October 31, 2014

PCR and Gel Electrophoresis

Today in the lab, we worked on our agrose gel electrophoresis, which separates the dyed DNA products on the basis of size and charge. This way we can  visualize and analyze the PCR product, to determine the presence and size of the PCR product. Below are the two substances that we used to create our gel. First we added 1 gram of the agrose powder, and the added 100 ml of the solution. We also added Ethidium Bromide , which will help us "see" where the DNA is in our gel. Before we let our gel set, we added a tool to one side of the gel, which will create small groves in the gel where we will be able to insert our DNA. It is presumably a "starting place" for our DNA.

After we let our gel set, we added a blue dye to our genes to make it easier for us to see the movement of the DNA across the gel. I did 4 practice insertions with just a mixture of dye and water. Then I was able to insert the real DNA's more efficiently. To insert the DNA's we used a pipette, which is pictured below, to precisely measure and imbed the empty groove with the DNA. We had to be mindful not to puncture the gel, or else that would effect the way the DNA would move across the gel. So once all the genes were in place, we connected our gel box to the power supply, where a positively charged cord was connected to one end of the box, and a negatively charged cord was connected to the other. the charges coming from the power supply box is also separating the Hydrogen to one side, and the Oxygen to the other. And since there is double the amount of Hydrogen than Oxygen, we saw more bubbles on the right side of the gel box than on the left. DNA is also negatively charged, so the DNA was being attracted and pulled by the positively charged side, which is what is makig the DNA move across the gel.

To  interpret our results, we look at the movement of the genes through the gel. Smaller DNA strands will move quicker and further, while larger DNA will move a lot slower. This is because smaller genes have  higher velocity and because they are so small they are able to move through the open holes in the gel with ease, while the larger genes are not traveling through the open holes as quickly. This whole process is called, gel electrophoresis, and through this process we can actually physically cut out our purified genes from the gel.

The picture up top is a picture of pipette, which is a tool that is used to measure and transfer precise amounts of substances.

This picture shows the power supply connected to the gel box by the two charged wires. If you look closely you can see the blue dye at the top the gel box. As time passes we will see bars form in a ladder formation, which will show the movment of the dyed genes.

• Polymerase Chain Reaction (PCR) article: http://www.nature.com/jid/journal/v133/n3/full/jid20131a.htm