NMR-spectroscopic characterization of phosphodiester bond cleavage catalyzed by the minimal hammerhead ribozyme

In order to relate the conformational dynamics of the hammerhead ribozyme to its biological function the cleavage reaction catalyzed by the hammerhead ribozyme was monitored by time-resolved nuclear magnetic resonance (NMR) spectroscopy. For this purpose, the two nucleosides around the scissile phosphodiester bond were selectively C-13 labelled in multi-step organic syntheses starting from uniformly C-13-labelled glucose. The phosphoamidites were incorporated using phosphoamidite chemistry in the hammerhead substrate strand. In addition, the 2'-OH group on the 5'-side of the hammerhead substrate strand was labelled with a photolabile protecting group. This labelling strategy enabled a detailed characterisation of the nucleotides around the scissile phosphodiester bond in the ground state conformation of the hammerhead ribozyme in the absence and presence of Mg2+ ions as well as of the product state. Photochemical induction of the reaction in situ was further characterized by time-resolved NMR spectroscopy. The detailed structural and dynamic investigations revealed that the conformation of the hammerhead ribozyme is significantly affected by addition of Mg2+ leading to an ensemble of conformations where dynamic transitions between energetically similar conformations occur on the ms-timescale in the presence of Mg2+. The dynamic transitions are localized around the catalytic core. Cleavage from this ensemble cannot be described by mono-exponential kinetics but follows bi-exponential kinetics. A model is described to take into account these experimental data.

Kinetics of photoinduced RNA refolding by real-time NMR spectroscopy

Philipp Wenter

By introducing a photolabile group in the Watson-Crick base-pairing site of a guanosine residue, a bistable 20-base RNA sequence was forced into a less stable conformation. A single laser pulse released the native sequence, and the subsequent refolding equilibration was monitored with time-resolved NMR spectroscopy. This permitted a quant. description of the refolding process. [on SciFinder (R)]

2005

Conformational dynamics of bistable RNAs studied by time-resolved NMR spectroscopy

Luc Reymond, Philipp Wenter

The structural transition between two alternate conformations of bistable RNAs has been characterized by time-resolved NMR spectroscopy. The mechanism, kinetics, and thermodynamics underlying the global structural transition of bistable RNAs were delineated. Both bistable RNA conformations and a partial unstructured RNA of identical sequence could be trapped using photolabile protecting groups. This trapping allowed for an investigation of the initial folding from an unfolded RNA to one of the preferred conformations of the bistable RNA and of the structural transitions involved. Folding of the secondary structure elements occurs rapidly, while the global structural transition of the bistable RNA occurs on a time scale of minutes and shows marked temperature dependence. Comparison of these results with bistable systems previously investigated leads to the prediction of activation enthalpies (Delta H-double dagger) associated with global structural transitions in RNA.

2007

Nitrous Oxide Abatement over Fe-Zeolite

Bryan Bromley

The use of zeolites for catalytic reactions is a field in continuous development. Since it was demonstrated that metal-zeolites are efficient catalysts for NOx abatement, decomposition of nitrous oxide (N2O) over Fe-containing zeolites has attracted great interest by the scientific community mainly due: N2O is the third most important gas contributing to global warming, its concentration in atmosphere is still on the rise and direct N2O decomposition to N2 and O2 is a sustainable alternative. N2O interaction with Fe-zeolite leads to the formation of "special" adsorbed oxygen (often called α-oxygen) with great potential for selective oxidation. Although the focus of a number of studies, the nature of the actives sites for the formation of this adsorbed oxygen is still unclear. The main objectives of this work are: 1) study the decomposition mechanism of N2O over isomorpously substituted Fe-ZSM-5 zeolite aiming on catalyst optimization and 2) optimization and further use of structured Fe-zeolite in novel micro-structured reactor. A number of refined transient kinetics methods were intensively used such as transient response, Temperature Programmed Desorption (TPD) and Temporal Analysis of Product (TAP). Density Functional Theory (DFT) and in situ IR spectroscopy studies were conducted in collaboration and our results support the following: In chapter 3, quantitative measurements have been carrier out to analyze the effect of temperature on the activation (under helium flow) and the irreversible deactivations that can happen during the pretreatment. The results obtained indicate that high temperature treatment (1273 K) results in the formation of a high amount of α-sites. The addition of a very low fraction of oxygen (2%) in the feed demonstrates that the catalyst is sensitive to its presence. Certain sites can be irreversibly destroyed, a result ascribed to the oxidation of active Fe(II) to Fe2O3 clusters which contain inactive Fe(III). Catalyst treatment at high temperature (1273 K) in He for up to 3 hours, also reduced irreversibly the concentration of α-sites. TPD measurements have shown desorption of oxygen at 3 different temperatures. Desorption at the lowest temperature (650 K) was assign to the α-oxygen recombination. The oxygen which desorbs at 700 K was associated to the oxygen from the deactivated sites. Oxygen which desorbs at the highest temperature (730 K) is originated from the surface NOx that desorbed as NO and O2. After a comparison of the concentration of the molecules accumulated, we propose that NO2 is the adsorbed specie. The mechanism of N2O decomposition on the binuclear oxo-hydroxo bridged extraframework iron core site [FeII(μ-O)(μ-OH)FeII]+ inside the ZSM-5 zeolite has been studied by combining theoretical and experimental approaches (see chapter 4). Rate parameters computed using standard statistical mechanics and transition state theory reveal that elementary catalytic steps involved into N2O decomposition are strongly dependent on the temperature. This theoretical result was contrasted with the experimentally observed steady state kinetics of the N2O decomposition and TPD experiments. As predicted by the theoretical study, the switch of the reaction order with respect to N2O pressure (from zero to one) occurs at around 800 K which confirms a change of the rate determining step from the α-oxygen recombination to α-oxygen formation. The proposed mechanism was also confirmed by O2-TD which confirmed the viability of the binuclear complex. The α-oxygen recombination at low temperature (

EPFL2010

Nitrous Oxide Abatement over Fe-Zeolite

Bryan Bromley

EPFL2010