FIG. 1.

An overview of the RNA mutually constrained folding problem. A set of mixture of reactivities is generated as the enzymatic/chemical probing information of two alternative structures from the same RNA sequence. Assume the probing enzymes/chemical reagents will preferentially attack the unpaired (loop) regions (the blue arrows) of the RNA structures. High reactivities are expected to be observed at these regions, while low reactivities are expected for the paired regions. With the presence of both alternative structures (assuming the partition is 50%–50%), their individual reactivities are attenuated by each other. Finally, a mixture of reactivities of both alternative structures are observed from the experiment. The problem we aim to solve is how to infer both alternative structures from the mixture of reactivities.