title: Synthesis, improved antisense activity and structural rationale for the divergent RNA affinities of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides.
abstract: The synthesis, biophysical, structural, and biological properties of both isomers of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides are reported. Synthesis of the FHNA and Ara-FHNA thymine phosphoramidites was efficiently accomplished starting from known sugar precursors. Optimal RNA affinities were observed with a 3'-fluorine atom and nucleobase in a trans-diaxial orientation. The Ara-FHNA analog with an equatorial fluorine was found to be destabilizing. However, the magnitude of destabilization was sequence-dependent. Thus, the loss of stability is sharply reduced when Ara-FHNA residues were inserted at pyrimidine-purine (Py-Pu) steps compared to placement within a stretch of pyrimidines (Py-Py). Crystal structures of A-type DNA duplexes modified with either monomer provide a rationalization for the opposing stability effects and point to a steric origin of the destabilization caused by the Ara-FHNA analog. The sequence dependent effect can be explained by the formation of an internucleotide C-F···H-C pseudo hydrogen bond between F3' of Ara-FHNA and C8-H of the nucleobase from the 3'-adjacent adenosine that is absent at Py-Py steps. In animal experiments, FHNA-modified antisense oligonucleotides formulated in saline showed a potent downregulation of gene expression in liver tissue without producing hepatotoxicity. Our data establish FHNA as a useful modification for antisense therapeutics and also confirm the stabilizing influence of F(Py)···H-C(Pu) pseudo hydrogen bonds in nucleic acid structures.
authors.affiliation: Department of Biochemistry, School of Medicine, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37232, USA. martin.egli@vanderbilt.edu
authors.forename: Martin
authors.initials: M
authors.lastname: Egli
authors.forename: Pradeep S
authors.initials: PS
authors.lastname: Pallan
authors.forename: Charles R
authors.initials: CR
authors.lastname: Allerson
authors.forename: Thazha P
authors.initials: TP
authors.lastname: Prakash
authors.forename: Andres
authors.initials: A
authors.lastname: Berdeja
authors.forename: Jinghua
authors.initials: J
authors.lastname: Yu
authors.forename: Sam
authors.initials: S
authors.lastname: Lee
authors.forename: Andrew
authors.initials: A
authors.lastname: Watt
authors.forename: Hans
authors.initials: H
authors.lastname: Gaus
authors.forename: Balkrishen
authors.initials: B
authors.lastname: Bhat
authors.forename: Eric E
authors.initials: EE
authors.lastname: Swayze
authors.forename: Punit P
authors.initials: PP
authors.lastname: Seth
mesh_terms: D008958:Models, Molecular; D008968:Molecular Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D013237:Stereoisomerism; D013402:Sugar Alcohols / Q000737:chemistry*
chemical_list: D009696:Nucleic Acids; D009841:Oligonucleotides; D013402:Sugar Alcohols; C543192:hexitol; D012313:RNA