Cheap Electrophoresis – Using Food Coloring
Experimental Procedure
Building the Gel Electrophoresis Chamber
To start this science project, you will first need to build your gel electrophoresis chamber. The plastic box
will be the actual gel chamber, the stainless steel wire will be the electrodes, the batteries will be the power
source, and you'll use the Styrofoam to make a comb for creating wells in your gel.
1. Cut two pieces of the stainless steel wire with your wire cutters. The wire should be slightly longer
than the width of the plastic box.
2. Bend the wires so that they hook over the sides of the plastic box and run the width of the box. Place
one wire at the top of the box; this will be your negative electrode. Place the other wire at the bottom
of your box; this will be your positive electrode.
Figure 2. Each stainless steel wire electrode is bent in such a manner that it hooks over the side of
the box.
3. Connect your five 9-volt batteries together in series by snapping the positive (+) terminal of one into
the negative (-) terminal of another until you've formed a battery pack with all five batteries. There
should be one positive and one negative terminal left exposed.
Figure 3. The five 9-volt batteries are clipped together to form one battery pack.
4. When you're ready to begin the experiment, connect one alligator clip lead to each of the exposed
terminals in the battery pack. Complete the circuit by attaching the lead from the negative terminal to
the negative electrode, and the lead from the positive terminal to the positive electrode. Now your gel
electrophoresis chamber should be fully powered. Remember, don't complete the circuit until your
experiment is set up.
5. Using a pair of scissors, cut out a comb out of the Styrofoam.
a. The comb will be placed vertically into the plastic box and need to stand upright, so it should
be wider at the top so that the comb can rest on the the edges of the plastic box.
b. The teeth should be evenly spaced and there should be at least 2 millimeters of space between
the bottom of the teeth and the bottom of the plastic box.
Figure 4. This Styrofoam comb will be used to create the wells in the gel for the samples.
Food Coloring Dye Separation Experiment
Once you've assembled your gel electrophoresis chamber, you are ready to start your food coloring dye
separation experiment.
1. The first step in the experiment is to make the buffer solution that you will use for both making the
agarose gel and running the samples. The buffer should be a 1% solution of baking soda. To make
this, combine 2 grams (g) of baking soda with 200 mL of bottled water in one of your bowls and stir
well. (If you don't have a kitchen scale, 2 g of baking soda is approximately ½ teaspoon.)
2. Make a 1% agarose gel solution by combining 1 g of agar powder with 100 mL of your buffer
solution in a microwave-safe bowl. (If you don't have a kitchen scale, 1 g of agar is approximately ¼
teaspoon.)
a. Heat the agar solution in a microwave to dissolve the powder. Stop the microwave every 10–
15 seconds to stir the solution.
b. When you see that the solution is starting to bubble, remove it from the microwave. The
solution should be translucent. Make sure to watch the agar solution carefully and remove it
promptly from the microwave; when it gets hot it will easily bubble over.
3. Remove the stainless steel wire electrodes from the gel chamber.
4. Insert the Styrofoam comb into either end of the gel chamber, leaving approximately 0.5 centimeters
(cm) between the end of the box and the comb. Gently pour the agar solution into the gel chamber.
Add just enough solution to the box so that the comb teeth are submerged approximately 0.5 cm. If
the gel is too thick, it will be difficult to observe good separation of the food coloring dyes.
Figure 5. To form the wells, there must be a few millimeters of space between the bottom of the comb's
teeth and the plastic box.
5. Wait until the gel solidifies, approximately 10 minutes.
6. Pour the remaining 100 mL of your buffer solution over the solidified gel. Add enough buffer to
submerge the gel.
7. Gently pull the comb out of the gel. The resulting wells will be used as reservoirs for your samples.
8. Using the butter knife, carefully cut a thin slice of the gel from the top and the bottom to make room
for the electrodes.
9. Re-attach the stainless steel wire electrodes.
10. Using a plastic syringe or medicine dropper, fill each well in the gel with a different color of food
dye. A small drop of food coloring dye is sufficient. You might find it easier to first put a drop of
food coloring dye on a piece of wax paper and then use a syringe or medicine dropper to transfer the
food coloring dye from the wax paper to the gel.
11. Using the alligator clip leads, attach the battery pack to the wires resting on the gel chamber. The
positive terminal of the battery pack should be connected to the positive electrode; this is the
electrode toward which you want the food coloring dye to migrate as it separates. You should see
bubbles forming around the electrodes in the buffer as the current passes through them.
a. If you don’t see bubbles, recheck all your electrical connections. Make sure the batteries are
properly placed in series, and that the batteries are fresh and fully charged.
Figure 6. Gel electrophoresis chamber running samples of food coloring dye. Notice the bubbles forming
around the electrodes.
12. Check the progress of your gel every 10–15 minutes. Run the gel until you see good migration and
separation of the food coloring dyes.
a. If you’ve used the electrophoresis chamber in a previous trial and feel that it is no longer
working as efficiently, you might need to troubleshoot the following:
1. Replace the batteries with fresh, fully charged ones. Running the electrophoresis
chamber can drain the batteries.
2. Make new stainless steel electrodes.
13. Compare each food coloring dye sample. How many bands do you see for each color? Which one ran
the farthest? Why? Using a ruler, measure how far from the wells each band migrated. Make a data
table, like the one below, for all your observations.
Food Dye Color
Number of Bands
Migration Distance of Each Band (cm)
Red
Blue
Green
Yellow
Black
Questions:
1. What dyes do each of the food colors separate into?
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2. Did any of the colors contain dyes that you did not expect?
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3. What dye moved the farthest? Why did this dye move farther than the rest?
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4. What dye moved the least farthest? Why did this dye not move as far as the rest?
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5. Is the yellow dye in the yellow food color and green food color the same? How do you
know?
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6. Are there any other food colors that have the same dyes?
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7. What two things help determine how far each dye moves?
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8. If all of the dyes are attracted to the positive electrode, what is the overall charge of the
dyes? Positive or Negative? Why?
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Next Step
Get the three unknown samples that are labeled — Crime scene, Suspect 1, and Suspect 2.
Design a procedure to determine which suspect committed the crime. This section will
require a formal lab report with pictures of your results. Your lab report should have Title,
Purpose, Procedure, Analysis (Pictures and a written description of your results.), and
Conclusion (A detailed analysis of how you arrived at your conclusions and notes for
improving results or analysis of possible errors.)
Teacher notes
For the unknown samples, mix various colors so that two of the samples are the same and one sample is
different. Use colors so that all samples appear to be black. I will use a premixed black color and then mix a
black (dark) color for the second unknown. (I don’t know exactly what mixture will work until I actually try
them. I will post my mixtures on the page with the video when I have them.)
Variations
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Are all food coloring dyes made from the same molecules? Compare different brands of food
coloring dyes. Do they migrate the same distance over time? Do they have the same color
composition?
What variables affect the rate of electrophoresis separation? There are many variables to explore.
Several to start with might be the type of electrode, the amount of power, and the agar percentage of
the gel.
Use your gel electrophoresis chamber to determine if two different types of plants use the same
molecule for pigment. To prepare your samples, take the flowers from a plant, grind up the flower,
add a little bit of isopropyl alcohol, and continue grinding. Once the solids settle, pour the pigmenttinted alcohol into a separate container. Let most of the alcohol evaporate and then add a drop or two
of your buffer solution to reconstitute the pigment.
Try combining this experiment with one of the DNA extraction science projects like the Do-ItYourself DNA or the Extracting Onion DNA Science Buddies project ideas. Can you see the DNA
you extracted on your gel? Are there different bands? Note: you will need to use a stain to visualize
the DNA. DNA stains are available from online science supply companies, like Science Kit catalog
#WW6488701 or Wards Natural Science catalog #38 V 9014.
For more science project ideas in this area of science, see Biotechnology Project Ideas.