FIGURE 4.

Conformational heterogeneity of MD-III RNA. (A) RNAs were synthesized in vitro using T7 polymerase, then electrophoresed on a 6% polyacrylamide gel, as described in Materials and Methods. Newly synthesized MD-III-2 RNA transcripts resolve as two bands, denoted Upper and Lower, on a nondenaturing gel. MD-III-2SF RNA, which contains mutations that destabilize the unbranched rod structure, resolves as a single band, commensurate in migration to the Upper band of MD-III-2 RNA. (B) Denaturing gel electrophoresis of MD-III-2 RNA isolated from the Upper and Lower bands of a nondenaturing polyacrylamide gel. Upper and Lower band RNAs were purified from the nondenaturing gel in (A), denatured and electrophoresed on a polyacrylamide gel containing 7 M Urea, as described in Materials and Methods.