Borate and DNA

Rafa Maldonado Rafael at
Fri Mar 4 18:48:06 EST 1994

> >> I have heard that borate can cause DNA damage so that some people stay away
> >> from borate containing buffers when the want to use the DNA for further
> >> cloning. 
> > The one time you can't
> > use TBE is when you intend to gel purify a fragment for ligation as the
> > borate inhibits the ligase (I don't know if this means *all* ligases).
> > Then I use TAE and run the gel overnight at low voltage.

I have been using TBE for everything too (Southern blots, probe
purification, insert purification for ligation and even melting and
ligation in agarose) and I have not had problems in any sense. Only in
Geneclean extractions. I think all the trouble is in using this usual
and lovely kit with borate, so *someone* have deduced that borate is
bad for DNA, and it isn't true. Borate is bad for disolving agarose
with INa and further binding of DNA to glassmilk, but nothing happens
to DNA.
Of course, enzymes ( T4 ligase among them) are inhibited by borate. But
also by acetate, NaCl, normal dirt, and many more things (obvious!),
it's only a question of concentration... Feel free of using TBE. It's
works better than TAE or TPE and your DNA will be happy and your
ligases too!

In my hands!


Rafael Maldonado
Howard Hughes Medical Insitute
University of Utah
Rafael at

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