9-(2′-Deoxy-β-D-xylofuranosyl)adenine Building Blocks for Solid-Phase Synthesis and Properties of Oligo(2′-deoxy-xylonucleotides)

Abstract

The 9-(2′-deoxy-à-D-threo-pentofuranosyl)adenine (=9-(2′-deoxy-à-D-xylofuranosyl)adeninc, xAd; 2) was protected at its 6-NH2 group with cither a benzoyl (5a) or a (dimethyfamino)methylidcnc (6a) residue and with a dimethoxytntyl 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 fib. The DNA building blocks were used for solid-phase synthesis of d[(xA)122-A] (8). The latter was hybridized with d[(xT)12-T] (Tm = 35°); in contrast, with d(T12), complex formation was not observed. Moreover, xAd and xTd were introduced into the self-complementary dodccamcr d(G-T-A-G-A-A-T-T-C-T-A-C) (12) at different positions lo give the oligomcrs 13–16. All oligonucleotides were characterised by temperature-dependent CD and UV spectroscopy, and in addition, 14 by T-jump experiments. From concentration-dependent Tm measurements, the thermodynamic paraneters of the melting as well as the tendency of hairpin formation of the oligonucleotides were deduced. Oligemer 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. Copyright © 1991 Verlag GmbH & Co. KGaA, Weinheim