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Ahoy,

In a way I hope you already solved the challenge and I am therefore too late.

But maybe not so I figure I may as well share my thoughts.
I do not know the exact composition of Qiagen N3 but since it is a silica binding buffer I would assume several things that may not be ideal for your purpose.

• DNA (Including Plasmids) is already precipitated -> spinning may lead to some loss.
• The precipitated DNA in N3 will be charged and therefore sticky -> changing tube leads to loss.
• Adding ethanol at this point might lead to salting out and general precipitation of unwanted contaminants.

I do not understand why you would presume that you would be selectively binding plasmids in the procedure you describe.
All in all I think what you propose wont work but maybe you have already tried it and can prove me wrong?

However, could you consider simply using Exonuclease 5 (V)?
From personal experience ExoV is amazingly good at chewing up anything non circular.

Cheers

Tim M

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