Kinetic solvent deuterium isotope effect in transesterification of RNA models

Weak Temperature Dependence of the Relative Rates of Chlorination and Hydrolysis of N2O5 in NaCl-Water Solutions

We have measured the temperature dependence of the ClNO₂ product yield in competition with hydrolysis following N₂O₅ uptake to aqueous NaCl solutions. For NaCl-D₂O solutions spanning 0.0054-0.21 M, the ClNO₂ product yield decreases on average by only 4 ± 3% from 5 to 25 °C. Less reproducible measurements at 0.54-2.4 M NaCl also fall within this range. The ratio of the rate constants for chlorination and hydrolysis of N₂O₅ in D₂O is determined on average to be 1150 ± 90 at 25 °C up to 0.21 M NaCl, favoring chlorination. This ratio is observed to decrease significantly at the two highest concentrations. An Arrhenius analysis reveals that the activation energy for hydrolysis is just 3.0 ± 1.5 kJ/mol larger than for chlorination up to 0.21 M, indicating that Cl^- and D₂O attack on N₂O₅ has similar energetic barriers despite the differences in charge and complexity of these reactants. In combination with the measured preexponential ratio favoring chlorination of 300_-200⁺⁴⁰⁰, we conclude that the strong preference of N₂O₅ to undergo chlorination over hydrolysis is driven by dynamic and entropic, rather than enthalpic, factors. Molecular dynamics simulations elucidate the distinct solvation between strongly hydrated Cl^- and the hydrophobically solvated N₂O₅. Combining this molecular picture with the Arrhenius analysis implicates the role of water in mediating interactions between such distinctly solvated species and suggests a role for diffusion limitations on the chlorination reaction.

Kinetic and NMR spectroscopic study of the chemical stability and reaction pathways of sugar nucleotides

The alkaline cleavage of two types of sugar nucleotides has been studied by ¹H and ³¹P NMR in order to obtain information on the stability and decomposition pathways in aqueous solutions under alkaline conditions. The reaction of glucose 1-UDP is straightforward, and products are easy to identify. The results obtained with ribose 5-UDP and ribose 5-phosphate reveal, in contrast, a more complex reaction system than expected, and the identification of individual intermediate species was not possible. Even though definite proof for the mechanisms previously proposed could not be obtained, all the spectroscopic evidence is consistent with them. Results also emphasise the significant effect of conditions, pH, ionic strength, and temperature, on the reactivity under chemical conditions.

Phosphodiester models for cleavage of nucleic acids

Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.

Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2+)

Solvent D2O and (18)O kinetic isotope effects on RNA 2'-O-transphosphorylation catalyzed by Zn(2+) demonstrate an altered transition state relative to specific base catalysis. A recent model from DFT calculations involving inner sphere coordination to the non-bridging and leaving group oxygens is consistent with the data.

Hydrolysis of the RNA model substrate catalyzed by a binuclear Zr(IV)-substituted Keggin polyoxometalate

The reactivity and solution behaviour of the binuclear Zr(IV)-substituted Keggin polyoxometalate (Et2NH2)8[{α-PW11O39Zr(μ-OH)(H2O)}2]·7H2O (ZrK 2 : 2) towards phosphoester bond hydrolysis of the RNA model substrate 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP) was investigated at different reaction conditions (pD, temperature, concentration, and ionic strength). The hydrolysis of the phosphoester bond of HPNP, followed by means of (1)H NMR spectroscopy, proceeded with an observed rate constant, kobs = 11.5(±0.42) × 10(-5) s(-1) at pD 6.4 and 50 °C, representing a 530-fold rate enhancement in comparison with the spontaneous hydrolysis of HPNP. (1)H and (31)P NMR spectra indicate that at these reaction conditions the only products of hydrolysis are p-nitrophenol and the corresponding cyclic phosphate ester. The pD dependence of kobs exhibits a bell-shaped profile, with the fastest rate observed at pD 6.4. The formation constant (Kf = 455 M(-1)) and catalytic rate constant (kc = 42 × 10(-5) s(-1)) for the HPNP-ZrK 2 : 2 complex, activation energy (Ea) of 63.35 ± 1.82 kJ mol(-1), enthalpy of activation (ΔH(‡)) of 60.60 ± 2.09 kJ mol(-1), entropy of activation (ΔS(‡)) of -133.70 ± 6.13 J mol(-1) K(-1), and Gibbs activation energy (ΔG(‡)) of 102.05 ± 0.13 kJ mol(-1) at 37 °C were calculated from kinetic experiments. Binding between ZrK 2 : 2 and the P-O bond of HPNP was evidenced by the change in the (31)P chemical shift and signal line-broadening of the (31)P atom in HPNP upon addition of ZrK 2 : 2. Based on (31)P NMR experiments and isotope effect studies, a mechanism for HPNP hydrolysis in the presence of ZrK 2 : 2 was proposed.

The mechanism of cleavage and isomerisation of RNA promoted by an efficient dinuclear Zn2+ complex

The cleavage and isomerisation of uridine 3'-alkylphosphates was studied in the presence of a dinuclear Zn(2+) complex, 3. The rate acceleration of the cleavage by 1 mM 3 is approximately 10(6)-fold under neutral conditions. Most remarkably, the complex also promotes the isomerisation of phosphodiester bonds, although the rate-enhancement is more modest: under neutral conditions complex 3 (1 mM) catalyses isomerisation by about 500-fold. The observation of this reaction shows that the reactions of these substrates catalysed by 3 proceed through a stepwise mechanism involving an intermediate phosphorane. A β(lg) value of -0.92 was determined for the 3-promoted cleavage reaction, and modest kinetic solvent deuterium isotope effects ranging from 1.5 to 2.8 were observed. Isomerisation was less sensitive to the nature of the esterifying group, with a β value of -0.5, and the kinetic solvent deuterium isotope effects were less than 1.5. Most of these characteristics of the 3-promoted cleavage are very similar to those for the cleavage of nucleoside 3'-phosphotriesters. These data are explained by a mechanism in which the complex primarily acts as an electrophilic catalyst neutralising the charge on the phosphate and stabilising an intermediate phosphorane, with general acid catalysis promoting the cleavage reaction. In contrast to the behaviour of triesters, isomerisation is significantly slower than cleavage; this suggests that the changes in geometry that occur during isomerisation lead to a much less stable complex between 3 and the phosphorane intermediate.

Kinetic isotope effects for RNA cleavage by 2'-O- transphosphorylation: nucleophilic activation by specific base

To better understand the interactions between catalysts and transition states during RNA strand cleavage, primary (18)O kinetic isotope effects (KIEs) and solvent D(2)O isotope effects were measured to probe the mechanism of base-catalyzed 2'-O-transphosphorylation of the RNA dinucleotide 5'-UpG-3'. The observed (18)O KIEs for the nucleophilic 2'-O and in the 5'-O leaving group at pH 14 are both large relative to reactions of phosphodiesters with good leaving groups, indicating that the reaction catalyzed by hydroxide has a transition state (TS) with advanced phosphorus-oxygen bond fission to the leaving group ((18)k(LG) = 1.034 +/- 0.004) and phosphorus-nucleophile bond formation ((18)k(NUC) = 0.984 +/- 0.004). A breakpoint in the pH dependence of the 2'-O-transphosphorylation rate to a pH independent phase above pH 13 has been attributed to the pK(a) of the 2'-OH nucleophile. A smaller nucleophile KIE is observed at pH 12 ((18)k(NUC) = 0.995 +/- 0.004) that is interpreted as the combined effect of the equilibrium isotope effect (ca. 1.02) on deprotonation of the 2'-hydroxyl nucleophile and the intrinsic KIE on the nucleophilic addition step (ca. 0.981). An alternative mechanism in which the hydroxide ion acts as a general base is considered unlikely given the lack of a solvent deuterium isotope effect above the breakpoint in the pH versus rate profile. These results represent the first direct analysis of the transition state for RNA strand cleavage. The primary (18)O KIE results and the lack of a kinetic solvent deuterium isotope effect together provide strong evidence for a late transition state and 2'-O nucleophile activation by specific base catalysis.

A kinetic study on the chemical cleavage of nucleoside diphosphate sugars

Nucleoside diphosphate sugars serve in essential roles in metabolic processes. They have, therefore, been used in mechanistic studies on glycosylation reactions, and their analogues have been synthesised as enzyme and receptor inhibitors. Despite extensive biochemical research, little is known about their chemical reactions. In the present work the chemical cleavage of two different types of nucleoside diphosphate sugars has been studied. UDP-Glc is phosphorylated at the anomeric carbon, whereas in ADP-Rib C-1 is unsubstituted, allowing hence the equilibrium between cyclic hemiacetal and acyclic carbonyl forms. Due to the structural difference, these substrates react via different pathways under slightly alkaline conditions: while UDP-Glc reacts exclusively by a nucleophilic attack of a glucose hydroxyl group on the diphosphate moiety, ADP-Rib undergoes a complex reaction sequence that involves isomerisation processes of the acyclic ribose sugar and results in a release of ADP.

Intra- and intermolecular interactions influence the reactivity of RNA oligonucleotides

The transesterification of RNA oligonucleotides was studied over a wide pH range. The rate constants obtained indicate that, under neutral conditions, oligonucleotides with an adenosine moiety as the 5'-linked nucleoside can be up to 1000-fold more reactive than the reference oligonucleotide, a 13-mer oligo-U (1). Experiments with the modified oligonucleotide with N6,N6-dimethyladenosine (9) as the 5'-linked nucleoside moiety suggest that the exocyclic amino group is involved in the reaction, influencing the reactivity of the neighboring phosphodiester bond. In addition to such intramolecular interactions, weak intermolecular interactions most probably contribute to the reactivity.