Hi
Two types of side reactions have been documented which can account for
N+1, etc. peaks. Fortunately, in both cases, the amount of N+1, etc. peaks
is small and not significant for most research purposes. However, those in
the antisense pharmaceutical industry have had to look very carefully at
them.
In one case, N+1 peaks arise because of detritylation of the
phosphoramidite reagents during the coupling step. The commonly used
tetrazole activator is acidic enough to cause trace detritylation,
especially when prolonged (10 min or longer) coupling times are used. This
problem can be reduced by minimizing coupling times or using less acidic
activators.
In the second case, alkylation of thymine bases by acrylonitrile
(produced by removal of the cyanoethyl protecting groups) produces
impurities which elute after the desired, unmodified products. Alkylation of
this type has been known for quite some time, but the seriousness of it in
oligonucleotide synthesis has just recently begun to be studied. This
problem can be resolved by using a different phosphate protecting group or
by adding a separate phosphate deprotection step to remove acrylonitrile
before proceeding with the rest of the deprotection.
Alain LAURENT wrote:
> Hello
>
> Concerning DNA synthesis and analysis of oligos with anion exchange
> Chromatography.
>
> How do you explain the peaks wich have an higher retention time than
> the main peak (n oligo in Nacl gradient, pH 12) ? Logicallly it should
> be species with higher POO- content. How is that possible ?
>
> Thank You and Best wishes
>
> Alain
>
> **************************************
> Alain LAURENT Ph. D
> DNA&Peptide Chemistry
> ESGS Groupe CYBERGENE
> 11, rue Claude Bernard
> 35 400 Saint MAL0
> FRANCE
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-- Richard T. Pon, Director, University Core DNA Services The University of Calgary, 3350 Hospital Drive N.W., Calgary, AB Canada, T2N 4N1 Tel: Lab. (403) 220-4277; Office (403) 220-4225. Fax: (403) 283-4907 Please direct DNA synthesis or sequencing orders to DNALAB@acs.ucalgary.ca
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