An equation for DNA electrophoretic mobility in agarose gels.

Assignment of molecular weight to DNA fragments on the basis of electrophoretic mobility in agarose gels is complicated by nonlinearity of the relationship between mobility and molecular weight. Graphical methods that linearize sigmoidal curves provide a simplified description of the mobility function when applied to normalized mobility data. This description is valid over a wide range of molecular weights. Linear duplex molecules of lengths ranging from 118 to 169,200 base pairs were electrophoresed at voltage gradients of 1 to 6 V/cm through horizontal slab gels ranging from 0.2 to 1.6% agarose. A logit transformation of the mobility graphed versus the logarithm of molecular weight, analogous to a Hill plot of enzyme kinetics, is a straight line. Changes in the voltage gradient or gel composition alter the position but not the slope or linearity of the data plotted by this method. The logistic representation is compared with the conventional graph of log molecular weight versus mobility, with the graph of molecular weight versus reciprocal mobility, and with Probit analysis of the mobility function. Parameters were determined for one equation that accurately describes DNA mobility as a function of the three tested variables. Curves are presented that are useful in predicting fragment length, migration, resolution, and gel performance.