title: Evaluation of six methods for extraction and purification of viral DNA from urine and serum samples.
abstract: The sensitivity and reliability of PCR for diagnostic and research purposes require efficient unbiased procedures of extraction and purification of nucleic acids. One of the major limitations of PCR-based tests is the inhibition of the amplification process by substances present in clinical samples. This study used specimens spiked with a known amount of plasmid pBKV (ATCC 33-1) to compare six methods for extraction and purification of viral DNA from urine and serum samples based on recovery efficiency in terms of yield of DNA and percentage of plasmid pBKV recovered, purity of extracted DNA, and percentage of inhibition. The most effective extraction methods were the phenol/chloroform technique and the silica gel extraction procedure for urine and serum samples, respectively. Considering DNA purity, the silica gel extraction procedure and the phenol/chloroform method produced the most satisfactory results in urine and serum samples, respectively. The presence of inhibitors was overcome by all DNA extraction techniques in urine samples, as evidenced by semiquantitative PCR amplification. In serum samples, the lysis method and the proteinase K procedure did not completely overcome the presence of inhibitors.
authors.affiliation: Department of Public Health and Microbiology, Virology Unit, University of Turin, Italy.
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Bergallo
authors.forename: Cristina
authors.initials: C
authors.lastname: Costa
authors.forename: Giorgio
authors.initials: G
authors.lastname: Gribaudo
authors.forename: Sonia
authors.initials: S
authors.lastname: Tarallo
authors.forename: Sara
authors.initials: S
authors.lastname: Baro
authors.forename: Alessandro
authors.initials: A
authors.lastname: Negro Ponzi
authors.forename: Rossana
authors.initials: R
authors.lastname: Cavallo
mesh_terms: D001739:BK Virus / Q000235:genetics / Q000302:isolation & purification; D002623:Chemistry Techniques, Analytical / Q000379:methods; D004279:DNA, Viral / Q000097:blood* / Q000652:urine*; D006801:Humans; D019800:Phenol / Q000737:chemistry; D016133:Polymerase Chain Reaction / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D058428:Silica Gel; D012822:Silicon Dioxide / Q000737:chemistry
chemical_list: D004279:DNA, Viral; D019800:Phenol; D058428:Silica Gel; D012822:Silicon Dioxide