9-(2'-DEOXY-BETA-D-XYLOFURANOSYL)ADENINE BUILDING-BLOCKS FOR SOLID-PHASE SYNTHESIS AND PROPERTIES OF OLIGO(2'-DEOXY-XYLONUCLEOTIDES)

Abstract

The 9-(2'-deoxy-beta-D-threo-pentofuranosyl)adenine (= 9-(2'-deoxy-beta-D-xylofuranosyl)adenine, xA(d); 2) was protected at its 6-NH2 group with either a benzoyl (5a) or a (dimethylamino)methylidene (6a) residue and with a dimethoxytrityl group at 5'-OH (5b, 6b). Compounds 5b and 6b were then converted into the 3'-phosphonates 5c and 6c; moreover, the 2-cyanoethyl phosphoramidite 6d was synthesized starting from 6b. The DNA building blocks were used for solid-phase synthesis of d[(xA)12-A] (8). The latter was hybridized with d[(xT)12-T] (T(m) = 35-degrees); in contrast, with d(T12), complex formation was not observed. Moreover, xA(d) and xT(d) were introduced into the self-complementary dodecamer d(G-T-A-G-A-A-T-T-C-T-A-C) (12) at different positions to give the oligomers 13-16. All oligonucleotides were characterized by temperature-dependent CD and UV spectroscopy, and in addition, 14 by T-jump experiments. From concentration-dependent T(m) measurements, the thermodynamic parameters of the melting as well as the tendency of hairpin formation of the oligonucleotides were deduced. Oligomer 14 was hydrolyzed by snake-venom phosphodiesterase in a discontinuous way implying a fast hydrolysis of unmodified 3'- and 5'-flanks followed by a slow hydrolysis of the remaining modified tetramer. In contrast to this, oligonucleotide 16 was hydrolyzed in a continuous reaction. In both cases, calf-spleen phosphodiesterase hydrolyzed the oligomer only marginally.