A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA/RNA helix

We propose a rapid chemical strategy for identifying base pairs in structured nucleic acid systems. The approach goes beyond traditional chemical mapping approaches by monitoring perturbations of each residue's chemical accessibility in response to systematic mutagenesis of residues that are distant in sequence but nearby in three dimensions. As a proof of concept, we present high-throughput dimethyl sulfate accessibility data for a chimeric DNA/RNA system in which every possible sequence variation and deletion in a 20 bp region has been synthesized and tested. The data demonstrate that 88% of the system's base pairs can be robustly inferred, with A/A and T/C DNA/RNA mismatches giving the strongest signals. These results point to the feasibility of rapid base pair inference in larger and more complex nucleic acid systems with unknown structure.