DAF optimization using Taguchi methods and the effect of thermal cycling parameters on DNA amplification

Taguchi methods, which are widely applied in industrial process design, were used to optimize DNA amplification fingerprinting (DAF). Quadratic loss functions that penalize deviations from prediction values and L-9 (3(4)) and L-18 (3(8)) orthogonal arrays revealed effects and interactions of amplification reaction components and thermal cycling parameters. Analysis of variance (ANOVA) decomposed the contribution of individual factors to the experimental response (amplification yield and product number), while verification experiments established that optimum conditions were predictable, verifiable and reproducible. While several amplification components (primer, magnesium and enzyme) conditioned the amplification reaction, annealing temperature and time were the only important thermal cycling contributing factors. The Taguchi strategy defined a robust and transportable amplification protocol based on high annealing temperatures (typically 48 degrees C) and primer concentrations (typically 8 mu M), which can be applied to the fingerprinting of a wide range of DNA templates of plant and fungal origin. The general strategy of robust experimental design holds potential as an optimization fool for other methods in molecular biology.