separation of ds-oligo (21-mer) from ss-oligo (also 21-mer)

Ingrid Jakobsen ingrid at
Tue Dec 21 01:52:23 EST 1993

This is indirectly related, but if you silver-stain an acrylamide gel,
the double-stranded DNA will be black and the single-stranded DNA more
a reddish colour. As Opus pointed out, glycerol is great for changing 
the relative mobility of single and double-stranded DNA, but it seems 
to vary a great deal whether it's the single or double stranded fragments
that run faster, hence the silver staining test.


In article <17DEC199318533382 at>, cjones at (OPUS) writes:
|> > 
|> >I trying to crystallize a DNA binding protein with its oligonucleotide
|> >binding site.  I have annealed two complementary single stranded 21-mers
|> >with a one base pair overhang on each end of the annealed product (A and T).
|> >The ss-oligos were HPLC purified prior to annealing.
|> > 
|> >When I run a 20% PAGE gel on the annealed product, I see two bands:  one
|> >is the more heavily staining band and the other (about 3-4 times less intense)
|> >is of lower molecular weight.
|> > 
|> >My question is twofold:  Does the lower MW band correspond to excess ss-oligo
|> >from the annealing reaction and, if so, how can I separate the ss from ds
|> >oligonucleotides??!
|> > 
|> >Is there some sort of nitrocellulose filter that I can use such that the ss
|> >DNA will stick and the ds DNA will go through the membrane?
|> > 
|> >Any advice would be a great help.
|> > 
|> >Thank you,
|> >Rob Willard
|> >The Wistar Institute/University of Pennsylvania Chemistry Department
|> hi, 
|>  i have been purifying a 120 BP frag from PCR and i see lots of single stranded
|> contamination of my fragment. there is a article by maniatas (in biochemistry, i
|> but can't find the ref) that gives the relative mobility of SS & DS DNA in
|> a variety of gel concentrations. I have successfully used a 10% acrylamide gel
|> with 5% glycerol in 0.5X TBE to separate the ss & ds species. I cut the bands
|> out of the gel, crush them with a glass rod, and elute with oligo extraction
|> buffer (Maniatas). I get ~90% recovery of my fragment. 
|>   If you are staining your gels with EtBr, then the heavily stained band is 
|> probably ds DNA, and the lighter is ss.
|> good luck
|> clyde jones
|> Clyde Jones       |       "There ain't no devil,
|> Tufts University  |         Just God when he's drunk"
|> 136 Harrison Ave  |              -Tom Waits
|>  Arnold 703       |
|> Boston MA 02144   |
|> 617/956-6874      |

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