Size selective DNA precipitation

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Kersten S. Rabe

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A very fast and easy method for the size-selective removal of smaller DNA from larger fragments. By adjusting the PEG and MgCl2 concentration the range of precipitated DNA fragments can be adjusted.



  • DNA to be separated
  • 30% (w/v) PEG 8000/30 mM MgCl2 (concentration of PEG 8000 can be varied to shift the size of the percipitated DNA. The concentration used here will remove DNA fragments with less than 300bp)
  • TE Buffer, pH 8.0 (10 mM TRIS-HCl, 1 mM EDTA, pH 8.0)


  • Centrifuge which can do up to 10.000 rcf (=g)
  • Appropriate tubes for the centrifuge
  • Pipettes
  • Vortexer


  • Mix 50 μL of sample with 150 µL of TE
  • Add 100 µL of PEG/MgCl2
  • Vortex
  • Centrifuge 15 min at 10.000 rcf at roomtemperature
  • Carefully remove supernatant not to disturb the pellet, which will be invisible
  • Dissolve the pellet in a appropriate amount of buffer of choice

Critical steps

  • Before centrifugation mark the tubes in order to know where the pellet will be expected afterwards, as the pellet will be (nearly) invisible



This protocol is being mention in the manual for the Gateway recombinational cloning system based on published methods.[1, 2, 3] Adjusting the PEG concentration can shift the threshold of the size of the precipitated DNA. The higher the final PEG concentration, the smaller the fragments that will be removed (which will stay in the supernantant).


Acnkowledge any help you had in development, testing, writing this protocol.


  1. [Website]
  2. Paithankar KR and Prasad KS. Precipitation of DNA by polyethylene glycol and ethanol. Nucleic Acids Res. 1991 Mar 25;19(6):1346. DOI:10.1093/nar/19.6.1346 | PubMed ID:2030954 | HubMed [Paithankar]
  3. Lis JT. Fractionation of DNA fragments by polyethylene glycol induced precipitation. Methods Enzymol. 1980;65(1):347-53. DOI:10.1016/s0076-6879(80)65044-7 | PubMed ID:6246357 | HubMed [Lis]

All Medline abstracts: PubMed | HubMed

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