Flexizymes: their evolutionary history and the origin of catalytic function

Transfer RNA (tRNA) is an essential component of the cell's translation apparatus. These RNA strands contain the anticodon for a given amino acid, and when "charged" with that amino acid are termed aminoacyl-tRNA. Aminoacylation, which occurs exclusively at one of the 3'-terminal hydroxyl groups of tRNA, is catalyzed by a family of enzymes called aminoacyl-tRNA synthetases (ARSs). In a primitive translation system, before the advent of sophisticated protein-based enzymes, this chemical event could conceivably have been catalyzed solely by RNA enzymes. Given the evolutionary implications, our group attempted in vitro selection of artificial ARS-like ribozymes, successfully uncovering a functional ribozyme (r24) from an RNA pool of random sequences attached to the 5'-leader region of tRNA. This ribozyme preferentially charges aromatic amino acids (such as phenylalanine) activated with cyanomethyl ester (CME) onto specific kinds of tRNA. During the course of our studies, we became interested in developing a versatile, rather than a specific, aminoacylation catalyst. Such a ribozyme could facilitate the preparation of intentionally misacylated tRNAs and thus serve a convenient tool for manipulating the genetic code. On the basis of biochemical studies of r24, we constructed a truncated version of r24 (r24mini) that was 57 nucleotides long. This r24mini was then further shortened to 45 nucleotides. This ribozyme could charge various tRNAs through very simple three-base-pair interactions between the ribozyme's 3'-end and the tRNA's 3'-end. We termed this ribozyme a "flexizyme" (Fx3 for this particular construct) owing to its flexibility in addressing tRNAs. To devise an even more flexible tool for tRNA acylation, we attempted to eliminate the amino acid specificity from Fx3. This attempt yielded an Fx3 variant, termed dFx, which accepts amino acid substrates having 3,5-dinitrobenzyl ester instead of CME as a leaving group. Similar selection attempts with the original phenylalanine-CME and a substrate activated by (2-aminoethyl)amidocarboxybenzyl thioester yielded the variants eFx and aFx (e and a denote enhanced and amino, respectively). In this Account, we describe the history and development of these flexizymes and their appropriate substrates, which provide a versatile and easy-to-use tRNA acylation system. Their use permits the synthesis of a wide array of acyl-tRNAs charged with artificial amino and hydroxy acids. In parallel to these efforts, we initiated a crystallization study of Fx3 covalently conjugated to a microhelix RNA, which is an analogue of tRNA. The X-ray crystal structure, solved as a co-complex with phenylalanine ethyl ester and U1A-binding protein, revealed the structural basis of this enzyme. Most importantly, many biochemical observations were consistent with the crystal structure. Along with the predicted three regular-helix regions, however, the flexizyme has a unique irregular helix that was unexpected. This irregular helix constitutes a recognition pocket for the aromatic ring of the amino acid side chain and precisely brings the carbonyl group to the 3'-hydroxyl group of the tRNA 3'-end. This study has clearly defined the molecular interactions between Fx3, tRNA, and the amino acid substrate, revealing the fundamental basis of this unique catalytic system.     

Performances of metal fluoride added carbon anodes with pre-electrolysis for electrolytic synthesis of NF3

Metal fluoride added carbon anodes treated by pre-electrolysis were investigated for electrolytic production of nitrogen trifluoride (NF₃) in molten NH₄F·KF·4HF at 100 °C. The conditions for pre-electrolysis were first optimized using a graphite sheet anode as a model anode. The formation of fluorine-graphite intercalation compounds (fluorine-GICs) with semi-covalent C–F bonds, (C_xF)_n, on the MgF₂ and CaF₂ added carbon anode surface was accelerated by pre-electrolysis at potentials less than 4.0 V. Critical current densities (CCD) on the MgF₂ added carbon anodes pre-electrolyzed under various conditions were determined, and the highest CCD was 290 mA cm⁻² obtained for that pre-electrolyzed at 3.5 V for 500 C cm⁻². This anode was successfully used in the electrolysis at 100 mA cm⁻² for 290 h and the maximum NF₃ current efficiency was 55%. From these results, it was concluded that the metal fluoride added carbon anode treated by pre-electrolysis has a high potential for electrolytic production of NF₃ at higher current density.     

Rate acceleration of Diels–Alder reactions utilizing a fluorous micellar system in water

A fluorous micellar system in water has been created to produce a large interfacial area between these media that retains substrates, effectively facilitating intermolecular Diels–Alder reactions due to repulsion effects from both media. Because LiFOS functioned not only as a surfactant but also as a supporting electrolyte, an electrochemical approach could be introduced to evaluate the rate acceleration effects. The measurement of the particle size distribution of the fluorous micelles clearly supported these evaluations.     

Determination of optical purity and absolute configuration of natural 12‐hydroxystearic acid by the 1H NMR anisotropy method

The enantiopure of (R)‐(?) MαNPA was allowed to react with racemic 18‐(tert‐butyldimethylsilyloxy)‐5‐octadecayne‐7‐ol which was derived from dodecane‐1,12‐diol, yielding diastereomeric esters mixture. These racemic esters were easily separated by HPLC on silica‐gel. The absolute configurations of the first‐eluted diastereomeric esters from the separated esters were determined using ¹H NMR anisotropy method. Analysis on ¹H NMR spectra and HPLC elution time of the synthesized esters and those of MαNP ester derived from natural methyl‐12‐hydroxystealate showed that the absolute configuration of natural 12‐hydroxystearic acid was R form, and the enantiomeric excess was over 99%.     

Fabrication of fluorine-terminated diamond-like carbon thin film using a hyperthermal atomic fluorine beam

Surface modification of diamond-like carbon (DLC) film was performed using a hyperthermal atomic fluorine beam on the purpose of production of hydrophobic surface by maintaining the high hardness of DLC film. By the irradiation of atomic fluorine beam of a 1.0 × 10²⁰ atoms/cm², the contact angle of a water drop against the DLC surface increased from 73° to 111°. The formation of CF₃, CF₂ and CF bonding on the modified DLC surface was confirmed from the measurements of X-ray photoelectron spectra and near-edge X-ray absorption fine structure spectra. Irradiation of hyperthermal atomic fluorine beam was concluded to produce insulator fluorine-terminated DLC film, which has high F content on the surface, by the taking of the use of neutral atomic beam as a fluorine source.     

Distance measurement between Tyr10 and Met35 in amyloid beta by site-directed spin-labeling ESR spectroscopy: implications for the stronger neurotoxicity of Abeta42 than Abeta40

The neurotoxicity of the 42-mer and 40-mer amyloid beta peptides (Abeta42 and Abeta40) is closely related to the radicalization at both Tyr10 and Met35. Abeta42 is more neurotoxic than Abeta40. Our previous structural analyses of Abeta42 suggested that Tyr10 and Met35 are brought closer together by the turn at positions 22 and 23, and the S-oxidized radical cation at position 35, which is the ultimate toxic radical species, can be produced effectively through oxidation by the phenoxy radical at position 10. To verify this idea, their separation was measured by site-directed spin labeling (MTSSL) by using ESR spectroscopy. Among the three kinds of Abeta42 derivatives, which are doubly or singly spin-labeled at position 10 and 35, only 10,35-MTSSL-Abeta42 showed a clear dipole coupling in continuous-wave ESR; this suggests that the intramolecular spin labels at position 10 and 35 in Abeta42 are located within approximately 15 A. In contrast, 10,35-MTSSL-Abeta40 did not give such signals. The distance between Tyr10 and Met35 in 10,35-MTSSL-Abeta40, which was successfully measured by pulsed ESR spectroscopy was 30 A long. The difference in the distance between Abeta42 and Abeta40 could explain in part the stronger neurotoxicity of Abeta42 compared to Abeta40.     

Synthesis and chiroptical properties of helical poly(phenylacetylene) bearing optically active chiral oxazoline Pendants

The novel optically active (S)-4-benzyl-2-(ethynylphenyl)-oxazoline (BnEPhOx) was successfully prepared and polymerized using rhodium catalyst ([Rh(nbd)Cl]₂) to obtain the moderate molecular weight poly(phenylacetylene)s bearing chiral oxazoline derivatives with high yields (≥90%). The ¹H NMR spectra demonstrated that the resulting polymers had high stereoregular structures. Moreover, the poly(phenylacetylene)s bearing chiral oxazoline exhibited better thermal stability than poly(phenylacetylene). The resulting polymers showed higher absolute values of optical specific rotation than the monomer. The polymers also exhibited intense CD signal in the region of the π-π1 band of the conjugated polyacetylene backbone in chloroform solution. The results of specific rotation and CD spectroscopy indicated that all the polymers adopted higher-order structure with predominantly one-handed screw sense.In addition, the resulting polymers emitted fluorescence under UV irradiation.     

Effects of Spraying Ozonated Water on the Severity of Powdery Mildew Infection on Cucumber Leaves

Effects of spraying ozonated water on the severity of powdery mildew infection, visible disorder/injury occurrence, and net photosynthesis in cucumbers were investigated. The severity in the ozonated water treatment was contained to almost the same level throughout the 14-day period of the experiment, while the severity steadily increased in the non-treated control and distilled water treatment. Neither visible disorder/injury on the leaves nor a large difference in net photosynthesis between before and after spraying the ozonated water was observed. The results indicate that ozonated water can be at least a partial alternative to agricultural chemical fungicides for powdery mildew on cucumber leaves.     

Adsorption characteristics of superplasticizers on cement component minerals

Adsorption characteristics of various superplasticizers on portland cement component minerals were investigated. Adsorption isotherms of various types of superplasticizers and ζ-potentials of cement component minerals at the maximum adsorption of the superplasticizers were measured. The value of the adsorption isotherm was calculated from the amount of the superplasticizer adsorbed on a cement component mineral in an equilibrated solution. The maximum amounts of adsorption and the adsorption isotherms varied with types of component mineral and superplasticizer. For all types of superplasticizers, a larger amount of superplasticizer was adsorbed on C₃A and C₄AF than C₃S and C₂S. However, the equilibrated concentration of each superplasticizer at the maximum adsorption was not influenced by types of superplasticizer. Without superplasticizer, C₃S and C₂S had negative ζ-potential. On the contrary, C₃A and C₄AF had positive ζ-potential. Therefore, accelerated coagulation of cement particles might occur due to their electrostatic potentials that are opposite each other. However, all component minerals of cement had negative ζ-potential when they were mixed with any superplasticizer. Fluidity of fresh cement paste is improved due to electrostatic repulsion acting between particles.