title: Quantitative and qualitative validations of a sonication-based DNA extraction approach for PCR-based molecular biological analyses.
abstract: The aim of this study was to comprehensively validate the sonication-based DNA extraction method, in hope of the replacement of the so-called 'standard DNA extraction method' - the commercial kit method. Microbial cells in the digested sludge sample, containing relatively high amount of PCR-inhibitory substances, such as humic acid and protein, were applied as the experimental alternatives. The procedure involving solid/liquid separation of sludge sample and dilution of both DNA templates and inhibitors, the minimum templates for PCR-based analyses, and the in-depth understanding from the bias analysis by pyrosequencing technology were obtained and confirmed the availability of the sonication-based DNA extraction method.
authors.affiliation: State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, China.
authors.forename: Xiaohu
authors.initials: X
authors.lastname: Dai
authors.affiliation: State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, China.
authors.forename: Sisi
authors.initials: S
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, China. Electronic address: lining@tongji.edu.cn.
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.affiliation: State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, China.
authors.forename: Han
authors.initials: H
authors.lastname: Yan
mesh_terms: D001419:Bacteria / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012722:Sewage / Q000382:microbiology*; D013010:Sonication / Q000379:methods*
chemical_list: D004269:DNA, Bacterial; D012722:Sewage
keywords: DNA extraction; Dilution; Pyrosequencing; Sonication