Development and application of a new pulsed-field gel-electrophoresis process based on molecular dynamics

Separation of DNA molecules according to size is an important step in molecular biology. Pulsed-field gel electrophoresis is the main experimental tool for carrying out this separation, and is one of the techniques used in the human genome megaproject. We have developed a new approach to the separation of biological molecules by choosing electric field pulses to activate specific stretching and relaxation modes of charged molecules moving through a gel. In our process, a particular sequence of electric field pulses provides the "code" (specific instructions) for the migration of a DNA fragment of a given size to a designated position on the gel. The entire pulse train (for the duration of the experiment) can then be used to predetermine the separation pattern of a large number of DNA molecules of different sizes. This allows, for example, for the movement of only nucleic acid fragments below a certain size through the gel, and simplifies DNA preparation techniques. We have developed new hardware and software to carry out this process in a routine fashion in a laboratory environment. In this paper we review the theoretical concepts that form the basis of this separation technique, and discuss its applicability to human chromosomes and proteins.