Solution structures and base pair stacking of a self-complementary DNA hexamer d(CGTACG)₂ have been studied at 5, 10 and 15° C, respectively. The stacking interactions among the center base pair steps of the DNA duplex are found to improve when the terminal base pairs became less stable due to end fraying. A new structural quantity, the stacking sum (Σ_s), is introduced to indicate small changes in the stacking overlaps between base pairs. The improvements in the stacking overlaps to maintain the double helical conformation are probably the cause for the observed temperature dependent structural changes in double helical DNA molecule. A detailed analysis of the helical parameters, backbone torsion angles, base orientations and sugar conformations of these structures has been performed.