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