1-(2'-DEOXY-BETA-D-XYLOFURANOSYL)CYTOSINE - BASE-PAIRING OF OLIGONUCLEOTIDES WITH A CONFIGURATIONALLY ALTERED SUGAR-PHOSPHATE BACKBONE

Abstract

Solid-phase synthesis of the oligo(2'-deoxynucleotides) 19 and 20 containing 2'-deoxy-beta-D-xylocytidine (4) is described. For this purpose, 1-(2-deoxy-beta-D-threo-pentofuranosyl)cytosine (= 1-(2-deoxy-beta-D-xyiofuranosyl)cytosine; 4) was protected at its 4-NH2 group with a benzoyl (-->5) or an isobutyryl (-->8) residue, and a dimethoxytrityl group was introduced at 5'-OH (-->7, 10; Scheme 2). Compounds 7 and 10 were converted into the 3'-phosphonates 11a,b. While 19 could be hybridized with 21 and 22 under formation of duplexes with a two-nucleotide overhang on both termini (19.21: T-m 29 degrees;19.22:T-m 22 degrees), the decamer 20 bearing four C-x(d) residues could no longer be hybridized with one of the opposite strands. Moreover, the oligonucleotides d[(xC)(8)-C] (13), d[(xC)(4)-C] (14), d[C-(xC)(4)-C] (15), and d[C-(xC)(3)-C] (16) were synthesized. While 13 exhibits an almost inverted CD spectrum compared to d(C-9) (17), the other oligonucleotides show CD spectra typical for regular right-handed single helices. At pH 5, d[(xC)(8)-C] forms a stable hemi-protonated duplex which exhibits a T-m of 60 degrees (d[(CH+)(9)].d(C-9): T-m 36 degrees). The thermodynamic parameters of duplex formation of (13H(+).13) and (17H(+).17) were calculated from their melting profiles and were found to be identical in Delta H but differ in Delta S (13H(+).13:Delta S = -287 cal/K mol; 17H(+).17: Delta S = -172 cal/K mol).