Template switching enables chemical probing of native RNA structures

Simulated primer masking demonstrates critical nucleotide reactivities. Secondary structure predictions based on exclusion of experimental Switch-MaP reactivities for nt −2 to 13 and 99 to +2 (indicated by blue highlight) of the SreA aptamer construct (left). Restoration of G13 reactivity generated the expected aptamer fold (center) and is equivalent to structural prediction encompassing full reactivity data for 5′ end (right).