alpha,beta-Oligodeoxyribonucleotides having alternating (3'to 3')-and (5'to 5')-internucleotidic phosphodiester linkages (altDNA) represent a unique class of synthetic oligonucleotide analogues achiral at phosphorus. These modified oligonucleotides exhibit superior resistance to nucleases than native beta-oligodeoxyribonucleotides, and possess the ability to form stable complexes with either complementary DNA or RNA sequences. In this context, altDNA-DNA duplexes are thermodynamically more stable than altDNA-RNA complexes and thus demonstrate the higher affinity of alt-DNA for single stranded DNA sequences than for RNA sequences. The reduced thermal stability of altDNA-RNA complexes may result from an inherent conformational incompatibility of altDNA within the A-type helical motif of the hybrids. A strategy designed at improving the affinity of altDNA for complementary RNA oligomers entails the substitution of the alpha-mononucleotides of altDNA for alpha-mononucleotides having a distinctive linker arm between the nucleobase and carbohydrate moieties. It is postulated that additional nucleobase flexibility imparted to altDNA may facilitate the formation of Watson-Crick base pairs with native RNA oligonucleotides through better alignment of complementary nucleobases and, hence, generate more stable A-type helices. To test this rationale, the chemical synthesis of nucleoside analogues having a methylene or an ethylene arm joining nucleobase and carbohydrate entities has been achieved. Improved methodologies have been developed during the course of this work to facilitate the large-scale preparation and purification of theses nucleosides. The novel nucleoside analogues have been fully characterized by NMR spectroscopy and mass spectrometry, and converted to their phosphoramidites derivatives for incorporation into oligonucleotides at selected positions according to defined internucleotidic motifs. The oligodeoxyribonucleotide analogues have been purified to homogeneity either by HPLC or PAGE. The physicochemical properties of these oligonucleotide analogues, and their affinity for complementary DNA or RNA sequences, are currently being evaluated in the laboratory.
