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How does PCR work?

The polymerase chain reaction (PCR) is a method to find the genes/DNA that make a particular plant genetically modified. The goal is to amplify specific sequences of DNA, for example the inserted herbicide gene. DNA is amplified by using specific short DNA sequences (called primers) that flank the region of the gene that is to be amplified. In other words, the primers allow us to find the "gene of interest" by latching onto the gene. At the onset of every PCR reaction we add DNA extracted (DNA extraction) from the GMO crop, primers, DNA polymerase and bases to a vial.

Remember from our biology classes that DNA is made up of two tightly bonded strands, turning in a helix. For our gene specific primers to work, we need to open or separate this DNA. A PCR thermocycler is a machine that heats the DNA helix so it opens (denatures). Once the DNA is separated into two strands, the temperature is dropped rapidly so that the primers can latch (hybridize) onto a single, complementary strand of DNA. This is the annealing step. The temperature of the thermocycler is raised again so that the DNA polymerase (an enzyme) produces more DNA. This is the extension step. A typical PCR program consists of 30-45 cycles of denaturing, annealing, and hybridizing steps. We then have enough of the gene/DNA synthesized for analysis.

Analysis: After the PCR reaction, the DNA from each vial is carefully pipetted onto a agarose gel. The gel is already stained with ethidium bromide so that the added DNA lights up under UV light. The charged DNA molecules "run" down the agarose gel and separate according to their size. For example, large DNA fragments stay on top of the gel, while smaller DNA fragments travel the bottom of the gel. A GMO plant would show a particular DNA fragment indicative of the gene, while a non-GMO plant would not show that DNA fragment on the gel. Please see a picture of a gel below:

Lane1: DNA marker with specific fragment sizes
Lane 2 non-GMO seed
Lane 3: GMO seed with two extra bands.


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