Optimization and the Robustness of BOX A1R PCR for DNA Fingerprinting Using Trout Lake E. coli Isolates

The rep-PCR DNA fingerprint technique using BOX A1R primer was investigated. DNA fingerprints were generated from Escherichia coli strains isolated from human, duck, goose, gull, and heron sources. Optimization tools (use of restriction enzymes, BSA, DMSO, and storage buffer) were used in an attempt to generate clear, well-defined DNA fingerprints from the Escherichia coli isolates. Initial studies revealed that although there were distinct fingerprint patterns emerging from the use of BOX A1R primer, the bands were faint and difficult to resolve. The use of optimization tools did not significantly improve the quality of the bands or the reproducibility of the method except for BSA. BSA seemed to improve the reproducibility of the method. This failure in optimizing the rep-PCR DNA fingerprinting technique may be due to the formation of primer dimers. Further research is required into this problem.