Selectivity of the separation of DNA fragments by capillary zone electrophoresis in low-melting-point agarose sol

The properties of solutions of low-melting-point agarose for the separation of DNA fragments were investigated as a function of temperature and applied voltage. Giddings et al.'s definition of the selectivity of the separation according to molecular size, S = (d In u)/(d ln p), where u is the electrophoretic mobility and p the number of base pairs, was adopted as a suitable phenomenological description of the capability of the system to separate DNA fragments. It was found that the selectivity of separation in 1% agarose has its maximum at about 600 base pairs, decreases with increasing applied voltage and is a complex function of temperature. No decrease in selectivity was observed even at temperatures above the melting point. The high selectivity of agarose at these temperatures is probably evidence for the positive effect of conformational entropy of DNA molecules. A development of an apparatus for thermostating the capillary within the range 10-70°C that allowed the measurements to be performed is reported.