Increased resolution of large DNA fragments by a two dimensional pulse field gel electrophoresis

Abstract

An electrophoretic method for separating well-defined large DNA fragments from higher and lower molecular weight molecules is described. It combines in a first dimension either a contour-clamped homogeneous electric field or an orthogonal field alternation gel electrophoresis technique followed by a perpendicular field inversion gel electrophoresis (FIGE) in a second dimension. A complex migration curve after the FIGE run is obtained depending on the applied pulse time, the forward/reverse ratio being kept constant at 3. However, a part of the curve appears as a straight line where the migration is inversely proportional to the molecular weight of the DNA fragments. In this zone, DNA molecules are particularly well separated from other fragments. When the forward pulse time increases, this part is displaced toward the higher molecular weights. Moreover a simple relationship between the middle part of the straight line and forward pulse time has been established.