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.     

Synthesis of All Stereoisomers of Monomeric Spectomycin A1/A2 and Evaluation of Their Protein SUMOylation-Inhibitory Activity

A synthetic methodology to access all possible stereoisomers of spectomycin A1 (SMA1) and A2 (SMA2) has been established through late-stage diversification. The key reaction for the construction of all four diastereomers is an intramolecular cyclization based on the umpolung of π-allyl palladium species with bis(pinacolato)diborane (B₂(pin)₂). Silyl group assisted direct benzylic oxidation of each isomer enabled construction of the fragile β-hydroxytetralone skeleton to provide the SMAs. The relative and absolute stereochemistry of SMA2 was also determined, and the absolute stereochemistry of SMA1 was extrapolated based on the optical rotation of SMA2. The axial chirality of SMAs is discussed based on circular dichroism spectra and DFT calculations, and it is concluded that the M isomer is predominant in solution. Biochemical assessment of all isomers in vitro revealed that the C9 hydroxyl group and dimeric structure were both important for protein SUMOylation-inhibitory activity.     

Proton Order–Disorder Phenomena in a Hydrogen‐Bonded Rhodium–η5‐Semiquinone Complex: A Possible Dielectric Response Mechanism

A newly synthesized one‐dimensional (1D) hydrogen‐bonded (H‐bonded) rhodium(II)–η⁵‐semiquinone complex, [Cp*Rh(η⁵‐p‐HSQ‐Me₄)]PF₆ ([ 1 ]PF₆; Cp*=1,2,3,4,5‐pentamethylcyclopentadienyl; HSQ=semiquinone) exhibits a paraelectric–antiferroelectric second‐order phase transition at 237.1 K. Neutron and X‐ray crystal structure analyses reveal that the H‐bonded proton is disordered over two sites in the room‐temperature (RT) phase. The phase transition would arise from this proton disorder together with rotation or libration of the Cp* ring and PF₆^? ion. The relative permittivity ε_b′ along the H‐bonded chains reaches relatively high values (ca., 130) in the RT phase. The temperature dependence of ¹³C CP/MAS NMR spectra demonstrates that the proton is dynamically disordered in the RT phase and that the proton exchange has already occurred in the low‐temperature (LT) phase. Rate constants for the proton exchange are estimated to be 10^?4–10^?6 s in the temperature range of 240–270 K. DFT calculations predict that the protonation/deprotonation of [ 1 ]⁺ leads to interesting hapticity changes of the semiquinone ligand accompanied by reduction/oxidation by the π‐bonded rhodium fragment, producing the stable η⁶‐hydroquinone complex, [Cp*Rh³⁺(η⁶‐p‐H₂Q‐Me₄)]²⁺ ([ 2 ]²⁺), and η⁴‐benzoquinone complex, [Cp*Rh⁺(η⁴‐p‐BQ‐Me₄)] ([ 3 ]), respectively. Possible mechanisms leading to the dielectric response are discussed on the basis of the migration of the protonic solitons comprising of [ 2 ]²⁺ and [ 3 ], which would be generated in the H‐bonded chain.     

Electrochemical Characteristics of a Triphenylamine Derivative by Microelectrode Voltammetry

With the objective of understanding the kinetic redox properties of triphenylamine derivatives in association with chemical reactions, for their future application in functional organic semiconductor devices, the electrochemical characteristics of 4‐(2,2‐diphenylethenyl)‐N,N‐bis(4‐methylphenyl)‐benzenamine (TPA) were evaluated. Based on cyclic voltammograms of TPA on Pt disk electrodes with diameters of 300 μm and 10 μm at slow and fast scan rates in an acetonitrile solution, the TPA^.+ is stable, while the TPA²⁺ is unstable. Importantly, the unstable TPA²⁺ appears to break down by a subsequent chemical reaction. A Cottrell plot analysis from chronoamperometry of a solution containing TPA reveals that both the first and second oxidations are one‐electron reactions. Concerning the stabilization mechanism of the first oxidation state of TPA, the results of molecular orbital calculations indicate that the electrons of the HOMO level are distributed in the triphenylamine group, which induces a resonance‐stabilized TPA^.+. Based on these results, TPA/TPA^.+ is suggested to have a sufficient stability for further application in organic semiconductor devices.     

Surface effects on the polarization reversal of the ferroelectric liquid crystal 8SI*

Abstract

The activation field for the switching time (τ_1/2) in the truly ferroelectric liquid crystal 8SI* (CE8; ΔS-(+)-4-(2′-methylbutyl) phenyl-4′-n-octylbiphenyl-4 carboxylate) has been studied for various surface conditions of the transparent electrode (SnO₂), in order to understand the memory effect, the polarization reversal mechanism and its surface effect. We prepared five different surfaces, namely one coated with polyvinyl alcohol (PVA) and the other four by scratching N-times(N = 0, 10, 20 and 30) with a paste made of Cr₂O₃ powder (about 0·1 μm). The number and the area of scratches on the electrode surface obviously increase with N. The polarization reversal processes are influenced by this treatment. τ_1/2 decreases with increasing N, but no change is observed in the contrast of the light transmittance. Two different activation fields, E _a1, for the applied field E > E ₀ and E _a2 for E < E ₀ are observed, where E ₀ is a certain field depending on the sample. Here E _a1 is much larger than E _a2; typically E _a1, = 260 kV cm^?1 and E _a2 = 144 kV cm^?1 for N = 0. This means that nucleation for the higher field needs a large activation energy which therefore has strong barriers. In contrast with this, nucleation for the low field occurs easily. Changing a surface condition, E _a2 clearly decreases with increasing N although E _a1 is almost independent of the surface scratching. This may suggest that E _a1 corresponds to the activation field for the bulk pinning and nucleation, and E _a2 for the surface pinning. The PVA treatment gives an intermediate influence between N = 0 and 10.     

Vinyl Polymerization. 418. Polymerization of Vinyl Monomer Initiated by Betaine-Type Polymers in Aqueous Solution

Abstract

Three kinds of betaine-type polymers, which are macromolecular amphoteric electrolytes, were found to be able to polymerize vinyl monomers in aqueous solution through a radical mechanism without any further initiator. Betain-type polymers form hydrophobic areas (HA) in water. Vinyl polymerization commenced in the HA. The effect of the pH of the aqueous solution on polymerization was investigated.     

Synthesis and Polymerization of N-(L-Menthylcarboxylatomethyl)maleimide

A new type of optically active N-(L-menthylcarboxylatomethyl)maleimide (MGMI) was synthesized from maleic anhydride, glycine, and L-menthol. Radical homopolymerization of MGMI was performed at 50°C for 24 h to give optically active polymer having [α]_D = -57°. Radical copolymerizations of MGMI (M ₁) were performed with styrene (ST, M ₂), methyl methacrylate (MMA, M ₂) in benzene at 50°C. From the results, the monomer reactivity ratios (r ₁, r ₂) and the Alfrey-Price Q, e values were determined as follows: r ₁ = 0.16, r ₂ = 0.006 for the MGMI-ST system; r ₁ = 0.15, r ₂ = 1.65 for the MGMI-MMA system, and Q ₁ = 0.72, e ₁ = 1.59 calculated from the MGMI-MMA system. Anionic homopolymerizations of MGMI were also carried out. Chiroptical properties of the polymers were investigated.