Electrophoresis of DNA in Nondenaturing Polyacrylamide Gels

For the majority of purposes, such as restriction mapping and sizing of cloned fragments, electrophoresis of DNA in horizontal agarose gels is perfectly adequate. As the size of the fragments of interest decreases to below 1000 base pairs (bp), however, the resolution deteriorates significantly, and an alternative is required. Polyacrylamide gels from 5% acrylamide upward provide a convenient system for analysis of fragments down to 10 bp. This type of gel is also very useful for checking for efficient blunt-end ligation of linkers if the linkers are labeled with 32 P.