Abbarent migration in agarose gels: interesting problem

un691cs at un691cs at
Fri Jul 25 02:28:19 EST 1997

Hello, I have an interesting problem.

I PCR a plasmid with one 3' primer, and several about 10 
5' primers:

                 ---->                             <----

the 3' primer is always the same.
As I know the promoter sequence in this construct, I 
can accuredly predict the size of the expected PCR products (150-1500bp).
I get single bands in each lanes, the PCR worked well, as far as i 
can see, products were checked by southern hybridization.

Now what happens is that several bands  do not run at the position
where I would expect them to migrate. This on a 2% gel. Then, If I run
the samples on a 1% gel, the positions of the bands are altered again,
but again not always to the expected position. for instance: a 450 bp signal
migrates as 800 on a 1% gel ! I can exclude a mix-up of samples.

Is my DNA 'bend' or what ? Where in the literature can I get additional 
info on this ? 

Could you answer by e-mail as well ?

thanks, Clemens

Uni Heidelberg 

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