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Nucleic Acids Research, 1987, Vol. 15, No. 4 1729-1743
© 1987

Articles

Mechanistic studies on the phosphoramidite coupling reaction in oligonucleotide synthesis. I. Evidence for nudeophilic catalysis by tetrazole and rate variations with the phosphorus substituents

Bjarne H. Dahl, John Nielsen and Otto Dahl*

Department of General and Organic Chemistry, The H.C.Ørsted Institute, University of Copenhagen, Universitetsparken 5 DK-2100 Copenhagen, Denmark

*To whom correspondence should be addressed

Received December 30, 1986. Accepted January 21, 1987.

Tetrazole catalyzed reactions of a series of phosphoramidites, 5' -O- DMTdT-3'-O-P(OR1)NRFormula (1a-h), with 3' O-SiButPh2-6-N-benzoyl-dA (2a) in acetonitrite solution have been studied. It is found that the coupling rate depends very much on whether tetrazole is added before or after 2a, and that dialkylammonium tetrazolide salts are inhibitors. These and other facts are evidence that the reactions are subjected to nucleophilic catalysis by tetrazole, in addition to acid catalysis. The rate variations with phosphorus substituents of 1a-h are NEt2 > Formula > N(CH2CH2)O > NMePh, and OMe > OCH2CH2CN > OCHMeCH2CN > OCMe2CH2CN >> OC6H4Cl. The inhibitor properties of dialkylammonium tetrazolides have practical consequences for the efficiency of DNA syntheses, when in situ prepared phosphramidites are used; the same would apply for segmented simultaneous syntheses or syntheses where recycling is performed.


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