2 '-Deoxy-2 '-fluoro-beta-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 su bstrates of RNase H. This enzyme is believed to be involved in the primary mechanism by which antisense oligonucleotides cause a reduction in target R NA levels in vivo. To gain a better understanding of the properties of arab inose based oligonucleotides, we have prepared a series of 2'F-ANA sequence s 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 relati ve to that of DNA and phosphorothioate DNA. The 2'-fluoroarabino modificati on showed favorable pairing to single-stranded DNA also. This is in sharp c ontrast to ANA, which forms weak ANA/DNA hybrids at best. According to the measured thermodynamic parameters for duplex formation, the increased stabi lity 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 favora ble enthalpy of hybridization. In addition, NMR spectroscopy revealed a fiv e-bond coupling between the 2'F and the base protons (H6/H8) of 2'-deoxy-2' -fluoro-beta-D-arabinonucleosides. This observation is suggestive of a thro ugh-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 resembla nce to DNA/RNA hybrids than to the pure RNA/RNA duplex. This feature is bel ieved to be an important factor in the mechanism that allows RNase H to dis criminate between 2'F-ANA/RNA (or DNA/RNA) and RNA/RNA duplexes.