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

Susanne Rohrer "srohrer(removethis)" at immv.unizh.ch
Thu Jan 11 11:59:15 EST 2001



"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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