Effects of ethidium bromide and SYBR Green I on different polymerase chain reaction systems

Evaluation of a homemade SYBR green I reaction mixture for real-time PCR quantification of gene expression

Real-time PCR is an accurate method that can be used for the quantification of specific DNA molecules. Here we provide a protocol for SYBR Green I in real-time PCR applications using plastic reaction tubes. We report that SYBR Green I is alkali labile and once degraded inhibits the PCR. In our optimized protocol, diluted aliquots of SYBR Green I remain stable for at least two weeks. We also evaluated different cDNA synthesis protocols for the quantification of multiple genes from the same cDNA preparation. The best result was obtained with cDNAs synthesized by OmniScript reverse transcriptase from 2.5 microg total RNA using oligo d(T)18 primers. The cDNA reactions could be diluted 1:25, allowing the quantification of up to 125 different medium expressed genes of Arabidopsis. Extension times ranged between 20 and 40 bp/s for accurate quantification of PCR products up to approximately 400 bp in the Rotor-Gene 2000 system. Using our optimized real-time PCR protocol, the reproducibility and amplification efficiency was high and comparable to a commercially available SYBR Green I kit. Furthermore, the sensitivity allowed us to quantify 10-20 copies of mRNA and dsDNA. Thus, the protocol eliminates the need for expensive pre-made kits.

PCR as a diagnostic and quantitative technique in veterinary parasitology

Over the past 15 years, there has been a dramatic evolution in molecular approaches to study parasites and parasitic diseases. Many of these advancements have been brought about through the development of new applications of the polymerase chain reaction (PCR). Enhancements in sensitivity that can be achieved using PCR now permit scientists to investigate changes at the level of a single cell, far below what is often needed for parasite-derived applications. PCR has had a substantial impact on advances made in the areas of parasite systematics and epidemiology, immunology and host-parasite interactions, recombinant DNA vaccine development and most recently, the analysis of whole genomes either through directly sequencing the DNA, the analysis of expressed sequence tags (ESTs) or through the rapidly growing field of functional genomics. This paper, however, focuses on the application of PCR methodology to parasite detection and differentiation, and the diagnosis of disease. Specific attention is given to advances provided by multiplex PCR, fluorescence-based "real-time" PCR, and the utilization of PCR as a quantitative technique.

Determination of Helicobacter pylori cagA, vacA genotypes with real-time PCR melting curve analysis

OBJECTIVES

genotypes of Helicobacter pylori are the focus of interest because they play a prominent role in mucosal injury. The purpose of this study was to determine cagA and vacA genotypes of H. pylori using real-time polymerase chain reaction (PCR) method with a double strain DNA binding SYBR Green I.dye, and to compare this with those of two immunohistochemical methods.

METHODS

forty-three paraffin-embedded biopsy tissue samples were examined by histology, epidermal growth factor receptor (EGFR), proliferating cell nuclear antigen (PCNA) immunohistochemistry and melting curve analysis of real-time PCR.

RESULTS

the presence of cagA gene was associated with a significantly higher frequency of gastritis (P=0.003) than that of vacA gene with intestinal metaplasia (P=0.045). Significant difference was found between the presence of cagA gene and EGFR expression in intestinal metaplasia cases in comparison with cagA negative samples (P=0.0418). Statistically significant difference was detected between increased cell proliferation and the presence of gastritis.

CONCLUSIONS

this method seems to be suitable for H. pylori genotype determination. Sensitivity, speed and simplicity are key areas in the development of PCR assays for H. pylori. Results supported the notion that infection with cagA positive H. pylori strain causes more augmentated cell proliferation in the stomach mucosa.