Eutectic phase in water-ice: a self-assembled environment conducive to metal-catalyzed non-enzymatic RNA polymerization

Information and catalytic polymers play an essential role in contemporary cellular life, and their emergence must have been crucial during the complex processes that led to the assembly of the first living systems. Polymerization reactions producing these molecules would have had to occur in aqueous medium, which is known to disfavor such reactions. Thus, it was proposed early on that these polymerizations had to be supported by particular environments, such as mineral surfaces and eutectic phases in water-ice, which would have led to the concentration of the monomers out of the bulk aqueous medium and their condensation. This review presents the work conducted to understand how the eutectic phases in water-ice might have promoted RNA polymerization, thereby presumably contributing to the emergence of the ancient information and catalytic system envisioned by the 'RNA-World' hypothesis.     

Time-resolved X-ray scattering study of actin polymerization from profilactin

The polymerization of actin in solutions of purified calf spleen actin or profilactin (1–10 mg·ml^-1) was followed by synchrotron radiation X-ray solution scattering. At the concentration used, polymerization of actin from profilactin or actin occurs without any lag phase. It is shown by a combination of solution scattering, model calculations and electron microscopy that contrary to the conclusions from previous viscometry studies, filaments form without any lag phase in profilactin solution but aggregate in bundles or networks. This phenomenon is independent of the method used to induce polymerization: slow temperature increase, temperature jump in the presence of polymerizing salts or fast mixing with salt. This aggregation explains the lower final viscosity levels, as compared to actin solutions, observed during the polymerization of actin from profilactin.     

Synthesis of pyrophosphates for in vitro selection of catalytic RNA molecules

Reported here are synthetic routes to pyrophosphates linking riboflavin with various nucleosides. The focus is on a flavin-uracil dinucleotide having a biotin tag on the uracil, a molecule that has potential value in the selection of RNA enzymes that catalyze the template-directed polymerization of RNA in the 3'-to-5' direction, which is the direction opposite that catalyzed by standard protein polymerases. Two detailed procedures are presented to prepare this new compound, as well as one procedure to prepare the new flavin-2,6-diaminopurine dinucleotide.     

Synthesis of polycardanol from a renewable resource using a fungal peroxidase from Coprinus cinereus

A fungal peroxidase from Coprinus cinereus (CiP) was successfully used for oxidative polymerization of cardanol in water–organic solvent mixtures. Cardanol is a phenol derivative from a renewable resource having the meta-substituent of a C15 unsaturated hydrocarbon chain mainly with one to three double bonds. So far, only uneconomic plant peroxidases, such as soybean peroxidase (SBP), have been used to polymerize cardanol. The fungal peroxidase used was easily produced by cultivating C. cinereus, and was purified by ultrafiltration and size exclusion chromatography. The purified peroxidase had a specific activity of 4960 U/mg. The CiP-catalyzed polymerization of cardanol was carried out in aqueous/organic solvents. Microbial CiP catalyzed the cardanol polymerization as efficiently as SBP. The structure and molecular weight of the polycardanol produced by CiP were comparable to those produced by SBP. A low reaction temperature of 10 and 15 °C produced polycardanol in high yield and the hydrogen peroxide feed rate was found to affect the initial reaction rate and the final conversion. From a practical point of view, it is believed that microbial CiP will be found more useful for the synthesis of a range of polyphenols from renewable resources than plant peroxidases.     

Preparation of vinyl thymidine ester catalyzed by protease and its chemical polymerization

Transesterification reaction of 0.25 M thymidine with 1 M divinyladipate in dimethylformamide (DMF) was catalyzed by an alkaline protease (5 mg ml^–1) from Streptomyces sp. (20 units mg^–1 min) at 30 °C for 7 days to give 5-O-vinyladipoyl thymidine (yield 77%) without formation of any by-products. Poly(vinyl alcohol) containing thymidine branches could be obtained by its free-radical polymerization.     

Continuous assay for DNA polymerization by light scattering

The time course of DNA polymerization, catalyzed by DNA polymerase I, can be monitored by following changes in light scattering that result from increases in molecular weight of the polymer. Increases in mass of 10% result in an easily measurable change in light scattering. It has been shown that the light scattering change is correlated with the incorporation of radioactive nucleotide, as measured by the filter binding method. Continuous monitoring of the time dependence of polymerization should prove useful in kinetic analysis of the polymerase reaction and related enzyme-DNA interactions.     

Kinetics of phenolic polymerization catalyzed by peroxidase in organic media

Phenolic polymerization was carried out by enzymatic catalysis in organic media, and its kinetics was studied by using high-pressure liquid chromatography (HPLC). Phenols and aromatic amines with electron-withdrawing groups could hardly be polymerized by HRP catalysis, but phenols and aromatic amines with electron-donating groups could easily be polymerized. The reaction rate of either the para-substituted substrate or meta-substituted substrate was higher than that of ortho-substituted substrate. When ortho-position of hydroxy group of phenols was occupied by an electron-donating group and if another electron-donating group occupied para-position of hydroxy group, the reaction rate increased. Horseradish peroxidase and lactoperoxidase could easily catalyze the polymerization, but chloroperoxidase and laccase failed to yield polymers. Metallic ions such as Mn(2+), Fe(2+), or Fe(3+), and Cu(2+) could poison horseradish peroxidase to various extents, but ions such as Co(2+), Cd(2+), Zn(2+), and K(+) were not found to inhibit the reaction. (c) 1995 John Wiley & Sons, Inc.     

Evidence of conformational switch in Streptococcus pneumoniae FtsZ during polymerization

FtsZ, the master coordinator of bacterial cell division, assembles into filaments in the presence of nucleotide. FtsZ from Streptococcus pneumoniae bears two tryptophan residues (W294 and W378) in its amino acid sequence. The tryptophan fluorescence of FtsZ increases during the assembly of FtsZ. We hypothesized that this increase in the fluorescence intensity was due to the change in the environment of one or both tryptophan residues. To examine this, we constructed two mutants (W294F and W378F) of FtsZ by individually replacing tryptophan with phenylalanine. The mutants displayed similar secondary structures, GTPase activity, and polymerization ability as the wild type FtsZ. During the polymerization, only one tryptophan (W294) showed an increase in its fluorescence intensity. Using time‐correlated single‐photon counting, the fluorescence lifetime of W294 was found to be significantly higher than W378, indicating that W294 was more buried in the structure than W378. The lifetime of W294 further increased during polymer formation, while that of W378 remained unchanged. Fluorescence quenching experiment suggested that the solvent exposure of W294 reduced during the polymerization of FtsZ. W294 is located near the T‐7 loop of the protein, a region important for the monomer‐monomer interaction during the formation of a protofilament. The results indicated that the region around W294 of S. pneumoniae FtsZ undergoes a conformational switch during polymerization as seen for FtsZ from other bacteria.     

Template-directed synthesis of oligonucleotides under eutectic conditions

Summary One of the most important sets of model prebiotic experiments consists of reactions that synthesize complementary oligonucleotides from preformed templates under nonenzymatic conditions. Most of these experiments are conducted at 4°C using 0.01–0.1 M concentrations of activated nucleotide monomer and template (monomer equivalent). In an attempt to extend the conditions under which this type of reaction can occur, we have concentrated the reactants by freezing at –18°C, which is close to the NaCl–H₂O eutectic at –21°C.The results from this set of experiments suggest that successful syntheses can occur with poly(C) concentrations as low at 5×10^–4 M and 2MeImpG concentrations at 10^–3 M. It was also anticipated that this mechanism might allow the previously unsuccessful poly(A)-directed synthesis of oligo(U)s to occur. However, no template effect was seen with the poly(A) and ImpU system. The failure of these conditions to allow template-directed synthesis of oligo(U)s supports the previously proposed idea that pyrimidines may not have been part of the earliest genetic material.Because of the low concentrations of monomer and template that would be expected from prebiotic syntheses, this lower temperature could be considered a more plausible geologic setting for template-directed synthesis than the standard reaction conditions.     

12 Reconstructing the RNA world

A critical event in the origin of life is thought to have been the emergence of an RNA molecule capable of self-replication as well as mutation, and hence evolution towards ever more efficient replication. As this primordial replicase appears to have been lost in time, we use synthetic biology to build modern-day “Doppelgangers” of the ancestral replicase to reconstruct and study their properties in an effort to learn more about life’s first genetic system. I will discuss our progress in the engineering and evolution of RNA polymerase ribozymes as well as the potential role that structured media such as the eutectic phase of water–ice may have played in the emergence of RNA self-replication.     

Chitosan‐templated bio‐coloration of cotton fabrics via laccase‐catalyzed polymerization of hydroquinone

There is an increasing interest in the development of enzymatic coloration of textile fabrics as an alternative to conventional textile dyeing processes, which is successful for dyeing protein fibers. However, unmodified cotton fabrics are difficult to be dyed through enzyme catalysis due to the lack of affinity of biosynthesized dyes to cotton fibers. In order to improve the enzyme‐catalyzed dyeability of cotton fibers, chitosan was used to coat cotton fabrics as template. A novel and facile bio‐coloration technique using laccase catalysis of hydroquinone was developed to dye chitosan‐templated cotton fabrics. The polymerization of hydroquinone with the template of chitosan under the laccase catalysis was monitored by ultraviolet‐vis spectrophotometer on the absorbance of reaction solution. A significant peak of UV‐vis spectrum at 246 nm corresponding to large conjugated structures appeared and increased with increasing the duration of enzymatic catalysis. The effect of different treatment conditions on the laccase‐catalyzed dyeing of cotton fabric was investigated to determine their optimal parameters of laccase‐catalyzed coloration. Fourier‐transform infrared spectroscopy spectra demonstrated the formation of H‐bond and Schiff base reaction between chitosan and polymerized hydroquinone. Scanning electron microscopy indicated that the surface of dyed cotton fiber was much rougher than that of the control sample. Moreover, X‐ray photoelectron spectroscopy also revealed the existence of the chitosan/polymerized hydroquinone complex and polymerized hydroquinone on the dyed cotton fibers. This chitosan‐templated approach offers possibility for biological dyeing coloration of cotton fabrics and other cellulosic materials.     

5 Efficient and high-fidelity copying of an RNA-like model prebiotic system

Nonenzymatic RNA replication would provide an important bridge to the RNA world. However, the demonstration of efficient and high-fidelity copying chemistry remains a great experimental challenge. It requires an efficient mechanism that can lead to both a high rate of polymerization and a high degree of fidelity in the copying chemistry. Previous experiments concerning nonenzymatic template-directed synthesis of RNA with activated monomers have led to the copying of short RNA templates, but these reactions are generally slow (taking days to weeks) and highly error-prone. Therefore, the ability to efficiently and accurately copy arbitrary template sequences remains frustratingly out of reach. N3′-P5′-linked phosphoramidate DNA is a highly reactive model for self-replicating genetic materials and has been used for studies of nonenzymatic RNA self-replication. It is also an excellent RNA mimic, due to its similar overall duplex structure, rigidity, and level of hydration (Tereshko, Gryaznov, & Egli, 1998). Our experiments show that the high reactivity imparted by the presence of an amino nucleophile allows rapid and efficient copying of all four nucleobases on both homopolymeric and mixed templates. On the other hand, G:T wobble pairing leads to a high error rate. We have, therefore, investigated the use of the modified nucleobase, 2-thio T (Ts) (Sintim & Kool, 2006), to suppress formation of the G:T wobble base-pair. Our results illustrate that the 2-thio modification can both increase polymerization rate and enhance fidelity in this self-replicating N3′-P5′-DNA system. These results suggest that this simple nucleobase modification may have played a role in primordial RNA (or proto-RNA) replication. In addition to suppressing the G:T mismatch, an additional benefit gained from its stronger base-pairing with A is that it also reduces A:C mismatch formation. Thus, simple modifications of nucleobases might provide a means of suppressing mismatches to yield better fidelity. Taken together, our results show that a high rate of polymerization and a high degree of fidelity are not mutually exclusive, but can be achieved simultaneously in nonenzymatic copying of N3′-P5′-linked phosphoramidate DNA. The structural similarity of NP-DNA to RNA suggests that these results could be translated to an RNA-only system.     

Penicillin acylase-catalyzed synthesis of cefazolin in water–solvent mixtures: enhancement effect of ethyl acetate and carbon tetrachloride on the synthetic yield

The effects of organic solvents on the penicillin acylase-catalyzed, kinetically controlled synthesis of cefazolin have been examined in various water–solvent mixtures. In the presence of water-miscible solvents, the initial rate and maximum yield of cefazolin (CEZ) synthesis reaction were found to be reduced. The extent of inhibition was increased with increasing hydrophobicity of the solvent in the reaction mixtures. Enzymatic synthesis of cefazolin was also carried out in the water–solvent biphasic systems. Among the water-immiscible solvents tested, ethyl acetate (EtOAc) and carbon tetrachloride (CCl₄) were found to markedly improve the yield of cefazolin in the two-phase reaction system. Our study showed that the enhancement effect of EtOAc and CCl₄ on the synthetic yield was mainly caused by a reduction of the hydrolysis of acyl donor and product in the two-phase system rather than extraction of the product into the solvent phase.     

Arginine cofactors on the polymerase ribozyme

The RNA world hypothesis states that the early evolution of life went through a stage in which RNA served both as genome and as catalyst. The central catalyst in an RNA world organism would have been a ribozyme that catalyzed RNA polymerization to facilitate self-replication. An RNA polymerase ribozyme was developed previously in the lab but it is not efficient enough for self-replication. The factor that limits its polymerization efficiency is its weak sequence-independent binding of the primer/template substrate. Here we tested whether RNA polymerization could be improved by a cationic arginine cofactor, to improve the interaction with the substrate. In an RNA world, amino acid-nucleic acid conjugates could have facilitated the emergence of the translation apparatus and the transition to an RNP world. We chose the amino acid arginine for our study because this is the amino acid most adept to interact with RNA. An arginine cofactor was positioned at ten different sites on the ribozyme, using conjugates of arginine with short DNA or RNA oligonucleotides. However, polymerization efficiency was not increased in any of the ten positions. In five of the ten positions the arginine reduced or modulated polymerization efficiency, which gives insight into the substrate-binding site on the ribozyme. These results suggest that the existing polymerase ribozyme is not well suited to using an arginine cofactor.     

Preparation of polysaccharide supramolecular films by vine-twining polymerization approach

In this study, we investigated the preparation of polysaccharide supramolecular films through the formation of inclusion complexes by amylose in vine-twining polymerization using carboxymethyl cellulose-graft-poly(?-caprolactone) (CMC-g-PCL) as a new guest polymer. First, hydrogels were prepared by phosphorylase-catalyzed enzymatic polymerization in the presence of CMC-g-PCL according to the vine-twining polymerization manner. The XRD result of a powdered sample obtained by lyophilization of the resulting hydrogel indicated the presence of inclusion complexes of amylose with the PCL graft-chains between intermolecular (CMC-g-PCL)s, which acted as supramolecular cross-linking points for the hydrogelation. Then, the supramolecular films were obtained by adding water to the powdered samples, followed by drying. The mechanical properties of the selected films examined by tensile testing were superior to those of a CMC film. The effect of the supramolecular cross-linking structures on the mechanical properties of the films was evaluated further by several investigations.     

Palmitoylation and polymerization of hepatitis C virus NS4B protein

Hepatitis C Virus (HCV) NS4B protein induces a specialized membrane structure which may serve as the replication platform for HCV RNA replication. In the present study, we demonstrated that NS4B has lipid modifications (palmitoylation) on two cysteine residues (cysteines 257 and 261) at the C-terminal end. Site-specific mutagenesis of these cysteine residues on individual NS4B proteins and on an HCV subgenomic replicon showed that the lipid modifications, particularly of Cys261, are important for protein-protein interaction in the formation of the HCV RNA replication complex. We further demonstrated that NS4B can undergo polymerization. The main polymerization determinants were mapped in the N-terminal cytosolic domain of NS4B protein; however, the lipid modifications on the C terminus also facilitate the polymerization process. The lipid modification and the polymerization activity could be two properties of NS4B important for its induction of the specialized membrane structure involved in viral RNA replication.     

Evaluation of 4-phenylamino-substituted naphthalene-1,2-diones as tubulin polymerization inhibitors

A series of 4-phenylamino-substituted naphthalene-1,2-dione derivatives were prepared and evaluated as effective antiproliferative agents. MTT assays showed that the compounds with a methyl group on the nitrogen linker exhibited potent antiproliferative activities against human cancer cells. The mechanistic study revealed that these compounds could induce mitochondrial depolarization, which resulted in intracellular ROS production, and they also acted as tubulin polymerization inhibitors. Moreover, the typical compound could arrest A549 cells in the G2/M phase, resulting in cellular apoptosis and induced mitotic arrest in A549 cells through disrupting microtubule dynamics.     

Comparative study of the molecularly imprinted polymers prepared by reversible addition–fragmentation chain transfer “bulk” polymerization and traditional radical “bulk” polymerization

Bisphenol A (BPA) and propranolol‐imprinted polymers have been prepared via both reversible addition–fragmentation chain transfer “bulk” polymerization (RAFTBP) and traditional radical “bulk” polymerization (TRBP) under similar reaction conditions, and their equilibrium binding properties were compared in detail for the first time. The chemical compositions, specific surface areas, equilibrium bindings, and selectivity of the obtained molecularly imprinted polymers (MIPs) were systematically characterized. The experimental results showed that the MIPs with molecular imprinting effects and quite fast binding kinetics could be readily prepared via RAFTBP, but they did not show improved template binding properties in comparison with those prepared via TRBP, which is in sharp contrast to many previous reports. This could be attributed to the heavily interrupted equilibrium between the dormant species and active radicals in the RAFT mechanism because of the occurrence of fast gelation during RAFTBP. The findings presented here strongly demonstrates that the application of controlled radical polymerizations (CRPs) in molecular imprinting does not always benefit the binding properties of the resultant MIPs, which is of significant importance for the rational use of CRPs in generating MIPs with improved properties. Copyright © 2013 John Wiley & Sons, Ltd.     

Living enantiosymmetric and enantioasymmetric polymerization of methylthiirane in homogeneous phase

The polymerization of racemic methylthiirane in homogeneous phase, initiated by bis(isopropyl-S-cysteinato) cadmium is a living process. The resulting polymers are isotactic and optically active at partial conversion. The optical purity of the residual monomer may reach 27% at half conversion. The propagation occurs mainly on one valency of Cd, however oligomers grow slowly on the second valency. The stereoregularity of the polymer chain appears only when the length of the oligomer becomes high enough, making possible a bicoordination of the Cd counterions. The stereoregularity of the polymer is characterized by the molar fraction σ of isotactic diads which varies from 0.5 for atactic chains—formed at the beginning—to about one for isotactic segments formed for longer chains. The stereospecifictity also depends on temperature of propagation and on initiator concentration. The kinetics observed (zero order in monomer and one-half in Cd) are explained by monomer coordination before insertion and dimeric association of the thiolate end groups. The enantioasymmetric process observed results from an unbalance in the number of the two different types of active sites and possibly from a difference in their reactivities. Enantioasymmetry has been found to decrease significantly when the dielectric constant ε of the medium increases.