Ultraviolet hyperchromicity experiments indicate that in DNA duplex formation, a C-T mismatch is destabilizing in the center of a duplex, but behaves as a stable base pair at the terminus of a duplex. The C-T base pair is thought to contain two hydrogen bonds, but has thermodynamic parameters (H° and G° of dissociation) that are similar to a G-C base pair. AMBER molecular mechanics calculations were performed to study the possible structural properties of DNA duplexes with central and terminal C-T combinations. These calculations also indicate that a central C-T pair destabilizes a duplex, while terminal C-T forms a stable base pair. Hydrogen bonding between cytosine and thymine occurs only in the energy-minimized structures when the helix diameter decreases and the propeller twist angle between the bases increases. These changes are found to occur only at the end of a duplex in the calculations, which may explain the experimental results.