AL's+Week+of+November+5

AL's Logbook

__11/5/07__ - Started reviewing other people's logbooks. What I'll probably do is make a table on a word document for my little reviews to make it easy to understand.

__11/6/07__ - In class I spent time reviewing people's logbooks. After school I went to the lab to analyze my new samples I made last week of the DNA. This sample is the DNA sample that has been deposited on the silicon substrate but with a cover slip put immediately afterwards, followed immediately by a washing of 18 mega ohm water and drying with Nitrogen. Normally what I do is wait for a deposition period of around 15 minutes for the DNA before applying the cover slip, or rinsing and drying. Under the AFM I could certainly tell that the DNA went through enzyme digestion. Some of the DNA was in the shape of a long crescent, with small points at the ends of them, which shows that the **DNA was cut by the enzyme (kp I enzyme)**.

__11/7/07__ - The process of the enzyme is more or less explained on the front page of the AFM-DNA page. What happens is the enzyme, through a chemical process, cuts the the sugar-phosphate backbone in between the base pairs at one or two locations on the circular DNA, depending on the kind of DNA plasmid and the kind of enzyme.

Here is a better image:



The circular shape is the DNA plasmid itself, the puc19 plasmid, which is the one I am using right now. The **kp I enzyme** cuts the DNA plasmid at the top right corner of this image, where you see a blue list of enzymes that cut at that specific point. I am trying to make the DNA bigger, or longer, when appearing under the AFM. Under the previous circumstances, the plasmids were coiled and small, not very visible. By cutting the DNA with a restriction enzyme, the circular plasmid would unravel, making the DNA easier to see. This new shape of the DNA would also make it easier to see the effects of the APTES and other solutions on the physical properties of the DNA.

Also today I have written more about the other logbooks...I've done 15 so far, but they're taking longer than I thought.