Fig. 2.
Kinetic competition experiment using complementary strands. (A) SPR sensorgram of DNA–DNA interaction between immobilized dG(TGGAA)2G and the ligand dC(TGGAA)2C at various ligand concentrations. (B) Same as A but with dC(TTCCA)2C as the ligand instead. (C) Illustration of the competition assay. Excess amount of d(TTCCA)n oligonucleotides was added to the d(TGGAA)n single molecule assay. Opening of the looped structure and formation of duplex DNA in the product state increases the distance between the two labeling sites (marked as red and green stars), resulting in low EFRET. (D) Time-dependent EFRET histograms of d(TGGAA)4 + d(TTCCA)4. (E) Representative time evolutions of the fraction of folded d(TGGAA)4 at various concentrations. The fraction was obtained using the population fraction with EFRET greater than 0.27. Single-exponential fits are overlaid as solid lines. (F) Concentration dependence of the apparent kinetic rate constants obtained for different number of repeats. Linear fits are overlaid as solid lines. The forward rate constants, obtained from the slopes of the linear fits, are shown in the inset. Error bars represent SDs of three individual experiments.