Take care with degenerate oligos

Trond Erik Vee Aune teva at online.no
Tue Oct 9 08:10:00 EST 2001

Thanks a lot! I'll remember this for later.

I've recently contacted some companies and asked if they can make my
library after a defined degenerate (also called "spiked"?) oligo that
I've constructed on paper. One of the companies refused and told me it
was not possible, the other said they have one machine able to
accomplish this task. They would charge 300$ for the set-up of the
machine and then normal price for each nucletide incorporated. They had
never received a similar request before, so designing a oligo-library
using degenerate ("spiked"??) oligos is obviously not usual. 

The oligo will be about 60 bps long, so I'm afraid it will cost a lot to
generate a large library.

Kind regards,
Trond Erik Vee Aune


"Hartley, Jim" wrote:
> It is very important to verify that the mixture of bases you specify is what
> is delivered.  Since there are eleven different base combinations, it is
> unlikely that any vendor will make up eleven different mixtures of amidites
> (very expensive and labile), and far more likely that the synthesizer will
> deliver a squirt of this, then a squirt of that, or some other less costly
> scheme.  I know someone who ordered an oligo with a number of N's and
> assumed that he would get approximately 25% of each base at those positions.
> But it turned out the N's were 70% G.  If getting anything like the
> degeneracy you order is critical to your experiment, you should call the
> vendor and ask how they achieve their degeneracies, i.e., what the plumbing
> details are, and how they know they deliver what they claim (different
> amidites have different reactivities). They may give you a refund but they
> can't give you back the time you waste.
> Jim Hartley
> jhartley at lifetech.com
> ---

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