DNA UFO catcher by team handai

   This section will mainly outline the annealing process, as most of the experiments done were concerning analysis, materials and methods for analytical methods are separated and inserted into analysis. During the annealing process, we had to decide the most suitable temperature and buffer. This optimal condition was achieved after several trials that is going to be explained in this page.

   Gel electrophoresis was performed to approximate the completion of the folding of the structure. As DNA has a phosphate group that is negatively charged, when put in a gel flowing with electricity, they will move from the negative terminal to the positive terminal. Larger structures will move more slowly and thus will have closer distance to the well after a certain amount of time current is applied. This technique was performed after every change in annealing condition.

All of the Gel electrophoresis was conducted by a standard procedure as follows:

1. 1. 3.5g of agarose gel powder was dissolved in 50ml of 10xTBE buffer.
2. 2. The solution was heated in microwave untill the agarose completely dissolved.
3. 3. The heated mixture was then poured into the plastic case and was left for 40 minutes at 4℃ (holes/wells were made to put          the samples).
4. 4. The hardened gel was set on the electrophoresis chamber.
5. 5. 2µL of sample was mixed with 2µL of loading dye.
6. 6. 4µL of each of the samples were inserted into the wells along with a high range DNA ladder in one separate well.
7. 7. 100V of electricty was applied for about 50 minutes.
8. 8. The finished gel was then immersed in SYBR™ Gold nucleic acid gel stain solution for 15 minutes on a shaker.
9. 9. The stained gel was then observed using a gel imager (ChemiDoc MP, BIO-RAD, USA).

During the determination of optimal temperature and buffer, the composition used for annealing was: