Figure 8.

Plausible idealized folding pathway of the basket-type GQ 143D. The structural schemes are visualized as in the Figure 1 and the flanking 5′-terminal adenine is depicted as a cyan circle. The green squares indicate structures that we found stable in simulations and the native basket-type GQ 143D. The blue square depicts the alternative basket fold Q2 with the same syn/anti pattern. The red squares indicate intermediates which we suggest are less likely to participate in the folding pathway. Those parts of the H1, H2 and T1-T4 structures that were not directly simulated are transparent in the schemes. Stability of the H12, H13 and H24 structures is assessed based on simulation behaviour of their separate G-hairpin parts. The model suggests a lack of a suitable pathway to the alternative topology Q2.