Coronavirus 5' proximal stem-loop 5 mutate-and-map
Multidimensional chemical mapping using the mutate-and-map procedure for coronavirus 5' proximal stem-loop 5 (SL5). The reactivity of the RNA to DMS/2A3 is read out as mutations introduced during reverse transcriptase. This chemical reactivity can guide the determination of RNA structure as DMS/2A3 preferentially modified unpaired bases. Furthermore, when mutations are introduced into the RNA prior to chemical modification, we expect to see changes in reactivity local to the mutation and the mutations base-pair. Hence, the change in reactivity upon mutation can further support secondary structure determination. In one experiment mutations were introduced into RNA using error prone PCR, in the other mutations were designed into an oligo library pool.