Basic Principles of RT-qPCR

Quantitative reverse transcription polymerase chain reaction, also called RT-qPCR, is used to detect and quantify RNA. Total RNA or mRNA is first transcribed into complementary DNA (cDNA). The cDNA is then used as the template for the quantitative PCR or real-time PCR reaction (qPCR). In qPCR, the amount of amplification product is measured in each PCR cycle using fluorescence. RT-qPCR is used in a variety of applications including gene expression analysis, RNAi validation, microarray validation, pathogen detection, genetic testing, and disease research.

RT-qPCR can be performed in a one-step or a two-step assay (Figure 1, Table 1). One-step assays combine reverse transcription and PCR in a single tube and buffer, using a reverse transcriptase along with a DNA polymerase. One-step RT-qPCR only utilizes sequence-specific primers. In two-step assays, the reverse transcription and PCR steps are performed in separate tubes, with different optimized buffers, reaction conditions, and priming strategies.

Figure 1. One-step vs. two-step RT-qPCR.

Learn more: One-step vs. two-step RT-qPCR

When designing a RT-qPCR assay it is important to decide whether to use total RNA or mRNA as the template for reverse transcription. mRNA may provide slightly more sensitivity, but total RNA is often used because it has important advantages over mRNA as a starting material. First, fewer purification steps are required, which helps ensure a more quantitative recovery of the template and a better ability to normalize the results to the starting number of cells. Second, by avoiding any mRNA enrichment steps, one can avoid the possibility of skewed results due to different recovery yields for different mRNAs. Taken together, total RNA is more suitable to use in most cases since relative quantification of the targets is more important for most applications than the absolute sensitivity of detection [1].

Explore: Total RNA isolation

To initiate reverse transcription, a short DNA oligonucleotide called a primer is required to anneal to the template RNA strand and provide reverse transcriptase a starting point for synthesis. Four different approaches can be used for priming cDNA reactions in two-step assays: oligo(dT) primers, random primers, or sequence specific primers (Figure 2 and Table 2). Often, a mixture of oligo(dT)s and random primers is used. Combining random primers and anchored oligo(dT) primers to diminish the generation of truncated cDNAs can help improve the reverse transcription efficiency and qPCR sensitivity.

Table 2. Primer considerations for the cDNA synthesis step of RT-qPCR

Explore: Primers for reverse transcription

Reverse transcriptase (RT) is the enzyme that makes DNA from RNA. Some reverse transcriptases have RNase activity to degrade the RNA strand in the RNA-DNA hybrid after transcription. If an enzyme does not possess RNase activity, an RNase H may be added for better qPCR efficiency. Commonly used enzymes include Moloney murine leukemia virus reverse transcriptase and Avian myeloblastosis virus reverse transcriptase. For RT-qPCR, it is ideal to choose a reverse transcriptase with high thermal stability, because this allows cDNA synthesis to be performed at higher temperatures, helping ensure successful transcription of RNA with high levels of secondary structure, while maintaining their full activity throughout the reaction to help produce higher cDNA yields.

Explore: Reverse transcription enzymes

RNase H activity degrades RNA from RNA-DNA duplexes to enable efficient synthesis of double-stranded DNA. However, with long mRNA templates, RNA may be degraded prematurely which can result in truncated cDNA. Hence, it is generally beneficial to minimize RNase H activity when aiming to produce long transcripts for cDNA cloning. In contrast, reverse transcriptases with intrinsic RNase H activity are often favored in qPCR applications because they can enhance the melting of RNA-DNA duplex during the first cycles of PCR (Figure 3).

Learn more: Reverse transcriptase properties

PCR primers for the qPCR step of RT-qPCR should ideally be designed to span an exon-exon junction, with one of the amplification primers potentially spanning the actual exon-intron boundary (Figure 4). This design can help reduce the risk of false positives from amplification of any contaminating genomic DNA, since the intron-containing genomic DNA sequence would not be amplified.

A minus reverse transcriptase control (“no RT” control) should be included in all RT-qPCR experiments to test for contaminating DNA (such as genomic DNA or PCR product from a previous run). Such a control contains all the reaction components except for the reverse transcriptase. Reverse transcription should not occur in this control, so if PCR amplification is seen, it is most likely derived from contaminating DNA.

1. Bustin S. (ed) (2004) A-Z of Quantitative PCR. IUL Biotechnology Series, International University Line, La Jolla, California.