Interpret+Results

In order to move the project anywhere, you must know the proper tools and procedures to interpreting your data, all involving the images you've taken. Part of the process of interpreting your data involves the program on Nanoscope hooked up to the AFM.

1.) __**Look at the Image**__ Make sure that on the image, you're seeing DNA. Sometimes there are particles that are plasmid shaped, but they may not necessarily be DNA. Compare and contrast the image of your plain sample versus the sample where you deposited DNA. Make sure that you spot clear differences between the two on the AFM image in order to properly decide whether or not you are seeing DNA. See the AFM process page to see two images. One with DNA, and one without.

2.) __**Take Section Analysis Height Measurements**__ Take height measurements of the DNA particles using the Nanoscope program on the computer hooked up to the AFM. Drag your mouse on the analyze screen of the monitor, and the computer will tell you the height and length of the DNA plasmid according to the points on the image you choose. The average DNA height is around 2.5 nm, but because of the strong positivity of the APTES, the heights may be smaller or larger as the DNA coils in on itself or stretches. Heights of the plasmids can range anywhere from .5 nm to 3 nm depending on the monolayer used. You will want to take between 25 and 60 height measurements per image. //Notice the bottom left box in the image below. In both red and green, you see the horizontal distance. This is the height of your selected points on the image as seen in the upper graph which shows the cross-section of a piece of the image.// When taking height measurements of plain samples for comparison value, there is a tool on the program that will take "all the heights" and find the **RMS or Root Mean Square** of the heights, such as the image below. You need to keep track of all the measurements.

The Section Analysis Screen looks like this:



3.) __**Average Number of Plasmids per Micrometer**__ In order to know if the plasmids are attaching to the monolayer and to see if your DNA concentration is correct, you will need to take your results and do a plasmid count per micron for the images you choose (generally the best ones). Count the number of plasmids in the image in every micrometer, and divide the total number of plasmids by the area of your image to get the number of plasmids per micrometer. In the image below (scale is in micrometers µm), **the area is 7.56 micrometers (length times width)**. If you have a low plasmid count, then you would need to change the concentration perhaps.



Comparing images, taking height measurements, and making plasmid counts allows you to take your project in new directions by using these as tools to interpret your results.