Richard Lab:Agarose Gel Electrophoresis

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This protocol is for the typical separation and purification of DNA done in the Richard Lab.
The consensus electrophoresis protocol should be consulted if deviating from the procedure outlined here.

Procedure

  1. Place the gel tray perpendicular in the electrophoresis to create a casting bay.
  2. Wipe the tray clean with a Kim-wipe and level the tray using the bubble level.
  3. Weigh out the desired amount of agarose and add it to 100ml of 1X TBE in a 300ml flask.
  4. Microwave the flask on high for 80 seconds. Be sure that it does not boil over.
  5. Swirl the microwaved agarose in the flask until the solution becomes clear.
  6. Pour the melted solution into the casting bay and insert the comb.
  7. Prepare the DNA ladder by combining the following:
    1. 10ul DNA ladder
    2. 1ul SYBR green (100X)
    3. 1ul Bromophenol Blue
  8. Prepare the DNA Samples by combining the following:
    1. 40ul DNA preparation
    2. 4ul SYBR Green (100X)
    3. 4ul Bromophenol Blue
  9. Remove the comb from the cured gel and realign the gel in the chamber.
  10. Adjust the buffer level by adding 1X TBE to the chamber until the buffer just covers the gel. The buffer can be reused a few times.
  11. Pipette the samples into the wells
  12. Apply 150 volts and run for approximately 60 minutes.
  13. Photograph the gel using the UVP transilluminator system.

Notes

  • Our "1X TBE" is technically 0.5X TBE but for our purposes we call it 1X TBE.
    • Correspondingly, the 10X TBE is officially 5X
  • Use the following table to determine the amount of agarose you want to use.
Agarose Concentration(g/100mL) Optimal DNA Resolution (kb)
0.5 1 - 30
0.7 0.8 - 12
1.0 0.5 - 10
1.2 0.4 - 7
1.5 0.2 - 3

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