Thermodynamic parameters for double strand formation have been measured for the sixteen double helices of the sequence dCA3XA3G·dCT3YT3G, with each of the bases A, C, G and T at the positions labelled X and Y. The results are analyzed in terms of nearest-neighbors and are compared with thermodynamic parameters for RNA secondary structure. At room temperature the sequence -A-A--T•-T•- is more stable than -A-A--U•-U•- and is similar in stability to -A-C--T•-G•- , -C-A--G•-T•- , -A-G--T•-C•- , -G-A--C•-T•- ; -A-T--T•-A•- and -T-A--A•-T•- are least stable. At higher temperatures the sequences containing a G·C base pair become more stable than those containing only A·T. All molecules containing mismatches are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. At room temperature the most stable mismatches are those containing guanine (G·T, G·C, G·A); the least stable contain cytosine (C·A, C·C). At higher temperatures pyrimidine-pyrimidine mismatches become the least stable.

Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,D