Synthesis, Improved Antisense Activity and Structural Rationale for the Divergent RNA Affinities of 3'-fluoro Hexitol Nucleic Acid (FHNA and Ara-FHNA) Modified Oligonucleotides

Overview

Journal J Am Chem Soc

Publisher American Chemical Society

Specialty Chemistry

Date 2011 Sep 17

PMID 21919455

Citations 18

Authors

Martin Egli

Pradeep S Pallan

Charles R Allerson

Thazha P Prakash

Andres Berdeja

Jinghua Yu

Sam Lee

Andrew Watt

Hans Gaus

Balkrishen Bhat

Eric E Swayze

Punit P Seth

Affiliations

Soon will be listed here.

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.

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