Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers

In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a “DNA Aptaomics” approach to systematically design functional aptamers as well as to obtain high affinity aptamers.     

Laser-induced fluorescence and infrared spectroscopic studies on the specific solvation of tris(1-(2-thienyl)-4,4,4-trifluoro-1,3-butanedionato)europium(III) in an ionic liquid

The extraction constant and the two-phase stability constant (K_D,Mβ₃) of tris(2-thenoyltrifluoroacetonato)europium(III) between 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C₄mim][Tf₂N]) as an ionic liquid and an aqueous phase were determined by considering the extraction equilibria including anionic tetrakis(2-thenoyltrifluoroacetonato)europate(III). Specific solute-solvent interactions between the neutral Eu(III) chelate and [C₄mim][Tf₂N] molecules were revealed from the relationships between the distribution constant of the enol form of 2-thenoyltrifluoroacetone (Htta) as a proton chelate and the distribution constant (K_D,M) of the neutral Eu(III) chelate because the [C₄mim][Tf₂N] system gave the high K_D,Mβ₃ value compared with those in conventional molecular solvents such as benzene and 1,2-dichloroethane. The coordination environment of Eu³⁺ in the neutral Eu(III) chelate in [C₄mim][Tf₂N] was investigated by time-resolved laser-induced fluorescence spectroscopy and infrared absorption spectroscopy. Both methods consistently indicated that not only the Eu(III) chelate extracted but also Eu(tta)₃(H₂O)₃ synthesized as a solid crystal were almost completely dehydrated in [C₄mim][Tf₂N] saturated with water. Consequently, the higher K_D,M or extractability of the neutral Eu(III) chelate in the [C₄mim][Tf₂N] system can be ascribed to the dehydration of the Eu(III) chelate, which is caused by the specific solvation with [C₄mim][Tf₂N] molecules.     

KINETICS AND MECHANISM OF PHOTOCYCLOADDITION OF DEOXYURIDINES TO 2,3-DIMETHYL-2-BUTENE

The mechanism of photocycloaddition of 2′-deoxyuridine (1a) and thymidine (1b) to 2,3-dimethyl-2-butene (Bu) in acetonitrile by UV irradiation has been studied. The reciprocal quantum yield for the cycloaddition increased linearly with reciprocal concentrations of Bu in acetonitrile to give limiting quantum yields at infinite concentration of Bu as 0.030 and 0.0096 for 1a and 1b , respectively. This shows that the cycloaddition proceeds in a two-step mechanism between the triplet state of 1 and Bu through biradical intermediates. Addition of cis-1,3-pentadiene quenched the reaction obeying the Stern–Volmer equation. The above quenching experiments and laser transient spectroscopy revealed that the triplet state of 1a reacts with Bu with much larger rate constant (1.3–1.6 × 10⁹ M^?1 s^?1) than that of 1b (4–5 × 10⁷ M^?1 s^?1) reflecting larger steric hindrance exerted in the reaction of 1b than that of 1a .     

Facile synthesis of biphenyl-fused BODIPY and its property

A biphenyl-fused BODIPY was synthesized through a facile oxidative cyclization of peripheral aryl-substituents at the β-position of the BODIPY unit. The extended π-system of the fused BODIPY induces near-infrared (NIR) absorption and strong π-π interactions in the solid state. These features are beneficial for the application of the dye as a functional material. The biphenyl-fused BODIPY dye was demonstrated to exhibit photocurrent conversion ability on the basis of its n-type semiconducting property.     

Lewis Acid-Catalyzed Hydrostannation of Acetylenes. Regio- and Stereoselective Trans-Addition of Tributyltin Hydride and Dibutyltin Dihydride

Lewis acids such as ZrCl(4) or HfCl(4) catalyze the hydrostannation of acetylenes 1 by tributyltin hydride to produce the cis vinylstannanes 2 by regio- and stereoselective anti-hydrostannation. The hydrostannation of acetylenes using dibutyltin dihydride was also catalyzed by ZrCl(4) to give the stereodefined Z-Z divinyltin derivatives 4 by an anti-hydrostannation pathway. The use of nonpolar solvents such as toluene or hexane was essential for obtaining high stereoselectivity and chemical yield. Since ZrCl(4) and HfCl(4) are not soluble in such solvents, the hydrostannations were carried out in a heterogeneous system. The reactions of internal acetylenes with Bu(3)SnH proceeded smoothly, although the use of stoichiometric amounts of ZrCl(4) gave better results. The ZrCl(4)-catalyzed hydrostannation at 0 degrees C gave better yields and stereoselectivities than the reaction at room temperature. To help clalify the reason, the reaction of Bu(3)SnH with ZrCl(4) was monitored by (1)H and (119)Sn NMR spectroscopy, and it was found that Bu(3)SnH reacted with ZrCl(4) at room temperature to afford a mixture of tributyltin hydride, dibutyltin dihydride, and tetrabutyltin.     

Fluorine-doped TiO2 powders prepared by spray pyrolysis and their improved photocatalytic activity for decomposition of gas-phase acetaldehyde

F-doped TiO₂ (FTO) powders were synthesized by spray pyrolysis (SP) from an aqueous solution of H₂TiF₆. The resulting FTO powders possessed spherical particles with a rough surface morphology and a strong surface acidity. The fluorine concentrations in the FTO powders calculated from XPS spectra significantly depended on SP temperature and ranged from 2.76 to 9.40 at.%. The FTO powder prepared at SP temperature of 1173 K demonstrated the highest photocatalytic activity for the decomposition of gas-phase acetaldehyde under both ultraviolet (UV) and visible light (vis) irradiations, and it was higher than that of commercial P 25. This high photocatalytic activity was ascribed to several beneficial effects produced by F-doping: enhancement of surface acidity, creation of oxygen vacancies, and increase of active sites. It was interesting to point out that the vis photocatalytic activity of FTO powders was achieved by the creation of surface oxygen vacancies rather than the improvement of optical absorption property of bulk TiO₂ in vis region.     

Domino allylation and cyclization of ortho-alkynylbenzaldehydes with allyltrimethylsilane catalyzed by Pd(II)-Cu(II) bimetallic systems

The reaction of ortho-alkynylated benzaldehydes 1 with allyltrimethylsilane under the Pd(OAc)₂-CuCl₂ catalyst system gave the isochromene derivatives 2 together with the chlorinated products 3. When the reaction was conducted in the presence of half equiv of H₂O, the formation of 3 was suppressed and 2 was obtained in good to high yields. When the reaction of 1a was carried out with trimethylsilylcyanide instead of allylsilane, the cyano group-substituted isochromene 9 was obtained in 94% yield.     

Optical microscopy and in situ Raman scattering of single crystalline ethylene hydrate and binary methane-ethylene hydrate at high pressures

Visual observations through a microscope and in situ Raman measurements have been made for single crystalline ethylene hydrate (EH) and binary methane-ethylene hydrate (MEH) at pressures up to 3.7 GPa and room temperature. Both hydrates showed pressure-induced phase transitions at 1.6, 2.0, and 3.0 GPa for EH and at 1.7, 2.1, and 3.3 GPa for MEH. The cubic sI phase of EH and MEH remains stable up to 1.6 and 1.7 GPa, respectively, which are more widely ranging values than the values for the methane hydrate sI phase. In this sI phase of binary MEH, the cage occupancies by methane and ethylene molecules are investigated from Raman spectra. Above P = 3.0 GPa for EH and 3.3 GPa for MEH, they decomposed by associating with the formation of the polyethylene.     

Study of adsorption of methylene blue and new methylene blue in liquid-solid interface by slab optical waveguide spectroscopy

A slab optical waveguide (SOWG) has been used for study of adsorption of both methylene blue (MB) and new methylene blue (NMB) in liquid–solid interface. Adsorption characteristics of MB and NMB on both bare SOWG and silanized SOWG by octadecyltrichlorosilane (ODS) were compared. Effect of pH on adsorption on MB and NMB was investigated. Binding rate constant analysis showed that both MB and NMB on bare SOWG demonstrates larger association constants than those on ODS-SOWG. Interactions of MB and NMB on bare SOWG and ODS-SOWG were analyzed by molecular mechanics calculation method. The binding energy change was in the following order: E_NMB–bare > E_MB–bare > E_NMB–ODS > E_MB–ODS.     

Aggregated structure analysis of polymer-protected platinum/ruthenium colloidal dispersions using EXAFS, HRTEM, and electron diffraction measurements

Polymer-protected platinum/ruthenium colloidal dispersions were prepared by refluxing mixed solutions of hexachloroplatinic(IV) acid and ruthenium(III) chloride in a mixture of ethanol/water (1/1 v/v) in the presence of poly(N-vinyl-2-pyrrolidone). The electronic spectra and transmission electron micrographs suggested that the colloidal dispersions are almost composed of the mixture of the small monometallic Pt and Ru clusters over all the ratio of Pt/Ru compositions. Extended X-ray absorption fine structure analyses and high resolution electron microprobe analyses indicated that no Pt/Ru alloy clusters exist in the dispersions, and the aggregation occurs between small monometallic Pt clusters (diameter ca. 15 A) and partially oxidized Ru microclusters (diameter less than 10 A). Electron diffraction measurements also suggested that the diffraction pattern of aggregated Pt/Ru cluster particles prepared by the simultaneous reduction of Pt and Ru ions is the same as that of the physical mixture of the small monometallic Pt and Ru clusters separately prepared. Therefore, it can be concluded that the aggregated Pt/Ru cluster particles, with 10 to 60 A in diameter, are built up by small monometallic Pt clusters and partially oxidized Ru microclusters, and that Pt/Ru alloy clusters are not formed.