Structural Characterization and Biological Evaluation of Small Interfering RNAs Containing Cyclohexenyl Nucleosides

CeNA is an oligonucleotide where the (deoxy)ribose sugars have been replaced by cyclohexenyl
moieties. We have determined the NMR structure of a CeNA:RNA duplex and have modeled this duplex
in the crystal structure of a PIWI protein. An N puckering of the ribose nucleosides, a 2H3 conformation of
the cyclohexenyl nucleosides, and an A-like helix conformation of the backbone, which deviates from the
standard A-type helix by a larger twist and a smaller slide, are observed. The model of the CeNA:RNA
duplex bound to the PIWI protein does not show major differences in the interaction of the guide CeNA
with the protein when compared with dsRNA, suggesting that CeNA modified oligonucleotides might be
useful as siRNAs. Incorporation of one or two CeNA units in the sense or antisense strands of dsRNA led
to similar or enhanced activity compared to unmodified siRNAs. This was tested by targeting inhibition of
expression of the MDR1 gene with accompanying changes in P-glycoprotein expression, drug transport,
and drug resistance.