Gel Electrophoresis Notes

Gel Electrophoresis

How Gel Electrophoresis Works

  • Electric current is applied to the gel.
  • DNA pieces wiggle through holes and spaces in the gel.
  • Shorter pieces wiggle faster than longer pieces.
  • Shorter pieces travel further down the gel.
  • Longer pieces get stuck higher up in the gel.
  • If the current keeps running, the pieces will eventually work their way through the gel.

Setting Up the Gel

  • Setting up four patients and a control, which is a known virus marker.
  • Comparing the patients to the control sample.
  • In the first lane of the gel, a marker (size standard or ladder) is placed.
  • Markers are standardized samples with set sizes.
  • Markers give a banding pattern to compare to the fragments.
  • In a genetics lab, one might look for a piece that's 250250 kilobases long.
  • Compare the bands to the samples to see if they have the same matching size.

Identifying a Virus

  • Looking for a banding pattern that exactly matches the known virus.
  • The sample bands might share bands in common, but must have all of their bands matching with no extra bonus bands.
  • If a patient's bands match the known virus, the patient has the virus.

Traditional Gel Procedure

  • Make the gel, pour it, and let it harden.
  • Lay the gel in a buffer tank.
  • The tank contains buffer, and the gel lays down inside it.
  • Apply a negative charge at one end and a positive charge at the other end.
  • Load the gel while it's in the buffer.
  • Use a pipette tip to insert the sample just below the buffer line into the well.
  • Trickle the sample slowly into the well.
  • Mix the sample with something more dense to help it sink.
  • If too shaky, the sample will disperse into the buffer.
  • If the gel is pierced too deeply the sample will squirt out the bottom.
  • Run the gel in the buffer bath.
  • Stain the gel with a dye that attracts to the bands.
  • The dye dyes the whole gel blue, so the gel has to be destained.
  • Destaining involves soaking the gel to wash away the extra dye so only the bands stain blue.
  • Some dyes can mutate DNA.
  • Running a gel can be a two or three-day process.

Electronic Gels (eGels)

  • Newer technology has created egels.
  • Make sure to change tips after every single patient.
  • Wear safety glasses.
  • Even though they're in a cassette, be careful not to pierce the gel.