Gels and pipet tips and sunburns (oh my!)

2/6/12
Today I had a lot of fun in the lab. Dr. Kirchman started off by telling me about another PCR he had run. In order to sequence the DNA, we are sending only the section of the DNA that we need to be sequenced rather than the whole thing. However, we need to make sure that this section of DNA is in good enough quality to be sequenced. Dr. Kirchman tested some of the PCR product and while there was some DNA there, it was very faint and not a bright band of good quality DNA. Today, we ran a larger amount of the PCR product (20 microliters) through a gel in order to hopefully get better quality DNA. This was no ordinary gel though. This was a gel that my own two hands created without Dr. Kirchman even in the lab with me :D I even avoided microwave explosions and air bubbles in my gel, and was deemed worthy of a thumbs up by Dr. Kirchman thanks to my nice work. While Dr. Kirchman quickly loaded some DNA samples from our latest three PCRs (choosing the samples with the highest quality DNA), I restocked the boxes that held pipet tips, improving my hand eye coordination in the process (I've noticed a trend where everything that has to do with DNA is usually tiny).
Then came the really fun part. After running the DNA through my gel, Dr. Kirchman and I used the big machine that produced ultraviolet light (that's where I got the pictures of the previous PCR's a couple posts below) to cut out the DNA from the gel. While I didn't quite have the hand eye coordination to participate (as I told Dr. Kirchman, I was never good at the game Operation as a kid) I donned a pair of protective goggles and stared captivated at the glowing strips of DNA along with how easy Dr. Kirchman made it seem to cut out minuscule blocks of DNA. Dr. Kirchman had to be very careful while cutting out the DNA, however, and make sure his sleeves and gloves were covering his skin, because it is possible for the UV rays to give you a sunburn.
After cutting out the DNA strips, Dr. Kirchman and I used a kit to clean up the DNA, or at least started to use the kit until we ran out of time. We first had to incubate the blocks of DNA and a mixture from the kit in order to melt down the gel.  The blocks of DNA were put in test tubes with 150 microliters of the mixture and then put in a little boat-type tray that would float in a machine that would keep the water at 50 degrees celcius. Special tubes that come with the kit contain filters that contain things that will cause the DNA to bind  to them, but allow the other stuff to filter through. Hopefully, when we are done with the kit, we will be left with some good quality DNA ready to be sequenced.