DNAOPT - A COMPUTER-PROGRAM TO AID OPTIMIZATION OF DNA GEL-ELECTROPHORESIS AND SDS-PAGE

Several methods and computer programs have been developed for estimati ng the size of DNA fragments from gel electrophoresis. However, method s are lacking that may facilitate in optimization of gel conditions. I n this article, a computer program called DNAOPT is described, which w as developed to assist researchers in tuning the gel conditions of gel electrophoresis. The DNAOPT program fits the reciprocal of the migrat ion distance vs. the size of the DNA fragments using the hyperbolic re gression method and computes the hyperbolic parameters such as signal, flatness and capacity (optimization parameters). The program further manipulates these parameters obtained by running gel electrophoresis u nder various conditions (i) to determine the relationship between the gel conditions (temperature, buffer concentration, electric field stre ngth, etc.) and optimization parameters; (ii) to demonstrate gel elect rophoresis curves and optimization parameters graphically; and (iii) t o represent the optimizing parameters at different gel conditions in t abular form. The above-mentioned program options aid the users in sele cting optimum gel conditions by running the gel repeatedly under vario us conditions in which the agarose concentration, electric field stren gth, temperature, buffer concentration and so on are varied in a syste matic way for each set of gel conditions. Similarly, this program can also be used to optimize gel conditions of sodium dodecyl sulfate poly acrylamide gel electrophoresis.