What is a probe-free PCR-based diagnostic assay?

Posted by Jack on December 8, 2022

PCR-based diagnostic assays are used to identify microorganisms, and are also useful in the diagnosis of diseases. There are two different types of PCR-based assays: RT-PCR and RCA. These assays are based on the use of primers and probes to amplify the DNA of an organism. However, a probe-free PCR-based assay, such as PCR-free ELISA, does not require the presence of a primer or probe.


RT-PCR, or reverse transcription quantitative polymerase chain reaction, is a probe-free PCR-based diagnostic assay used for detection of nucleic acids and RNA pathogens. It has become a first line diagnostic test for many microorganisms. Several types of chemistries and instruments can be used to perform RT-qPCR.

For RT-qPCR, a double-stranded cDNA serves as the first step. This cDNA is then fed into a standard PCR-based amplification process. This amplification process is repeated over and over to produce new copies of viral DNA. A fluorescent dye is then measured by the machine to determine the presence of the virus.

RT-qPCR can be performed with a wide range of protocols. However, the performance of one assay may vary considerably from that of another. These differences are caused by different reagents and instruments, and by the target of interest.

There are two types of RT-qPCR, one-step and two-step. Both have similar steps, but the difference is in the sequence of these steps. A one-step assay involves reverse transcription and qPCR amplification of a target sequence, whereas a two-step assay separates RT-qPCR and qPCR.

The two-step approach results in a lower mismatch between the primers and the target of interest. This is important because a mismatch can affect the sensitivity of an RT-qPCR assay. Assays that perform poorly often do so because of the effect of a mismatch. Increasing the concentration of a mismatched reverse primer can improve sensitivity.

In addition to detecting specific genetic material of a pathogen, RT-qPCR can also detect changes in gene expression after treatment with inhibitors. This is useful for investigating gene expression changes upon treatment with model systems.

In order to understand a virus's development, it is important to know what has been a past infection. In some cases, a virus can develop without symptoms. Therefore, other methods are needed to track past infections.


RCA (Rolling Circle Amplification) is a method for clonally amplifying RNA or DNA. It is used in a variety of applications, such as the diagnosis of infectious human diseases. The advantages of RCA include low cost, easy diagnosis, and rapid amplification of viral genomes.

The RCA technique can be applied to a wide range of targets, including microRNAs, RNA, and cytokines. In addition, it is very sensitive to a small amount of pathogen.

One benefit of RCA is that it requires minimal instrumentation and can be performed in a mixed biological environment. RCA is often resistant to contaminants, and can replicate thousands of complementary template copies. RCA may also be used as a surveillance tool for infectious disease.

Recently, the GenMark ePlex(r) SARS-CoV-2 test was developed to automate the process of amplification. The test integrates RNA extraction, amplification, and analysis. It is a point-of-care diagnostic device that provides rapid, accurate, and cost-effective detection of SARS-CoV-2.

The assay was based on the principle of rolling circle amplification. The rolling circle structure was employed as the basis for amplification, and a polymerase enzyme copied a circular DNA template. RNA ligation was conducted simultaneously with the rolling circle amplification reaction. The test was tested against different concentrations of SARS-CoV-2 target molecules.

The total assay time was about 100 minutes. The results were directly quantitative and could be displayed graphically. Several outliers were removed from the data. The assay was able to detect SARS-CoV in liquid phase. The SARS-CoV-2 outbreak required urgent medical attention. The RCA assay is also more sensitive than other methods, as shown in the figure.

The use of CRISPR/Cas-based systems has expanded the scope of diagnostic devices. These devices use a single guide RNA to bind to a target sequence. The RNA is then cleaved by the CRISPR/Cas enzyme to generate a signal. This technology is a powerful tool in nucleic acid diagnostics, and offers a potential alternative to POC RT-PCR devices.

T-blocker assay

Using probe-free PCR-based diagnostic assays could reduce the cost and time required for screening, as well as increase overall testing capacity. The use of such a test may relieve the burden on central laboratories. Using a probe-free assay, however, may also lead to a false negative result. Therefore, the presence of PCR inhibitors needs to be assessed and identified.

PCR inhibitors can have an effect on a variety of sample types. A number of different methods have been developed to remove them from samples.

Several substances can inhibit amplification, including polyphenols, heparin, and proteins. These substances can be introduced into the PCR mixture during preparation, or they can be present in the sample. The resulting inhibition can lead to a decrease in sensitivity. The inhibitors also cause false negative results.

RT-PCR is a powerful investigative tool in life sciences. It is used to determine the presence of pathogens in samples. It is also used for molecular cloning of genes of interest.

A real-time assay for coronaviruses is a strong contender for rapid diagnostics in public health emergencies. It is highly sensitive and selective, and it can be scaled up onto large automated qPCR machines. It is also useful for the detection of hepatitis A virus in seafood. RNA-extraction-free protocols, which are compatible with existing PCR-based testing pipelines, could help expand the ability to screen for COVID-19.

A number of commercial kits are available to perform PCR-based diagnostics. Unfortunately, they do not include human gene targets, which can affect the quality of the test results. This is why standardized controls are recommended for substantiating diagnostic PCR results.

Standardized controls can be used to compare the efficiency of various PCR protocols. This allows for the identification of PCR systems that are less susceptible to inhibitors.

Dye-based real-time PCR

Using a dye-based real-time PCR diagnostic assay to analyze samples is a fast and easy way to evaluate a large number of samples. Compared to conventional methods, real-time PCR is more sensitive. It can also be performed on high-throughput equipment. This type of assay can be used to detect the presence of pathogens and amplify nucleic acids.

A dye-based real-time PCR diagnostics assay uses a fluorescent dye that binds to double stranded DNA (dsDNA) during amplification. The fluorescence intensity increases proportionally to the amount of dsDNA that is present. The dye's fluorescence is measured by a qPCR instrument.

Choosing the detection chemistry depends on the characteristics of your experiment. You may need to consider primer specificity, as well as the stability of the primers. You can use multiple primer pairs with the same fluorescent dye.

The standard qPCR assay includes intercalating and hydrolysis probes. New-generation intercalating dyes have improved melt curve analysis and have lower background noise.

Real-time PCR can be conducted in a thermal cycler, which uses the physicochemical properties of nucleic acids to rapidly chill and heat the sample. This allows amplification of the sample and simultaneous detection of changes in the amplicon concentration.

This assay is not suitable for tracking past infections. It is also not accurate for detecting the presence of multiple targets. You will need other methods to investigate the spread of a virus.

When you use a dye-based real-time RT-PCR diagnostic assay, you will need to use two different sequence-specific primers for each GOI. You will also need to consider the primer's stability in order to ensure accurate results.

Variation can be caused by a variety of factors. Amplification efficiency is one of the major contributors to variations. However, if you account for the reverse transcription control, you can make sure that the overall results are similar.


Various clinical institutions have developed molecular diagnostic assays to detect SARS-CoV-2. Several assays are available for commercial use. RT-PCR, real time RT-PCR and dual target assays are available for clinical diagnosis of SARS-CoV-2. A dual-target assay consists of two or more specific target genes. A single-target assay is more susceptible to sequence variation. The WHO requires two genomic targets for diagnostic tests.

As an alternative to duplex assays, probe-based assays are used to maximize sample throughput and decrease unexpected discrepancies. TaqMan probe-based assays enable multiplexing of viral specific target probes with human control probes. This assay is highly sensitive and accurate.

A study was conducted to identify and evaluate mutations in the SARS-CoV-2 virus. The study consisted of 26 clinical specimens that were investigated using primer sets for the human RNase P gene. The assay was validated by real-time RT-PCR. The results showed no non-specific amplification products. The assay is capable of detecting human nucleic acid and is highly specific for SARS-CoV-2.

The study also evaluated the sensitivity of SARS-CoV-2 in vitro synthesized RNA. The results showed a reduction in Ct value with increasing concentration of RNA. In addition, the assay was found to be 100% specific.

A SARS-CoV-2 probe-free PCR-based assay has been developed to improve detection of the SARS-CoV-2 virus. This assay has similar detection limit to RT-PCR. It has been tested on five popular real-time PCR cyclers. It provides quick, portable, and unbiased analysis of raw qRT-PCR data. It has a turnaround time of less than 2 hours. This assay is ideal for clinical diagnosis of SARS-CoV-2. It is also applicable to the clinical management of the COVID-19 outbreak.

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