OBJECTIVETo develop a rapid and effective method for genomic DNA extraction with magnetic bead-based semi-automatic system.

METHODSDNA was extracted from whole blood samples semi-automatically with nucleic acid automatic extraction system.The concentration and purity of samples was determined by UV-spectrophotometer. Orthogonal design was used to analyze the main effect of lysis time, blood volume, magnetic bead quantity and ethanol concentration on the DNA yield; also the 2-way interaction of these factors.

RESULTSLysis time, blood volume, magnetic bead quantity and ethanol concentration were associated with DNA yield (P<0.05), but no interaction existed. DNA yield was higher under the condition with 15 min of lysis time, 100 μl of blood volume, 80 μl of magnetic beads and 80 % of ethanol. A significant association was found between the magnetic bead quantity and DNA purity OD260/OD280 (P=0.008). Interaction of blood volume and lysis time also existed (P=0.013). DNA purity was better when the extracting condition was 40 μl of magnetic beads, 15 min of lysis time and 100 μl of blood volume. Magnetic beads and ethanol concentration were associated with DNA purity OD260/OD230 (P=0.017 and P<0.05), the result was better when magnetic beads was 40 μl and ethanol concentration was 80 %.

CONCLUSIONThe results indicate that the optimized conditions with 40 μl magnetic beads will generate higher quality of genomic DNA from the whole blood samples.

Analysis of Variance ; DNA ; blood ; isolation & purification ; Humans ; Immunomagnetic Separation ; methods

Brucella ; genetics ; isolation & purification ; DNA, Bacterial ; blood ; isolation & purification ; Polymerase Chain Reaction ; methods

OBJECTIVETo compare the detection rates of Epstein-Barr virus (EBV) DNA in the serum/plasma between apparently healthy adults (AHAs) and nasopharyngeal carcinoma (NPC) patients in attempt to evaluate the efficiency of EBV DNA assay for serodiagnosis of NPC.

METHODSThe plasma and serum were obtained from 58 AHAs and 66 untreated NPC patients. EBV DNA W-fragment was detected using nested ploymerase chain reaction (PCR). Immunoenzymatic assay for titration of IgA-VCA was also adopted.

RESULTSEBV DNA detection rate (84.85%) in the plasma/serum of 66 NPC patients was significantly higher than that (10.34%) in 58 AHAs. The sensitivity of plasma/serum EBV DNA assay (0.8485) was higher than that (0.8030) of titrating IgA-VCA (positive criterion >/= 1:40) though the specificities of these two tests were the same (0.8966). The correct rate, predictive value of a positive test, and Odds ratio of dual positivity (0.8387, 0.9792 and 141.0, respectively) were higher than those of single positivity either to plasma/serum EBV assay (0.5242, 0.7333 and 1.1423, respectively) or to IgA-VCA >/= 1:40 test (0.4839, 0.5385 and 1.0480, respectively).

CONCLUSIONThe EBV DNA detection in the plasma/serum using nested PCR may be a useful indicator for serodiagnosis of NPC.

Antigens, Viral ; blood ; DNA, Viral ; blood ; Herpesvirus 4, Human ; isolation & purification ; Humans ; Immunoglobulin A ; blood ; Nasopharyngeal Neoplasms ; diagnosis ; virology ; Serologic Tests

PURPOSE: The extraction of nucleic acid is initially a limiting step for successful molecular-based diagnostic workup. This study aims to compare the effectiveness of three automated DNA extraction systems for clinical laboratory use. MATERIALS AND METHODS: Venous blood samples from 22 healthy volunteers were analyzed using QIAamp(R) Blood Mini Kit (Qiagen), MagNA Pure LC Nucleic Acid Isolation Kit I (Roche), and Magtration-Magnazorb DNA common kit-200N (PSS). The concentration of extracted DNAs was measured by NanoDrop ND-1000 (PeqLab). Also, extracted DNAs were confirmed by applying in direct agarose gel electrophoresis and were amplified by polymerase chain reaction (PCR) for human beta-globin gene. RESULTS: The corrected concentrations of extracted DNAs were 25.42 +/- 8.82 ng/microLiter (13.49-52.85 ng/microLiter) by QIAamp(R) Blood Mini Kit (Qiagen), and 22.65 +/- 14.49 ng/microLiter (19.18-93.39 ng/microLiter) by MagNA Pure LC Nucleic Acid Isolation Kit I, and 22.35 +/- 6.47 ng/microLiter (12.57-35.08 ng/microLiter) by Magtration-Magnazorb DNA common kit-200N (PSS). No statistically significant difference was noticed among the three commercial kits (p > 0.05). Only the mean value of DNA purity through PSS was slightly lower than others. All the extracted DNAs were successfully identified in direct agarose gel electrophoresis. And all the product of beta-globin gene PCR showed a reproducible pattern of bands. CONCLUSION: The effectiveness of the three automated extraction systems is of an equivalent level and good enough to produce reasonable results. Each laboratory could select the automated system according to its clinical and laboratory conditions.
Automation/methods ; DNA/blood/*isolation & purification ; Humans ; Polymerase Chain Reaction ; *Reagent Kits, Diagnostic ; Reproducibility of Results

The aim of this study was to investigate the feasibility of using RASSF1A gene as a universal fetal marker in maternal plasma. Two methods of circulating cell-free fetal DNA (cffDNA) extracted from maternal plasma were compared. The better one was chosen for extraction of cffDNA in the 20 pregnant samples. The SRY gene and the RASSF1A gene treated with methylation-sensitive restriction enzyme were amplificated by RT-PCR and the PCR system was optimized. The results showed that the SRY gene was found in 11 out of the 20 pregnant samples, which was consistent with the postnatal sex. Using the optimized PCR system, the specifically amplified fetal-associated methylated RASSF1A gene was found after treatment with BstUI in 18 of the 20 pregnant samples, while the 2 samples failed in detection. It is concluded that the methylated fetal-specific RASSF1A gene can be used as a universal fetal marker for the presence of cffDNA in maternal plasma without fetal gender restrictions. So, it can be used for noninvasive prenatal diagnosis.
DNA ; isolation & purification ; Female ; Fetus ; Humans ; Pregnancy ; Prenatal Diagnosis ; methods ; Tumor Suppressor Proteins ; blood ; genetics

OBJECTIVE: To study DNA quantification and STR typing of samples pre-treated with pyramidon. METHODS: The blood samples of ten unrelated individuals were anticoagulated in EDTA. The blood stains were made on the filter paper. The experimental groups were divided into six groups in accordance with the storage time, 30 min, 1 h, 3 h, 6 h, 12 h and 24h after pre-treated with pyramidon. DNA was extracted by three methods: magnetic bead-based extraction, QIAcube DNA purification method and Chelex-100 method. The quantification of DNA was made by fluorescent quantitative PCR. STR typing was detected by PCR-STR fluorescent technology. RESULTS: In the same DNA extraction method, the sample DNA decreased gradually with times after pre-treatment with pyramidon. In the same storage time, the DNA quantification in different extraction methods had significant differences. Sixteen loci DNA typing were detected in 90.56% of samples. CONCLUSION Pyramidon pre-treatment could cause DNA degradation, but effective STR typing can be achieved within 24 h. The magnetic bead-based extraction is the best method for STR profiling and DNA extraction.
Aminopyrine/pharmacology* ; Blood Stains ; DNA/isolation & purification* ; DNA Fingerprinting ; Forensic Medicine ; Humans ; Polymerase Chain Reaction ; Reproducibility of Results ; Specimen Handling

OBJECTIVE: To establish a new method for RNA and DNA co-extraction from the same sample by TRIzol reagent. METHODS: After the aqueous phase which contained total RNA was removed by traditional TRIzol method, the values of pH of the interphase phase and organic phase were adjusted. The DNA was precipitated with ethanol and purified with DNA IQ system. The purified DNA was measured in quality and quantity. As the template, it was amplified and typed by PCR-STR. The data was compared with that extracted by traditional TRIzol method. RESULTS: The DNA extracted by this modified method showed a better result of quality and quantity than that by traditional TRIzol method and a good STR typing. CONCLUSION The modified TRIzol method is advisable and reliable to simultaneously extract both DNA and RNA from the same sample. It could be used for individual identification and paternity testing to satisfy the need of forensic science.
Blood Chemical Analysis/methods* ; DNA/isolation & purification* ; DNA Fingerprinting ; Forensic Medicine ; Guanidines/chemistry* ; Humans ; Hydrogen-Ion Concentration ; Phenols/chemistry* ; Polymerase Chain Reaction ; RNA/isolation & purification* ; Reagent Kits, Diagnostic

OBJECTIVE: To explore the feasibility of biological method to identify the biological attribute of samples at crime scene. METHODS: Thirty samples of ten blood stains, ten saliva stains and ten semen stains were selected, and all the samples were processed by the routine method and biomolecular method, respectively. Both RNA and DNA were isolated using DNA-RNA co-extraction technology and the mRNA was converted into cDNA using reverse transcription PCR (RT-PCR). Three pairs of specific primers were designed for blood stain, saliva stain and semen stain based on the different target genes in three specific tissues and the primers were amplified using real-time fluorescent quantitative PCR. The differences in these biological samples were evaluated by melting temperature (Tm) values and the size of the amplification fragment. RESULTS: The Tm values of blood stain, saliva stain and semen stain were (84.5 +/- 0.2) degrees C, (76.9 +/- 0.3) degrees C and (88.5 +/- 0.2) degrees C, respectively. The length of PCR fragments of them was 177bp, 134bp and 294bp, respectively. CONCLUSION Compared with the routine method, RT-PCR with real-time fluorescent quantitative PCR is highly specific, sensitive and reliable to identify the biological attribute of evidence, and can be potentially applied to determine evidence attribute in forensic practice.
Blood Stains ; DNA/isolation & purification* ; DNA Primers ; Forensic Medicine/methods* ; Genetic Markers ; Humans ; Male ; Polymerase Chain Reaction/methods* ; RNA/isolation & purification* ; RNA, Messenger/analysis* ; Saliva ; Semen ; Sensitivity and Specificity

To compare two different methods for extracting genomic DNA from cord blood and to evaluate their applications for HLA genotyping, the genomic DNA from 72 samples was extracted by guanidine hydrochloride (Gu * HCl) and modified guanidine hydrochloride, the DNA yield and purity were evaluated by spectrophotometry and detected by PCR with sequence-specific primers. The result showed that the genomic DNA was successfully isolated from whole blood by both methods. The modified Gu * HCl method used was better than Gu * HCl method as the modified method produces better quality of DNA and less ambiguous bands in PCR. It is concluded that modified Gu * HCl method has the advantages of low-cost, simple operation, high quality output and clear positive bands in HLA-genotyping, the modified method is optimal for extracting DNA from multiple samples of cord blood bank.
DNA ; blood ; isolation & purification ; Fetal Blood ; chemistry ; Genotype ; Guanidine ; HLA Antigens ; genetics ; Humans ; Polymerase Chain Reaction ; methods

Covalently closed circular DNA (cccDNA) is the existing form of the HBV DNA in the nucleus of host cells and also the original template of HBV replication; its long-term presence in the nucleus makes it difficult to be eliminated by current antiviral drugs; and it becomes the key factor of continuous HBV infection and relapse after antiviral suspension. Detection of HBV cccDNA is of great significance for further understanding the life cycle of HBV and providing guidance for antiviral treatment. This article aims to review the detection and its clinical significance to the advancement of researches on hepatitis B virus cccDNA.
DNA, Circular ; blood ; genetics ; DNA, Viral ; blood ; genetics ; Hepatitis B virus ; genetics ; isolation & purification ; Hepatitis B, Chronic ; virology ; Humans ; Polymerase Chain Reaction ; methods