Amplicon

An amplicon is a DNA or RNA sequence that has been amplified. This amplification is typically achieved through polymerase chain reaction (PCR) or other nucleic acid amplification techniques. Amplicons represent the product of this amplification process, meaning they are multiple copies of a specific DNA or RNA region.

The targeted region for amplification is determined by the primers used in the amplification reaction. Primers are short, synthetic oligonucleotides that are complementary to the sequences flanking the target region. During amplification, these primers bind to the template DNA or RNA and initiate the copying process, leading to the exponential increase in the number of copies of the sequence between the primers.

Amplicons are widely used in molecular biology and diagnostics. They serve as the basis for various applications, including:

• DNA sequencing: Amplicons can be sequenced to determine the exact nucleotide sequence of a specific region of DNA.
• Genotyping: Amplicons can be used to identify specific genetic variants or polymorphisms.
• Gene expression analysis: Amplicons derived from RNA (cDNA) can be quantified to measure the levels of gene expression.
• Diagnostic assays: Amplicons can be used to detect the presence of specific pathogens or genetic markers associated with disease.

The size of an amplicon can vary, but it is typically in the range of a few hundred to a few thousand base pairs. The size is primarily determined by the distance between the primer binding sites on the template DNA or RNA. Optimizing amplicon size can be important for the efficiency and accuracy of downstream applications. Factors affecting amplicon creation and quality include primer design, polymerase selection, and PCR cycling parameters. Contamination is a major concern as it can lead to false positives or inaccurate results.