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Make Your Own Markers

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Do you ever wonder how markers are made? Where do all of those colors come from? Many of the colorful dyes we use come from plants. Could you create vibrant colored natural dyes? Could you turn these dyes into art supplies? You can! In this science project, become a scientist and engineer and make your own marker using homemade plant dye!


Areas of Science
Time Required
Very Short (≤ 1 day)
Material Availability
A kit is available from our partner Home Science Tools. See the Materials section for details.
Low ($20 - $50)
Adult supervisions is required while using the stove, hot water, and cutting knife.
Sara Agee, PhD, Science Buddies Alumni
Sabine De Brabandere, PhD, Science Buddies
  • Kool-Aid® is a registered trademark of Kraft Foods Holdings, Inc.
  • Crayola® is a registered trademark of Crayola LLC.


Make plant-based natural dye and use paper chromatography to compare color molecules in your plant dye to those in water-soluble markers.


Many modern products—like food, plastics, art supplies, and fabric— are brightly colored. The variety of colors come from colored molecules that are mixed into the materials used to make the products. Some colored molecules are synthetic, like the famous Yellow #5, found in many candies and food products. Synthetic-colored molecules are man-made molecules. Others are made from nature and can be found in plants and other organic material.

A color molecule is a molecule that reflects a certain color of light from the Sun. This color is reflected and seen by your eye, which tells your brain that you are seeing a certain color. Oftentimes, the colors that we see are a combination of the light reflected by a mixture of different-colored molecules. Even though our eye sees the result as one color, each of the separate-colored molecules stays true to its own color in the mixture. One way to see this is to find a way to separate the individual colored molecules from the mixture, to reveal their unique colors.

Paper chromatography is a way chemists separate the components of a mixture. The components of the mixture start out in one place on a strip of paper. A liquid is allowed to run up the paper. As it does so, it takes part of the mixture with it. Some molecules run up the paper faster than others depending on their interactions with the paper and the liquid, as shown in Figure 1. As a result, components of the mixture separate and, in this case, become visible as strips of color on the chromatography paper. Imagine that you and your parents are running through a densely crowded park. You might get to the other side faster because your parents might stick around to talk to and interact with friends in the park while you might be driven to reach the other side. Similarly, molecules that interact less with the paper will run up faster and molecules that rather stick to the paper, will run more slowly up the paper strip.

Diagram of a homemade paper chromatography testing box

A homemade paper chromatography testing box is made from a tall box with a lid. A dowel spanning the width of the box is placed near the top to allow a binder clip to hold a paper strip that has been marked by colored pigments. The paper strip is long enough to reach the bottom of the box where there is a small pool of solvent. As the solvent is absorbed by the paper and moves upward it brings some of the colored pigment markings with it.

Figure 1. Paper chromatography. Molecules are separated from each other, depending on how fast they migrate with the solvent up the chromatography paper. (Wikipedia, 2008.)

You can learn more about paper chromatography in the video. The video gives an overview of what paper chromatography is, shows how it is done, explains the separation processes involved, and also provides tips and tricks for troubleshooting your experiment.

In this science project, you will learn how to extract a dye from plants. A dye is a coloring solution; in other words, it is made up of color molecules that are dissolved in a solution like water or oil. Paper chromatography will help you separate the color molecules in the dye so you can compare them to synthetic color molecules used in watercolor markers. Will the natural and synthetic dyes have the same or different color components? Can you use your homemade dye to make your own markers?

Terms and Concepts

To do this science project, you should know what the following terms mean. Have an adult help you search the Internet or take you to your local library to find out more.



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Experimental Procedure

Note: Natural dyes can be strong, and stains can be difficult to remove from surfaces and fabric. Protect your work surface and clothes at all times as you do this project.

Prepare Your Dye

  1. Pick out a plant source to extract your dye from. Make sure you have enough of the plant source to cover the bottom of a saucepan.
  2. If your plant source is large, you will need to finely chop it into little pieces using your knife and cutting board. Have an adult help you with this step. If the color is concentrated into the skin, you might want to peel the skin off and use only the skin.
  3. Add the plant material to your saucepan and add just enough water to cover the plant source. If you selected tea or a spice, add enough water so that it is floating or mixed into the liquid and not just absorbing the water or turning into a paste.
  4. Bring the mixture to a boil and simmer covered on the stove for approximately 10-15 minutes. The pigment from the plant material will slowly begin to color the water in your saucepan.
    1. Safety Notes: Do not leave the plant-water mixture unattended on the stove. Remain nearby to make sure it does not burn. It is also a good idea to do this in a well-ventilated area, or with the stove top fan running, in case the cooking plants release bad-smelling fumes.
  5. If the color of your water is too faint, you may want to concentrate the color by removing the lid of the saucepan and continue boiling until enough liquid has evaporated, leaving behind a darker liquid.
  6. When the color of the water is rich in color, remove the saucepan from the heat and allow the dye to cool. If there are pieces of material in your saucepan, separate the dye into another bowl using a strainer and set the bowl of dye aside. If your plant source dissolved, just pour the liquid into a bowl and set it aside.
  7. Now that you have your homemade dye, you will want to compare it to a dye from a similar color of water-soluble marker.

Chromatography Test

To make sure you can compare your results, as many of your materials as possible should remain constant. This means that the temperature, type of water used, size of paper strips, where the dye is placed onto the paper, etc. should remain the same throughout the experiment.

  1. Cut the chromatography paper into strips approximately 2 centimeters (cm) wide by 6.5 cm long. Prepare a total of 6 chromatography strips this way.
    1. Science Buddies Kit: The kit comes with 20 long strips of chromatography paper; two 6.5 cm strips can be cut from each long strip.
  2. Take one of the chromatography strips and use a ruler and pencil to draw a line across it horizontally 1 cm from the bottom. This is the origin line or baseline, see Figure 2 for details. Repeat this step for all 6 of the chromatography strips.
An origin line is drawn 1 centimeter from the bottom of a vertical paper strip used for chromatography
Figure 2. Draw an origin line (baseline) on the chromatography strip. The dye to be tested will be spotted in the middle of the origin line.
  1. Using the pipette, place a small dot of dye at the center of the origin line of one chromatography strip. The drop size should be about the size of a pencil eraser. This is your natural dye spotted sample. Let the spot air dry and then apply another layer of your dye onto the same spot. Ideally, you want to repeat this step 5–10 times to increase the concentration of your dye on the paper. The more concentrated the dye is on the paper, the better your results will be!
    1. Use a pencil to label the chromatography strip "natural dye". Do not use a pen to label the strips: the ink might run when the water passes through the strips.
    2. Allow the spot to dry. If the spot is still too faint, you will need to thicken your dye (see step 5 of the Prepare Your Dye section) and repeat step 3 on a new strip.
  2. Using the water-soluble marker that is the same color as your dye, take a new chromatography strip and make a dot the size of a pencil eraser in the middle of the origin line of the strip. This is your marker-spotted sample, as shown in Figure 3.
    1. Use a pencil to label this the chromatography strip "marker."
    2. Allow the spot to dry.
A marker places a black dot on the origin line of two paper chromatography strips
Figure 3. A single spot of dye or a marker dot should be placed in the middle of the origin line on the chromatography strips.
  1. Using your binder clips, clip the two prepared chromatography strips to a wooden splint, as shown in Figure 3. Make sure the two strips do not touch each other and that the bottoms align.
  2. Rest the wooden splint on top of the 500 mL beaker so that the strips hang into the beaker and do not touch the sides of the beaker, nor the bottom of the beaker. Estimate the distance between the bottom of the beaker and the end of the chromatography strips.
  3. Remove the wooden splint with the chromatography strips and add water to the beaker so the water would just reach the end of the chromatography strips if they are placed back.
  4. Place the wooden splint back on top of the beaker. Do both strips touch the water? The goal is to have the strip just touching the surface of the water, as shown in Figure 4. As long as the water touches the strips and the water level is below the dye dots, you are good to go!
    1. If necessary, repeat step 6 and 7 until you reach the desired water level, when the ends of the strips just touch the water.
Two paper chromatography strips slowly absorb alcohol from a beaker
Figure 4. The ends of the chromatography strips should just touch the water.
  1. Watch as the water rise up the strips. What happens?
  2. Let the water run up until it is about 0.5 cm from the top. This can take anywhere from 30 minutes to several hours. Then remove the strips from the water by taking the wooden splint out.
    1. Be patient and do not remove your paper strips from the solvent early. The longer you leave the paper strips in the solvent, the better your separation will be!
  3. Let the strips dry on a clean waterproof surface, like a plate.
  4. Lay your strips side by side to compare the color components. Make a drawing of each strip in your lab notebook. What do you notice? Make a list of similarities and differences.
  5. Scientists repeat experiments several times before drawing conclusions to ensure the experiments are done correctly. You will do the same, repeating steps 3–11 two more times for a total of three trials.
  6. Analyze your results:
    1. Were your findings for the three trials identical? If so, your experiments were reproducible and you can make strong conclusions.
    2. Were your findings different? Which ones were the same in each trial and which ones varied? What can you conclude from your experiments?

Optional: Do-It-Yourself Marker

  1. Now you are ready to make your dye into a marker.
  2. Pour some of your natural homemade dye that you made earlier in the project in a glass until the dye reaches about 1 cm up the glass.
  3. Gather all your materials. Figure 5 shows everything you need to make one marker.
Tweezers, wooden hammer, dye and a Crayola marker refill pack
Figure 5. Materials needed to make your homemade marker.
  1. Start by pressing one tip into the narrow side of the marker barrel.
  2. Place a marker core into the glass filled with about 1 cm of dye and watch how it soaks up the dye. Consult Figure 6 whenever you feel unsure about a step. The illustrations can guide you through the process.
  3. Once the core is completely soaked, use your tweezers to press the core into the barrel, as shown in Figure 6.
  4. Snap on the plug and cap.
  5. Place your marker cap down on a hard surface.
  6. Ask an adult for help or supervision with this step. Give a quick hit on the plug with a hammer. Be careful not to hit any fingers!
  7. If you see that the tip soaked up the dye, you know everything snapped together well. The marker is finished!
Six photos show a core soaking up dye then being sealed into a marker body where it can hydrate the marker tip
Figure 6. To make a marker, let the core soak up the dye before you place the core into the barrel. Add the plug and cap, and a quick tap of a hammer will snap it all together. If all has been done well, you will see the dye coloring the tip of your homemade marker.
  1. Now you are ready to write a message or draw a picture with your new homemade marker!
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Ask an Expert

Do you have specific questions about your science project? Our team of volunteer scientists can help. Our Experts won't do the work for you, but they will make suggestions, offer guidance, and help you troubleshoot.


  • Try other sources of material to get new and different colors of dye. Can you try to make yourself a complete set of homemade markers? Which materials made the best colors?
  • Another fun chromatography project is to use Kool-Aid® as a source of pigment. Conduct an experiment using your favorite flavors of Kool-Aid. Do some of the different flavors use some of the same coloring agents? Which flavors contain mixtures of different-colored molecules?
  • Some plant pigments change color when they are mixed with an acid (like vinegar) or a base (like baking soda). Conduct an experiment on different plant dyes to see which ones have this amazing color-changing ability!

For some slightly more advanced chromatography projects, see

For a fun paper chromatography activity, see


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General citation information is provided here. Be sure to check the formatting, including capitalization, for the method you are using and update your citation, as needed.

MLA Style

Agee, Sara, and Sabine De Brabandere. "Make Your Own Markers." Science Buddies, 11 Nov. 2023, https://www.sciencebuddies.org/science-fair-projects/project-ideas/Chem_p014/chemistry/make-your-own-markers?from=Blog. Accessed 27 Feb. 2024.

APA Style

Agee, S., & De Brabandere, S. (2023, November 11). Make Your Own Markers. Retrieved from https://www.sciencebuddies.org/science-fair-projects/project-ideas/Chem_p014/chemistry/make-your-own-markers?from=Blog

Last edit date: 2023-11-11
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