W0387

Structural Origins of the Different RNA Affinities Exhibited by DNAs Containing either 2’-O-(N-Methylcarbamate)- or 2’-O-(N-Methylacetamide)-Thymidines. R Pattanayek¹, C Pan¹, M Prhavc², T P. Prakash², M Manoharan², M Egli¹,¹Dept. of Biological Sciences, Vanderbilt University, Nashville, TN 37235, ²Dept. of Medicinal Chem., Isis Pharmaceuticals Inc., Carlsbad, CA 92008.

Chemically modified nucleic acids that can downregulate protein synthesis by interfering with gene expression at the mRNA level are currently being evaluated as antisense compounds for potential therapeutic applications. An important criterion for the usefulness of a particular modification in an antisense oligonucleotide (AON) is whether it combines improved resistance with enhanced RNA affinity. We are investigating the structural changes in oligonucleotides caused by modifications, with the goal of creating a structural database for oligonucleotide analogs.

The focus of the present study is a detailed understanding of the structural origins of the differences in RNA affinity and duplex stability of AONs with incorporated 2’-O-(N-methylcarbamate)- (NMC) and 2’-O-(N-methylacetamide)- (NMA) T residues. Incorporation of NMC residues results in a reduction of the thermodynamic stability of modified-DNA:RNA duplexes by ca. 2.5°C/nucleotide¹, while NMA incorporation stabilizes modified duplexes by ca. 2.5°C/nucleotide². To allow a direct comparison between the structural properties of the NMC and NMA modifications, the structures of the duplexes [d(GCGTAT*ACGC)]₂ (T*=NMC-T/NMA-T) were determined at 1.25 and 1.30 Å resolution, respectively. A comparison between the conformational properties of the NMC- and NMA-modified residues in the duplex context and the observed stability differences will be presented.