Investigation on the influence of the ROX reference fluorescence correction on the real-time quantitative RT-PCR assessment for Nrf2 mRNA

Abstract

Objective To evaluate the normalized correction effect of the ROX reference fluorescence on the real-time quantitative RT-PCR assessment for the Nrf2 mRNA.Methods The Taq-man probe was utilized in the real-time quantitative RT-PCR method to assess the Nrf2 mRNA; The reaction specificity of the Nrf2 PCR products obtained from the rat cDNA was assessed using gel electrophoresis and sequencing identification.The PCR calibrators with different concentrations varied at 10 gradients(from 2.0 × 109 to 2.0 × 100) were prepared for real-time quantitative RT-PCR assessment,and then the influence of the ROX reference fluorescence correction on the linear range of the PCR standard curve was investigated experimentally.The recombinant plasmids with different concentration levels(e.g,high,medium or low concentration) were assessed by the real-time RT-PCR and 20 replicate measurements were performed for all the samples in both intra- and inter-assays.The repeatability differences of both the inter- and intra-assays were analyzed systemically with/without the ROX reference fluorescence correction.Results The primers and probes required for Nrf2 mRNA real-time quantitative RT-PCR assessments were constructed,and the reaction system and conditions were also established.The length of the amplified fragment agreed well with the expected length(122 bp),and the sequencing analysis showed the amplified fragment was verified by the sequencing identification.After applying the ROX reference fluorescence correction,the linear range ofthe PCR standard curve was measured as 2.0 × 109 -2.0 × 100 copies/μl(R2 ＞ 0.99),which was 100times wider than that measured without ROX reference fluorescence correction(2.0 × 109 - 2.0 × 102copies/μl,R2 ＞ 0.99).Without the ROX reference fluorescence correction,the intra-assay CVs of the Ct value were measured as 4.1%,2.7% and 2.1% for the recombinant plasmids with high-,medium-,and low-level concentration,respectively.The inter-assay CVs of the Ct value were 4.3% 、3.0% 、2.4%.By contrast,with the ROX reference fluorescence correction,the intra-assay CVs of the Ct value became 0.7%,0.5%,0.4% and the inter-assay CVs of the Ct value turned to 1.0%,0.8% and 0.7%.The discrete degree of the Ct value with the correction was lower than that without the correction.The intra- and interassay Ct values of the high- and medium-level samples exhibited statistic significance for the measurements with/without the correction.In the high-level group,the t values of the intra- and inter-assays were 4.843 and 2.566,with P＜0.05.In the medium-level group,the t values of the intra- and inter-assays were 4.293 and 4.423,with P＜0.05.However,no statistic significance was observed the low-level group(the t values of the intra- and inter-assays were 0.753 and 1.279,with P ＞.0.05).Conclusions The utilization of the ROX reference fluorescence in the real-time quantitative PCR assessment for Nrf2 mRNA could widen the linear range of the standard PCR calibration curve and improve the repeatability of the assessment,which should be quite helpful for accurately assessing the expression level of the Nrf2 mRNA. Key words: NF-E2-related factor 2; Reverse transcriptase polymerase chain reaction; Succinimides; Rhodamines