ON USING DNA-TRAPPING ELECTROPHORESIS TO INCREASE THE RESOLUTION OF DNA-SEQUENCING GELS

It was previously shown that labeling one of the ends of single-strand ed DNA molecules with streptavidin increases the interband separation of such DNA molecules when they are electrophoresed in denaturing poly acrylamide gels. This electrophoretic method was called DNA-trapping e lectrophoresis and seemed to be a promising method to increase the res olution of DNA sequencing ladders. Here, we show that this method requ ires inverted gel preruns to obtain optimal resolution, and we present a method to calculate the velocity of end-labeled DNA molecules in de naturing polyacrylamide gels. We use this method to elucidate the trap ping mechanism and to characterize the electric field dependence of th e critical size beyond which end-labeled DNA molecules are strongly tr apped. Our results show that DNA-trapping electrophoresis cannot be us ed to increase the resolution of DNA sequencing ladders because, in th e strong trapping regime, the bandwidths increase more than the gain i n interband distances. On the other hand, it might be possible to use DNA-trapping electrophoresis to develop isoelectric focusing-like tech niques using monotonic electric field gradients.