Matrix effects suggest an important influence of DNA-polyacrylamide interactions on the electrophoretic mobility of DNA.

The electrophoretic mobilities of 34 DNA fragments with a varied phasing of two A-tract bends have been determined in different polyacrylamide gels. They are perfectly described by a cosine function. A systematic variation of the polyacrylamide gel matrix revealed that not only the absolute electrophoretic mobilities of these distance variants, but also their amplitudes and the positions of their extrema, depend on the polyacrylamide content. The displacement of the extrema with increasing polyacrylamide content is attributed to gel-induced unwinding of the DNA. None of these matrix effects can be explained by the change of the pore sizes, which is generally regarded as the central parameter determining electrophoretic mobility of DNA in gels. Instead, we hypothesize an interaction between the electrophoresed DNA and the polyacrylamide matrix and discuss a new qualitative model for electrophoresis of DNA in polyacrylamide gels which accounts for these observations.