Use+the+AFM

The AFM is used to see the fruits of your labor and look at the DNA under the AFM and analyze what you have. Before beginning, turn on the AFM and the computer that it is hooked up to as the computer is needed for me to analyze the sample using Nanoscope.

1.) The first step is to take a small cantilever and slide it into a small cantilever holder using small clean tweezers. The cantilever contains a tip that analyzes the sample in the AFM. Insert the cantilever holder into the AFM, and then the sample, which you should tape to a magnetic puck and place directly under the tip holder also using tweezers.

2.) There is a small camera next to the AFM that shows you a picture of what the camera and tip see and what part of the sample the AFM is focused in on. There is a red laser that appears in the AFM that must be directed on top of the tip so the AFM can process the information analyzed by the cantilever tip. On the base of the AFM there is a dial and by turning the knobs on the dial, the number will change. The number should read as close to zero as possible in order for the information to be processed correctly and shown on the computer.

3.) After that, bring up the Nanoscope software and tune the tip, by simply pressing a button that is labeled appropriately, then go to the screen and have the AFM bring the tip down to the sample by clicking the button “Approach sample” and then watch as the tip on the camera will move back and forth and what the tip goes over, will appear on the computer screen as different colors which denote different heights in the sample. If you have cleaned the sample well, it will be relatively smooth with little color variation besides the DNA samples which are about 2 nm in height.

4.) If you find a worthy or insightful image, take a picture of it using the program feature that shows a button with a camera on it. Press it and then when the image is fully analyzed by the tip, the picture will automatically be taken and saved to the disk. Finally, disengage the tip, remove the sample, cleanup, and turn off the AFM.

Here is a sample AFM image. This sample has nothing on it except a plain APTES layer, hence the smooth surface. Notice the scale on the upper right hand corner that tells you the various heights of the image surface, and the bottom right corner which tells you the AFM setting you set. All of this is seen through a computer hooked up to the AFM. Knowing what the image is telling you is pivotal to using the AFM.



Here is another sample AFM image of unlinearized DNA plasmids on a PEG solution surface. You can view this image on the front of the AFM-DNA page. The straight yellow lines are samples of DNA. I've circled a few of the DNA plasmids in black just to point them out. Notice the difference between this and the image above which contains no DNA.



Next Milestone - Convert Images to Tiff File Images