Purifying halogenated DNA?

[Satish Nair]

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
chromatogram).

Try a shallower gradient to resolve the peaks further.