Microelectrophoresis for the separation of DNA fragments

Abstract

A methodology has been developed which significantly reduces the linear dimension necessary for the electrophoretic separation of DNA fragments and oligonucleotides. DNA fragments are rapidly separated into compact, resolvable microscopic banding patterns which can be detected using a high‐resolution electronic imaging system. Separations can be carried out in either capillary tube or thin‐layer (slab) microgel formats of one centimeter or less in length. The complete separation of all eleven fragments (1353 to 72 base pairs) of the ΦX174 DNA/ HaeIII restriction ladder was achieved in a total running distance of less than 2 mm and in less than 2 min. The observed band widths for the larger fragments (1353–603 bp) ranged from 18 to 25 μm, with the intermediate and smaller fragments (310 to 72 bp) ranging from 30 μm to 60 μm. The ethidium bromide‐stained microgels were analyzed using an epifluorescent microscope combined with an intensified charged coupled device imaging system. In other experiments, single‐base resolution of fluoresceinated oligonucleotides in the 20–30 nucleotide range was demonstrated. DNA sequencing may be possible with further optimization. This new methodology departs from the conventional gel formulations and electrophoretic procedures used for the separation DNA fragments. High voltage gradients and the use of highly concentrated and crosslinked homogeneous polyacrylamide gels effects the rapid separation of DNA fragments in very short distances. Analysis of the microgels with proteins of known size (Stokes radius) indicates that separations are occurring in gels with pore sizes close to the diameter of double‐stranded DNA. In the extreme, single‐stranded oligonucleotides could be effectively separated in gels with pore diameters that completely excluded double‐stranded oligomers of the same length.