size of the (CH 3 O) 2 SO 2 probe, yet have low coverage, since the alkylating agent only reacts to adenine and cytosine.