Figure 5.

(A) Comparison of ethidium bromide and compound 4 as agarose gel fluorescent probes. Two agarose gels were prepared in parallel. Ethidium bromide (left) or compound 4 (right) (both at 0.4 µM final concentration) were added at 65°C to pre-melted 2.5% agarose, 1× TAE gels. Reading gels from left to right, samples 1–3 (duplex molecular weight markers, 1 µg) and 4–6 (intramolecular quadruplexes, 21, 22A and 28G, 1 µg each) were prepared in a 1× TAE buffer solution with 0.1 M KCl and incubated at room temperature for 1 h. Equivalent amounts (20 µl) of each sample were loaded in each gel. (B) Sensitivity assay. Two-fold stepwise dilutions of an intramolecular quadruplex solution (28G, in 0.1 M KCl, decreasing strand concentrations: 8, 4, 2, 1, 0.5, 0.25, 0.12 and 0.06 µM) were prepared, incubated at 20°C for 1 h and loaded on an agarose gel containing 0.4 µM compound 2 (upper left), 0.4 µM compound 4 (upper right) or 0.1 µM compound 2 (lower left). In each of these gels, the dye was added at 65°C to a pre-melted 2.5% agarose solution, mixed and poured in a standard agarose gel cuvette.