Quantitation and purification of polymerase chain reaction products by high-performance liquid chromatography

Optimal Conditions for the Asymmetric Polymerase Chain Reaction for Detecting Food Pathogenic Bacteria Using a Personal SPR Sensor

We have been developing quick and simple system for detecting food-poisoning bacteria using a combination of an asymmetric PCR and a portable surface plasmon resonance (SPR) sensor. The system would be suitable for point-of-care detection of food-poisoning bacteria in the field of food industry. In this study, we established a novel method for quantifying the amplified forward (F) and reverse (R) chains of Staphylococcus aureus separately by high-performance liquid chromatography (HPLC). The concentration of single-stranded DNA amplicon excessively amplified, which is crucial for the system, could be calculated as the difference between those of the F- and R-chains. For the R-chain, a correction based on the F-chain concentration in the sample was used to obtain a more accurate value, because the determination of the R-chain concentration was affected by that of the coexisting F-chain. The concentration values were also determined by fluorescence imaging for electrophoresis gels of amplicons with FITC- or Cy5-conjugated primers, and they were in good agreement with the values by the HPLC. The measured concentration of the single-strand F-chain correlated well with the value of the SPR response against the probe that was a complementary sequence of the F-chain, immobilized on the sensor chip of the SPR sensor.

Real time detection of the tri5 gene in Fusarium species by lightcycler-PCR using SYBR Green I for continuous fluorescence monitoring

LightCycler technology combines rapid in vitro amplification of DNA with real time detection and quantification of the amount of target molecules present in a sample. The system enables a 35-cycle PCR with 32 samples do be completed in 45 min, including quantification and identification of the product. It is therefore well suited for routine analysis of large numbers of samples in quality control and for defining HACCP concepts. Based on PCR primers specific to the tri5 gene, a quantitative group specific assay was established for Fusarium species producing trichothecenes. In the assay, SYBR Green I was used as fluorescent dye enabling real time detection of PCR products. Characterisation of the amplicons was achieved by melting point analysis (85 +/- 0.1 degrees C). Nonspecific products such as primer dimers could readily be distinguished from the product by their lower melting points. Composition of the amplification buffer was optimised and various hot start methods were tested in order to achieve the highest sensitivity of the assay. Uracil DNA glycosylase was added to prevent amplification of nonspecific products due to DNA carryover. The spectrum of species detected was generally in accordance with the results found in conventional PCR using the Tox5 primer pair. Reproducibility in six parallel experiments of the assay was determined to be 98% in the range between 0.05 and 6 ng of purified Fusarium graminearum DNA. The assay was used to analyse 30 wheat samples contaminated with toxigenic Fusarium spp. Contamination ranged from 0% to 78% as revealed by mycological analysis, and this is compared with results from the LightCycler. This is the first report on the use of the LightCycler system in combination with SYBR Green I for the quantification and identification of fungal DNA in pure cultures and sample material.

A new PCR MIMIC strategy to quantify low mdr1 mRNA levels in drug resistant cell lines and AML blast samples

Determination of the MDR-phenotype in patients suffering from AML is an important hallmark of treatment outcome but is often complicated by technical problems in P-gp assessment. A PCR-MIMIC strategy was employed to construct PCR-fragments for a competitive and quantitative mdr1 reverse transcription-PCR-assay. Using K562 cells, which had been selected for drug resistance to the epipodophyllotoxin VP16, a stepwise increase of mdr1 levels depending on the concentration of VP16 was shown with the MIMIC technique. Comparison of mdr1 levels in drug selected K562 cells with the corresponding levels for P-gp and functional data indicated a mRNA threshold that has to be exceeded for the full expression of the MDR-phenotype. Subsequently mdr1 levels of 34 samples of de novo acute myeloid leukemia were determined with the PCR-MIMIC strategy. Ten patient samples could be identified with elevated mdr1 levels which were substantially lower than the levels observed in the MDR-cell line K 562 0.7 microM VP16. Outcome analysis revealed that eight of the ten patients had an unfavourable prognosis and did not achieve CR after induction chemotherapy. Coexpression of mdr1 and CD 34 was not associated with CR in all examined cases. Moreover all these patients had unfavourable cytogenetic aberrations. These data indicate a sensitive technique with applicability in patient material.