The thermal stabilities and structures of B-Z junction forming DNA duplexes possessing A/C or G/T base pair mismatches were compared to those of corresponding duplexes possessing perfect matched base pairs. The upper strands of the duplexes have a generalized sequence 5'-(5meCG)-LMN-GACTG-3', where L stands for A or G while M and N are permutations of pyrimidines. The lower strands were either complementary or were such as to create an A/C or G/T mismatch at the position corresponding to L, M, or N. Optical melting and circular dichroism studies were used to investigate the thermal stabilities and structures of both the mismatched base pair and the perfect matched base pair duplexes. Incorporating mismatched A/C or G/T base pairs did not noticeably affect the conformations of the duplexes in 115 mM Na+ but resulted in perturbed B-Z conformations at 4.5 M Na+. For any mismatched base pair duplex, the B-DNA domain of the hybrid B-Z structure formed at 4.5 M Na+ is significantly perturbed while the Z-DNA domain is less perturbed by the presence of the mismatched base pairs. The presence of a mismatch destabilizes a duplex relative to the perfect matched base pair duplex by 1.7-10.0 kcal/mol depending upon position of the mismatch, type of mismatch base pair involved, and Na+ concentration. The thermodynamic destabilization of a mismatched base pair duplex relative to the perfect matched base pair duplex arises from perturbations in nearest neighbor interactions and hydrogen bonding. In general, we observed that the incorporation of an A/C or G/T base pair mismatch in place of a perfect matched base pair at or near a B-Z junction results in a relatively large change in enthalpy and entropy to produce a significant change in the free energy of the duplex to single strand transition. At 4.5 M Na+, where the duplexes possess perturbed B-Z junctions, the farther away from the junction that the mismatch is, the greater the extent of the destabilization.