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Nucleic Acids Research, Vol 24, Issue 5 890-897, Copyright © 1996 by Oxford University Press

ARTICLES

Synthesis and characterization of 8-methoxy-2'- deoxyadenosine- containing oligonucleotides to probe the syn glycosidic conformation of 2'-deoxyadenosine within DNA

RG Eason, DM Burkhardt, SJ Phillips, DP Smith and SS David
Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.

The synthesis of 8-methoxy-2'-deoxyadenosine (moA) protected at N6 as an N,N-dimethylformamidine derivative and incorporation of the modified nucleoside into oligodeoxynucleotides via the phosphoramidite method are described. UV thermal denaturation studies were conducted on duplexes containing moA:G, moA:C and moA:T base pairs to determine the thermodynamic stability of duplexes containing moA relative to their adenosine (A)-containing counterparts. In the case of moA:G base pairs the effect of moA substitution is sequence dependent. In A:G mismatch- containing sequences, which have been shown by structural characterization to have a syn conformational preference at the glycosidic bond of A, moA substitution results in stabilization of the duplex. In contrast, in sequences where the A in the A:G mismatch has been shown to prefer the anti conformation moA substitution is destabilizing to the duplex. Thus moA may be a useful probe for investigating the conformational preferences of the N-glycosidic bond of adenosine within DNA. In addition, moA nucleoside is more resistant to acid-catalyzed depurination than previously described 8-bromo-2'- deoxyadenosine, allowing for facile incorporation into oligonucleotides via automated solid phase DNA synthesis.
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