Figure 4.

The intensity and pattern of transcription blockages changes with the type of cation in solution. (A) Upper panel. In vitro transcription by T7 RNA polymerase conducted in the presence of 2 mM Mn²⁺. Note the new product corresponding to a transcript truncated 5 bases upstream of the H-DNA edge (designated ‘up’) in addition to the previously observed ‘up’, ‘m’ and ‘dn’ blockage positions (see the scheme in Figure 3C). Due to poor resolution of the gel, the ‘m’ and ‘dn’ positions form a single blockage band. Full-length products appear at their usual 320 nt location, but also in positions above 330 nt. Lower panel. Quantification of the results in the upper panel reveals that arrest at up’-position constitutes 33.5% of the all RNA transcripts; up-transcripts and (m- + dn-) transcripts account for 21.7 and 33.1% respectively. The full-length product makes only 11.6% of the total product. (B) Upper panel. Triplex-mediated transcription arrests observed at 80 mM K⁺ or at 80 mM Li⁺. Lower panel. Quantification of these data reveal that intensities of blockages in quadruplex-favoring (K⁺) conditions are similar to intensities in conditions (Li⁺) that do not favor quadruplexes.