Gel electrophoresis is a forensic method used to compare different DNA and identify similarities between them. This is useful in maternity and paternity tests, identification of person responsible for a crime, and can also be used to find out the cause of an infectious disease including foodborne disease outbreak. DNA samples are usually very small in quantity. Hence, they are hard to analyze. To amplify samples to analyzable amounts, they are generally cloned using a method known as polymerase Chain Reaction (PCR). The technique involves heating the DNA sample to separate (or denature) the double helix followed by adding a lab-made primer at the ends of the separated DNA strands. These primers are used to “prime” a certain enzyme called DNA polymerase to copy the rest of DNA bases to complete the DNA strand. Consider if I ask you what the capital of France is and tell you that it starts with the letter “P”. You are then primed to tell me the other letters in the word i.e. “aris” for the word Paris. In this general sense, the enzyme is primed by the primer to complete the rest of the letters on the DNA sequence.
Once the copies of the DNA is made, it is denatured again, primers re-added, and more DNA copied. This process is repeated until there are millions to billions of copies available for analysis.
When there is enough DNA copied, the sample can then be digested using restriction enzymes (nucleases). Restriction enzymes are bacteria-based enzymes used by bacteria to cut up viral DNA that may infect it. These enzymes have the ability to identify specific sequences of nucleotides along the DNA strand and cut them out. Restriction enzymes do the same thing with DNA, producing DNA fragments that contain the same sequence of nucleotides and hence the same size. This enables size separation using electrophoresis.
In electrophoresis, different samples of digested DNA are placed side-by-side in wells made of agarcose gel. An electric current is applied to the wells, causing the DNA to move from the negative side of the electrode to the positive side. Larger DNA will move slower, producing bands that are closer to the anode (negatively charged end) while smaller DNA fragments will be able to travel farther and closer to the cathode (positive electrode). Since DNA are electrophoresed side-by-side, the distance the bands travel in the gel can be easily compared. Bands that line up with each other are the same genetic sequence and hence show relationship with each other.
In summary, DNA is collected and then amplified by PCR. Restriction enzymes are then added to cut the DNA at specific regions and create fragments of different sizes. Finally, electrophoresis is done to separate DNA by size. We find relationship between samples by looking for bands located at the same position in the gel.