Locked 2′-Deoxy-2′,4′-Difluororibo Modified Nucleic Acids: Thermal Stability, Structural Studies, and siRNA Activity

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 (T m) data of duplexes was consistent with the 2′,4′-diF-rU nucleotides adopting a rigid North (RNA-like) sugar conforma...

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Bibliographic Details
Published in:ACS chemical biology 2015-09, Vol.10 (9), p.2016-2023
Main Authors: Martínez-Montero, Saúl, Deleavey, Glen F, Martín-Pintado, Nerea, Fakhoury, Johans F, González, Carlos, Damha, Masad J
Format: Article
Language:English
Subjects:
Base Sequence
DNA - chemistry
Floxuridine - analogs & derivatives
Floxuridine - chemistry
HeLa Cells
Humans
Models, Molecular
Nucleic Acid Conformation
Nucleic Acid Denaturation
Oligonucleotides - chemistry
RNA - chemistry
RNA Interference
RNA, Small Interfering - chemistry
RNA, Small Interfering - genetics
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Summary: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 (T m) 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 T m 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.
ISSN:1554-8929
1554-8937
DOI:10.1021/acschembio.5b00218