Oligos: Who is cheapest?

The Great American Gene Company geneco at ix.netcom.com
Wed Feb 12 13:33:25 EST 1997

In article <5dsum6$177k at piglet.cc.uic.edu>,
	levenson at uic.edu (Victor Levenson) wrote:

>cstryker at unlinfo.unl.edu (cynthia stryker) wrote:
>>Who is the cheapest supplier of oligos these days?  We need small 
>>scale, 40 nm, primarily for primers.  TIA!  Cindy, UNL
>Keep in mind that SOME cheap oligos are  ... "incorrect", let's put it
>this way: a friend recently has encountered this problem, when, after
>amplificvation he sequenced several ends and found out that the primer
>was "slightly" off base - enough to send him to step 1 of his
>On the other hand, IDT and GreatAmericanGeneCompany, are probably the
>least expensive and still OK for routine amplification (GAGC charges
>$0.85 per base for 5 OD, EtOH precip; IDT slightly higher)
>No affiliation, blah,blah,blah.
>Res Asst Prof
>UIC, Dept of Genetics
>levenson at uic.edu 

 Dear Victor et al.

Here are the things you need to know about synthetic oligos:
(1) The quality, regardless of supplier, is pretty much the same, since the
amidites and the chemicals all come from a handful of sources.
(2) The oligo is very often not the problem.  Look at other threads in this
newsgroup relating to error rates in various polymerases, refusal of some
polymerases to deal with inosines, etc.  Possibly the oligo IS the problem,
but is unfair to everyone to conclude that everything else MUST be okay.
(3) If it is the oligo, it is almost never a sequence problem.  It is much
more likely that it is either:
  (a) wrong oligo (humans make mistakes, i.e. somebody else got yours)
  (b) failure of the underlying chemistry (synthetic oligos are not perfect
because the underlying chemistry is not perfect), particularly important
with longer oligos.
  (c) synthesizer failure.  Sometimes poor upkeep, sometimes poor
maintenance of equipment.

It is important to understand that no supplier can possibly sequence the
oligos for quality control.  If there were chemical errors, or synthesizer
failures, for example, they do not turn up in QC.  All you can do is look at
the trityl (a qualitative evaluation of whether or not there was an overt
failure during synthesis), then look at the oligo by denaturing gel
electrophoresis.  It it is a single band and appears where it should, you
must assume that it was competently synthesized.  Unless, of course, you
have a bunch of boneheads running the place.

-Mike (obviously an affiliation)

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