Denaturation of plasmid DNA

Thu Nov 30 19:52:45 EST 1995

Here's a basic question for which I should know the answer.  Basically, I'm
working with a mixed population of cDNAs cloned into a plasmid and I want
to anneal a primer (with an affinity tag) to the specific constructs in
solution to try and recover the homologous constructs intact.  When you
want to separate the strands of plasmid DNA and you have mostly ccc DNA
(say, from a Qiagen prep), what's the best way to separate the strands only
partially so that when you reanneal, one strand from any particular plasmid
will reanneal with the other strand from the same plasmid molecule, rather
than those of other homologous plasmid molecules?  Please don't flame me if
you think this is stupid - I'm trying to be serious.  Thanks in advance for
your help.

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