Fig. 2. Self-assembly channels for recognition-encoded trimers. The first base-pairing interaction can take place in an intermolecular or intramolecular fashion, leading to the 1,2 or 1,3 folding channels. The second base-pairing interaction can be intramolecular, initiating duplex formation or intermolecular, leading to the networks channel. The outcome depends on the concentration, C, the association constant for the intermolecular base-pairing interaction, K, and the effective molarities for folding, (EMf-1,2, EMf-1,3), duplex initiation and propagation (EMi, EMd).
