FIGURE 5.
Free energy diagram for simple duplex formation zipper model. In the zipper model, nucleation involves the formation of 2–3 bp, after which subsequent base-pair formation is favored over the dissociation of the nucleation complex. The bimolecular association rate between two ssRNA molecules is limited by this nucleation rate (kduplex). Because the formation of these 2–3 bp is uphill in energy from an initial encounter between the two strands, the association rate for duplex formation (kduplex) is slower than diffusional encounter (kdiff).
