Oligonucleotide purification

[Edward Wang]

Lynn Hughes (lynn.hughes at jcu.edu.au) wrote:
: Hello, I'm hoping someone can help me with the following problem.  I have 
: 2 10mer oligonucleotides which I want to anneal, they will give me a 
: HindIII sticky end, 6 base pair double stranded region then an EcoRI 
: sticky end.  This should be easier enough to do.  However I then need to 
: purify this configuration away from my starting  2 single stranded 
: oligos, and I am not sure how to do this.  Being such a small fragment of 
: DNA I don't think I will be able to use methods such as kits available 
: for purifying DNA from agarose gels.  If anyone has any methods I could 
: try I'd be very grateful to hear from them
: 
: Thanks
: 
: Lynn Hughes

Could you not let the EcoRI end stick to a longer piece of DNA with an
EcoRI end, and then gel purify that (acrylamide?). and then, cut the piece
off?  Or am I completely off the mark?
Or maybe just run a non-denaturing acrylamide gel.  The single and double
stranded DNA will run differently on a gel.  I am pretty sure you could
run a 10 mer on a gel because the oligo synthesis guy here always run the
primers (finished product) on a acrylamide gel to check the quality.  Let
me know if my ideas help at all...




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Edward H. Wang                 *
Staff Resch. Assc.             *
Dept. Internal Med. -Nephrology*
UC Davis                       *
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