Synthesis and pairing properties of 3'-deoxyribopyranose (4' -> 2')-oligonucleotides ('p-DNA')

The prepn. and the pairing properties of the new 3'-deoxyribopyranose (4'->2')-oligonucleotide (= p-DNA) pairing system, based on 3'-deoxy-b-D-ribo-pyranose nucleosides is presented. D-Xylose was efficiently converted to the prefunctionalized 3-deoxyribopyranose deriv. 4-O-[(tert-butyl)dimethylsilyl]-3-deoxy-D-ribo-pyranose 1,2-diacetate (obtained as a 4:1 mixt. of a- and b-D-anomers). From this sugar building block, the corresponding, appropriately protected thymine, guanine, 5-methylcytosine, and purine-2,6-diamine nucleoside phosphoramidites were prepd. in a minimal no. of steps. These building blocks were assembled on a DNA synthesizer, and the corresponding p-DNA oligonucleotides were obtained in good yields after a one-step deprotection under std. conditions, followed by HPLC purifn. Qual., p-DNA shows the same pairing behavior as p-RNA, forming antiparallel, exclusively Watson-Crick-paired duplexes that are much stronger than corresponding DNA duplexes. Duplex stabilities within the three related (i.e., based on ribo-pyranose nucleosides) oligonucleotide systems p-RNA, p-DNA, and 3'-O-Me-p-RNA were compared with each other. Intrinsically, p-RNA forms the strongest duplexes, followed by p-DNA, and 3'-O-Me-p-RNA. However, by introducing the nucleobases purine-2,6-diamine and 5-methylcytosine instead of adenine and cytosine, a substantial increase in stability of corresponding p-DNA duplexes was obsd. [on SciFinder (R)]