Heather came in on Saturday to check on our DNA library that we had left on the heat block overnight. She discovered that the liquid at the bottom of the tubes was brown. It seemed like some of the liquid had evaporated. This was not good, so she vortexed them and hoped for the best.
We spent Tuesday morning washing our beads. The beads are magnetic and can attach to the DNA. Using magnetic beads is great for ancient DNA because they prevent tiny DNA fragments from escaping. Washing the beads was very visually pleasing because they were brown as opposed to clear. Moreover, we got to use the magnetic rack, which has magnets that pull the beads to one side of the tube. We would start by adding a wash buffer to the tube with the magnets and the solution would be brown. We would then place the tube on the magnetic rack and watch the solution gradually become transparent (video) with a small ball of beads huddling by the magnet.
In the afternoon we made a qPCR to see if our DNA library was successful. Unfortunately it was not. The samples started amplifying at around 25-28 cycles and looked no different than the qPCR blank. Last year the samples started amplifying at 20 cycles. It is possible something went wrong with the qPCR machine, but we guessed that the library didn’t work because of Saturday’s discovery of the brown liquid and evaporation. Luckily, a heated lid for the heat block would prevent evaporation and the formation of brown liquid. We are ordering one now.
On Wednesday afternoon we did a DNA demonstration with Miller Farm’s kids’ camp. We showed 7 kids ages 5-8 strawberry DNA and let them help us mash the strawberries. We added dish soap and Gatorade to break down the strawberry cells and then pineapple juice, which has enzymes that break down proteins. Finally we added cold alcohol to separate out the DNA. After letting the test tube sit, we could see a layer of white, goopy stuff that was the DNA.
We then let the kids see their own DNA. After swishing Gatorade in their mouths for two minutes, they spit into test tubes. We added dish soap and cold alcohol and showed the kids how to use a transfer pipettes to add the pineapple juice. The kids loved using the transfer pipettes. While waiting for the DNA to separate out, we had the kids make DNA bracelets. They got to choose a DNA sequence from options such as human, butterfly, cobra, flesh-eating microbe, and cockroach DNA. They had to read the sequence and put colored beads corresponding to A,T,C, and G on one string and then figure out the corresponding base pairs to put on the other string. After they finished the bracelets their DNA had separated from the Gatorade and soap. We put the DNA in a little test tube and attached the test tube to a string to make a necklace. It was a nice change of pace to be outside with the kids, and the kids seemed to enjoy learning about DNA.