Removing Oligonucleotides - (Nov/25/2004 )

Hello,

I need to remove a high concentration of small single and double stranded oligos (20-40bp) from a preparation of chromatin.
The chromatin pieces are 5-50 Kb in length, and fixed in formaldehyde.

Is it possible to use rate zonal or ispycnic centrifugation to efficiently separate the oligos from the chromatin?

I don't know much about this kind of centrifugation, so any advice/protocols would be really appreciated.

Thanks!
Dave

You can purchase columns from Biorad etc. or prepare your own resin available from biorad or other companies that exclude small pieces of DNA.

I always use Microcon Millipore centrifuge tubes. They always work well for me. In your case,you can choose the cutoff length <1Kbp.