Synthesis of (2-Deoxy-α- and -β-D-erythro-pentofuranosyl)(thymin-1-yl)alkanes and Their Incorporation into Oligodeoxyribonucleotides. Effect of Nucleobase-Sugar Linker Flexibility on the Formation of DNA-DNA and DNA-RNA Hybrids

摘要

On the basis of modeling studies, the (2-deoxy-α- and β-D-erythro-pentofuranosyl) (thymin-1-yl) alkanes 1a,b and 2a,b were selected as potential conformational probes for altDNA oligonucleotides. A straightforward approach to the synthesis of 1a,b and 2a,b from commercial 2-deoxy-D-ribose (3) and 1-O-methyl-2-deoxy-3,5-di-O-p-toluoyl-D-erythro-pentofuranose (13), respectively, was developed. These nucleoside analogues were converted to the phosphoramidite derivatives 27a,b-30a,b and incorporated into oligonucleotide 31 at predetermined sites and defined internucleotidic motifs. The insertion of la,b according to either a (3′ → 5′)- or a (3′ → 3′)-internucleotidic polarity produced oligonucleotides exhibiting a slightly higher affinity for their complementary unmodified DNA sequence than for the corresponding RNA sequence (Table 3). Conversely, the incorporation of 2a into 31 according to a (3′ → 3′)-orientation generated, for the first time, an altDNA oligonucleotide displaying a greater affinity for its complementary unmodified RNA sequence (ΔT_m = 6℃) than for the corresponding DNA sequence (ΔT_m = 10 ℃). This hybrid was, however, thermodynamically less stable than the duplex having unmodified α-2′-deoxythymidine similarly incorporated into 31 (ΔΔT_m = 3℃).