RM's+Week+of+July+7

Back to RM's Summer Research


 * July 7, 2008**

I have returned....so I made a new sample with 5 ul DNA + 5 ul buffer mixed as a homogenous solution, depositing 5 ul of the solution for 3 minutes. The cleaning process for mica included cleaning with tape, rinsing with 18 mega ohm water, and drying with nitrogen gas. After deposition, the sample was "vigorously rinsed" with 18 mega ohm water and dried with nitrogen gas.

I also had a few questions for Dr. Lieberman which were answered as follows: I also received some additional advice.
 * 1) How many images of DNA rafts must I take before the Flory-Schultz statistics can be applied?
 * 2) 100 particles (at least) had to measured.
 * 3) Into what will this project branch if the results from the samples do not follow these statistics?
 * 4) If the data don't follow the statistics, then we will attempt to put order to the results.
 * Use 512 pixels versus 256 pixels if the images are a bit fuzzy.
 * Take the cross-sections of the samples and analyze them.
 * Using the same timp that scanned the sample, scan a gold particle with a known width of 5.7 nm. Then, we can "deconvolute" my images by adjusting them for the difference of the measured reading of the gold particle to what it should actually be. These gold particles can be deposited on mica. The reason this is important is that an AFM tip is between 10-15 nm wide. The width of a DNA raft is only 8 nm. Thus, the lateral reading of the DNA raft is either that of the tip or distorted in some other way. So, I will attempt this soon.


 * July 8, 2008**

I actually got time in the Afm and captured a few decent images. Additionally, I did some more research, looking at Dr. Sarveswaran's published papers and finding some interesting and useful articles on the Flory-Schultz statistics. I finally feel that I have a grasp of what they are. Next, I worked on my weekly report.


 * July 9, 2008**

I was in the AFM for 3 hours this morning. I obtained a couple good, clear images of the rafts. The sample viewed under the AFM had 3 ul of the DNA solution and 7 ul of the buffer. What I've also been noticing is that when I'm scanning the surface, the image I see immediately on the computer screen is different than when the image has been captured and flattened. What I see when the surface is scanned, in other words, basically disappears when the image is flattened.


 * July 10, 2008**

I made a new 30% sample with a deposition time of 3 minutes. Strange Happenings: When I take images, the particles are between 1.5-3 nm on the color scale. However, when I conducted section analysis, the height read BELOW 1 nm. Apparently, the same is happening to some of my fellow researchers. On the positive side, however, I did see quite a few DNA necklaces. Next, I read an article entitled, "How flat is an air-cleaved mica surface?" What I learned is that when water is present on the surface of mica, then a contaminant layer forms from the adsorption of carbonaceous gases. However, when the surface is submerged in a liquid, contaminants do not build upon the surface. Even thermal treatment doesn't remove these carbonaceous particles. After this, I made another sample, except this time I used 2 ul of the DNA solution and 8 ul of the buffer. I deposited 5 ul of this solution on the mica surface for 3 minutes.


 * July 11, 2007**

I just sat in the AFM and took many, many images.