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Method: Primer Extension Labeling of DNA in Low Melt Agarose


C. Helms


Special reagents:

Time required:


  1. Restrict clone DNA and run a low melt agarose gel in TA buffer + ethidium bromide. A minigel can be run if the fragments can be separated adequately. Excise the band using long wavelength UV lightbox and a clean razor blade. Trim the gel slice of as much extra agarose as possible before placing in an eppendorf tube.
  2. Melt the gel slice at 70 degrees C for 5- 15 minutes, remove 0.1 g (up to 34 l) and place in a fresh tube. Often it is difficult to estimate concentrations. However if you try to stay close to or below 0.1 g of DNA per reaction, the specific activity of the probe will be high. Add sterile dH2O to bring the volume to 34 l. Place in the boiling water bath for 5 minutes to denature the probe. Place in a 37 degrees C waterbath or heatblock and quickly add the following:

    2.0 l OL solution primer (1mg/ml pd(N)6 ), see primer extension protocol
    5.0 l 10X salts (recipe below)
    2.5 l 20 X dNTPs - C (recipe below)
    1.0 l BSA (10 mg/ml)
    5.0 l 32P dCTP
    0.5 l Klenow fragment
    16 l total volume added

    Mix well by pipetting up and down with a pipetman.

  3. Incubate at room temperature for 3 hours to overnight, or at 37 degrees C for 1-2 hours. Stop the reaction with 40 l Labeling Stop Mix and put at 65 degrees C for about 10 minutes until the mixture is liquified.
  4. Warm up the TE used to elute the probe from the P60 column in a 50 degrees C incubator, and prerinse the column with 1 ml of the warmed TE. Apply the probe to the column as usual, but be sure to begin the elution as soon as the probe mix has entered the column to prevent the agarose from solidifying on the column, and work with one column at a time. Collect the 500 l containing the light blue (dextran blue) dye. Count the probe and use as usual.



Feinberg, A. P., and B. Vogelstein. (1983) "A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity." Anal. Biochem. 132: 6-13.

Feinberg, A. P., and B. Vogelstein. (1984) " Addendum: A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity." Anal. Biochem. 137: 266.

Struhl, K. (1985). "A rapid method for creating recombinant DNA molecules". BioTechniques 3: 452-453.

CRI Laboratory Manual: RFLPs Project (1989).