? How to destroy DNA chemically (to reuse DNA columns)

Dennis J. Templeton djt2 at po.CWRU.Edu
Tue Dec 22 11:17:17 EST 1992


Well, the old cheapskate (me) has broken down and bought a bunch of
silica-based columns for DNA column purification (plasmid).  We went with
those from Machery Nagel (Nucleobond) bought in the US from The Nest Group.
These are similar to the Qiagen columns, but the Nest Technical support was
more informative and they were a little cheaper.

They work fine, as many of you have attested previously.

They are expensive, though, and I'm toying with how to re-use them.  The
critical element is to avoid pH above 9 for long periods (in minutes, I'm
told). The important aspects would be to 1) retain binding ability and 2)
remove DNA that might contribute to the next prep.

We tried washing the column with DNAse solution (200 ug/ml in Mg++
containing buffer, RT for 60 minutes) and re-stripping.  When we
re-stripped again, though, we recovered plasmid "contaminant" that amounted
to about 10e-5 of the original amount, based on amp-containing transfection
units.  I think this is too much to allow re-use.

I'm thinking now about *chemical* methods of degrading/destroying the DNA
bound to the column.  1M NaOH is out (that destroys the silica column) and
I'm not too keen on 4 M HCl for the same reason.  I guess I'm leaning
towards an alkylation agent, maybe Acetic anhydride, though I really don't
have a good feel for what might work best. Maybe an oxidative reagent, like
peracetic acid.

So... any chemists out there?  What should we try that works near neutral
pH in aqueous or anhydrous conditions that should destroy the biological
activity of the residual DNA, that is safe and relatively cheap?  If you
have reasonable suggestions, I'll try it out and post a followup.

dennis



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