DNA marker in PCR 


AffiDYE® DL15000 DNA Marker

DNA markers : 

DNA markers are commonly used in PCR (Polymerase Chain Reaction) as a tool to detect and analyze specific DNA sequences. They serve as reference points or indicators within the amplified DNA fragments to help researchers identify and characterize genetic variations or specific regions of interest. 

Here's how DNA markers are used in PCR : 
  • Marker selection:

Choose a DNA marker that is suitable for your specific research or application. Common types of DNA markers used in PCR include microsatellites, restriction fragment length polymorphisms (RFLPs), and single nucleotide polymorphisms (SNPs). The marker selected should have variations or polymorphisms that allow for distinguishing between different samples or individuals.

  • PCR primer design:

Design specific primers that flank the target region containing the DNA marker. These primers are typically designed to anneal to the regions adjacent to the marker sequence. The primers are essential for amplifying the DNA region of interest during PCR.

  • PCR amplification:

Perform the PCR amplification using the designed primers and the DNA template, which may include genomic DNA or cDNA, depending on the experiment. The PCR reaction mixture typically contains the DNA template, primers, nucleotides (dNTPs), a DNA polymerase enzyme, and a suitable buffer.


  • Gel electrophoresis:

After PCR amplification, analyze the amplified DNA fragments using gel electrophoresis. Prepare an agarose gel with appropriate concentration and run the PCR products alongside a DNA marker of known fragment sizes. The DNA marker is loaded into one or more lanes of the gel to serve as a size reference.

  • Visualization and analysis:

Apply an appropriate DNA stain, such as ethidium bromide or a fluorescent dye, to the gel to visualize the DNA bands. DNA markers typically produce distinct bands of known sizes, acting as reference points. By comparing the sizes of the amplified PCR products with the DNA marker bands, you can estimate the sizes of the PCR products and identify any size variations or polymorphisms.

  • Interpretation:

Analyze and interpret the results based on the research objectives or application. DNA markers can be used to determine the presence or absence of specific genetic variations, assess genetic diversity, identify genetic traits, or validate the success of PCR amplification.