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

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posted on 29.04.2008, 00:58 by Kevin A Wilkinson, Robert J Gorelick, Suzy M Vasa, Nicolas Guex, Alan Rein, David H Mathews, Morgan C Giddings, Kevin M Weeks

(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).