Strand Dissociation and Cooperative Melting of Double-Stranded DNAs Detected by Denaturant Gradient Gel Electrophoresis1

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Abstract
Precise analysis using the denaturant gradient gel electrophoresis which was devised by Fischer and Lerman ( Cell 16, 191–200, 1979), was found to present specific patterns of fine structures for double stranded DNA fragments. These seem to be a mobility change of DNA fragments caused by specific denaturation processes. The effect of denaturants on DNA melting was ascertained to be similar to the effect of temperature. The observed patterns, in comparison with the melting processes of DNAs theoretically obtained, were closely related to DNA meltings and strand dissociations. A number of electrophoretic mobility transitions showed the retardation correspondent to each of the cooperative meltings. Strand dissociations occurred under the conditions theoretically predicted. The degree of retardation in electrophoresis for DNA fragments seemed to correspond to the size of melted regions. Methods presented here were proved to have advantages over the conventional ones for the study of DNA stability maps.