Figure 1.

Overview of DNA substrates. (A) DNA substrate design. Tertiary structure is shown schematically, indicating obstacle positions relative to the target residue location (marked by a lollipop). Secondary structure diagrams show the intended base pairing of the DNA substrates. Obstacles in substrates SL1, SL2 and SL1-2 are created by a 6-bp DNA helix capped at both ends with tetraloops, which is connected to the DNA substrate via a four-way junction (see text for details and Supplementary Table S1 for oligonucleotide sequences). Schematic diagrams are adapted from (30). (B) Relative mobilities of DNA substrates. Fluorescein-labelled substrates S, SL1, SL2 and SL1-2 were subjected to electrophoresis at 100 V for 4 h in a 5% non-denaturing polyacrylamide gel.