Figure 5: SHAPE-JuMP interactions detected for the RNase P RNA in the presence and absence of Mg²⁺.

(A) SHAPE-JuMP interactions for the most frequent 3% of deletions for RNase P in the presence (left) and absence (right) of Mg²⁺. Experimentally measured distances are shown with black lines; gray histograms represent distances of all nucleotide pairs in reference structure. (B) Internucleotide crosslinks, detected as cDNA deletions, superimposed on the secondary structure, colored by through-space distance as calculated from the reference structure¹⁶. Nucleotides not visualized in the reference structure are shown within gray circles.