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Purifying halogenated DNA?

Satish Nair nairs at rockvax.rockefeller.edu
Thu Oct 22 10:16:42 EST 1998

Ng wrote:
>      Hi.  I am having some problems purifying bromo and iodo DNA
>  oligomers (10 and 12 mers).  During purification by anion exchange
> in 7M urea with KCl gradient,
> I usually see 2-3 significant peaks which overlap.  I don't see these
> peaks when purifying non-modified DNA.  What are the components of
> these peaks?  And what is a good way to identify the correct peak? 
> Thanks!

As there is a difference in pKa between halogenated bases and 
unmodified bases, what you are seeing is the resolution of oligos that
have lost the halogen (photo-labile) and the appropriately modified
DNA.  On an anion exchange resin, the halogenated DNA should be
retained the best (ie. it corresponds to the last peak in your

Try a shallower gradient to resolve the peaks further.

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