Analyzing DNA

Electrophoresis of Dyes (activity)

  1. Prepare a 1% agarose gel by adding 60ml Tris-Borate-EDTA buffer (TBE) to 0.6g agarose in an erlenmeyer flask
  2. Place flask in microwave or on heat until agarose is melted
    • stop periodically and swirl solution and do not permit to boil over
  3. Assemble the casting tray by blocking the ends with tape or plastic gaskets
  4. Place the comb into the center of the casting tray
  5. You may place the casting trays inside a refrigerator and pour the solution into the tray
  6. Wait until the gel is solidified
  7. Carefully separate the gaskets from the tray
  8. Remove the comb and place the casting tray into an electrophoresis chamber
  9. Cover the gel with TBE buffer
  10. Using a micropipettor, load 40-50μl dye samples sequentially into  the wells
  11. Cover the electrophoresis chamber with the lid and ensure good contact between electrodes
    • It is conventional that the POSITIVE side of the tank is nearest to you
    • With the POSITIVE side nearest to you, load the samples from left to right
  12. Set the power supply to 100-120V and press the Run button (you should see bubbles at each electrode) and allow to run for at least 40 minutes
  13. After 40 minutes, stop the current and remove the gel in casting tray
  14. Place tray on a white background and document your gel

Activity Follow-up

  1. What colors were the dyes originally before loading into the wells?
  2. How many separate bands of dye are in each well following the run?
  3. What does it mean that there are multiple bands in a lane? What does it mean that there is only one band in a lane?
  4. What does the length of migration illustrate to us about the properties of the dye molecules?
  5. In which direction did the dye molecules migrate? What does the direction of migration indicate about the analytes?
  6. Are there lanes where there are multiple bands of the SAME color?