Gel matrices in N-methylformamide for separation of DNA fragments

Capillary gel electrophoresis is a powerful method for separation of DNA fr agments. Usually, water based poly(acrylamide) gels are employed. In order to release compressions due to intra-molecular base pairing within DNA frag ments, it is often necessary to incorporate denaturing agents (e.g. urea, f ormamide) and/or to operate at elevated temperatures. In this work we have studied the performance of gels in non-aqueous solvents. Poly(dimethylacryl amide) gels in both formamide and N-methyl formamide were prepared. The for mamide based gels showed a poor stability under normal capillary electropho resis conditions, rapidly developing voids at moderate electric field stren gths. However, N-methyl formamide based gels were more stable and could be employed for electrophoretic separations of oligonucleotides. Sieving prope rties similar to those of regular water-based poly(acrylamide) gels, were o bserved. Non-aqueous gels without any additives had a considerable denaturi ng power, in fact, comparable to water-based gels containing 7 M urea. Inte resting influences on the separation selectivity when utilizing different c oncentrations of N-methyl formamide were observed, which are discussed in t he paper.