Gel electrophoresis with discontinuous rotation of the gel: An alternative to gel electrophoresis with changing direction of the electrical field

Abstract

AbstractWhen using agarose gel electrophoresis to fractionate linear DNA longer than 40–60 kilobases (kB), improved resolution by length has previously been obtained by periodically and discontinuously changing the direction the electrical field. This change of the field's direction was accomplished by alternately activating two sets of electrodes. However, some of the procedures used produce inhomogeneous electrical fields and with all of these procedures it is comparatively difficult to either change the angle between the two directions of the field or suppress formation of local pH gradients. To overcome these problems, a procedure is presented for changing the direction of the electrical field by rotating the gel. During agarose gel electrophoresis, a commercially available stepping motor and indexer are used to periodically rotate a gel on a circular disk within a conventional, horizontal, submerged gel electrophoresis apparatus. Because of the homogeneous field used, DNA forms comparatively sharp, undistorted bands. The previously achieved improved resolution of 40–166 kB, linear, double‐stranded DNÀ has been achieved here by rotating the gel. Dependence of length resolution on both the angle of rotation and the temperature has been measured.