Smolke:Protocols/Gel extraction

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Comb size

  • Single wells from the smallest comb (15 wells per row) can hold up to 20 ul
  • Single wells from un-taped medium comb (8 wells per row) can hold up to 50 ul

Agarose density

  • Above 3 kb: 0.8%
  • 1-3 kb: 1%
  • 250-1000 bp: 1.5%
  • Below 250 bp: 2%
  • 75V for 45 min, or 85V for 35 min
  • Minimizing the amount of agarose in the cutout band seems to improve yields


  • I clean the razor blade between each use with a Kimwipe and do not change blades until it is dull or known to be contaminated. I have never had cross-contamination in my gel extraction doing it this way. --YC
  • Using the nano-drop to determine DNA concentration from a gel extraction is inaccurate. If you really need a concentration, run a small sample of the eluent on a gel and determine the concentration by comparing the brightness to that of the ladder at known concentration.