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[BioBus]

Hi  ChIPpest,

Could I use  the non- reverse  sonicated  aliquot on Agarose  gel  to check the sonication efficiency ?

If  remeber correctly , at least one plant  ChIP  in Nature protocols just check the  sonication
efficiency  with  non- reverse Agarose  gel  ( an aliquot , 5-10 %  of  quantity of IP chromatin )

Like gel shift ,  it is understandable that non reversed  DNA  could appear up- shift
in comparison with the reversing.  

The picture attached is non- reversed , could it work or further sonication needed?

The bottom smear ( <  300 bp)  could be  RNAs, but the the > 500 bp  could be the
fragmented DNAs or  just something messy ??  ( in this forum,  on post reply  tells that
SDS can  bind EtBr.  an dhere  1% SDS in the lysis buffer used ).



If it could work ; it makes  thing simpler and save time.

Any suggestion is greatly appreciated.

bioBus

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Edited by BioBus, 28 June 2009 - 06:19 AM.

[TracyDuke]

You can do a quick Proteinase K digestion at 45 degree for 1 hour. Then you run it on the gel, it appears almost as good as after revers cross-linK plus purification.