Sonication DNA - (May/01/2008 )

Has anyone sonicated DNA to shotgun sizes (a few hundred bases) before?
Any tips on sonicating DNA in general? It will be my first time doing this.

You might find it easier to find a small bore hypodermic needle and 1 ml syringe (tuberculosis needles) and push your DNA through it a few dozen times. I don't know if you can get to 200 bp this way, but it is trivial to get 2000-5000 bp fragments, and a lot easier, in my opinion, than sonication. High pressure and small diameter needles are the key. Push hard.

Search this subforum by "sonication" or read some of the pinned threads you can find many useful information here.

Hey,

I've sonicated DNA for Methylated DNA Immunoprecipitation and for improved bisulfite conversion efficiency. Basically I used Weber's method (sorry can't think of the reference right now) which is very simple. In order to produce 300-800 bp fragments we use 5 ug DNA in 350 ul TE and sonicate 10X at power 30 (sonics sonicator, which is about 1/4 strength) for 20 second bursts with 40 second rests on ice. This method works for bisulfite conversion, antibody precipitation and methylation PSQ.

Good luck,

Bram

The best advice I can give is do NOT use sonicators where you have to dip a tip in the tube.

Use the ones waterbath based, where you just float all your tubes in chilled circulating water, close the chamber, and zap. Very uniform sonication in all your samples once you have identified right settings (pulse time/interval/power).

HTH/