Capillary zone electrophoresis of DNA fragments in a novel polymer network: poly(N-acryloylaminoethoxyethanol).

Migration of DNA fragments in the 51 to 21226 bp size range has been investigated by capillary zone electrophoresis in entangled solutions of linear poly(N-acryloylaminoethoxyethanol) from 8 to 16%. Plots of log mobility vs. log size (in base pairs, bp) clearly evidence three different migration regimes: according to Ogston (i.e. as spherical globules) up to 200 bp, reptation without stretching up to 3-4000 bp and reptation with partial stretching for larger fragments. Guidelines on the % polymer to be used for optimum resolution can be obtained from plots of peak spacing (in seconds per base pair) vs. % of polymer in solution and from standard plots of peak resolution vs. % polymer. An optimum linear poly(N-acryloylaminoethoxyethanol) concentration, allowing for good resolution of most fragments, from small to large, is found in the range 10% to 12% polymer (as opposed to conventional polyacrylamide, where a sharp maximum is obtained at 6% polymer). It is hypothesized that in situ polymerization allows for formation of a large distribution of polymer sizes, 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. Due to the fact that the novel monomer is 500 times more resistant to hydrolysis and more hydrophilic than acrylamide, its polymeric solutions allow repeated sample injections (> 35) with minimal absolute standard deviations (of the order of +/- 3%). No carry-over nor sample precipitation at the injection port is experienced with the new matrix composed of poly(N-acryloylaminoethoxyethanol).