Enzyme Restriction Activity

(Any way of coming up with a long strip of paper, string, etc should be fine)

  1. Start with plain letter size paper and cut them vertically in 2 inch wide strips (a letter size paper should give you 4 2x11 inch strips)
  2. Tape these 4 strips together to get a single piece of 2x44 inch long DNA molecule. (This represents the DNA molecule of one suspect)
  3. If you want to show that the same DNA molecule can be cut by 2 separate enzymes to give different banding on the gel, then you need to make 2 DNA paper strips for each suspect. (For 4 suspects that means 8 paper strips)
  4. For each duplicate DNA strips, create the same restriction site pattern. I placed the restriction sites so that the fragment sizes can be easily distinguished (at full or half length of the 4 paper pieces taped together at step 2) In this exercise some suspects have the same fragment pattern if cut with one enzyme, but they have different patterns when cut with the second enzyme to emphasize why it might be important to use more than one enzyme. Also 1 of the suspect's DNA is cut in half by one of the enzymes, producing only 1 band on the gel to emphasize they can only see differences in DNA fragment sizes and if two different fragments are the same size they will produce only 1 band. Please see the attached figure for the patterns.
  5. Using 2 different colored tape for the 2 unique restriction sites worked well. This way you can use same colored scissors as the enzymes.
  6. Before starting the class, draw two gels on the board, one marked as "red" enzyme, the other as "blue" enzyme. And also draw the banding pattern for a DNA ladder. (I used one that had 0.5 units, 1 unit, 2 units, 3 units and 4 units long DNA molecules as the ladder.) You can draw the DNA pattern for the crime scene sample either at the beginning or after students draw theirs
  7. Have 4 students as suspects and have them hold the paper DNA (only 1 strip from the duplicate set) first showing the site that has nothing and emphasize that DNA in a tube looks the same but there are intrinsic differences that can let us differentiate them. And then have them flip the piece of paper to reveal the restriction sites.
  8. Ask another student to be the enzyme and tell them to cut wherever they see the specific color. Each suspect ends up with 2 or 3 fragments.
  9. Ask each suspect to draw the banding pattern on the gel diagram on the board. (Here asking about how DNA moves on a gel is a good idea, to emphasize the importance of size and charge). You might need to help the first student if they are not sure how to do it.
  10. Ask the class to compare the banding patterns and decide who they think committed this crime. (There should be at least 2 suspects that have the same pattern as the sample from the crime scene)
  11. Now hand each suspect the other DNA strip that is exactly the same as the previous one they had.
  12. Ask another student to be the other enzyme and hand them a different colored scissor and tell them to cut wherever they see the matching restriction site.
  13. Ask the suspects to draw the banding pattern for the new fragments on the second gel diagram. (Have the new banding pattern of the sample found at the crime scene on the second gel diagram)
  14. Ask the class if they can conclude who committed the crime if they only can see the second gel (There should be at least 2 samples that match the crime scene sample. Since there are two possibilities from each enzyme restriction, there should be only 1 person that is implicated on both gels)
  15. Now ask them, if they can reach a conclusion when they observe both gels together. They should be able to ID the criminal.
  16. At this point, there can be more discussions about what would happen if two enzymes were put in the tube at the same time to have a double digest, or the need to use probes when the whole human DNA is digested and there are too many fragments to visualize, or the use of PCR forensic crime detection, etc...
  17. Pattern for this Activity