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Preparation of Agarose Gels

Use the tables below corresponding to the AquaPor agarose of choice to determine the percentage gel to cast. (LE = general-purpose; LM = low melting; ES = extra strength; HR = high resolution).

AquaPor LE
(all-around performance)
Gel % Size Range (bp)
2 200-3,000
1.75 250-4,000
1.5 300-5,000
1 400-12,000
0.75 1,000-23,000

AquaPor LM
(low melting)
Gel % Size Range (bp)
4 <500
3 200-800
2 300-3,000
1 500-20,000
0.75 600-25,000

AquaPor ES
(extra strength)
Gel % Size Range (bp)
1.5 300-5,000
1 400-12,000
0.75 800-15,000
0.5 1,000-25,000
0.3 5,000-50,000

AquaPor HR
(high resolution)
Gel % Size Range (bp)
4.5 50-200
4 75-300
3 100-700
2.5 125-800
2 150-1,000

Preparing an Agarose Gel

Before preparing an agarose gel it is first important to select a quality comb and the correct buffer.  Use a thin comb (less than 1 mm) with wide teeth for the sharpest, best-resolved bands.

Buffer selection depends on the condition and/or use of DNA.  We recommend the following guidelines:

  • Use 1X TBE for optimal resolution of DNA < 12 kb when the DNA will not be recovered.
  • Use 1X TAE for the best separation of DNA from 12 kb to 50 kb, or for DNA < 12 kb if the DNA will be recovered from the gel.
  • Use 1X Tris-Acetate (TAE without EDTA) if the DNA will be used for in-gel enzymatic processing.

Casting a Gel

  1. Add buffer (at room temperature) to a flask that is 2.5 - 4 times the volume of gel solution. Add a teflon-coated stir bar.
  2. Add AquaPor powder while stirring vigorously so the agarose is dispersed uniformly. Stir for 2 minutes to hydrate the agarose.
  3. Tare the flask and solution.
  4. Place in a microwave oven and heat at 100% power using 20-60 second intervals. Swirl gently between intervals to resuspend the agarose.
  5. Continue the cycle of heating and swirling until the agarose is completely dissolved (no visible particles are present).
  6. Add distilled water to return the solution to its initial weight and mix.
  7. Cool the solution to 50-60°C before pouring the gel. Pour the solution into the mold so as to dispense the entire amount in 30-60 seconds, without generating bubbles.
  8. After casting, chill the gel for 30 minutes prior to comb removal when using AquaPor LM, HR, and low (<1%) concentrations of AquaPor LE and ES. This will complete gelation, increase gel strength, and enhance DNA resolution.

 

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