GEL MATRICES IN N-METHYLFORMAMIDE FOR SEPARATION OF DNA FRAGMENTS

Abstract

Capillary gel electrophoresis is a powerful method for separation of DNA fragments. Usually, water based poly-(acrylamide) gels are employed. In order to release compressions due to intra-molecular base pairing within DNA fragments, it is often necessary to incorporate denaturing agents (e.g. urea, formamide) and/or to operate at elevated temperatures. In this work we have studied the performance of gels in non-aqueous solvents. Poly(dimethylacrylamide) gels in both formamide and N-methyl formamide were prepared. The formamide based gels showed a poor stability under normal capillary electrophoresis conditions,1 rapidly developing voids at moderate electric field strengths. However, N-methyl formamide based gels were more stable and could be employed for electrophoretic separations of oligonucleotides. Sieving properties similar to those of regular water-based poly(acrylamide) gels, were observed. Non-aqueous gels without any additives had a considerable denaturing power, in fact, comparable to water-based gels containing 7 M urea. Interesting influences on the separation selectivity when utilizing different concentrations of N-methyl formamide were observed, which are discussed in the paper.