RM's+Week+of+June+30

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 * June 30, 2008**

Today, I made another sample (surprise) with a deposition time of 3 minutes. It dawned on me that the manner in which I deposited the buffer and DNA solution was incorrect. What I should have done (and what I did for this sample) was to make another homogenous mixture of the buffer and DNA in a separate tube. Then, after mixing it, I should have deposited 5 microliters onto the mica surface. For, it seemed that perhaps the buffer dried and formed clumps (i.e. the elevated dots in the past image).

Next, I made a new stock solution. The components were as follows: 80 microliters of DNA + 20 microliters of Mg/TAE 2+ 10x buffer + 100 microliters of 18 mega ohm water, for a total volume of 200 microliters. The buffer was therefore diluted to 1x.


 * July 1, 2008**

I looked at the sample prepared yesterday (it was kept in the dessicator overnight) and obtained some good images. I also prepared a sample with the new stock solution made yesterday afternoon. It came out of the thermocycler this morning. This new sample's preparation: Later today, we went to the cleaning room as a group to learn the proper techniques of cleaning surfaces in the sterile environment. I was barely able to get 45 minutes in the AFM as a result of that.
 * 1) Cleaned the mica by peeling off 2 layers of the surface with tape (a process that I had used for all the samples until now).
 * 2) Deposited the DNA on the mica surface, letting it soak the surface for 3 minutes.
 * 3) Rinsed the mica surface with 18 mega ohm water.
 * 4) Dried the sample with nitrogen gas.


 * July 2, 2008**

Today, I made 2 new samples as variations of the one I made yesterday. Sample 1: mica, 10 ul (microliters) DNA solution with a deposition time of 3 minutes. The preparation technique was different, however. Preparation: Sample 2: mica, 5 ul of DNA solution + 5 ul of TAE/Mg 2+ buffer, with a deposition time of 3 minutes. The preparation differed in that I did not rinse the mica surface with water after peeling off 2 layers of the surface. I deposited the homogenous solution of the DNA and buffer onto the surface directly after cleaning the mica with tape.
 * 1) Cleaned the mica by peeling off 2 layers of the surface with tape.
 * 2) Rinsed the mica surface with 18 mega ohm water.
 * 3) Dried the surface with nitrogen gas.
 * 4) Deposited the DNA solution. Deposition time was 3 minutes.
 * 5) Repeated steps 2 and 3.


 * July 3-6, 2008**

I was away for a tournament.