FIGURE 6.

Catalysis of hairpin hybridization by an opening strand. (A) Displacement of an opening strand bound to hairpin H (l = 40, n = 16) by the complementary hairpin . The schematic diagram shows the FRET labels on the opening strand used to observe the progress of the reaction. Black and gray lines show the time dependence of the reaction for opening strands with seven-base internal and external toeholds, respectively. The dots show a fit to the data assuming second-order kinetics with a rate constant of 5.1 × 10⁴ M⁻¹ s⁻¹. (B) Catalysis of the reaction between complementary hairpins H and (l = 40, n = 16) by an opening strand with a seven-base external toehold. Bands in the native polyacrylamide gel correspond to the reactants (individual hairpins , H and kissed complex k), the duplex product d, and the intermediate formed by the opening strand bound to H. Controls: o, annealed H and opening strand; a, annealed H and . See text for descriptions of experiments and Materials and Methods for experimental details.