Nested PCR is a technique that involves two rounds of PCR amplification to increase the specificity and sensitivity of DNA detection.

Why are controls important in PCR?

Controls help validate the results by ensuring that the amplification is specific and that there is no contamination.

How does nested PCR improve specificity?

By using two sets of primers, nested PCR reduces the chances of amplifying non-target sequences, leading to more accurate results.

What are the key components of the PCR master mix?

The master mix typically includes DNA polymerase, dNTPs, primers, and a buffer solution.

Can nested PCR be used for other applications?

Yes, nested PCR can be adapted for various applications in molecular biology, including genetic testing and pathogen detection.

Nested-PCR to Detect a Specific Viral Genomic Sequence

JoVE Encyclopedia of Experiments

Biological Techniques

0 views • 3:20 min • July 8th, 2025

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Nested polymerase chain reaction, nested PCR, can selectively amplify specific gene sequences.

To detect a target viral sequence, begin with a master mix containing outer primers complementary to a larger DNA region containing the targeted viral sequence, dNTPs, and thermostable DNA polymerase in an appropriate buffer.

Add double-stranded viral DNA, extracted from the virus-infected cells, to this mix. Transfer the tube to a thermocycler; run the first PCR cycle.

During denaturation, the double-stranded DNA produces two single-stranded templates. At an appropriate annealing temperature, outer primers bind to their corresponding target sequences. Later, DNA polymerase extends the primers using dNTPs, producing large amplicons, containing the specific sequence within the amplified DNA.

Transfer these amplicons to a new tube. Supplement with a fresh master mix containing inner or nested primers targeting a smaller, more specific sequence within the larger amplified DNA. Run the second PCR.

During the second PCR, the DNA strand denatures. After denaturation, the nested primers bind the target sites on the single-stranded template, followed by polymerase-mediated primer extension.

Repeat the second PCR cycle several times to exclusively amplify the targeted viral sequence.

Analyze the PCR product to visualize the smaller amplicons, confirming the presence of the specific viral sequence.

Retrieve the necessary reagents and keep them on ice in a clean room until ready to use. When ready, thaw and vortex the reagents. Next, prepare 48 microliters of first-round PCR mix for each sample in a 1.5-milliliter centrifuge tube, as outlined in Table 2 of the text protocol, and divide the reaction mix into 0.2-milliliter PCR tubes.

In a PCR workstation in a template room, add a 2-microliter sample of the cDNA into the first-round PCR mix. Include two microliters of CVS-11 cDNA as a positive control and two microliters of double-distilled water as a negative control. Then, transfer the sealed tubes into a PCR thermal cycler and cycle using the parameters listed in Table 3 of the text protocol.

To begin, prepare 48 microliters of second-round PCR mix for each sample in a 1.5-milliliter centrifuge tube, as outlined in Table 4 of the text protocol, and divide the reaction mix into 0.2-milliliter PCR tubes. Add two microliters of the first-round PCR product into the second-round PCR mix. Include double-distilled water as a negative control for this round of PCR. Then, perform PCR thermal cycling using the parameters listed in Table 3 of the text protocol.