posted on 2015-09-18, 00:00authored bySaúl Martínez-Montero, Glen F. Deleavey, Nerea Martín-Pintado, Johans F. Fakhoury, Carlos González, Masad J. Damha
2′-Deoxy-2′,4′-difluorouridine
(2′,4′-diF-rU)
was readily incorporated into DNA and RNA oligonucleotides via standard
solid phase synthesis protocols. NMR and thermal denaturation (Tm) data of duplexes was consistent with the
2′,4′-diF-rU nucleotides adopting a rigid North (RNA-like)
sugar conformation, as previously observed for the nucleoside monomer.
The impact of this modification on Tm is
neutral when incorporated within RNA:RNA duplexes, mildly destabilizing
when located in the RNA strand of a DNA:RNA duplex, and highly destabilizing
when inserted in the DNA strand of DNA:RNA and DNA:DNA duplexes. Molecular
dynamics calculations suggest that the destabilization effect in DNA:DNA
and DNA:RNA duplexes is the result of structural distortions created
by A/B junctions within the helical structures. Quantum mechanics
calculations suggest that the “neutral” effect imparted
to A-form duplexes is caused by alterations in charge distribution
that compensate the stabilizing effect expected for a pure North-puckered
furanose sugar. 2′,4′-diF-RNA modified siRNAs were able
to trigger RNA interference with excellent efficiency. Of note, incorporation
of a few 2′,4′-diF-rU residues in the middle of the
guide (antisense) strand afforded siRNAs that were more potent than
the corresponding siRNAs containing LNA and 2′-F-ANA modifications,
and as active as the 2′-F-RNA modified siRNAs.