Acceleration of the Zn2+-promoted phosphodiester hydrolysis of oligonucleotides by the 3′-terminal monophosphate group: intrastrand participation over several nucleoside units

Abstract

The Zn²⁺-promoted hydrolysis of the 5′-terminal ribonucleoside phosphodiester bond in chimeric ribo/deoxyribo oligonucleotide 3′-monophosphates, Up(Tp)₄ and Up(Tp)₉, and their dephosphorylated analogue, Up(Tp)₃T, has been studied at various metal ion and substrate concentrations, and in the presence and absence of deoxyribooligonucleotide 3′-monophosphates, (Tp)_n, containing no cleavable ribonucleoside phosphodiester bond. The results strongly suggest that the rate-accelerating effect of the 3′-terminal monophosphate group on the phosphodiester hydrolysis is of intramolecular origin: the Zn²⁺ ion bridges the favoured site of coordination, i.e. the terminal monophosphate group, and the cleaving phosphodiester bond. The 3′-monophosphate group also causes the reaction order in [Zn^{2 +}] to deviate from unity, the values obtained with Up(Tp)₃T, Up(Tp)₄ and Up(Tp)₉ being 1.1, 1.4 and 1.7, respectively. Possibly, the intramolecular participation of the 3′-monophosphate bound Zn²⁺ ion is facilitated by another Zn²⁺ ion that stabilizes the folded conformation of the oligonucleotide chain in the reactive Zn^{2 +}/substrate macrochelate.