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

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• 作者：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
• 刊名：Journal of the American Chemical Society
• 出版年：2011
• 出版时间：October 19, 2011
• 年：2011
• 卷：133
• 期：41
• 页码：16642-16649
• 全文大小：1012K
• 年卷期：v.133,no.41(October 19, 2011)
• ISSN：1520-5126

文摘

The synthesis, biophysical, structural, and biological properties of both isomers of 3鈥?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鈥?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鈥揊路路路H鈥揅 pseudo hydrogen bond between F3鈥?of Ara-FHNA and C8鈥揌 of the nucleobase from the 3鈥?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)路路路H鈥揅(Pu) pseudo hydrogen bonds in nucleic acid structures.