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Use high frequency sound wave to break down either cellular membranes and the release the contents of the cell or random fragmentation of DNA.

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Materials Needed


  • Bath Sonicator
  • Probe Sonicator

Sample (Protein or DNA)

Ice bath



Ear protection should be worn when using sonication.

This includes everyone in the room while a sonicator is in use.

Beginning with an appropriate centrifuged culture:

Protein Extracts

  • If your protein is extracellular:
    • Keep the supernatant from centrifuged culture.
  • If your protein is intercellular:
    • Dispose of supernatant
    • resuspend pellet in an appropriate extraction buffer
      • Must preserve protein integrity and activity
    • Place sample container in water bath
      • Energy released into the cell suspension will be converted to heat. Therefore if the sample is not kept effectively cooled the sample and the container can be irreversibly damaged.
    • Place sample into sonicator, and set the intermittent pulses to the appropriate setting to break open the cultured cells.
      • If necessary add ice to the water bath to ensure proper cooling!
    • Spin down the sample - your protein should be in the supernatant.

DNA Fragmentation

  • Place sample in solution in appropriate contain (typically micro centrifuge tube)
    • To avoid nonrandom fragmentation at ends circulate and concatenated sample in by placing in ligation buffer.
  • Insert sonicator tip into solution as far as possible without touching the tube.
    • Keep sample in ice bath or the sample may be irreversibly damaged due to heat.
  • Set the amplitude as appropriate (higher amplitude will yield smaller fragments more quickly)
  • Use intermittent burst of sonication (example @ 5 μm: 5 seconds sonication, 15 seconds cooling[1])
    • Supercoiled DNA will take fewer bursts
  • Precipitate DNA
  • Fragment ends can be repaired with T4 DNA Polymerase
    • Do to the nature of this method the DNA does not have uniform ends for incorporation.


Sample DNA Fragmentation Protocol

Textbook Explanation

User notes


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  1. Deininger, PL (1983) Random subcloning of sonicated DNA: application to shotgun DNA sequence analysis. Anal. Biochem. 129 216-23 PubMed EcoliWiki page