DNAOPT: a computer program to aid optimization of DNA gel electrophoresis and SDS-PAGE

Several methods and computer programs have been developed for estimating the size of DNA fragments from gel electrophoresis. However, methods are lacking that may facilitate in optimization of gel conditions. In this article, a computer program called DNAOPT is described, which was developed to assist researchers in tuning the gel conditions of gel electrophoresis. The DNAOPT program fits the reciprocal of the migration distance vs. the size of the DNA fragments using the hyperbolic regression 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 under various conditions (i) to determine the relationship between the gel conditions (temperature, buffer concentration, electric field strength, etc.) and optimization parameters; (ii) to demonstrate gel electrophoresis curves and optimization parameters graphically; and (iii) to represent the optimizing parameters at different gel conditions in tabular form. The above-mentioned program options aid the users in selecting optimum gel conditions by running the gel repeatedly under various conditions in which the agarose concentration, electric field strength, temperature, buffer concentration and so on are varied in a systematic way for each set of gel conditions. Similarly, this program can also be used to optimize gel conditions of sodium dodecyl sulfate polyacrylamide gel electrophoresis.