Our “Standard” RT-PCR Mastermix for RNA-Based Detection

In this blog post, we delve into the intricacies of RNA-based assays, focusing on the detection capabilities enhanced by multiplexed kits in Standard RT-qPCR mastermixes. We will explore how kits from PCRassays.com are revolutionizing RNA detection, the challenges they address in RT-qPCR, and the specific enhancements they bring to multiplex detection in molecular diagnostics.

scientific laboratory scene depicting a team of researchers working on RT-qPCR

Overcoming RT-qPCR Challenges

RT-qPCR is a powerful tool in molecular diagnostics, however, it is not without its challenges. Understanding and addressing these challenges is key to enhancing the efficiency and accuracy of RNA-based assays.

Mutation Rates and Primer Design

One of the most significant challenges in RT-qPCR is accounting for the mutation rates in RNA, especially in rapidly evolving viruses. Precision in primer design is critical to ensure assays remain effective even as genetic sequences evolve. Using PanelPlex-Consensus, from DNA Software, allows for organization of all relevant accessions in our inclusivity playlist to be confirmed by ThermoSleuth for detection in the PCRassay kit.

Sensitivity and Specificity

Achieving high sensitivity to detect low levels of RNA targets without compromising specificity is a delicate balance. This is particularly important in diagnostic tests, where false negatives or positives can have significant implications.

Sample Size and Quality

Often, only limited sample material is available, and the quality of RNA can be variable. Techniques to amplify even small quantities of RNA reliably are crucial in such scenarios.

Technological Solutions

Advances in technology have led to innovative solutions to these challenges. Enhanced enzyme formulations, optimized reaction conditions, and advanced instrumentation all play a part in overcoming the limitations of traditional RT-qPCR. Namely, our multiplexed kits at PCRAssays.com have been formulated for our “Standard  RT-qPCR mastermix”.  We have worked with the enzymology team at Fortis to custom the formulation our mastermix and enhancing performance by:

  • minimizing primer dimer artifacts
  • optimizing Cq performance
  • optimizing RT activity

Minimizing Primer Dimer Artifacts in RT-qPCR

A key aspect of optimizing RT-qPCR assays involves minimizing primer dimer artifacts. Primer dimers occur when primers bind to each other instead of the target RNA, leading to non-specific amplification. This can significantly impact the accuracy and efficiency of RT-qPCR assays. Using ThermoSleuth to account for the appropriate scoring metrics of mismatch thermodynamics, we can confirm hybridization to the intended targets and be certain that there are no off target effects or unintended hybridization.

Understanding Primer Dimer Formation

Primer dimers form due to complementary base pairings at the ends of primers. This unwanted interaction can be exacerbated by factors like primer concentration and reaction conditions. All PCRassays have been designed using DNA Software, which has uncovered five different mechanisms for primer dimer formation, and as a result our assays have superior performance in

Impact on Assay Reliability and Resultant Benefits

Enhanced RT activity leads to higher yield and quality of cDNA, which in turn improves the sensitivity and specificity of the RT-qPCR assays. It ensures that even low-abundance RNA targets are accurately quantified, which is especially crucial in diagnostics and quantitative gene expression studies.

The team at PCRassays.com and DNA Software have further refined the overall effectiveness of RT-qPCR assays through our database driven and “best-in-class” software, formulated mastermix and wide portfolio of assay offering for infectious disease detection by qPCR to deliver more value to our customers.