Buffer catalyzed cleavage of uridylyl-3′,5′-uridine in aqueous DMSO: comparison to its activated analog, 2-hydroxypropyl 4-nitrophenyl phosphate

Abstract

Buffer catalysis of the cleavage and isomerization of uridylyl-3',5'-uridine (UpU) has been studied over a wide pH range in 80% aq. DMSO. The diminished hydroxide ion concentration in this solvent system made catalysis by amine buffers (morpholine, 4-hydroxypiperidine and piperidine) visible even at relatively low buffer concentrations (10-200 mmol L(-1)). The observed catalysis was, however, much weaker than what has been previously reported for the activated RNA model 2-hydroxypropyl 4-nitrophenyl phosphate (HPNP) in the same solvent system. In the case of morpholine, contribution of both the acidic and the basic buffer constituent was significant, whereas with 4-hydroxypiperidine and piperidine participation of the acidic constituent could not be established unambiguously. The results underline the importance of using realistic model compounds, along with activated ones, in the study of the general acid/base catalysis of RNA cleavage.

Ribonuclease Activity of an Artificial Catalyst That Combines a Ligated CuII Ion and a Guanidinium Group at the Upper Rim of a cone-Calix[4]arene Platform

“…Because of the different temperatures at which the kinetics were carried out, namely, 50 vs 25 °C, a convenient way to compare catalytic efficiencies in the cleavage of diribonucleoside monophosphates vs HPNP is to resort to catalytic rates relative to background ( k obs / k bg ), under the assumption that the temperature coefficients of the k obs / k bg ratios are not too different. In line with expectations, comparison of the k obs / k bg values in Table with the corresponding value for HPNP ( k obs / k bg = 3.2 × 10 5 in Table ) shows that 2 H + –Cu catalyzes the cleavage of GpA, GpU, and UpU much more efficiently than the cleavage of HPNP, but the reverse holds for CpA . Since the value of k bg of the latter is similar to that of the other diribonucleoside monophosphates, the low rate of catalytic cleavage cannot be ascribed to the inherently low reactivity of CpA, but presumably to unfavorable interactions between the catalyst and the altered substrate in the transition state, that are either absent or less important for the more reactive diribonucleoside monophosphates.…”

Phosphodiester models for cleavage of nucleic acids

“…The situation seems, however, to be rather different with dinucleoside-3´,5´-monophosphates. The buffer-catalyzed reaction of UpU is not so much faster than the buffer-independent reaction, in 0.1 mol L −1 piperidine buffer only 4-fold faster [ 68 ]. No second-order dependence of rate on buffer concentration was observed.…”

Guanidinium Promoted Cleavage of Phosphoric Diesters: Kinetic Investigations and Calculations Provide Indications on the Operating Mechanism

“…In the cleavage of small RNA fragments as well as diribonucleoside monophosphate and other phosphoric diesters several cleavage mechanisms contemplate the pseudorotation of a phosphorane intermediate. 28,29 The pseudorotation of pentacoordinated phosphorus compounds consists in an interconversion in which two of the equatorial ligands become apical and vice versa, whereas the third equatorial ligand remains in equatorial positions (see Figure 5). When two ligand atoms are covalently bound to a fivemembered ring, as in the case of a cyclic phosphate on the ribose ring, one of them is equatorial and the other is apical.…”