Sonication of DNA for cloning

NJ njuni at
Mon Mar 5 02:52:57 EST 2001

I think the statement in your protocol means that you can not obtain
well-fragmented DNA using DNase 1 with Mg++. In the presence of Mg++, DNase
1 attacks each strand independently and predominantly makes nicks instead of
double strand breaks. In the presence of Mn++, on the other hand, it cleaves
both strand at approximately the same position to yield DNA fragments with
blunt-ends or short protrusions. See "Molecular Cloning".

in article 97fsgp$1c7e$1 at, salanti at ali at wrote on
2/27/01 6:42 PM:

> I am going to make a small library from a 7kb PCR fragment. I plan to
> fragment the big PCR product by sonication, then treat it with Klenow.
> But what happens to the "nicks" in the DNA that will occur from the
> sonication?
> In a protocol using DNAse 1 to digest the DNA, they point out that it is
> important to use a Mn+ buffer instead of Mg+ in order to avoid nicking of
> DNA!! My question is : Is it OK to sonicate DNA for cloning purposes
> Thank you
> Salanti

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