Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A center dot A, C center dot C, G center dot G, and T center dot T mismatches

Thermodynamic measurements are reported fur 51 DNA duplexes with A.A, C.C, G.G, and T.T single mismatches in all possible Watson-Crick contexts. These measurements were used to test the applicability of the nearest-neighbor m odel and to calculate the 16 unique nearest-neighbor parameters for the 4 s ingle like with like base mismatches next to a Watson-Crick pair. The obser ved trend in stabilities of mismatches at 37 degrees C is G.G > T.T approxi mate to A.A > C.C. The observed stability trend for the closing Watson-Cric k pair on the 5' side of the mismatch is G.C greater than or equal to C.G g reater than or equal to A.T greater than or equal to T.A. The mismatch cont ribution to duplex stability ranges from -2.22 kcal/mol for GGC.GGC to +2.6 6 kcal/mol for ACT.ACT. The mismatch nearest-neighbor parameters predict th e measured thermodynamics with average deviations of Delta G degrees(37) = 3.3%, Delta H degrees = 7.4%, Delta S degrees = 8.1%, and T-M = 1.1 degrees C. The imino proton region of 1-D NMR spectra shows that G.G and T.T misma tches form hydrogen-bonded structures that vary depending on the Watson-Cri ck context. The data reported here combined with our previous work provide for the first time a complete set of thermodynamic parameters for molecular recognition of DNA by DNA with or without single internal mismatches. The results are useful for primer design and understanding the mechanism of tri plet repeat diseases.