title: Locked 2'-Deoxy-2',4'-Difluororibo Modified Nucleic Acids: Thermal Stability, Structural Studies, and siRNA Activity.
abstract: 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.
authors.affiliation: Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8.
authors.forename: Saúl
authors.initials: S
authors.lastname: Martínez-Montero
authors.affiliation: Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8.
authors.forename: Glen F
authors.initials: GF
authors.lastname: Deleavey
authors.affiliation: Instituto de Química Física Rocasolano , CSIC, C/. Serrano 119, 28006 Madrid, Spain.
authors.forename: Nerea
authors.initials: N
authors.lastname: Martín-Pintado
authors.affiliation: Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8.
authors.forename: Johans F
authors.initials: JF
authors.lastname: Fakhoury
authors.affiliation: Instituto de Química Física Rocasolano , CSIC, C/. Serrano 119, 28006 Madrid, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: González
authors.affiliation: Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8.
authors.forename: Masad J
authors.initials: MJ
authors.lastname: Damha
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D005467:Floxuridine / Q000031:analogs & derivatives* / Q000737:chemistry; D006367:HeLa Cells; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics
chemical_list: C000593434:2'-deoxy-2',4'-difluorouridine; D009841:Oligonucleotides; D034741:RNA, Small Interfering; D005467:Floxuridine; D012313:RNA; D004247:DNA