AL's+Week+of+November+12th

AL's Logbook

__11/12/07__ - I used this day to finish up my logbook reviews. Overall I found them to be pretty good with much similarity in format and amount of detail including my own.

__11/13/07__ - Today I went to the lab and worked on copying images from the computer connected to the AFM (where all the images are stored) and putting them on a floppy disk, as the disk drive doesn't work properly on the computer. This is relatively time consuming because all the images must be converted to TIFF files before being put on the disk. Afterwards I spent my time putting the images on to a powerpoint file for easy storage. This way I can have all images stored on one file. I will post my images later.

__11/14/07__ - Here are some TIFF file AFM images that I took yesterday in the AFM.

The image below is of the DNA that has gone through the enzyme digestion on the APTES solution. I am still trying to figure out major differences between this sample and the regular plasmids as you can tell from the images on the main AFM page. The DNA plasimds here are all the squiggly like lines and shapes you see that dot the image. They are much longer looking than the regular DNA plasmids. This is because the bonds at one point of the sugar-phosphate backbone have been cut, uncoiling the DNA. I hereby call this __//**IMAGE A**//__.



The image below is of linearized DNA (it has gone through enzyme digestion) on silicon with an APTES layer like all my other samples so far. There is a difference however, between the deposition process of the image below and IMAGE A. In the image below, immediately after putting the DNA solution droplet on to the silicon, I placed a coverslip on the droplet and dragged it across the surface in the hopes of "flattening" and straightening the DNA on the substrate. After that, I washed the sample with water and dried it with Nitrogen gas to get rid of excess DNA, solution, and particles as I always do. In this sample (a69sm34), there was virtually no time for the DNA to attach to the surface, as it was only on the surface for a few seconds. Most of the time the deposition of the DNA droplet on the silicon chip is around 10 - 15 minutes.

On this image you see various balck holes dotting the surface. I've seen similar features on other samples. They are probably holes in the monolayer (APTES layer) on the silane surface. This can be caused by short deposition time of the silicon in the APTES solution.



__11/15/07__ - Today in the lab I deposited the linearized DNA on to the silicon substrate. I left it there for 15 minutes to make sure the DNA stuck to the surface. However, instead of washing it off with water and drying with the nitrogen, I used a micropipette to suck the plasmid solution droplet off the slicon substrate. This was to see if the suction from the pippette would affect the position and the look of the DNA under the AFM. Hopefully the DNA will straighten out and look longer, so its features can better be studied.