Week+of+December+10

AL's Logbook

__12/10/07__ - Today was spent catching up on my logbook and organizing my lab book for Notre Dame where i keep the details of my experiments. Since I have started the project, I have run out of linearized DNA so I now have to make more. It is a long and annoying process, but I think now would be a good time to get the process online so that I will better understand what I must do on Tuesday (tomorrow) and for my milestones.

__**1.) Initial Materials in Tube**__

Kpn I - Restriction Enzyme, 5 μL Buffer (10x) - 10 μL BSA (100x) - bovine serum albumin; it ensures 100% activity in the enzyme reaction, 1 μL. It comes from cows, hence bovine. 1 μg/μL concentration DNA plasmid - 5 μL Water - 79 μL


 * //Total://** 100 μL solution

2.) Put tube in 37**° C** temperature distilled water for 12 hours, then take out and put in freezer. 37**° is the optimum incubation temperature for the enzyme.**

3.) Put the tube in ice and get 100 μL of phenol (ph level 8). The phenol will stop the reaction and gets rid of protein.Mix this into the solution for 5 minutes.

4.) Put the DNA into the centrifuge then put a tube of water in the opposite end for about 5 minutes. This brings the dissolved particles to the bottom of the tube.

5.) Take out 100 μL of this solution and put it into another tube. Add another 100 μL of Chlorophorm Iso Amy Alcohol and put into the tube and put the tube in the vortex again. Then put in centrifuge again for only 1 minute.

6.) Take the top 100 μL layer (you should see different concentrations in the tube/layers) and put the substance in yet another tube. Add 3 M of sodium acetate (CH3OO- Na+). 3 M is equivalent to 10 μL. Add 300 μL of Ethyl alcohol or ethanol.

7.) Afterwards, put in -20° C either for 1 hour or overnight**. It doesn't matter.**

8.) After being put in freezer, take the tube out and into the cool room for 20 minutes in the centrifuge.. After, remove ethanol from tube, and there should be a pellet in there.

9.) Wash pellet in cold 70% ethanol and dissolve the pellet in 20 μL of water, then 5 μg of DNA in the 20 μL of water...and that's it.

__12/11/07__ - Today I talked to Dr. Loughran about the format of my milestone map and the content of my milestone. What I figured out is that there is no one format for every single milestone. Certain formats work best depending on your objective in each milestone, be it explaining what you've learned, a command or procedure, or what lies ahead in your project.

In the lab, I watched Renula take an image of mica with plain DNA (non linearized). Koshala explained to me the importance of using a semi-conductor such as silicon and the role DNA plays in the big picture. This the gist of what I think she's talking about:

The silicon must be a semi-conductor because it will be etched into (lithographed) by an electron beam after a polymer layer has been placed on top of the silicon substrate. This etching allows the DNA, which will act as scaffolding for various molecules.

===I made this image on MS Paint displaying what this would look like from the side... __**EDIT: Apologies, but my etching is wrong.The nanoparticles should be placed on top of the DNA scaffolding. Otherwise the image is fine.**__===



For the top-bottom view of nanoparticles with DNA scaffolding, I found this image while browsing the [|Nature Materials website journals]. The yellow cirlces are the nanoparticles and the gray helices are obviously DNA...



__12/12/07__ - Today I made a specific outline of what my Milestone Map will look like.

__**Milestone Outline**__

The Properties of DNA

Why DNA Tiling?

Overview of my Project

The Silicon and Mica

The AFM

The Monolayer of the DNA and the Buffer: Buffer Solution, APTES, TMX, PEG, OTS

Enzyme Digestion of DNA

Linearized DNA

I am thinking of putting the different monolayers as different milestones.

__12/13/07__ - Today for Science Research, I went back and emailed Dr. Sarveswaran about my remaining questions on my project such as result interpretations. Also, I am not sure the diagram I made of the lithographed silicon is entirely correct. I will make apropriate changes as I see my errors. Also, lab was again canceled today.

__12/14/07__ - I thought it would be best to post an image of a centrifuge to help people visualize what I'm talking about. You put the tube in the slots you see along the circle which in turn is around the center of the centrifuge.