Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme

Background: RNA and DNA are polymers that lack the diversity of chemical functionalities that make proteins so suited to biological catalysis. All naturally occurring ribozymes (RNA catalysts) that catalyze the formation, transfer and hydrolysis of phosphodiesters require metal-ion cofactors for their catalytic activity. We wished to investigate whether, and to what extent, DNA molecules could catalyze the cleavage (by either hydrolysis or transesterification) of a ribonucleotide phosphodiester in the absence of divalent or higher-valent metal ions or, indeed, any other cofactors.Results: We performed in vitro selection and amplification experiments on a library of random-sequence DNA that incorporated a single ribonucleotide, a suitable site for cleavage. Following 12 cycles of selection and amplification, a ‘first generation’ of DNA enzymes (DNAzymes) cleaved their internal ribonucleotide phosphodiesters at rates ∼ 10⁷-fold faster than the spontaneous rate of cleavage of the dinucleotide ApA in the absence of divalent cations. Re-selection from a partially randomized DNA pool yielded ‘second generation’ DNAzymes that self-cleaved at rates of ∼ 0.01 min⁻¹ (a 10⁸-fold rate enhancement over the cleavage rate of ApA). The properties of these selected catalysts were different in key respects from those of metal-utilizing ribozymes and DNAzymes. The catalyzed cleavage took place in the presence of different chelators and ribonuclease inhibitors. Trace-metal analysis of the reaction buffer (containing very high purity reagents) by inductively coupled plasma-optical emission spectrophotometry indicated that divalent or higher-valent metal ions do not mediate catalysis by the DNAzymes.Conclusions: Our results indicate that, although ribozymes are sometimes regarded generically to be metalloenzymes, the nucleic acid components of ribozymes may play a substantial role in the overall catalysis. Given that metal cofactors increase the rate of catalysis by ribozymes only ∼ 10²−10³-fold above that of the DNAzyme described in this paper, it is conceivable that substrate positioning, transition-state stabilization or general acid/base catalysis by the nucleic acid components of ribozymes and DNAzymes may contribute significantly to their overall catalytic performance.     

An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling

DNA enzymes are single-stranded DNA molecules with catalytic capabilities that are isolated from random-sequence DNA libraries by "in vitro selection". This new class of catalytic biomolecules has the potential of being used as unique molecular tools in a variety of innovative applications. Here we describe the creation and characterization of an RNA-cleaving autocatalytic DNA, DEC22-18, that uniquely links chemical catalysis with real-time fluorescence signaling capability in the same molecule. A trans-acting DNA molecule, DET22-18, was also developed from DEC22-18 that behaves as a true enzyme with a k(cat) of approximately 7 min(-1)-a rate constant that is the second largest ever reported for a DNA enzyme. It cleaves a chimeric RNA/DNA substrate at the lone RNA linkage surrounded by a closely spaced fluorophore-quencher pair-a unique structure that permits the synchronization of the chemical cleavage with fluorescence signaling. DET22-18 has a stem-loop structure and can be conjugated with DNA aptamers to form allosteric deoxyribozyme biosensors.     

RNA-cleaving DNA enzymes with altered regio- or enantioselectivity

In vitro evolution methods were used to obtain DNA enzymes that cleave either a 2',5'-phosphodiester following a D-ribonucleotide or a 3',5'-phosphodiester following an L-ribonucleotide. Both enzymes can operate in an intermolecular reaction format with multiple turnover. The DNA enzyme that cleaves a 2',5'-phosphodiester exhibits a k(cat) of approximately 0.01 min(-1) and catalytic efficiency, k(cat)/K(m), of approximately 10(8) M(-1) min(-1). The enzyme that cleaves an L-ribonucleotide is about 10-fold slower and has a catalytic efficiency of approximately 4 x 10(5) M(-1) min(-1). Both enzymes require a divalent metal cation for their activity and have optimal catalytic rate at pH 7-8 and 35-50 degrees C. In a comparison of each enzyme's activity with either its corresponding substrate that contains an unnatural ribonucleotide or a substrate that instead contains a standard ribonucleotide, the 2',5'-phosphodiester-cleaving DNA enzyme exhibited a regioselectivity of 6000-fold, while the L-ribonucleotide-cleaving DNA enzyme exhibited an enantioselectivity of 40-fold. These molecules demonstrate how in vitro evolution can be used to obtain regio- and enantioselective catalysts that exhibit specificities for nonnatural analogues of biological compounds.     

Optimisation d’une sélection in vitro d’enzymes

Optimisation of an in vitro enzyme selection. Isolation of a catalyst for a given chemical reaction may be achieved by in vitro selection of enzymes from a protein library. Here, we investigate the polymerisation reaction on filamentous phage and the cross-linking of substrate on phage to optimise an in vitro selection for DNA polymerase activity. The efficiency of the optimised selection is measured by enrichment factors up to 3.8 × 10³, the highest described so far for an in vitro selection of proteins for catalysis. It should be useful for directed polymerase evolution towards novel catalytic activities. To cite this article: E. Orsi, J.-L. Jestin, C. R. Chimie 6 (2003).     

An RNA-Cleaving DNAzyme That Requires an Organic Solvent to Function

Engineering functional nucleic acids that are active under unusual conditions will not only reveal their hidden abilities but also lay the groundwork for pursuing them for unique applications. Although many DNAzymes have been derived to catalyze diverse chemical reactions in aqueous solutions, no prior study has been set up to purposely derive DNAzymes that require an organic solvent to function. Herein, we utilized in vitro selection to isolate RNA-cleaving DNAzymes from a random-sequence DNA pool that were “compelled” to accept 35 % dimethyl sulfoxide (DMSO) as a cosolvent, via counter selection in a purely aqueous solution followed by positive selection in the same solution containing 35 % DMSO. This experiment led to the discovery of a new DNAzyme that requires 35 % DMSO for its catalytic activity and exhibits drastically reduced activity without DMSO. This DNAzyme also requires divalent metal ions for catalysis, and its activity is enhanced by monovalent ions. A minimized, more efficient DNAzyme was also derived. This work demonstrates that highly functional, organic solvent-dependent DNAzymes can be isolated from random-sequence DNA libraries via forced in vitro selection, thus expanding the capability and potential utility of catalytic DNA.     

Bridging the gap between proteins and nucleic acids: a metal-independent RNAseA mimic with two protein-like functionalities.

Two synthetically modified nucleoside triphosphate analogues (adenosine modified with an imidazole and uridine modified with a cationic amine) are enzymatically polymerized in tandem along a degenerate DNA library for the combinatorial selection of an RNAse A mimic. The selected activity is consistent with both electrostatic and general acid/base catalysis at physiological pH in the absence of divalent metal cations. The simultaneous use of two modified nucleotides to enrich the catalytic repertoire of DNA-based catalysts has never before been demonstrated and evidence of general acid/base catalysis at pH 7.4 for a DNAzyme has never been previously observed in the absence of a divalent metal cation or added cofactor. This work illustrates how the incorporation of protein-like functionalities in nucleic acids can bridge the gap between proteins and oligonucleotides underscoring the potential for using nucleic acid scaffolds in the development of new materials and improved catalysts for use in chemistry and medicine.     

In vitro selection of a novel nuclease-resistant RNA phosphodiesterase

BACKGROUND: Ribonucleotide-based enzymes (ribozymes) that cleave pathological RNAs are being developed as therapeutic agents. Chemical modification of the hammerhead ribozyme has produced nuclease-resistant catalysts that cleave targeted mRNAs in cell culture and exhibit antitumor activity in animals. Unfortunately, stabilizing modifications usually reduce the catalytic rate in vitro. An alternative to rationally designed chemical modifications of existing ribozymes is to identify novel motifs through in vitro selection of nuclease-stable sequence space. This approach is desirable because the catalysts can be optimized to function under simulated physiological conditions. RESULTS: Utilizing in vitro selection, we have identified a nuclease-stable phosphodiesterase that demonstrated optimal activity at simulated physiological conditions. The initial library of 10(14) unique molecules contained 40 randomized nucleotides with all pyrimidines in a nuclease-stabilized 2'-deoxy-2'-amino format. The selection required trans-cleaving activity and base-pairing specificity towards a resin-bound RNA substrate. Initial selective pressure was permissive, with a 30 min reaction time and 25 mM Mg(2+). Stringency of selection pressure was gradually increased until final conditions of 1 mM Mg(2+) and less than 1 min reaction times were achieved. The resulting 61-mer catalyst required the 2'-amino substitutions at selected pyrimidine positions and was stable in human serum (half-life of 16 h). CONCLUSIONS: We demonstrated that it is possible to identify completely novel, nuclease-resistant ribozymes capable of trans-cleaving target RNAs at physiologically relevant Mg(2+) concentrations. The new ribozyme motif has minimal substrate requirements, allowing for a wide range of potential RNA targets.     

Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes

Although DNA has not been found responsible for biological catalysis, many artificial DNA enzymes have been created by "in vitro selection." Here we describe a new selection approach to assess the influence of four common divalent metal ions (Ca(2+), Cu(2+), Mg(2+), and Mn(2+)) on sequence diversity, metal specificity, and catalytic proficiency of self-phosphorylating deoxyribozymes. Numerous autocatalytic DNA sequences were isolated, a majority of which were selected using Cu(2+) or Mn(2+) as the divalent metal cofactor. We found that Cu(2+)- and Mn(2+)-derived deoxyribozymes were strictly metal specific, while those selected by Ca(2+) and Mg(2+) were less specific. Further optimization by in vitro evolution resulted in a Mn(2+)-dependent deoxyribozyme with a k(cat) of 2.8 min(-1). Our findings suggest that DNA has sufficient structural diversity to facilitate efficient catalysis using a broad scope of metal cofactor utilizing mechanisms.     

Catalysis of the kemp elimination by natural coals

Commercially available coals were found to be efficient heterogeneous catalysts of the Kemp elimination reaction in aqueous solutions. A pH-rate profile study suggests that catalysis originates from specific catalytic groups and not simply from the large graphitic surface area. The low-quality lignite coals, which exhibit similar catalytic efficiency per weight to that of molecularly imprinted polymers, are better catalysts for this reaction in comparison with the bituminous coals.     

喹啉及其衍生物的多相不对称氢转移反应

喹啉及其衍生物的多相不对称氢转移是制备杂环手性化合物的理想策略.多相手性催化体系具有催化剂可循环利用及产物分离提纯容易等优势.然而,喹啉及其衍生物的多相手性高效催化体系鲜有报道.这主要是由于多相手性氢转移为水-油-固三相反应,在反应的过程中,传质问题极大影响固体催化剂的催化性能.因此,发展具有相转移功能的手性催化材料,是提高多相氢转移体系催化效率的有效途径.本文采用一锅法合成策略,通过离子液体(ILs)为连接基团实现了TsDPEN手性配体在SBA-15介孔孔道中的嫁接.与Rh盐配位后,获得手性固体催化剂SBA-ILBF4-TsDPEN-Rh.FI-IR光谱和13C NMR结果表明,手性催化活性中心成功负载在SBA-15中,随着手性活性中心负载量的增加,SBA-ILBF4-TsDPEN-Rh的比表面积、孔径和孔容逐渐降低.在喹啉衍生物不对称氢转移反应中,SBA-ILBF4-TsDPEN-Rh系列催化剂催化得到产物的ee值为91％,表明多相手性催化剂具有较高的手性选择性.多相手性催化剂的催化活性随着活性中心负载量的上升而呈现下降的趋势,这主要是由于活性中心负载量较低的多相催化剂具有更高的比表面积和孔容,更有利于催化过程中的传质.与均相手性催化剂相比,优化后的多相手性催化剂表现出更高的催化活性(TOF值分别为75和92 h-1).作为对比,本文还合成了采用烷基链为连接基团的SBA-TsDPEN25-Rh,并以其为基础进一步嫁接了ILs基团,得到SBA-TsDPEN20-ILBF4-Rh.在相同的反应条件下,SBA-ILBF4-TsDPEN50-Rh表现出更高的催化活性.上述结果证实了ILs基团在反应过程中起到相转移以及富集氢源甲酸盐的作用,极大促进了喹哪啶不对称氢转移多相催化体系的活性,并且ILs基团和手性活性中心在空间距离上的接近更有利于催化活性的提高.此外,本文还研究了反应体系pH值对固体催化剂上反应速率的影响,随着反应的进行,反应溶液的pH会呈现明显上升的趋势,导致反应速率减缓以及底物转化受限.通过在反应过程中加入适量甲酸或者选用浓度更高的缓冲溶液可以有效防止催化过程中反应速率的减慢.综上可见,负载手性催化剂中的连接基团对多相手性催化剂的催化性能有重要影响.通过改变手性配体的连接基团提高手性固体催化剂的催化活性和手性选择性的策略可以拓展到其他多相手性催化体系.     

Function of the Metallomicelle from an Aza-Crown Ether Complex with an Acetamide Branch as a Highly Potent Promoter of Phosphate Diester Hydrolytic Cleavage

This study reports the synthesis method of a new aza-crown ether with an acetamide branch ligand, 2-(1,10-dioxa-4,7,13,16-tetraaza-cyclooctadec-4-yl)-acetamide (L), and determines the chemical composition of the cerium complex containing the aza-crown ether ligand by a new fluorescence spectrophotometric method. In the report, the cerium complex and its metallomicellar systems were used as catalysts in the hydrolysis of bis(4-nitrophenyl)phosphate ester (BNPP), and their catalytic activity was studied by the comparative method. The interaction between the metallomicelle and BNPP was proved by the fluorescence spectrum. The catalytic rate of BNPP hydrolysis was measured kinetically using the UV-Vis spectrophotometric method. The results indicated that the metallomicellar system of the anionic surfactant exhibited excellent catalytic function and relatively higher catalytic activity than that of the complex solution, the metallomicelle of nonionic and cationic surfactants, and the micelle provided an effective catalytic environment for the catalytic reaction. The experimental results also showed that the best acidity for the metallomicelle catalysis is pH 8.0, and the mono-hydroxy complex may be the real active species uaed as a catalyst in BNPP catalytic hydrolysis. The reaction mechanism was proposed on the basis of the research results.     

In Situ Microfocus Chemical Computed Tomography of the Composition of a Single Catalyst Particle During Hydrogenation of Nitrobenzene in the Liquid Phase

Heterogeneous catalysis performed in the liquid phase is an important type of catalytic process which is rarely studied in situ. Using microfocus X‐ray fluorescence and X‐ray diffraction computed tomography (μ‐XRF‐CT, μ‐XRD‐CT) in combination with X‐ray absorption near‐edge spectroscopy (XANES), we have determined the active state of a Mo‐promoted Pt/C catalyst (NanoSelect) for the liquid‐phase hydrogenation of nitrobenzene under standard operating conditions. First, μ‐XRF‐CT and μ‐XRD‐CT reveal the active state of Pt catalyst to be reduced, noncrystalline, and evenly dispersed across the support surface. Second, imaging of the Pt and Mo distribution reveals they are highly stable on the support and not prone to leaching during the reaction. This study demonstrates the ability of chemical computed tomography to image the nature and spatial distribution of catalysts under reaction conditions.     

Discovery and characterization of catalysts for azide-alkyne cycloaddition by fluorescence quenching

Copper-based catalysts for the 1,3-dipolar cycloaddition of azides and alkynes were screened in parallel fashion using a fluorescence quenching assay. The method was designed to identify systems able to accelerate the coupling of reactants at micromolar concentrations in aqueous mixtures and to obtain quantitative comparisons of their activities. In addition to the tris(triazolylamines) previously reported, two types of compounds (bipy/phen and 2-pyridyl Schiff bases) were found to exhibit significant ligand-accelerated catalysis, with one complex showing especially dramatic rate enhancements. Preliminary explorations of the dependence of reaction rate on pH, ligand:Cu ratio, and Cu concentration are described.     

Advances in the electrochemical catalytic reduction of CO2 with metal complexes

Electrocatalytic CO₂ reduction has emerged as a promising strategy to effectively produce fuels and chemicals sustainably. In this regard, the study of electrochemical catalytic reduction of CO₂ with metal complexes is a powerful tool for both the development of catalysts that operated under desired conditions (low overpotentials, high catalytic rates and selectivity, and extended durability) and the understanding of basic principles in catalysis. To illustrate the state-of-the-art, this revision presents a selection of the most recent and remarkable findings reported in terms of key strategies to improve reaction rates, selectivity and mechanism understanding for the leading families of homogeneous catalysts.     

Dual Gold Catalysis: σ,π‐Propyne Acetylide and Hydroxyl‐Bridged Digold Complexes as Easy‐To‐Prepare and Easy‐To‐Handle Precatalysts

A series of dinuclear gold σ,π‐propyne acetylide complexes were prepared and tested for their catalytic ability in dual gold catalysis that was based on the reaction of an electrophilic π‐complex of gold with a gold acetylide. The air‐stable and storable catalysts can be isolated as silver‐free catalysts in their activated form. These dual catalysts allow a fast initiation phase for the dual catalytic cycles without the need for additional additives for acetylide formation. Because propyne serves as a throw‐away ligand, no traces of the precatalyst are generated. Based on the fast initiation process, side products are minimized and reaction rates are higher for these catalysts. A series of test reactions were used to demonstrate the general applicability of these catalysts. Lower catalyst loadings, faster reaction rates, and better selectivity, combined with the practicability of these catalysts, make them ideal catalysts for dual gold catalysis.     

Synthesis of thermoregulated phase-separable triazolium ionic liquids catalysts and application for Stetter reaction

A series of polyether-substituted triazolium ionic liquids catalysts have been first synthesized for resolving the problem of separation and reuse of Stetter catalysts. The catalysts possess the properties of critical solution temperature (CST) and inverse temperature-dependent solubility in toluene/heptane solvents. Based on these properties, the catalysts can achieve the catalytic process named as thermoregulated phase-separable catalysis (TPSC) with the characteristic of homogeneous reaction at higher temperature and phase-separation at lower temperature. The novel TPSC system has been successfully applied for Stetter reaction of furfural or butanal with ethyl acrylate. The experimental results have showed that the novel catalysts exhibit excellent TPSC with high recycling efficiency.     

Metalloporphyrin‐Based Hypercrosslinked Polymers Catalyze Hetero‐Diels–Alder Reactions of Unactivated Aldehydes with Simple Dienes: A Fascinating Strategy for the Construction of Heterogeneous Catalysts

We describe a novel and intriguing strategy for the construction of efficient heterogeneous catalysts by hypercrosslinking catalyst molecules in a one‐pot Friedel–Crafts alkylation reaction. The new hypercrosslinked polymers (HCPs) as porous solid catalysts exhibit the combined advantages of homogeneous and heterogeneous catalysis, owing to their high surface area, good stability, and tailoring of catalytic centers on the frameworks. Indeed, a new class of metalloporphyrin‐based HCPs were successfully synthesized using modified iron(III) porphyrin complexes as building blocks, and the resulting networks were found to be excellent recyclable heterogeneous catalysts for the hetero‐Diels–Alder reaction of unactivated aldehydes with 1,3‐dienes. Moreover, this new strategy showed wide adaptability, and many kinds of homogeneous‐like solid‐based catalysts with high catalytic performance and excellent recyclability were also constructed.     

光热协同效应在催化反应中的应用研究进展

近几年,随着催化研究的逐渐深入,将两种或多种手段耦合,能够明显地改善催化性能,其中光热协同催化是当前新型催化技术研究的焦点.我们介绍了光热协同催化在能源合成领域的应用,尤其在光热催化CO_2转化、污染物降解、制氢和费托合成等反应.研究结果表明,两者的有效结合可以超越单独热催化或光催化所能达到的效果,在某些反应中能够明显提高产物的收率,改善目标产物的选择性以及降低反应的温度.最后还展望了光热协同催化发展的前景,以及目前仍然面临反应机理尚不明确和合适催化剂的筛选等问题.     

Improving metal ion specificity during in vitro selection of catalytic DNA

Metal ions play important roles in both the structure and function of catalytic DNA and RNA. While most natural catalytic RNA molecules (ribozymes) are active in solutions containing Mg(2+), in vitro selection makes it possible to search for new catalytic DNA/RNA that are specific for other metal ions. However, previous studies have indicated that the in vitro selection protocols often resulted in catalytic DNA/RNA that were equally active or sometimes even more active with metal ions other than the metal ion of choice. To improve the metal ion specificity during the in vitro selection process, we implemented a negative selection strategy where the nucleic acid pool was subjected to a solution containing competing metal ions. As a result, those nucleic acids that were active with those metal ions are discarded. To demonstrate the effectiveness of the negative selection strategy, we carried out two parallel in vitro selections of Co(2+)-dependent catalytic DNA. When no negative selection was used in the selection process, the resulting catalytic DNA molecules were more active in solutions of Zn(2+) and Pb(2+) than in Co(2+). On the other hand, when the negative selection steps were inserted between the normal positive selection steps, the resulting catalytic DNA molecules were much more active with Co(2+) than in other metal ions including Zn(2+) and Pb(2+). These results suggest strongly that in vitro selection can be used to obtain highly active and specific transition metal ion-dependent catalytic DNA/RNA, which hold great promise as versatile and efficient endonucleases as well as sensitive and selective metal ion sensors.     

A Pt-cluster-based heterogeneous catalyst for homogeneous catalytic reactions: X-ray absorption spectroscopy and reaction kinetic studies of their activity and stability against leaching

The design and development of metal-cluster-based heterogeneous catalysts with high activity, selectivity, and stability under solution-phase reaction conditions will enable their applications as recyclable catalysts in large-scale fine chemicals production. To achieve these required catalytic properties, a heterogeneous catalyst must contain specific catalytically active species in high concentration, and the active species must be stabilized on a solid catalyst support under solution-phase reaction conditions. These requirements pose a great challenge for catalysis research to design metal-cluster-based catalysts for solution-phase catalytic processes. Here, we focus on a silica-supported, polymer-encapsulated Pt catalyst for an electrophilic hydroalkoxylation reaction in toluene, which exhibits superior selectivity and stability against leaching under mild reaction conditions. We unveil the key factors leading to the observed superior catalytic performance by combining X-ray absorption spectroscopy (XAS) and reaction kinetic studies. On the basis of the mechanistic understandings obtained in this work, we also provide useful guidelines for designing metal-cluster-based catalyst for a broader range of reactions in the solution phase.