Thermodynamic parameters for duplex formation were determined from CD melting curves for r(GGACGAGUCC)2 and d(GGACGAGTCC)2, both of which have been demonstrated to form two consecutive 'sheared' A:G base pairs at the center by our previous studies. The parameters were determined also for r(GGACUAGUCC)2 and d(GGACTAGTCC)2, where the A:G mismatches are replaced by Watson-Crick A:U(T) base pairs. Thermodynamic properties for duplex formation are compared between the sheared and the Watson-Crick base pairs, and between RNA and DNA. Difference in the thermodynamic stability is analyzed and discussed in terms of enthalpy and entropy changes.