running ssDNA (30-1000nt) in denatured conditions

TC via methods%40net.bio.net (by tracyscience from gmail.com)
Tue Nov 4 14:51:37 EST 2008


Hi all,

I am trying to run DNA under denatured conditions. Has anyone run single
stranded DNA (30nt to 1000nt) under denatured conditions.

I am trying to decide whether to run a low percentage urea acrylamide gel or
an alkaline agarose gel.  Any thoughts/ideas?  I am thinking maybe running a
low percentage (3-4%) urea acrylamide gel, but wonder that it may not be
able to resolve ssDNA above couple hundred nucleotides in length even in low
acrylamide such as 3-4%?  Any thoughts?  Has anyone run alkaline agaorse for
ssDNA 30nt-1000nt?  If so, may I ask for your conditions?

THANKS!

Tracy


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