RNA Conformational Changes That Differentiate Ex Virio and In Vitro Transcript States

(A) The in vitro transcript forms a loop-loop dimer. Identical samples of the transcript RNA were resolved in nondenaturing gels, either omitting or containing 7 mM MgCl2. Markers for monomeric (M) and dimeric (D) conformations are shown.

(B) SHAPE reactivity as a function of nucleotide position for ex virio (red) and transcript (black) RNAs. Difference plot in lower panel has been smoothed over a 5-nt window.

(C) Secondary structure model for the primer binding site in the absence of tRNA(lys3).