HELP ! get DNA (< 500bp) out of gel

Nico Dantuma N.P.Dantuma at biol.ruu.nl
Sat Jun 15 09:54:19 EST 1996


ez026048 at rocky.ucdavis.edu (Hong Lin) wrote:

>I had problem of isolating small DNA fragments from gel. I had tried 
>promega "Wizard" DNA purification system and Bio 101 Geneclean product.
>Both did not end up satisfied result. I have no problem, however, in 
>isolating longer DNA fragment (eg >1000 bp) using the same methods above. 
>I did slightly modify the procedure; for example, add 5 ul of 10% of 
>acetic acid for each ml of NaI in Bio-101 geneclean kit, or incubation 
>DNA samples before elute it out. I guess, I can only get less than 20 % 
>of recovery from gel.
>Can anyone provide any information or advice for eluting small bp DNA out of 
>gel with satisfied recovery. Or other alternative methods (I had tried 
>dialysis method too). Thanks in advance

Why do you think the poor recovery of the small fragment is due to
elution from the gel. I would assume that it is mainly caused by a
substantial loss of the DNA during precipitations, as you do not have
poor recoveries with the larger fragments, which are more difficult to
elute but easier to precipitate. The poor precipitation of small DNA
fragments is a well known problem, that can be solved by precipitating
the fragments in the presence of carrier molecules, for example
linearized acrylamide. I think that protocols can be found in standard
manuals.

Nico Dantuma 




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