Dna Amplicon Analysis
Dna Amplicon Analysis - Related Videos
08:38
Targeted DNA Methylation Analysis by Next-generation Sequencing
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Cited by 83 •
2015
Bisulfite amplicon sequencing (BSAS) is a method for quantifying cytosine methylation in targeted genomic regions of interest. This method uses bisulfite conversion paired with PCR amplification of target regions prior to next-generation sequencing to produce absolute quantitation of DNA methylation at a base-specific level.
03:41
Agarose Gel Electrophoresis of DNA Amplicons Post PCR: A Method to Analyze Products of Multiplex PCR and Evaluate PCR Reaction Success
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2025
In this video, we demonstrate the separation of bacterial PCR-amplified DNA using agarose gel electrophoresis. Agarose gel functions as a molecular sieve, enabling the negatively-charged DNA to migrate based upon their size under an applied electric field.
08:57
Amplicon Sequencing using the Long-Read Sequencing Technologies
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2025
This protocol was optimized for targeted deep sequencing of 18 drug-resistance regions in Mycobacterium tuberculosis using a long-read sequencing platform, followed by analysis with a tuberculosis-specific bioinformatics pipeline designed for long-read data.
12:34
DNA Methylation: Bisulphite Modification and Analysis
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Cited by 75 •
2011
The gold standard for DNA methylation analysis is genomic sequencing of bisulphite converted DNA. This method takes advantage of the increased sensitivity of cytosine compared with 5-methylcytosine (5-MeC) to bisulphite deamination under acidic conditions. Unmethylated cytosines can be distinguished from methylated cytosines after PCR amplification of the target genomic DNA.
08:47
DNA Methylation Analysis
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2023
Methylation at CpG dinucleotides is a chemical modification of DNA hypothesized to play important roles in regulating gene expression. In particular, the methylation of clusters of methylation sites, called “CpG islands”, near promoters and other gene regulatory elements may contribute to the stable silencing of genes, for example, during epigenetic processes such as genomic imprinting and X-chromosome inactivation. At the same time, aberrant CpG methylation has been shown to be associated with...
FAQs
Primers define the boundaries of the locus that PCR will copy, so their sequence determines which genetic region enters the analysis. This targeted selection focuses sequencing and computational interpretation on a chosen marker rather than the entire DNA content of a sample. Consequently, primer design strongly influences whether the resulting data represent the intended organisms or genetic variation.
Primer specificity affects how accurately the amplified products reflect the intended target. If primers do not selectively capture the chosen locus, the resulting sequence dataset may provide a misleading picture of genetic variation, taxonomic identity, or community composition. Evaluating specificity is therefore essential when comparing samples or drawing conclusions from targeted biological measurements.
Sequencing reveals the nucleotide sequences present in the amplified products, while computational analysis interprets those sequences for a defined purpose. Depending on the study design, the results can identify sequence variation, assign taxonomic identities, or estimate the composition of a biological community. These outputs connect a targeted DNA measurement with questions about identity, diversity, and abundance.
Three factors highlighted by the method are primer specificity, amplification quality, and sequencing accuracy. Specific primers help focus the assay on the intended locus, successful amplification provides suitable material for downstream analysis, and accurate sequencing supports trustworthy interpretation. Weakness in any of these stages can affect taxonomic assignments, variation detection, or estimates of community composition.
A typical workflow begins by selecting a defined DNA region and designing or applying primers for that locus. PCR then amplifies the selected region, after which the products undergo sequencing. Computational analysis follows to interpret the sequences, such as detecting variation, assigning taxonomic identities, or evaluating community composition. Each stage contributes to the final biological conclusion.
Researchers may choose this approach when they need focused information from a selected genetic region across complex biological samples. Its targeted design can provide efficient and cost-effective insights for microbial profiling, species identification, pathogen surveillance, genotyping, or biodiversity studies. The approach is especially useful when the research question centers on a defined locus or marker.
In microbial studies, sequence data from selected loci can support profiling of organisms and estimation of community composition. In biodiversity research, the same strategy can help identify species or compare genetic sequences among samples. These applications allow researchers to examine complex biological material using targeted measurements, while interpretation remains dependent on amplification and sequencing quality.