Synthesis and biophysical properties of arabinonucleic acids (ANA): Circular dichroic spectra, melting temperatures, and ribonuclease H susceptibility of ANA center dot RNA hybrid duplexes

Arabinonucleic acid (ANA), the 2'-epimer of RNA, was synthesized from arabi nonucleoside building blocks by conventional solid-phase phosphoramidite sy nthesis. In addition, the biochemical and physicochemical properties of ANA strands of mixed base composition were evaluated for the first time. ANA e xhibit certain characteristics desirable for use as antisense agents. They form duplexes with complementary RNA, direct RNase H degradation of target RNA molecules, and display resistance to 3'-exonucleases, Since RNA does no t elicit RNase H activity, our findings establish that the stereochemistry at C2' (ANA versus RNA) is a key determinant ill the activation of the enzy me RNase II. Inversion of stereochemistry at C2' is most likely accompanied by a conformational change in the furanose sugar pucker from C3'-endo (RNA ) to C2'-endo ("DNA-like") pucker (ANA) [Noronha and Damha (1998) Nucleic A cids Res. 26, 2665-2671; Venkateswarlu and Ferguson (1999) J, Am. Chem. Soc . 121, 5609-5610], This produces ANA/RNA hybrids whose CD spectra (i.e., he lical conformation) are more similar to the native DNA/RNA substrates than to those of the pure RNA/RNA duplex. These features, combined with the fact that ara-2'OH groups project into the major groove of the helix (where the y should not interfere with RNase H binding), help to explain the RNase H a ctivity of ANA/RNA hybrids.