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Nucleic Acids Research, 1994, Vol. 22, No. 20 4187-4194
© 1994

STRUCTURAL BIOLOGY

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

M.J.J. Blommers*, U. Pieles1 and A.De Mesmaeker1

Physics Research PO Box, CH-4002 Basel, Switzerland 1Central Research, Ciba-Geigy AG PO Box, CH-4002 Basel, Switzerland

*To whom correspondence should be addressed

Received September 21, 1994. Revised September 25, 1994. Accepted August 25, 1994.

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.


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