Conventional Nested PCR Assays vs. Real-Time PCR Assays

What's the Difference?

Conventional Nested PCR assays and Real-Time PCR assays are both widely used molecular techniques for amplifying and detecting specific DNA sequences. However, they differ in several aspects. Conventional Nested PCR involves two rounds of amplification, where the first round uses outer primers to amplify the target DNA, and the second round uses inner primers to amplify a specific region within the first amplicon. This technique requires gel electrophoresis to visualize the amplified products. On the other hand, Real-Time PCR, also known as quantitative PCR, allows for the detection and quantification of DNA in real-time. It uses fluorescent probes or DNA-binding dyes to monitor the amplification process, enabling the measurement of DNA concentration during the exponential phase of amplification. This real-time monitoring eliminates the need for gel electrophoresis and provides more accurate and quantitative results.


AttributeConventional Nested PCR AssaysReal-Time PCR Assays
PrincipleAmplification of DNA in multiple cyclesAmplification of DNA in real-time
Detection MethodGel electrophoresisFluorescence detection
QuantificationNot suitable for quantificationQuantitative results can be obtained
SpeedSlower compared to real-time PCRReal-time results are obtained during amplification
SensitivityLess sensitive compared to real-time PCRHigh sensitivity due to continuous monitoring
SpecificityHigh specificityHigh specificity
CostRelatively lower costHigher cost due to specialized equipment
ApplicationsResearch, diagnosticsResearch, diagnostics, quantification

Further Detail


PCR (Polymerase Chain Reaction) is a widely used molecular biology technique that allows for the amplification of specific DNA sequences. Over the years, different variations of PCR have been developed to suit various research and diagnostic needs. Two commonly used PCR methods are Conventional Nested PCR Assays and Real-Time PCR Assays. While both techniques serve the purpose of DNA amplification, they differ in several aspects, including their principles, workflow, sensitivity, specificity, and applications.


Conventional Nested PCR Assays and Real-Time PCR Assays are based on the same fundamental principle of DNA amplification through repeated cycles of denaturation, annealing, and extension. However, the key difference lies in the detection method. In Conventional Nested PCR, the amplified DNA is visualized after the completion of the PCR reaction using gel electrophoresis. On the other hand, Real-Time PCR allows for the continuous monitoring of DNA amplification in real-time using fluorescent probes or DNA-binding dyes.


The workflow of Conventional Nested PCR involves two rounds of amplification. In the first round, outer primers are used to amplify the target DNA region of interest. Then, a small aliquot of the first-round PCR product is used as a template for the second round, where inner primers amplify a smaller, specific region within the first amplicon. This nested approach increases the specificity of the assay. In contrast, Real-Time PCR is a one-step process where amplification and detection occur simultaneously. The reaction mixture contains all the necessary components, including primers, probes, and DNA polymerase, allowing for the real-time monitoring of DNA amplification.

Sensitivity and Specificity

Conventional Nested PCR assays are known for their high sensitivity and specificity. The nested approach increases specificity by targeting a smaller region within the initial amplicon, reducing the chances of non-specific amplification. However, the sensitivity of Conventional Nested PCR can be affected by the risk of contamination during the multiple handling steps involved in the assay. On the other hand, Real-Time PCR assays offer excellent sensitivity and specificity as well. The continuous monitoring of DNA amplification allows for the detection of even low copy numbers of the target DNA. Additionally, the closed-tube system minimizes the risk of contamination, making Real-Time PCR a preferred choice for diagnostic applications.


Conventional Nested PCR assays have been widely used in research settings for the detection and identification of various pathogens, including viruses, bacteria, and parasites. The ability to amplify specific DNA regions makes it suitable for genotyping, sequencing, and phylogenetic studies. However, the labor-intensive nature of the assay limits its application in high-throughput diagnostic settings. Real-Time PCR assays, on the other hand, have revolutionized the field of molecular diagnostics. The rapid and quantitative nature of Real-Time PCR makes it ideal for the detection and quantification of pathogens, genetic mutations, gene expression analysis, and viral load monitoring. Its ability to provide results in real-time has made it an invaluable tool in clinical laboratories.

Advantages and Limitations

Conventional Nested PCR assays offer several advantages. They are relatively simple and cost-effective, requiring basic laboratory equipment. The nested approach enhances specificity, and the use of gel electrophoresis allows for the visualization of the amplified DNA. However, the assay is time-consuming, labor-intensive, and prone to contamination. Real-Time PCR assays overcome many of these limitations. They provide rapid results, eliminate the need for post-PCR processing, and offer higher throughput capabilities. The closed-tube system reduces the risk of contamination, and the quantitative nature of the assay allows for accurate quantification of the target DNA. However, Real-Time PCR assays are more expensive due to the requirement for specialized equipment and fluorescent probes or dyes.


Conventional Nested PCR assays and Real-Time PCR assays are both valuable tools in molecular biology and diagnostics. While Conventional Nested PCR offers high sensitivity and specificity, it is labor-intensive and time-consuming. Real-Time PCR, on the other hand, provides rapid and quantitative results, making it ideal for diagnostic applications. The choice between the two methods depends on the specific requirements of the experiment or diagnostic test. Researchers and clinicians must consider factors such as sensitivity, specificity, workflow, cost, and throughput when selecting the appropriate PCR assay for their needs.

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