NMR structure of an antisense DNA center dot RNA hybrid duplex containing a 3 '-CH2N(CH3)-O-5 ' or an MMI backbone linker

The solution structure of an antisense DNA RNA hybrid duplex, d(CGCGTT-MMI- TTGCGC). r(GCGCAAAACGCG) (designated Ri), containing an MMI backbone linker [3'-CH2N(CH3)-O5'], is elucidated. The structural derails of the MMI linke r, its structural effects on the neighboring residues, and the molecular ba sis of the MMI effects are examined. The lipophilic N-methyl group of MMI i s peripheral to the helix, assuming a conformation that is most stable with regard to the N-O torsion angle. The MMI Linker promotes a 3'-endo conform ation for the sugar moieties at both 3'- and 5'-adjacent positions and a ba ckbone kink involving distant residues along the 3'-direction. Comparison o f R4 with other analogous hybrid duplexes previously studied in this labora tory reveals a new family of low-energy helical conformations that can be a ccommodated in stable duplexes and a common feature of C3'-modified sugars for adopting a C3'-endo pucker. The results of these studies emphasize the interplay of several factors that govern the formation of stable hybrid dup lexes and provide a basis for the understanding of the biological role of t he MMI modifications, which are important building blocks far a family of p romising chimeric antisense oligonucleotides.