NMR Structure of an Antisense DNA·RNA Hybrid Duplex Containing a 3‘-CH₂N(CH₃)-O-5‘ or an MMI Backbone Linker

Abstract

The solution structure of an antisense DNA.RNA hybrid duplex, d(CGCGTT-MMI-TTGCGC).r(GCGCAAAACGCG) (designated R4), containing an MMI backbone linker [3'-CH(2)N(CH(3))-O5'], is elucidated. The structural details of the MMI linker, its structural effects on the neighboring residues, and the molecular basis of the MMI effects are examined. The lipophilic N-methyl group of MMI is 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 conformation for the sugar moieties at both 3'- and 5'-adjacent positions and a backbone kink involving distant residues along the 3'-direction. Comparison of R4 with other analogous hybrid duplexes previously studied in this laboratory reveals a new family of low-energy helical conformations that can be accommodated 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 duplexes and provide a basis for the understanding of the biological role of the MMI modifications, which are important building blocks for a family of promising chimeric antisense oligonucleotides.

Synthesis and properties of 4'-ThioDNA: unexpected RNA-like behavior of 4'-ThioDNA

“…Thus far, oligonucleotide N3′ → P5′phosphoramidates ( 29 ) and ONs containing 3′-methylene backbones (3′-methylene phosphonate backbone, methylene methylimino backbone and amide backbone) ( 30 – 32 ) composed of 2′-deoxyfuranose-based nucleosides are known RNA-like molecules. The nucleoside units of those modified ONs prefer the 3′-endo sugar conformation in solution ( 31 , 33 ), while that of 4′-thioDNA adopts a 2′-endo sugar conformation in solution and crystals ( 34 ). It is nevertheless worth noting that, despite such structural differences in nucleoside units, 4′-thioDNA can adopt an RNA-like conformation.…”

The Medicinal Chemistry of Therapeutic Oligonucleotides

“…The PO linkage can also be replaced with other nitrogen containing achiral four atom linkages. 74 Sanghvi et al showed that the methylene-(methylimino) (MMI) linkage can be an effective replacement for the PO linkage (Figure 6). 75 Like the amide linkage, the thermal stability of MMI linked dimers can be further enhanced by incorporating a fluorine atom or a methoxy group at the 2′position (ΔT m 3.2 to 3.7 °C per dimer modification).…”

“…The PO linkage can also be replaced with other nitrogen containing achiral four atom linkages . Sanghvi et al showed that the methylene­(methylimino) (MMI) linkage can be an effective replacement for the PO linkage (Figure ).…”

Stabilization of a Bimolecular Triplex by 3′‐S‐Phosphorothiolate Modifications: An NMR and UV Thermal Melting Investigation

“…Planarity constraints were applied to all except the terminal base‐pairs 49. Backbone torsion angles were loosely constrained to a range which encompassed typical values for both A‐ and B‐type helices, in accordance with the literature 49,50. For the modified triplex, torsion angles were not additionally constrained for the Hoogsteen bonded strand 51.…”