Figure 2.

The dissociation constants for the oligonucleotide substrate from the open and closed complexes can be used to determine the equilibrium constant for docking (K_dock). A. The free energy diagram for a closed complex substrate, which allows measurement of ${(\mathrm{\Delta }{\mathrm{G}}_{\text{off}}^{‡})}_{\mathrm{c}}$. ΔG_dock can be obtained from the difference between ${(\mathrm{\Delta }{\mathrm{G}}_{\text{off}}^{‡})}_{\mathrm{c}}$ and ${(\mathrm{\Delta }{\mathrm{G}}_{\text{off}}^{‡})}_{\mathrm{o}}$ [i.e., $\mathrm{\Delta }{\mathrm{G}}_{\text{dock}}={(\mathrm{\Delta }{\mathrm{G}}_{\text{off}}^{‡})}_{\mathrm{c}}-{(\mathrm{\Delta }{\mathrm{G}}_{\text{off}}^{‡})}_{\mathrm{o}}$] B. The free energy diagram for an open complex substrate, which allows measurement of ${(\mathrm{\Delta }{\mathrm{G}}_{\text{off}}^{‡})}_{\mathrm{o}}$ The values of ΔG and the corresponding dissociation rate and equilibrium constants can be interconverted via standard equations as described in Measurement of docking equilibria in Materials and Methods.