Diffusion in Gels

Diffusion in Gels
Bring the following pieces of equipment to your lab bench:

1. Computer
2. 1% agarose gel, poured into petri dishes
3. 20-30 microliter pipette
4. Digital camera
5. light box and shroud

First get dye started

1. Use a plastic pipette to remove a small core of gel from the center of the dish
2. Into the hole left by the core, pipette 20-30 microliters of biphenol blue (bpb).
3. This will now diffuse over the next several days. Make a plan with you partners to take pictures of the gel several times per day over the next three days. Should you take the pictures more closely together at first, at the same interval throughout, or more closely spaced at the end? Collecting images
   1. Turn on the light box and place the gel in the center.
   2. Turn on the camera and set it to close-up, then insert into shroud and place shroud over the light box.
   3. Using the timed exposure, take a picture
   4. Note the time of the picture, download the image to the computer and note the file name and identify it with your gel number.
   5. Repeat for all gels.
   Analyzing images
   1. Start ImageJ and load in an image.
   2. Draw a line through the center of the gel and under the analyze menu, select Plot Profile.
   3. Is the curve what you expected? Why?
   4. Repeat for all gels and make a table of FWHM for each of the images.
   5. From a plot of FWHM vs. time, what conclusions do you draw about diffusive motion?