GEL-ELECTROPHORESIS OF END-LABELED DNA .2. DYNAMICS AND DETRAPPING INPULSED FIELDS

A theory for field-inversion gel electrophoresis of a flexible polyele ctrolyte bearing an uncharged bulky label at one end is described, and the evolution of the mobility with chain length, field strength, fric tion of the label, and the duration of the forward and reverse pulses is predicted. A new critical size, N-detrap, is introduced, and its va lue calculated. It increases roughly linearly with the duration of the reverse pulses. Chains smaller than N-detrap are detrapped by reverse pulses, and may have a high mobility, whereas chains larger than N-de trap are not trapped, and have a very small mobility. This leads to an increase of the mobility (as compared with constant held) in a given range of sizes, and to a strong selectivity around N (detrap). Dependi ng on the parameters, numerous other effects, including a secondary mo bility plateau and band inversion, may appear. The corresponding regim es are predicted and discussed. All predictions are qualitatively cons istent with available experimental data. We use them to suggest effici ent conditions for the development of pulsed-field trapping electropho resis, a possible tool for improved DNA sequencing. In particular, we recommend using a ramping of pulse times, with a constant ratio of for ward to reverse time in the range 3 to 5.