Removing Oligonucleotides - (Nov/25/2004 )
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.
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.