SS dna analysis

Darren Natale camdna at ubvmsb.cc.buffalo.edu
Fri Feb 12 14:58:00 EST 1993


In article <12FEB199307160147 at aardvark.ucs.uoknor.edu>, broe at aardvark.ucs.uoknor.edu (Bruce Roe) writes...
>In article <44864 at sdcc12.ucsd.edu>, wsun at jeeves.ucsd.edu (Fiberman) writes...
>>Hello, netters,
>> 
>>What kind of gels can I run to analyze my SS DNA?  Maniatis says
>>to use alkali gels, but then it says I need to radiolabel the SS
>>DNA to see it.  Is there an easier way?  And how would SS DNA
>>migrate compared to DS DNA?
>> 
>>-fm
> 
>	This depends on the size of your ssDNA,  for ssM13's
>just run out on an agarose gel (we use Tris/Acetate/EDTA gels).
>As for ssDNA oligo's, use PAGE (such as a sequencing gel without urea).
>To visualize the ssM13 use ethidium bromide (there's enough secondary
>structure to get the dye to bind) and for oligos try UV shadowing.
>As for migration, ssM13's travel faster than dsSuperCoiled m13Rf on
>our agarose gels.

ssDNA can be easily visualized using acridine orange. It stains ds and
ssDNA differently (one is orange, the other is green) when viewed under
UV light. I don't have any details (I can't find my copy of the paper
describing its use :( ) but the reference is McMaster and Carmichael (1977)
PNAS 74:4835-4838.

DN



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