What is the maximum length of synthetic oligonucleotide ?

Dr. Michael T. MacDonell sendero at ix.netcom.com
Tue May 13 10:07:42 EST 1997


Dear Troels:

The information you received is not entirely
correct. You can make a 200-mer since coupling
efficiencies are good enough these days to allow
it. The oligo will be seriously impacted by spurious
chemical damage, however, and this CANNOT be
purified by any means whatever.  The simple fact
is that the underlying chemistry does not support
the synthesis of very long oligos. You can link
the monomers together, but the product will be
suspect.

You will notice that most suppliers of synthetic
oligos get nervous about oligos longer than about
60 bases. The reason is that the cumulative damage
begins to be significant, and results in mis-
reading, etc. at about that length.

Some of the most common chemical errors include
transamination of C, and the generation of 
diaminopurine through the phosphitylation of G.
The latter misreads as A.

So, there are TWO answers. If you just want to
make an oligo, and do not actually require 
sequence (or reading) fidelity, the answer is
"more than 200 bases". If you have a restriction
site in it, you should start getting nervous at
about 55 bases or thereabouts.

Being in the business, I can tell you that, to
the best of my knowledge, everyone supplying
synthetic oligos is doing an excellent job of
it. Nobody can work miracles, and all of us
are constrained by the limitations of the under-
lying chemistry.

Best Regards!
Mike


In article <5l9pr7$p0l at bioalp.biobase.dk>,
	wind at biobase.dk (Troels Wind) wrote:
>Lee Jae-Hyun (leejh at worak.kaist.ac.kr) wrote:
>: Is there anybody who knows about the maximum length of synthetic
>
>: oligonucleotide commercially available ?
>
>: And where can I get those long synthetic oligonucleotide ?
>
>I just talked to the company from where I usually by my oligos and asked
>them if it would be a problem to get a 75mer. Thet said that it wouldnt
>be a problem, as long as the oligo is purified by HPLC or the like.
>The issue (according to the company) is that the coupling reaction has
>a 99% efficiency, therefore increasing amounts of shorter oligos will
>be present in the final pool as the oligo gets longer, and of course these has
>to be removed by purification. 
>I dont know if there is a practical maximum...
>
>Troels
>





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