Anomalous electrophoresis of deoxyribonucleic acid restriction fragments on polyacrylamide gels

A detailed study has been made of the polyacrylamide gel electrophoresis of DNA restriction fragments obtained from two plasmids, pBR322 and p82-6B. Variables studied were molecular weight, gel concentration, temperature, and electric field strength. The retardation coefficients of the larger fragments (greater than 800 base pairs) were independent of molecular weight. The retardation coefficients of the smallest fragments (less than or equal to 300 base pairs) were proportional to Mr1/3, and therefore to the mean geometric radii of the fragments. The logarithm of the relative mobility of all fragments was also proportional to Mr1/3. The anomalous migration of certain fragments on polyacrylamide gels was found to be "transportable" into fragments generated by different restriction enzymes. Anomalous migration was enhanced at lower temperatures and disappeared upon increasing the temperature. A fragment which migrated anomalously slowly migrated even more anomalously when dimerized; dimerizing a normally migrating fragment resulted in the normal migration of the dimerized fragment. Anomalously migrating fragments were found to be localized in distinct regions of the pBR322 circle.