Science Buddies: "Ask an Expert"

Hi!

I want to use PCR to amplify the DNA and then use Gel Electrophoresis to determine whether the Alu gene is present. But, which option would leave me the smallest room for possible error - if I obtain the DNA through cheek swab, fingerprint, rinsing with a saline solution, or do you have any other suggestions?


Thanks in advance for your time and help!

Hi adriahna_jae,

Rinsing with a saline solution should work fine. You will want to really swish it around in your mouth, and if you are really worried that you will not get enough DNA you could gently scrape the sides of your tongue a cheek with your teeth while you are at it. Do not hurt your self while doing this! Harvesting of old cells will not require much scraping. See the beginning section of the following protocol- http://biology.arizona.edu/sciconn/less ... ro/dna.htm

Good luck,
Emily

Ms. Emily,
Thank you so much for your help and the article!

I have another question though, if I'm running gel electrophoresis on DNA that is about 300bp what concentration of agarose gel should I make? Do you know of any other websites that have like a "template" for how much % concentration the gel should be based on the size of the DNA?

Thank you

Hi Adriahna,

For separating linear DNAs by agarose gel electrophoresis, the rule is the smaller the DNA piece the higher the concentrated of agarose. I have never seen a 'template' for calculating agarose percentage to separate a particular size range of DNA. If you are just looking for one small fragment of 300 bp then a 1.5 to 2.0% gel will work just fine.

Are you running a DNA size standard in one lane along with your sample on the gel? It's a good idea to do that in order to check the size of your fragment. Also, when you run the gel adjust the voltage so that your current doesn't exceed 75-80 mA so it doesn't get too hot.

If you are including bromophenol blue as your running dye in the loading buffer, remember that this dye runs about as fast as a 300 bp piece of DNA, so you can use it as a marker for when to stop the electrophoresis and look at your gel.

Lastly, gel electrophoresis uses DC electricity at voltages and currents that can be high enough to give you a bad shock, so be especially careful around the chamber when it is running.

Good luck, and do let us know how your run comes out.

Best wishes,

SciB