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.     

Skeletal Transformation Triggered by C−F Bond Activation after Photochemical Rearrangement of Fluorinated [7]Helicenes

Tri- and tetra-fluorinated [7]helicenes are photolabile and undergo a double fluorine atom transfer. Herein, we show that the transferred product further undergoes a skeletal transformation on silica gel. The transformation begins with activation of the allylic C−F bond on the silanol surface. Then, the resulting carbocation readily undergoes a regioselective nucleophilic aromatic substitution with water, depending on the position of the fluorine substituents. Hexafluoro-2-propanol also activated the allylic C−F bond and acted as a nucleophile. These findings support the generation of a highly reactive cationic electrophilic intermediate in the successive transformations involving fluorine atoms.     

Detailed Analysis of the Crystal Structures and Magnetic Properties of a Dysprosium(III) Phthalocyaninato Sextuple-Decker Complex: Weak f–f Interactions Suppress Magnetic Relaxation

In the research field of single-molecule magnets (SMMs), lanthanoid–lanthanoid interactions, so-called f–f interactions, are known to affect the SMM properties, although their magnitudes are small. In this article, an SMM with very weak f–f interactions is reported, and the effects of the interactions on the SMM properties are discussed. X-ray structural analysis of the Dy^III-Cd^II-phthalocyaninato sextuple-decker complex (Dy₂Cd₃) reveals that the intramolecular Dy−Dy length in Dy₂Cd₃ is more than 13 Å, which is longer than the intermolecular Dy−Dy length. Even though the two Dy^III ions are far apart, intermolecular ferromagnetic dipole–dipole interactions are observed in Dy₂Cd₃. From detailed analysis of ac magnetic susceptibilities, quantum tunneling of the magnetization (QTM) in Dy₂Cd₃ is partially suppressed owing to the existence of very weak Dy−Dy interactions. Our results show that even very weak Dy−Dy interactions act as a dipolar bias, suppressing QTM.     

Controlled Reduction of Carboxamides to Alcohols or Amines by Zinc Hydrides

New protocols for controlled reduction of carboxamides to either alcohols or amines were established using a combination of sodium hydride (NaH) and zinc halides (ZnX₂). Use of a different halide on ZnX₂ dictates the selectivity, wherein the NaH‐ZnI₂ system delivers alcohols and NaH‐ZnCl₂ gives amines. Extensive mechanistic studies by experimental and theoretical approaches imply that polymeric zinc hydride (ZnH₂)_∞ is responsible for alcohol formation, whereas dimeric zinc chloride hydride (H?Zn?Cl)₂ is the key species for the production of amines.     

Radical polymerization of trifluoromethyl‐substituted methyl methacrylates and their application for use in pressure‐sensitive paint

Three CF₃‐substituted methyl methacrylates (MMAs), 2,2,2‐trifluoroethyl methacrylate (TFEMA), 1,1,1,3,3,3‐hexafluoroisopropyl methacrylate (HFIPMA) and nonafluoro‐tert‐butyl methacrylate (NFTBMA), were polymerized by conventional radical polymerization to give oxygen‐permeable polymers for application in pressure‐sensitive paint (PSP). The radical copolymerizations of styrene with TFEMA, HFIPMA, or NFTBMA were carried out to examine the effect of CF₃ groups on the polymerizability. The e values increased in the order of MMA (0.40) < TFEMA (0.76) < HFIPMA (1.19) < NFTBMA (1.31). The homopolymers of TFEMA, HFIPMA and NFTBMA (PTFEMA, PHFIPMA, and PNFTBM, respectively) were examined as polymers for use in PSP using 5,10,15,20‐tetrakis(pentafluorophenyl)porphinato platinum(II) (PtTFPP). The PSP consisting of PNFTBMA and PtTFPP exerted very high pressure sensitivity and very low temperature sensitivity. In the absence of oxygen, the temperature sensitivity decreased in the order of PTFEMA > PHFIPMA > PNFTBMA = PMMA, which corresponds to the order of glass transition temperatures (T_g). However, the activation energies of the overall process of the luminescence quenching by oxygen were found to be 16.8 (PMMA), 13.0 (PTFEMA), 6.8 (PHFIPMA), and 4.3 kJ mol^?1 (PNFTBMA). Therefore, the low temperature sensitivity of PNFTBMA was attributed to its high degree of substitution with CF₃ groups and to its relatively high T_g value. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52, 963–972     

Polymerization-induced self-assembly of amino-acid-based nano-objects by reversible addition–fragmentation chain-transfer dispersion polymerization

A series of amino-acid-based amphiphilic diblock copolymer nano-objects having different morphologies were developed by reversible addition–fragmentation chain-transfer (RAFT) dispersion polymerization of styrene (St) in methanol. This was mediated by six different hydrophilic poly(N-acryloyl amino acid) macro-chain transfer agents (CTAs), including three carboxylic-acid-containing ones, poly(N-acryloyl-l -proline) (PAProOH), poly(N-acryloyl-4-trans-hydroxy-l -proline) (PAHypOH), and poly(N-acryloyl-l -threonine) (PAThrOH) prepared by RAFT polymerization, and their methyl ester forms, PAProOMe, PAHypOMe, and PAThrOMe. The effects of polymerization conditions on RAFT dispersion polymerization of St using a dithiocarbamate-terminated PAProOH was investigated. A systematic study of the effects of monomer conversion and concentration afforded the formation of various morphologies (i.e., spheres, worms, and vesicles). The effects of hydrogen-bonding and ionic interactions of the macro-CTAs on the assembled structures of the nano-objects were evaluated using six different macro-CTAs. Transforming the products from methanol to water via dialysis produced amino-acid-based block copolymer nano-objects, exhibiting pH-responsive morphological change, in aqueous solution.     

Control of Axial Chirality by Planar Chirality Based on Optically Active [2.2]Paracyclophane

Optically active X-shaped molecules based on the planar chiral [2.2]paracyclophane building block were prepared, in which di(methoxy)terphenyl units were stacked on the central benzene rings. At 25 °C, anisolyl rings freely rotate in solution, while in the crystal form, they are fixed by intramolecular CH–π interactions, thereby leading to the expression of the axial chirality, i.e., propeller chirality was exhibited by the planar chiral [2.2]paracyclophane moiety. The X-shaped molecule exhibited good circularly polarized luminescence (CPL) profiles with moderate Φ_PL and a large g_lum value in the order of 10⁻³ at 25 °C, in solution. In contrast, at −120 °C, dual CPL emission with opposite signs was observed. According to the theoretical studies, the rotary motion of the anisolyl units is suppressed in the excited states, and so emission from two isomers could be observed. These results demonstrate that the axial chirality was controlled by the planar chirality, leading ultimately to propeller chirality.     

Rhodium-Catalyzed ortho-Bromination of O-Phenyl Carbamates Accelerated by a Secondary Amide-Pendant Cyclopentadienyl Ligand

It has been established that a newly developed cyclopentadienyl rhodium(III) [Cp^ARh^III] complex, bearing an acidic secondary amide moiety on the Cp ring, is able to catalyze the ortho-bromination of O-phenyl carbamates with N-bromosuccinimide (NBS) at room temperature. The presence of the acidic secondary amide moiety on the Cp^A ligand accelerates the bromination by the hydrogen bond between the acidic NH group of the Cp^A ligand and the carbonyl group of NBS.     

The resonant secondary emission of the F center in alkali halides

The secondary radiation after resonant excitation of F center and its linear polarization P correlated to the polarization of resonant light have been measured for five alkali halides at low temperatures. In KC1, the spectrum of P over the whole Stokes region is divided into three successive regions, the depolarization range at the one-phonon Raman scattering, the near plateau range, and the depolarization range down to vanishing. The former two have common relevance to resonant energy and symmetries of coupled phonons. These relevances are interpreted adopting a configuration coordinate model for 2s- and 2p-like excited states.