OPTIMIZATION OF SEPARATION CONDITIONS IN THE SIZE-SELECTIVE CAPILLARYELECTROPHORETIC SEPARATION OF DNA FRAGMENTS

We report herein the development and initial evaluation of a computer program to determine optimal separation conditions for the size-select ive capillary electrophoretic (SSCE) separation of DNA fragments. The program uses the simplex method to optimize for those conditions which are most influential in these types of separations. Since base-pair e lectrophoretic behavior is largely independent of sequence, an empiric al equation can be used to predict DNA fragment mobility in methyl cel lulose running buffers. This allows column length and methyl cellulose concentration to be adjusted for optimal separation performance. The program generates a chromatographic response function which serves as a measure of the success of the separation. Reasonable correlation bet ween computational and experimental work is demonstrated, as are the i nfluences of adjustable parameters on the quality of the separation an d the function of the computational methods. Also presented is the abi lity of the program to function for samples that were not used in the initial data set. (C) 1996 John Wiley & Sons, Inc.