Synthesis and conformational properties of oligonucleotides incorporating 2 '-O-phosphorylated ribonucleotides as structural motifs of pre-tRNA splicing intermediates
H. Tsuruoka et al., Synthesis and conformational properties of oligonucleotides incorporating 2 '-O-phosphorylated ribonucleotides as structural motifs of pre-tRNA splicing intermediates, J ORG CHEM, 65(22), 2000, pp. 7479-7494
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 accor
ding to our previous phosphorylation procedure. These phosphoramidite units
6a-d were not contaminated with 3'-regioisomers and were successfully appl
ied to solid-phase synthesis to give oligodeoxyuridylates 15, 16 and oligou
ridylates 21, 22. Self-complementary Drew-Dickerson DNA 12mers 24-28 replac
ed by a 2'-O-phosphorylated ribonucleotide at various positions were simila
rly synthesized. In these syntheses, it turned out that KI3 was the most ef
fective reagent for oxidative desulfurization of the initially generated th
iophosphate group to the phosphate group on polymer supports. Without using
this conversion step, a tridecadeoxyuridylate 17 incorporating a 2'-O-thio
phosphorylated 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, T-m measurement of the self-complementary oligonucleo
tides obtained and MD simulation of heptamer duplexes 33-36 were carried ou
t. 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 signif
icantly affect the stability of the DNA duplex. On the other hand, the 2'-m
odified ribose moiety was expelled to give a C3'-endo conformation in RNA d
uplexes so that the RNA duplexes were extremely destabilized.