FIGURE 6.

Folding mechanisms of the wild-type and the G39-C65 base pair aptamers. The wild-type adenine aptamer folds from the unfolded (U) to an intermediate state (I) by the formation of the P1-P3 coaxial stacking interaction. The folded state (F) is then adopted by the formation of the loop-loop interaction. The G39-C65 aptamer most likely folds directly from the U to the F state without going through the I state. The absence of the I structure most likely results from the formation of the G39-C65 base pair. Folding schemes only represent global structures and not structural differences that occur at the local level in core domains.