MOVEMENT OF DNA FRAGMENTS DURING CAPILLARY ZONE ELECTROPHORESIS IN LIQUID POLYACRYLAMIDE

Migration of DNA fragments in the 51-23 130 base pair (bp) size range was investigated by capillary zone electrophoresis in solutions of linear polyacrylamide of concentration from 4 to 10%. Plots of log (mobility) vs. log [size (in bp)] clearly indicate three different migration regimes: according to Ogston (i.e., as spherical globules) up to 200 bp, reptation-without-stretching up to 3000-4000 bp and reptation with partial stretching for larger fragments. Guidelines on what percentage of the polymer should be used for optimum resolution can be obtained from plots of peak spacing (in seconds per base pair) versus percentage of polymer in solution and from standard plots of peak resolution versus percentage of polymer. An optimum linear polyacrylamide concentration, allowing for good resolution of most fragments, from small to large, is found at a level of 6% polymer. It is hypothesized that in situ polymerization allows for the formation of a large distribution of polymer sizes (centred at M(r) approximate to 100 000), thus facilitating simultaneous separation of short and long DNA fragments based on the principle that shorter polyacrylamide chains will sieve shorter DNA fragments and vice versa.