The thermal stability of DNA fragments with tandem mismatches at a d(CXYG)center dot d(CY'X'G) site

Temperature-Gradient Gel Electrophoresis (TGGE) was employed to determine the thermal stabilities of 28 DNA fragments, 373 bp long, with two adjacent mismatched base pairs, and eight DNAs with Watson-Crick base pairs at the same positions. Heteroduplex DNAs containing two adjacent mismatches were formed by melting and reannealing pairs of homologous 373 bp DNA fragments differing by two adjacent base pairs. Product DNAs were separated based on their thermal stability by parallel and perpendicular TGGE, The polyacrylamide gel contained 3.36 M urea and 19.2% formamide to lower the DNA melting temperatures. The order of stability was determined in the sequence context d(CXYG). d(CY'X'G) where X . X' and Y . Y' represent the mismatched or Watson-Crick base pairs. The identity of the mismatched bases and their stacking interactions influence DNA stability, Mobility transition melting temperatures (T-u) of the DNAs with adjacent mismatches were 1.0-3.6 degrees C (+/-0.2 degrees C) lower than the homoduplex DNA with the d(CCAG). d(CTGG) sequence. Two adjacent G . A pairs, d(CGAG). d(CGAG), created a more stable DNA than DNAs with Watson-Crick A . T pairs at the same sites. The d(GA). d(GA) sequence is estimated to be 0.4 (+/-30%) kcal/mol more stable in free energy than d(AA). d(TT) base pairs. This result confirms the unusual stability of the d(GA). d(GA) sequence previously observed in DNA oligomers. All other DNAs with adjacent mismatched base pairs were less stable than Watson-Crick homoduplex DNAs. Their relative stabilities followed an order expected from previous results on single mismatches. Two homoduplex DNAs with identical nearest neighbor sequences but different next-nearest neighbor sequences had a small but reproducible difference in T-u value. This result indicates that sequence dependent next neighbor stacking interactions influence DNA stability.