what is the effect of a 5' overhang on gel mobility

Mr JN Goulding jgouldin at hgmp.mrc.ac.uk
Thu Jan 18 07:02:30 EST 2001


I have a 20bp marker ladder which works well; it's by advanced
biotechnologies (I think, but I can't find my it at the moment)

Jon

On Thu, 11 Jan 2001, Susanne Rohrer wrote:

> 

> "WILLIS GAVIN (RM1) Norfolk and Norwich NHS Trust" wrote:
> 
> > The product will be about 25bp. The reason I want it to migrate at the same
> > speed is that there is another 25bp fragment that will be present in mutant
> > individuals. I will then get 50 bp =normal, 25 bp = mutant. Because thy are
> > so small the fragments are pretty faint so co migration would be nice though
> > not essential. Under the conditions I am using there is also a nice window
> > around 25 bp between  primer related artefact and other restriction
> > fragments. I don't want to denature because that would make the fragments
> > hard to see and the pattern more complex.
> 
> I'd try to use oligos. as a standard. either go through the trouble and do a
> denaturing gel or use annealed, complementary oligos. or see if any supplier
> sells really small markers. I'd definitely go for an acrylamide gel (10% or
> higher) rather than low melting agarose.
> 
> 






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