Evaluation of optimized DNA extraction methods from bacteria and whole blood for Polymerase Chain Reaction

Abstract

The quality of DNA extracted from clinical samples is crucial for the accuracy and reliability of Polymerase Chain Reaction (PCR) in molecular diagnostics. This study compares five optimized DNA extraction methods—Phenol Chloroform (PC), Phenol Chloroform with column (PCC), Boiling (BM), Boiling with Ethanol Precipitation (BME), and a Commercial Kit (CK)—for their efficacy in isolating DNA from bacterial suspension and whole blood from human. The evaluation focused on DNA yield, purity, PCR compatibility, and cost-effectiveness, with a particular emphasis on their use in resource-limited settings. DNA concentration was highest with BM for bacterial samples and with PC for blood samples, though the CK method offered better reproducibility. Significant differences in DNA purity were observed across methods, particularly in E. coli and blood samples. PCR amplification was successful for most methods; however, DNA extracted from CK method failed to amplify E. coli DNA. Time and cost analyses revealed that while the PC was the most cost-effective, it was also the most time-consuming. Conversely, the CK method was the fastest but most expensive. This study underscores the importance of selecting DNA extraction methods that align with the specific needs of molecular biology applications, balancing cost, time, and performance in resource-limited environments.