Evaluation and Optimization of Methodsfor the DNA Extraction from Drinking water

Abstract

Tap water qualification is quite important for human health, the DNA extraction from tap water is a current challenge since the microbes inside is limited. This article aims to evaluate various DNA extraction methods and based on the different reagents or procedures and their influence to do some modifications for better extraction. DNA yield, purity and fragment size are three evaluation criteria for extracted DNA, while the reproducibility and operational convenience are also taken into evaluation for each method. According to the results, extraction methods could be recommended for different situations. It is concluded that commercial kits show better reproducibility in yield and quality aspects and more convenient in operation than phenol/chloroform based methods. The modified method which adds enzymatic and chemical lysis method into standard commercial kit protocol, shows the highest DNA yield. The phenol/chloroform based methods give the best average purity, especially for protein contaminants. Considering the fragment size, the DNA extracted from Quick-DNA HMW MagBead kit (ZYMO Research, USA) distributes widest with more HMW DNA among all methods. The results presented here suggest that that the DNA extraction method of choice for tap water samples should be the modified Quick-DNA HMW MagBead kit.