DNA Catalysis: The Chemical Repertoire of DNAzymes

Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.

Ion concentration and deduced chemical compounds of the GRIP and Dome Fuji ice cores, Greenland and Antarctica

We have proposed a method of deducing the chemical compounds found in deep polar ice cores by analyzing the balance between six major ions (Cl-, NO3-, SO4**2-, Na+, Mg2+, and Ca2+). The method is demonstrated for the Holocene and last glacial maximum regions of the Dome Fuji and GRIP ice cores. The dominant compounds depend only on the ion balance and the sequence of chemical reactions. In priority order, the principle salts are calcium sulfate, other sulfates, nitrate, chloride, and carbonate. The chemical abundances deduced by this method agree well with the results of Raman spectroscopy on individual salt inclusions. The abundances in the ice cores are shown to reflect differences in climatic periods (the acidic environment of the Holocene versus the reductive environment of the last glacial maximum) and regional conditions (the marine environment of Antarctica versus the continental environment of Greenland).

Some physical and chemical proceddes in fluids

The ability to reproduce reduced gravity conditions for long periods is one of the reasons why the orbiting laboratory is so attractive. In this paper several fluid dynamics problem areas are reviewed in which zero-gravity conditions are of great importance. Although emphasis is placed on space processing, there are some older problems also in which gravity masks the phenomcna, impeding a reasonably simple approach to the solution. Three problems are considered: Thermal convection under reduced gravity. The dumping effect ofsurface gravity waves at the outset of convection induced by surface tractions is discussed in particular. The existence of convection is of concern for some satellite thermal control techniques presently used, and for most of the proposed manufacturing processes. Whereas convection should be normally avoided, problems related to the containerless stirring ofa melt constitute an exception. Secondly, gravity and chemical reactions. Although chemical reactions are independent of gravity because of the small mass of the molecules and atoms involved, in many cases the reaction rate dcpends on the arrival of the species to the reaction zone. When the arrival process is buoyancy-controlled, the net specd of the reaction will be affected by the gravity. Thirdly, two-phase flows under reduced gravity provkle interesting problems from boiling heat transfer to degasslng of melts. This part of the paper deals only with the measurement of sound veiocity in a liquid containing bubbles. It is suggested that such measurements should be mude under reduced gravity to provide reliable residís.

Peroxo-iron and oxenoid-iron species as alternative oxygenating agents in cytochrome P450-catalyzed reactions: switching by threonine-302 to alanine mutagenesis of cytochrome P450 2B4.

Among biological catalysts, cytochrome P450 is unmatched in its multiplicity of isoforms, inducers, substrates, and types of chemical reactions catalyzed. In the present study, evidence is given that this versatility extends to the nature of the active oxidant. Although mechanistic evidence from several laboratories points to a hypervalent iron-oxenoid species in P450-catalyzed oxygenation reactions, Akhtar and colleagues [Akhtar, M., Calder, M. R., Corina, D. L. & Wright, J. N. (1982) Biochem. J. 201, 569-580] proposed that in steroid deformylation effected by P450 aromatase an iron-peroxo species is involved. We have shown more recently that purified liver microsomal P450 cytochromes, including phenobarbital-induced P450 2B4, catalyze the analogous deformylation of a series of xenobiotic aldehydes with olefin formation. The investigation presented here on the effect of site-directed mutagenesis of threonine-302 to alanine on the activities of recombinant P450 2B4 with N-terminal amino acids 2-27 deleted [2B4 (delta2-27)] makes use of evidence from other laboratories that the corresponding mutation in bacterial P450s interferes with the activation of dioxygen to the oxenoid species by blocking proton delivery to the active site. The rates of NADPH oxidation, hydrogen peroxide production, and product formation from four substrates, including formaldehyde from benzphetamine N-demethylation, acetophenone from 1-phenylethanol oxidation, cyclohexanol from cyclohexane hydroxylation, and cyclohexene from cyclohexane carboxaldehyde deformylation, were determined with P450s 2B4, 2B4 (delta2-27), and 2B4 (delta2-27) T302A. Replacement of the threonine residue in the truncated cytochrome gave a 1.6- to 2.5-fold increase in peroxide formation in the presence of a substrate, but resulted in decreased product formation from benzphetamine (9-fold), cyclohexane (4-fold), and 1-phenylethanol (2-fold). In sharp contrast, the deformylation of cyclohexane carboxaldehyde by the T302A mutant was increased about 10-fold. On the basis of these findings and our previous evidence that aldehyde deformylation is supported by added H202, but not by artificial oxidants, we conclude that the iron-peroxy species is the direct oxygen donor. It remains to be established which of the many other oxidative reactions involving P450 utilize this species and the extent to which peroxo-iron and oxenoid-iron function as alternative oxygenating agents with the numerous isoforms of this versatile catalyst.

Iron isotope and chemical compositions of sediments and basalts drilled seaward of the Mariana Trench

The purpose of this work is to study the mobility and budget of Fe isotopes in the oceanic crust and in particular during low-temperature interaction of seawater with oceanic basalt. We carried out this investigation using samples from Ocean Drilling Program (ODP) Site 801C drilled during Leg 129 and Leg 185 in Jurassic Pacific oceanic crust seaward of the Mariana Trench. The site comprises approximately 450 m of sediment overlying a section of 500 m of basalt, which includes intercalated pelagic and chemical sediments in the upper basaltic units and two low-temperature (10-30°C) ocherous Si-Fe hydrothermal deposits. Fe was chemically separated from 70 selected samples, and 57Fe/54Fe ratios were measured by MC-ICP-MS Isoprobe. The isotopic ratios were measured relative to an internal standard solution and are reported relative to the international Fe-standard IRMM-14. Based on duplicate measurements of natural samples, an external precision of 0.2? (2 sigma) has been obtained. The results indicate that the deep-sea sediment section has a restricted range of d57Fe, which is close to the igneous rock value. In contrast, large variations are observed in the basaltic section with positive d57Fe values (up to 2.05?) for highly altered basalts and negative values (down to ?2.49?) for the associated alteration products and hydrothermal deposits. Secondary Fe-minerals, such as Fe-oxyhydroxides or Fe-bearing clays (celadonite and saponite), have highly variable d57Fe values that have been interpreted as resulting from the partial oxidation of Fe(2+) leached during basalt alteration and precipitated as Fe(3+)-rich minerals. In contrast, altered basalts at Site 801C, which are depleted in Fe (up to 80%), display an increase in d57Fe values relative to fresh values, which suggest a preferential leaching of light iron during alteration. The apparent fractionation factor between dissolved Fe(2+) and Fe remaining in the mineral is from 0.5? to 1.3? and may be consistent with a kinetic isotope fractionation where light Fe is stripped from the minerals. Alternatively, the formation of secondary clays minerals, such as celadonite during basalt alteration may incorporate preferentially the heavy Fe isotopes, resulting in the loss of light Fe isotopes in the fluids. Because microbial processes within the oceanic crust are of potential importance in controlling rates of chemical reactions, Fe redox state and Fe-isotope fractionation, we evaluated the possible effect of this deep biosphere on Fe-isotope signatures. The Fe-isotope systematics presented in this study suggest that, even though iron behavior during seafloor weathering may be mediated by microbes, such as iron-oxidizers, d57Fe variations of more than 4? may also be explained by abiotic processes. Further laboratory experiments are now required to distinguish between various processes of Fe-isotope fractionation during seafloor weathering.

A dictionary of chemical equations.

Mode of access: Internet.

Toxicity reduction through chemical and biological modification of spent pulp bleaching liquors /

Mode of access: Internet.

Industrial uses of isotopes, chemical reaction mechanisms and kinetics, and radiochemistry : a selected list of references /

This bibliography contains 417 annotated references on uses of isotopes in industry and in chemical reaction mechanisms and kinetics. The references were taken from the 1957-1958 open literature. Also included are a list of journals from which the references were selected, an author index, an isotope index, and a graphical depiction of typical applications.

A multi-scaled approach for simulating chemical reaction systems

In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge–Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E. coli, and conclude with a discussion on the significance of this work.

Chemical kinetic investigation of a commercial batch reactor process

The aim of this investigation was to study the chemical reactions occurring during the batchwise production of a butylated melamine-formaldehyde resin, in order to optimise the efficiency and economics of the batch processes. The batch process models are largely empirical in nature as the reaction mechanism is unknown. The process chemistry and the commercial manufacturing method are described. A small scale system was established in glass and the ability to produce laboratory resins with the required quality was demonstrated, simulating the full scale plant. During further experiments the chemical reactions of methylolation, condensation and butylation were studied. The important process stages were identified and studied separately. The effects of variation of certain process parameters on the chemical reactions were also studied. A published model of methylolation was modified and used to simulate the methylolation stage. A major result of this project was the development of an indirect method for studying the condensation and butylation reactions occurring during the dehydration and acid reaction stages, as direct quantitative methods were not available. A mass balance method was devised for this purpose and used to collect experimental data. The reaction scheme was verified using this data. The reactions stages were simulated using an empirical model. This has revealed new information regarding the mechanism and kinetics of the reactions. Laboratory results were shown to be comparable with plant scale results. This work has improved the understanding of the batch process, which can be used to improve product consistency. Future work has been identified and recommended to produce an optimum process and plant design to reduce the batch time.

Fundamental Pd0/PdII redox steps in cross-coupling reactions:homogeneous, hybrid homogeneous-heterogeneous to heterogeneous mechanistic pathways for C-C couplings

C–C bond-forming, cross-coupling reactions of organohalides with nucleophilic compounds, catalysed by palladium, are amongst the most important chemical reactions available to the synthetic chemist. The intimate mechanisms of these reactions, involving Pd0/PdII redox steps, have been of great historical interest and continue to be so. The myriad of possible mechanisms is reviewed in this chapter. The interplay of mononuclear Pd species with higher order Pd species, e.g. nanoclusters/nanoparticles are considered as being equally important in cross-coupling reaction mechanisms. A focus is placed on trichotomic behaviour of cross-coupling catalytic manifolds, from homogeneous to hybrid homogeneous–heterogeneous to truly heterogeneous behaviour. For the latter, surface chemistry and metal atom leaching (and various experimental techniques) are broadly discussed. It is now clear that mechanism for general cross‐coupling reactions, that is as presented to undergraduate students studying Chemistry degrees across the world, is undoubtedly more complex than first thought. New opportunities for catalyst design have therefore emerged in the area of Pd nanoparticles and nanocatalysis, with some wonderful applications especially in chemical biology, providing a snapshot of what the future might hold.

Chemical and physical effects of ultrasound: sonoluminescence and materials

When a liquid is irradiated with ultrasound, acoustic cavitation (the formation, growth, and implosive collapse of bubbles in liquids irradiated with ultrasound) generally occurs. This is the phenomenon responsible for the driving of chemical reactions (sonochemistry) and the emission of light (sonoluminescence). The implosive collapse of bubbles in liquids results in an enormous concentration of sound energy into compressional heating of the bubble contents. Therefore, extreme chemical and physical conditions are generated during cavitation. The study of multibubble sonoluminescence (MBSL) and single-bubble sonoluminescence (SBSL) in exotic liquids such as sulfuric acid (H2SO4) and phosphoric acid (H3PO4) leads to useful information regarding the intracavity conditions during bubble collapse. Distinct sonoluminescing bubble populations were observed from the intense orange and blue-white emissions by doping H2SO4 and H3PO4 with sodium salts, which provides the first experimental evidence for the injected droplet model over the heated-shell model for cavitation. Effective emission temperatures measured based on excited OH• and PO• emission indicate that there is a temperature inhomogeneity during MBSL in 85% H3PO4. The formation of a temperature inhomogeneity is due to the existence of different cavitating bubble populations: asymmetric collapsing bubbles contain liquid droplets and spherical collapsing bubbles do not contain liquid droplets. Strong molecular emission from SBSL in 65% H3PO4 have been obtained and used as a spectroscopic probe to determine the cavitation temperatures. It is found that the intracavity temperatures are dependent on the applied acoustic pressures and the thermal conductivities of the dissolved noble gases. The chemical and physical effects of ultrasound can be used for materials synthesis. Highly reactive species, including HO2•, H•, and OH• (or R• after additives react with OH•), are formed during aqueous sonolysis as a consequence of the chemical effects of ultrasound. Reductive species can be applied to synthesis of water-soluble fluorescent silver nanoclusters in the presence of a suitable stabilizer or capping agent. The optical and fluorescent properties of the Ag nanoclusters can be easily controlled by the synthetic conditions such as the sonication time, the stoichiometry of the carboxylate groups to Ag+, and the polymer molecular weight. The chemical and physical effects of ultrasound can be combined to prepare polymer functionalized graphenes from graphites and a reactive solvent, styrene. The physical effects of ultrasound are used to exfoliate graphites to graphenes while the chemical effects of ultrasound are used to induce the polymerization of styrene which can then functionalize graphene sheets via radical coupling. The prepared polymer functionalized graphenes are highly stable in common organic solvents like THF, CHCl3, and DMF. Ultrasonic spray pyrolysis (USP) is used to prepare porous carbon spheres using energetic alkali propiolates as the carbon precursors. In this synthesis, metal salts are generated in situ, introducing porous structures into the carbon spheres. When different alkali salts or their mixtures are used as the precursor, carbon spheres with different morphologies and structures are obtained. The different precursor decomposition pathways are responsible for the observed structural difference. Such prepared carbon materials have high surface area and are thermally stable, making them potentially useful for catalytic supports, adsorbents, or for other applications by integrating other functional materials into their pores.

ENZYME-FREE UBIQUITIN LIGATION. FROM NATIVE CHEMICAL LIGATION AND SPIN LABELING TO DIMERIZATION BY INTER-UBIQUITIN MIMICKING LINKAGE AND PH-DEPENDENT CONFORMATIONAL SWITCH

The delicate balance between the production and disposal of proteins is vital for the changes required in the cell to respond to given stimulus. Ubiquitination is a protein modification with a range of signaling outcomes when ubiquitin is attached to a protein through a highly ordered enzymatic cascade process. Understanding ubiquitination is a growing field and nowadays the application of chemical reactions allows the isolation of quantitative materials for structural studies. Therefore, in this dissertation it is described some of these suitable chemical methodologies to produce an isopeptide bond toward the polymerization of ubiquitin bypassing the enzymatic control with the purpose of showing if these chemical modifications have a direct impact on the structure of ubiquitin. First, the possibility of incorporating non-natural lysine analogs known as mercaptolysines into the polypeptide chain of Ubiquitin was explored when they were attached to ubiquitin by native chemical ligation at its C terminus. The sulfhydryl group was used for the attachment of a paramagnetic label to map the surface of ubiquitin. Second, the condensation catalyzed by silver nitrate was used for the dimer assembly. In particular, the main focus was on examining whether orthogonal protection and deprotection of each monomer have an impact on the reaction yield, since the synthetic strategy has been previously attempted successfully. Third, the formation of ubiquitin dimers was approached by building an inter-ubiquitin linkage mimicking the isopeptide bond with two approaches, the classic disulfide exchange as well as the thiol-ene click reaction by thermal initiation in aqueous conditions. After assembling the dimeric units, they were studied by Nuclear Magnetic Resonance, in order to establish a conformational state profile which depends on the pH conditions. The latter is a very important concept since some ligands have a preferred affinity when the protein-protein hydrophobic patches are in close proximity.

Reduced models of chemical reaction in chaotic flows

We describe and evaluate two reduced models for nonlinear chemical reactions in a chaotic laminar flow. Each model involves two separate steps to compute the chemical composition at a given location and time. The “manifold tracking model” first tracks backwards in time a segment of the stable manifold of the requisite point. This then provides a sample of the initial conditions appropriate for the second step, which requires solving one-dimensional problems for the reaction in Lagrangian coordinates. By contrast, the first step of the “branching trajectories model” simulates both the advection and diffusion of fluid particles that terminate at the appropriate point; the chemical reaction equations are then solved along each of the branched trajectories in a second step. Results from each model are compared with full numerical simulations of the reaction processes in a chaotic laminar flow.

Chemical Reaction Dynamics of the Liquid/Vapor Interface Studied by Mass Spectrometry

This thesis presents investigations of chemical reactions occurring at the liquid/vapor interface studied using novel sampling methodologies coupled with detection by mass spectrometry. Chapters 2 and 3 utilize the recently developed technique of field-induced droplet ionization mass spectrometry (FIDI-MS), in which the application of a strong electric field to a pendant microliter droplet results in the ejection of highly charged progeny droplets from the liquid surface. In Chapter 2, this method is employed to study the base-catalyzed dissociation of a surfactant molecule at the liquid/vapor interface upon uptake of ammonia from the gas phase. This process is observed to occur without significant modulation of the bulk solution pH, suggesting a transient increase in surface pH following the uptake of gaseous ammonia. Chapter 3 presents real-time studies of the oxidation of the model tropospheric organic compound glycolaldehyde by photodissociation of iron (III) oxalate complexes. The oxidation products of glycolaldehyde formed in this process are identified, and experiments in a deoxygenated environment identify the role of oxygen in the oxidation pathway and in the regeneration of iron (III) following photo-initiated reduction. Chapter 4 explores alternative methods for the study of heterogeneous reaction processes by mass spectrometric sampling from liquid surfaces. Bursting bubble ionization (BBI) and interfacial sampling with an acoustic transducer (ISAT) generate nanoliter droplets from a liquid surface that can be sampled via the atmospheric pressure interface of a mass spectrometer. Experiments on the oxidation of oleic acid by ozone using ISAT are also presented. Chapters 5 and 6 detail mechanistic studies and applications of free-radical-initiated peptide sequencing (FRIPS), a technique employing gas-phase free radical chemistry to the sequencing of peptides and proteins by mass spectrometry. Chapter 5 presents experimental and theoretical studies on the anomalous mechanism of dissociation observed in the presence of serine and threonine residues in peptides. Chapter 6 demonstrates the combination of FRIPS with ion mobility-mass spectrometry (IM-MS) for the separation of isomeric peptides.