Separation of DNA fragments.

[wetsel_r at wums.wustl.edu]

>jaf-  I have to disagree with a posted followup that says to use a 4% 
>gel; this would work with a smaller fragment but not with 3.4k.
> 
>We have had good luck by digesting the set with an enzyme that cuts in the
>middle of the piece you *don't* want, effectively removing it from the
>piece you do.  It's surprising how often a good enyme for this can be
>found.
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> 
>dennis
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Yes, I agree with Dennis.  However, we have used both techniques to 
separate DNA fragments, high percentage gel and restriction enzyme to 
remove the contaminating band.  Dennis' approach is the better for the 
reasons he stated.  I assumed that enzymes were not a viable option (which 
has occured with our research) leaving us the only option of high 
percentage gel.

If you can "remove" or clear the contaminating band out of the way with an 
enzyme, that's your best approach.

David