Abstract
It was previously shown that labeling one of the ends of single-stranded DNA molecules with streptavidin increases the interband separation of such DNA molecules when they are electrophoresed in denaturing polyacrylamide gels. This electrophoretic method was called DNA-trapping electrophoresis and seemed to be a promising method to increase the resolution of DNA sequencing ladders. Here, we show that this method requires inverted gel preruns to obtain optimal resolution, and we present a method to calculate the velocity of end-labeled DNA molecules in denaturing polyacrylamide gels. We use this method to elucidate the trapping mechanism and to characterize the electric field dependence of the critical size beyond which end-labeled DNA molecules are strongly trapped. Our results show that DNA-trapping electrophoresis cannot be used to increase the resolution of DNA sequencing ladders because, in the strong trapping regime, the bandwidths increase more than the gain in interband distances. On the other hand...
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