The RNA molecular wire: the pH-dependent change of the electronic character of adenin-9-yl is transmitted to drive the sugar and phosphate torsions in adenosine 3?, 5?-bisphosphate

Abstract

The change of the electronic character of adenin-9-yl in adenosine 3′,5′-bisphosphate (EtpApMe, 1) in the neutral versus protonated form, in contrast to its abasic counterpart [Etp(apurinic)pMe, 2], is transmitted to modulate the sugar conformation by an interplay of stereoelectronic anomeric and gauche effects, which in turn dictate the phosphate conformation by tuning the 3′-O—P—O(ester) anomeric effect. It was found that with the change of protonation ⇌ deprotonation equilibrium the electronic character of the aglycone changes, which is evident from the change of the pD-dependent chemical shift of the aromatic protons (δH2 and δH8). This change in chemical shift (δH2, δH8) is linearly correlated with the pD-dependent change of ΔG° of the N ⇌ S pseudorotational equilibrium of the sugar moiety (from −2.8 kJ mol−1 at pD 7.9 to −1.7 kJ mol−1 at pD 1.0), as well as with the pD-dependent change of ΔG° of the two-state ϵt ⇌ ϵ− equilibrium along the phosphate backbone (from −1.9 kJ mol−1 at pD 7.9 to −1.5 kJ mol−1 at pD 1.0). Finally, the pD-dependent change of ΔG° of the N ⇌ S pseudorotational equilibrium is also linearly correlated with that of the pD-dependent ϵt ⇌ ϵ− equilibrium, thereby unequivocally showing that the pD-dependent change of the electronic character of adenin-9-yl moiety (to its protonated form) is indeed propogated to drive the constituent sugar and phosphate backbone conformations in a concerted manner. The absence of such a correlation in the apurinic phosphodiester 2 implies that the change of the sugar conformation in 1 is independent of the electronic character of the phosphate. This tunable one-way stereoelectronic transmission is modulated intramolecularly by a cascade of orbital overlaps basing on the donor and acceptor properties of various bonding, non-bonding and antibonding orbitals, which cause a single-stranded RNA to behave as molecular wire. Copyright © 2000 John Wiley & Sons, Ltd.