Synthesis and Conformational Properties of Oligonucleotides Incorporating 2‘-O-Phosphorylated Ribonucleotides as Structural Motifs of Pre-tRNA Splicing Intermediates

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Abstract
To synthesize oligonucleotides containing 2‘-O-phosphate groups, four kinds of ribonucleoside 3‘-phosphoramidite building blocks 6a−d having the bis(2-cyano-1,1-dimethylethoxy)thiophosphoryl (BCMETP) group were prepared according to our previous phosphorylation procedure. These phosphoramidite units 6a−d were not contaminated with 3‘-regioisomers and were successfully applied to solid-phase synthesis to give oligodeoxyuridylates 15, 16 and oligouridylates 21, 22. Self-complementary Drew−Dickerson DNA 12mers 24−28 replaced by a 2‘-O-phosphorylated ribonucleotide at various positions were similarly synthesized. In these syntheses, it turned out that KI3 was the most effective reagent for oxidative desulfurization of the initially generated thiophosphate group to the phosphate group on polymer supports. Without using this conversion step, a tridecadeoxyuridylate 17 incorporating a 2‘-O-thiophosphorylated uridine derivative was also synthesized. To investigate the effect of the 2‘-phosphate group on the thermal stability and 3D-structure of DNA(RNA) duplexes, Tm measurement of the self-complementary oligonucleotides obtained and MD simulation of heptamer duplexes 33−36 were carried out. According to these analyses, it was suggested that the nucleoside ribose moiety phosphorylated at the 2‘-hydroxyl function predominantly preferred C2‘-endo to C3‘-endo conformation in DNA duplexes so that it did not significantly affect the stability of the DNA duplex. On the other hand, the 2‘-modified ribose moiety was expelled to give a C3‘-endo conformation in RNA duplexes so that the RNA duplexes were extremely destabilized.