Avoid some cheap oligos

Ransom Hill Bioscience visla at ix.netcom.com
Wed Apr 22 13:46:36 EST 1998


In article <353E0E1B.865722D4 at uchc.edu>,
	Zheng-yu Peng <peng at uchc.edu> wrote:

>Everyone knows that cheap is not always the best.  But when comes to
>oreder large number of oligonucleotides for our alanine scanning
>project, we found "Genemed Synthesis" in California who had an Ad. in
>the back of "Science" claiming charging only 70 cents per base. What a
>good deal, plus, they gave us  a further discount  since we were
>ordering large volume of oligos at the same time.  We have ordered, over
>the past half year or so, over 60 oligos for site-directed mutagenesis,
>for linkers, or for using as sequencing primers.  The result:  many
>double mutations (some triple mutations) were found in our genes
>although the oligo were designed for getting single mutations.   For
>those which were used as linkers,  missing bases were found at the
>linker region whcih caused frame shift.  However, we think the oligos
>used as sequencing primers are fine.  So our experience is:  for
>sequencing primer, it is OK to order from them but  we won't trust their
>oligos to be used for any other purpose.
>
>Some of the same oligo designs were then ordered from other companies
>and the results were all fine.
>

 I find myself in the unusual position of coming to the defense of one of the companies that
competes with us, since we (Ransom Hill Bioscience, and our subsidiary company, The Great
American Gene Company) are also suppliers of oligos.

 I believe that the blame is not with GeneMed, or any other supplier, and I firmly believe that
there is little, if any, real difference in quality between suppliers of oligos. The simple fact
of the matter is that years ago, when synthetic oligos were a "new and wonderful" thing,
researchers read about them, and they understood the limitations of the underlying chemistry. In
the intervening years, those limitations have not changed but the perceptions of the users of
oligos have. Nowadays, oligos are thought of much the same as eppendorf tubes or pipet tips,
i.e. as a commodity. Unfortunately, it is not true.

 Three of the bases, A,G, and C are susceptible to a large number of chemical modifications, and
these accumulate so as to make longer oligos particularly vulnerable to damage. Oligos in the
20-mer range are ALWAYS going to be of better quality than oligos in the 40-mer range, and those
are going to be of better quality than oligos in the 60-mer range, and so on.

 Indeed, it is no more fair to point a finger at GeneMed, or any other supplier than it is for
GeneMed (or other supplier) to say that scientists from a particular country have a higher
problem rate with synthetic oligos. 

 With oligo, as with any other tool, an if you take the time to educate yourself about their
strengths and limitations, you will find that your results get a lot better. You will probably
find that even "poor quality" oligos start to work for you.

 Best Regards,
 Mike MacDonell, Ph.D.
 Chief Scientific Officer
 Ransom Hill Bioscience, Inc.




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