An approach to the structure determination of nucleic acid analogues hybridized to RNA. NMR studies of a duplex between 2′-OMe RNA and an oligonucleotide containing a single amide backbone modification

摘要

The backbone modification amide-3, in which -CH₂-NH-CO-CH₂- replaces -C5'H₂-O5'-PO₂-O3'-, is studied in the duplex d(G₁-C₂-G₃-T₄-T₅-G₆-C₇-G₈)mr(C₉-G₁₀-C₁₁-A₁₂-A₁₃-C₁₄-G₁₅-C₁₆) where indicates the backbone modification and mr indicates the 2′-0Me RNA strand. The majority of the exchangeable and non-exchangeable resonances have been assigned. The assignment procedure differs from standard methods. The methyl substituent of the 2′-0Me position of the RNA strand can be used as a tool in the interpretation. The duplex structure is a right-handed double helix. The sugar conformations of the 2′-0Me RNA strand are predominantly N-type and the 2′-0Me is positioned at the surface of the minor groove. In the complementary strand, only the sugar of residue T₄ is found exclusively in N-type conformation. The incorporation of the amide modification does not effect very strongly the duplex structure. All bases are involved in Watson - Crick base pairs.