Chemical Synthesis of a 5'-Terminal TMG-Capped Triribonucleotide m(3)(2,2,7)G(5)(')pppAmpUmpA of U1 RNA

The 5'-terminal TMG-capped triribonucleotide, m(3)(2,2,7)G(5)(')pppAmpUmpA, has been synthesized by condensation of an appropriately protected triribonucleotide derivative of ppAmpUmpA with a new TMG-capping reagent. During this total synthesis, it was found that the regioselective 2'-O-methylation of 3',5'-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-N-(4-monomethoxytrityl)adenosine was achieved by use of MeI/Ag(2)O without affecting the base moiety. A new route to 2-N,2-N-dimethylguanosine from guanosine via a three-step reaction has also been developed by reductive methylation using paraformaldehyde and sodium cyanoborohydride. These key intermediates were used as starting materials for the construction of a fully protected derivative of pAmpUmpA and a TMG-capping reagent of Im-pm(3)(2,2,7)G. The target TMG-capped tetramer, m(3)(2,2,7)G(5)(')pppAmpUmpA, was synthesized by condensation of a partially protected triribonucleotide 5'-terminal diphosphate species, ppA(MMTr)mpUmpA, with Im-pm(3)(2,2,7)G followed by treatment with 80% acetic acid. The structure of m(3)(2,2,7)G(5)(')pppAmpUmpA was characterized by (1)H and (31)P NMR spectroscopy as well as enzymatic assay using snake venom phosphodiesterase, calf intestinal phosphatase, and nuclease P1.

Synthesis of oligonucleotide having a bent structure by incorporation of an interresidually cyclized uridylyl (3'-5')uridine unit

The chemical synthesis and conformational properties of interresidually cyclized uridylyl(3'-5')uridine derivatives were studied in order to introduce a stable turn structure into oligonucleotides. These cyclized molecules were analogs of uridylyl(3'-5')5-[methylamino(methyl)]-uridine which is the component of the U turn structure of tRNAarg E. coli. The conformational properties of these cyclic dinucleoside monophosphates were studied using NMR and CD spectroscopy with the aid of molecular mechanics and molecular dynamics simulations. These experiments indicated that the turn conformation could be stabilized by introducing a cyclic structure as expected. On the basis of these results, the chemical synthesis of phosphoramidite units of these cyclic dinucleoside monophosphate derivatives were studied to construct oligonucleotides having a stable bent structure.