Influence of nearest neighbor sequence on the stability of base pair mismatches in long DNA: determination by temperature-gradient gel electrophoresis

Temperature-gradient gel electrophoresis (TGGE) was employed to determine the thermal stabilities of 48 DNA fragments that differ by single base pair mismatches. The approach provides a rapid way for studying how specific base mismatches effect the stability of a long DNA fragment. Homologous 373 bp DNA fragments differing by single base pair substitutions in their first melting domain were employed. Heteroduplexes were formed by melting and reannealing pairs of DNAs, one of which was 32P-labeled on its 5′-end. Product DNAs were separated based on their thermal stability by parallel and perpendicular temperature-gradient gel electrophoresis. The order of stability was determined for all common base pairs and mismatched bases in four different nearest neighbor environments; d(GXT)d(AYC), d(GXG)d(CYC), d(CXA)d(TYG), and d(TXT)d(AYA)withX,Y = A,T,C, or G. DNA fragments containing a single mismatch were destabilized by 1 to 5˚C with respect to homologous DNAs with complete Watson - Crick base pairing. Both the bases at the mismatch site and neighboring stacking interactions influence the destabilization caused by a mismatch. G ▪ T, G ▪ G and G ▪ A mismatches were always among the most stable mismatches for all nearest neighbor environments examined. Purine-purine mismatches were generally more stable than pyrimidine-pyrimidine mispairs. Our results are in very good agreement with data where available from solution studies of short DNA oligomers.