Denaturing gradient gel electrophoretic analysis of minisatellite alleles

By two-dimensional DNA fingerprinting, an electrophoretic method which combines separation according to size with separation in a denaturing gradient, virtually all minisatellite sequences detected with a minisatellite core probe can be resolved (Uitterlinden et al., Proc. Natl. Acad. Sci. USA 1989, 86, 2742-2746). To investigate the electrophoretic behavior in denaturing gradient gels of allelic restriction fragments containing minisatellite sequences, we analyzed alleles of the two highly polymorphic minisatellite loci D7S22 and D2S44. The results obtained indicate that for these loci, depending on the restriction enzyme used to digest genomic DNA, alleles of different sizes migrate to regions of similar denaturant concentration, i.e. to isothermal positions in the denaturing gradient. Denaturing gradient gel electrophoresis also allows for the discrimination of restriction fragments which are the result of the presence of internal recognition sites in the minisatellite and, therefore, to distinguish between VNTR and restriction site polymorphisms.