2′-Deoxy-2′-fluoro-β-d-arabinonucleosides and oligonucleotides (2′F-ANA): synthesis and physicochemical studies

Recently, hybrids of RNA and d-arabinonucleic acids (ANA) as well as the 2′-deoxy-2′-fluoro-d-arabinonucleic acid analog (2′F-ANA) were shown to be substrates of RNase H. This enzyme is believed to be involved in the primary mechanism by which antisense oligonucleotides cause a reduction in target RNA levels in vivo. To gain a better understanding of the properties of arabinose based oligonucleotides, we have prepared a series of 2′F-ANA sequences of homopolymeric (A and T) and mixed base composition (A, T, G and C). UV thermal melting and circular dichroic (CD) studies were used to ascertain the thermodynamic stability and helical conformation of 2′F-ANA/RNA and 2′F-ANA/DNA hybrids. It is shown that 2′F-ANA has enhanced RNA affinity relative to that of DNA and phosphorothioate DNA. The 2′-fluoroarabino modification showed favorable pairing to single-stranded DNA also. This is in sharp contrast to ANA, which forms weak ANA/DNA hybrids at best. According to the measured thermodynamic parameters for duplex formation, the increased stability of hybrids formed by 2′F-ANA (e.g., 2′F-ANA/RNA) appears to originate from conformational pre-organization of the fluorinated sugars and a favorable enthalpy of hybridization. In addition, NMR spectroscopy revealed a five-bond coupling between the 2′F and the base protons (H6/H8) of 2′-deoxy-2′-fluoro-β-d-arabinonucleosides. This observation is suggestive of a through-space interaction between 2′F and H6/H8 atoms. CD experiments indicate that 2′F-ANA/RNA hybrids adopt an ‘A-like’ structure and show more resemblance to DNA/RNA hybrids than to the pure RNA/RNA duplex. This feature is believed to be an important factor in the mechanism that allows RNase H to discriminate between 2′F-ANA/RNA (or DNA/RNA) and RNA/RNA duplexes.