Synthesis and Properties of 2′-Deoxy-2′,4′-difluoroarabinose-Modified Nucleic Acids

Abstract

We report the synthesis, thermal stability, and RNase H substrate activity of 2′-deoxy-2′,4′-difluoroarabino-modified nucleic acids. 2′-Deoxy-2′,4′-difluoroarabinouridine (2,′4′-diF-araU) was prepared in a stereoselective way in six steps from 2′-deoxy-2′-fluoroarabinouridine (2′-F-araU). NMR analysis and quantum mechanical calculations at the nucleoside level reveal that introduction of 4′-fluorine introduces a strong bias toward the North conformation, despite the presence of the 2′-βF, which generally steers the sugar pucker toward the South/East conformation. Incorporation of the novel monomer into DNA results on a neutral to slightly stabilizing thermal effect on DNA–RNA hybrids. Insertion of 2′,4′-diF-araU nucleotides in the DNA strand of a DNA–RNA hybrid decreases the rate of both human and HIV reverse transcriptase-associated RNase H-mediated cleavage of the complement RNA strand compared to that for an all-DNA strand or a DNA strand containing the corresponding 2′-F-araU nucleotide units, consistent with the notion that a 4′-fluorine in 2′-F-araU switches the preferred sugar conformation from DNA-like (South/East) to RNA-like (North).

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

“…The therapeutic potential use of LNA (27) has led to the synthesis of a wide number of related analogues known as BNAs (bicyclic nucleic acids) (28). Our laboratory has had a long standing interest in nucleosides modified with fluorine at C2´ (11,(29)(30)(31)(32)(33) and more recently at both the C2´ and C4´ positions (34,35). 4´-Fluoro nucleosides are relatively unexplored in the literature, investigated in only a handful of studies (36)(37)(38)(39)(40), most of which encountered acid instability of the glycosidic linkage, which precluded these molecules from further studies and incorporation within oligonucleotides.…”

Synthesis and Antisense Properties of 2′β-F-Arabinouridine Modified Oligonucleotides with 4′-C-OMe Substituent

“…Since the RNA-selective hybridization ability was highly related to the conformational preorganization of the sugar, we investigated the 1 H– 1 H J -coupling constants of H2″/H3′ and H1′/F2′ to determine the sugar conformation. According to the Karplus equation’s prediction [ 17 ], a northern conformer will have a large 3 J H2″H3′ coupling constant, whereas a southern conformer will have a large 3 J H1′F2′ value. The experimental 3 J H2″H3′ and 3 J H1′F2′ values of 2′-F,4′- C -OMe–araU in D 2 O were 5.6 and 9.0 Hz, respectively, whereas those for 2′-F–araU were 3.0 and 17.5 Hz, respectively ( Supplementary Materials, Table S2 ).…”

“…This conformational behavior is highly beneficial to the binding affinity to complementary RNA [ 15 , 16 ]. Moreover, Damha et al [ 17 ] demonstrated that introduction of 4′-F into 2′-F–araU switched the preferred sugar conformation from DNA-like to RNA-like by the similar anomeric effect of 4′-F. Hence, it was predicted that the 4′- C -alkoxy-2′-F–arabinonucleotide derivatives would also pre-organize the sugar ring toward a north conformation, and enhance the hybridization properties for antisense oligonucleotides.…”

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

“…Also other fluorinated nucleic acids such as 2’-fluorocyclohexenyl nucleic acid (F-CeNA, Fig. 1) [27] and other modifications [28–31] have been analyzed on their antisense properties.…”