Skip to main content
. 2004 Feb;10(2):254–264. doi: 10.1261/rna.5176604

FIGURE 2.

FIGURE 2.

Anomalous electrophoretic migration of K-turn RNA is dependent on the presence of magnesium ions. Comparison of electrophoretic mobility of 120-bp RNA duplexes containing a central Kt-7 sequence or variant with duplexes kinked by virtue of a central oligoadenine bulge. (A) Central sequences of the RNA species employed. Each is a 120-bp duplex with either the Kt-7 sequence (K, top), a derivative in which the three G•A mismatches have been each converted into a Watson-Crick base pair (K′, middle), or an oligoadenine bulge (An, bottom). (B,C) Electrophoretic mobilities in the presence of 5 mM magnesium ions (B) or 2 mM EDTA (C). Note that the Kt-7 sequence migrates very slowly in magnesium ions, indicating a highly kinked structure, comparable to the A7 bulged species. By comparison, the same species migrates much faster in EDTA, similar to an A3 bulged duplex. Lane 1, Kt-7; 2, K′ sequence, lacking the G•A mismatches; 3–8, oligoadenine An bulge-containing species, where n = 0 (i.e., perfect duplex), 1, 3, 4, 5, or 7, respectively.