Figure 2.

Given here are the A-A mismatch conformations for the main minima associated with the free energy landscapes. The letters denote different conformations: A, anti-anti; B, syn-anti; and C, syn-syn. Here D1 is a special case, because the χ-angle corresponds to syn-syn, but the base conformation looks like anti-anti due to the twisting of the sugar rings that become parallel to the bases. Note also that the hydrogen bonds associated with each of the conformations are also marked. To see this figure in color, go online.