detection of small changes in DNA size

[Bart Janssen]

In article <42o7u3$ogj at elaine3.Stanford.EDU>, ladasky at leland.Stanford.EDU
(John Ladasky) wrote:

> In article <DEJIGp.32I at uns.bris.ac.uk>,
> AJ. Murray <biajm at zeus.bris.ac.uk> wrote:
> >I have a 6.4kb vector with EcoRI and BamHI sites 9bp between the cut 
> >sites. I would like to be able to detect on a gel if the enzymes are both 
> >cutting, either by seeing the 9bp fragment on a gel, or detecting the 
> >difference in the vector size. 
> 
>         Well, you don't have a snowball's chance of seeing the difference in
> vector size.  If you pour a high-molecular weight acrylamide gel (>8%?), you
> might be able to see your 9 bp band.

Bio101 make a special agarose that they use for separating oligos. 
According to their pictures you can easily see 12bp oligos on a 6% gel. 
I've never tried it.

Personally the way I do what you are trying to do is run single digests
with each enzyme to confirm that the enzyme/DNA is OK then just cut with
the second enzyme and *believe* that they've both cut.  The NEB catalogue
has a great table showing which enzymes have trouble cutting near the end
of the DNA, very few enzymes have problem with a 9 bp "tail", and EcoRI
and BamHI definately don't have problems.

cheers
Bart