Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis.

Pistol ribozyme (Psr) is a distinct class of small endonucleolytic ribozymes, which are important experimental systems for defining fundamental principles of RNA catalysis and designing valuable tools in biotechnology. High-resolution structures of Psr, extensive structure-function studies, and computation support a mechanism involving one or more catalytic guanosine nucleobases acting as a general base and divalent metal ion-bound water acting as an acid to catalyze RNA 2'-O-transphosphorylation. Yet, for a wide range of pH and metal ion concentrations, the rate of Psr catalysis is too fast to measure manually and the reaction steps that limit catalysis are not well understood. Here, we use stopped-flow fluorescence spectroscopy to evaluate Psr temperature dependence, solvent H/D isotope effects, and divalent metal ion affinity and specificity unconstrained by limitations due to fast kinetics. The results show that Psr catalysis is characterized by small apparent activation enthalpy and entropy changes and minimal transition state H/D fractionation, suggesting that one or more pre-equilibrium steps rather than chemistry is rate limiting. Quantitative analyses of divalent ion dependence confirm that metal aquo ion pKa correlates with higher rates of catalysis independent of differences in ion binding affinity. However, ambiguity regarding the rate-limiting step and similar correlation with related attributes such as ionic radius and hydration free energy complicate a definitive mechanistic interpretation. These new data provide a framework for further interrogation of Psr transition state stabilization and show how thermal instability, metal ion insolubility at optimal pH, and pre-equilibrium steps such as ion binding and folding limit the catalytic power of Psr suggesting potential strategies for further optimization.

Syntheses and structures of two benzoyl amides: 2-chloro-4-eth-oxy-3,5-dimeth-oxy-N-(3-oxo-cyclo-hex-1-en-1-yl)benzamide and 2-chloro-N-(5,5-dimethyl-3-oxo-cyclo-hex-1-en-1-yl)-4-eth-oxy-3,5-di-meth-oxy-benzamide.

The first title benzoyl amide, C17H20ClNO5 (3a), crystallizes in the monoclinic space group P21/c with Z = 4 and the second, C19H24ClNO5 (3b), also crystallizes in P21/c with Z = 8 (Z' = 2), thus there are two independent mol-ecules in the asymmetric unit. In 3a, the phenyl ring makes a dihedral angle of 50.8 (3)° with the amide moiety with the C=O group on the same side of the mol-ecule as the C-Cl group. One meth-oxy group is almost in the plane of the benzene ring, while the eth-oxy and other meth-oxy substituent are arranged on opposite sides of the ring with the eth-oxy group occupying the same side of the ring as the C=O group in the amide moiety. For one of the two mol-ecules in 3b, both the amide and 5,5-dimethyl-3-oxo-cyclo-hex-1-en-1-yl moieties are disordered over two sets of sites with occupancies of 0.551 (2)/0.449 (2) with the major difference between the two conformers being due to the conformation adopted by the cyclo-hex-2-en-1-one ring. The three mol-ecules in 3b (i.e., the undisordered mol-ecule and the two disorder components) differ in the arrangement of the subsituents on the phenyl ring and the conformation adopted by their 5,5-dimethyl-3-oxo-cyclo-hex-1-en-1-yl moieties. In the crystal of 3a, N-H⋯O hydrogen bonds link the mol-ecules into a zigzag chain propagating in the [001] direction. For 3b a combination of C-H⋯O and N-H⋯O inter-molecular inter-actions link the mol-ecules into a zigzag ribbon propagating in the [001] direction.

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.