Efforts to expand the genetic alphabet: identification of a replicable unnatural DNA self-pair

Six unnatural nucleotides featuring fluorine-substituted phenyl nucleobase analogues have been synthesized, incorporated into DNA, and characterized in terms of the structure and replication properties of the self-pairs they form. Each unnatural self-pair is accommodated in B-form DNA without detectable structural perturbation, and all are thermally stable and selective to roughly the same degree. Furthermore, the efficiency of polymerase-mediated mispair synthesis is similar for each unnatural nucleotide in the template. In contrast, the efficiency of polymerase-mediated self-pair extension is highly dependent on the specific fluorine substitution pattern. The most promising unnatural base pair candidate of this series is the 3-fluorobenzene self-pair, which is replicated with reasonable efficiency and selectivity.     

Ligand binding properties of myoglobin reconstituted with iron porphycene: unusual O2 binding selectivity against CO binding

Sperm whale myoglobin, an oxygen storage hemoprotein, was successfully reconstituted with the iron porphycene having two propionates, 2,7-diethyl-3,6,12,17-tetramethyl-13,16-bis(carboxyethyl)porphycenatoiron. The physicochemical properties and ligand bindings of the reconstituted myoglobin were investigated. The ferric reconstituted myoglobin shows the remarkable stability against acid denaturation and only a low-spin characteristic in its EPR spectrum. The Fe(III)/Fe(II) redox potential (-190 mV vs NHE) determined by the spectroelectrochemical measurements was much lower than that of the wild-type. These results can be attributed to the strong coordination of His93 to the porphycene iron, which is induced by the nature of the porphycene ring symmetry. The O2 affinity of the ferrous reconstituted myoglobin is 2600-fold higher than that of the wild-type, mainly due to the decrease in the O2 dissociation rate, whereas the CO affinity is not so significantly enhanced. As a result, the O2 affinity of the reconstituted myoglobin exceeds its CO affinity (M' = K(CO)/K(O2) < 1). The ligand binding studies on H64A mutants support the fact that the slow O2 dissociation of the reconstituted myoglobin is primarily caused by the stabilization of the Fe-O2 sigma-bonding. The IR spectra for the carbon monoxide (CO) complex of the reconstituted myoglobin suggest several structural and/or electrostatic conformations of the Fe-C-O bond, but this is not directly correlated with the CO dissociation rate. The high O2 affinity and the unique characteristics of the myoglobin with the iron porphycene indicate that reconstitution with a synthesized heme is a useful method not only to understand the physiological function of myoglobin but also to create a tailor-made function on the protein.     

Characterization of p-aminobenzamidine-based sorbent and its use for high-performance affinity chromatography of trypsin-like proteases

An affinity sorbent, hydrophilic polymer-based carrier of different pore size (Toyopearl) with immobilized p-aminobenzamidine (ABA), has been prepared. Its basic properties and some applications for protein purification were studied. ABA, which is a synthetic inhibitor for trypsin-like proteases, was covalently immobilized to Toyopearl by reductive amination. The ligand density and binding capacity for porcine trypsin varied depending on the pore size of Toyopearl. The maximum binding capacity of the immobilized p-aminobenzamidine Toyopearl (ABA-Toyopearl) for trypsin was more than 40 mg/ml gel. ABA-Toyopearl thus obtained was very stable below pH 8 and was successfully used for high-performance affinity chromatography of trypsin-like proteases such as trypsin, thrombin, tissue-type plasminogen activator or urokinase in a single step at 25 degrees C.     

Degradation of nitrilotriacetic acid (NTA) by oxidation with lead dioxide suspension

Degradation of nitrilotriacetic acid (NTA) by oxidation with lead dioxide suspension has been studied by differential pulse polarography. The NTA was degraded over the pH range from 4 to 9, with formation of glycine or a mixture of iminodiacetic acid and glycine. After shaking with lead dioxide for 1 hr at 30 degrees and pH ~7, the NTA was almost completely decomposed, the molar reacting ratio of Pb(IV) to NTA being ~17:1; down to 1 x 10(-5)M NTA was decomposed in a shaking time as short as 15 min and at a temperature as low as 5 degrees . The iron(III)-NTA complex was also degraded under the same conditions, and the iron released was adsorbed on the lead dioxide.     

Dinuclear zinc(II) double-helicates of homochirally substituted bis(dipyrromethene)s

[structure: see text] A series of bis(dipyrromethene)s substituted with aromatic amide and aliphatic ester homochiral auxiliaries have been prepared and complexed with zinc(II) ions to form double-helical dinuclear complexes. CD analysis of the crude complexes revealed that the helicates formed in a diastereoselective manner. The helicates have been resolved into their constituent M and P helices by HPLC, indicating that the helical sense of the complexes is stable to racemization.     

Studies on the mechanism of 1,2-dihydropyrazin-2-one ring formation from dipeptidyl chloromethyl ketone and its chemical properties: immediate deamination during catalytic hydrogenation

1,2-Dihydropyrazin-2-one derivatives, which have two aminoalkyl groups at the positions 3 and 6, were found to be efficient tools for the construction of potent, selective and long-acting opioid mimetics. During the course of preparation, we found that the catalytic hydrogenation of 3,6-bis(benzyloxycarbonylaminomethyl)-5-methyl-1,2-dihydropyrazin-2-one to remove the benzyloxycarbonyl groups resulted in a side reaction. By MS and NMR studies and by preparation of additional 1,2-dihydropyrazin-2-one derivatives, the structure of the by-product was identified as 3-aminomethyl-5,6-dimethyl-1,2-dihydropyrazin-2-one. Preparation of additional compounds substituted with deuterium provided us with sufficient information to confirm the structure of the product and to support a cyclization mechanism in its formation.     

N-tert-Butoxy-1-aminopyrenyl Radicals. Isolation,Electronic Structure,and Magnetic Characterization

N-tert-Butoxy-2,7-di-tert-butyl-1-pyrenylaminyl (4), N-tert-butoxy-2-tert-butyl-1-pyrenylaminyl (5), and N-tert-butoxy-7-tert-butyl-1-pyrenylaminyl (6) free radicals were generated by the reaction of the lithium amides of the corresponding 1-aminopyrenes with tert-butyl peroxybenzoate in THF at -78 degrees C. Although 6 could not be isolated due to the gradual decomposition in solution, 4 and 5 were quite persistent and could be isolated as monomeric radical crystals. The X-ray crystallographic analyses for the isolated free radicals were successfully carried out, indicating that the N and O atoms are almost coplanar with the pyrene ring. The ESR spectra of 4 and 5 were very complex due to the presence of many magnetically unequivalent protons. Therefore, the proton hyperfine coupling (hfc) constants were determined by (1)H ENDOR/TRIPLE resonance spectroscopy. To assign the hfc constants for the pyrene ring protons, a partially deuterated radical, 4-d(4), was prepared and the ENDOR and ESR spectra were measured. To discuss the spin density distribution for 4 and 5 ab initio molecular orbital calculations were performed by the DFT UBecke 3LYP method, using the STO 6-31G basis set. Magnetic susceptibility measurements were carried out for 4 and 5 with a SQUID magnetometer. For 4 a weak antiferromagnetic interaction was observed, and for 5 a very strong antiferromagnetic interaction was observed. The antiferromagnetic interactions were explained by their crystal structures.     

Effects of beta-sheet breaker peptide polymers on scrapie-infected mouse neuroblastoma cells and their affinities to prion protein fragment PrP(81-145)

The effects of Soto's 'beta-sheet breaker peptide' and its polymer on PrPSc formation in ScN2a cells were investigated. Surface plasmon resonance study indicated that direct binding between PrP(81-145) and the 'beta-sheet breaker peptide' is not specific and may not play a major role in the inhibition of PrPSc formation.     

Mössbauer study of new vanadate glass with large charge-discharge capacity

Charge-discharge capacity and cyclicity of lithium ion battery (LIB) was evaluated in which 15Li₂O·10Fe₂O₃·xSnO₂·5P₂O₅·(70–x)V₂O₅ glass (x?=?0 and 20 in mol%, abbreviated as xLFSPV) was used as a cathode. A local structure of xLFSPV glass before and after charging was investigated by ⁵⁷Fe- and ¹¹⁹Sn-Mössbauer spectroscopies. ⁵⁷Fe-Mössbauer spectrum of xLFSPV glass with ‘x’ of 20 was composed of a doublet with isomer shift (δ) of 0.35_±0.02 mm s^???1 and quadrupole splitting (Δ) of 0.88_±0.03 mm s^???1 due to distorted Fe^IIIO₄ tetrahedra. ¹¹⁹Sn-Mössbauer spectrum of this glass consisted of a doublet with δ of 0.08_±0.01 and Δ of 0.52_±0.01 mms^???1 due to distorted Sn^VIO₆ octahedra. After discharging the battery from 4.5 to 1.0 V, larger δ of 0.40_±0.03 mm s^???1 and Δ of 0.94_±0.04 mm s^???1 were obtained, indicating that both iconicity of Fe-O bonds and local distortion of Fe^IIIO₄ tetrahedra were increased. On the contrary, identical δ of 0.09_±0.01 mm s^???1 and Δ of 0.50_±0.01 mm s^???1 were observed in the ¹¹⁹Sn-Mössbauer spectrum of 20LFSPV glass after the discharge, indicating that chemical environment of Sn^IVO₆ octahedra was not affected after the discharge. Charge-discharge curve of LIB containing 20LFSPV glass as a cathode active material recorded under the current density of 8.3 mA g^???1 (0.011 mA cm^???2) between 1.0 and 4.5 V showed a large initial charge capacity of 431.1 mAh g^???1 and discharge capacity of 382.3 mAh g^???1, respectively. These results indicate that 20LFSPV glass could be a new cathode active material for LIB.