Make a d-strand from ss oligonucleotide ?

Dave.Segal ds1539 at u.cc.utah.edu
Fri Nov 26 22:22:12 EST 1993


WANGNN at UCBEH.SAN.UC.EDU wrote:
: Hi Netters:

: I am going run the gel retardation to show the band shifting using my protein
: and a small fragment DNA.   The small fragment is about 20 bases, which is
: planned to  be synthesized.  For sure, the synthesis of a 20-mer of
: oligonucleotide is much cheaper than that of two strands to make a ds DNA.

: My question is if some methods can be used to synthesis such small ds DNA
: fragment (20bp) from the single strand oligonucleotide. 

: Any suggestion will be appreciated.

Dear Hong,
All DNA polymerases require a short primer to initiate synthesis.  Even RNA
polymerases require a promoter site.

If you were really clever, you could design a DNA hairpin structure which 
would fold back on itself to give you a double-stranded region (really 
just a big stem-loop).  You could use the Zucker folding program 
(available on several computer platforms) to help predict the folding, and
you would have to be sure to anneal at low concentration to avoid 
intermolecular annealing.  This would allow you to save the setup charge
associated with oligo synthesis, but the oligo would naturally have to 
be about 50 nt.

However, IMHO, even that would be a waste of time (because of new
uncertainties, prification of full length oligo, etc...) and money. 
Perhaps the best method is to use a crowbar on your wallet and spring for
the second 20-mer.  And quite frankly, this would produce the most
convincing result.

Good luck!

- Dave Segal
- Biochemistry, U. of Utah
- Dave.Segal at m.cc.utah.edu
  



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