The Dynamics of DNA Gel Electrophoresis

Gel electrophoresis of DNA has improved greatly in the last decade, mostly owing to the invention of pulsed-field gel electrophoresis (1 ). This has enabled the separation of DNA more than two orders of magnitude longer than what was previously possible (2 –4 ). This chapter will review what is understood about the microscopic behavior of DNA undergoing electrophoresis, which has reached a stage of sophistication allowing one to predict the mobility of a specified DNA molecule in a given system. The author’s own research will be emphasized, much of the most elaborate calculations done in collaboration with Thomas L. Madden (5 –9 ) and J. D. Reger (10 ). It is hoped that this chapter will be comprehensible to most biologists, and to this end, it eschews a complete technical treatment of the subject that can be found in the cited literature.