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.     

Liquid crystalline epoxy resin with improved thermal conductivity by intermolecular dipole–dipole interactions

To address tremendous needs for developing efficiently heat dissipating materials with lightweights, a series of liquid crystalline epoxy resins (LCEs) are designed and synthesized as thermally conductive matrix. All prepared LCEs possess epoxies at the molecular side positions and cyanobiphenyl mesogenic end groups. Based on several experimental results such as differential scanning calorimetry, polarized optical microscopy, and X‐ray diffraction, it is found that the LCEs exhibited liquid crystalline mesophases. When LCE is cured with a diamine crosslinker, the cured LCE maintains the oriented LC domain formed in the uncured state, ascribing to a presence of dipole–diploe and π–π interactions between cyanobiphenyl mesogenic end groups. Due to the anisotropic molecular orientation, the cured LCE exhibits a high thermal conductivity of 0.46 W m^?1 K^?1, which is higher than those of commercially available crystalline or amorphous epoxy resins. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 708–715     

Fabrication of Carbon Nanotube Thin Films for Flexible Transistors by Using a Cross-Linked Amine Polymer

Owing to their remarkable properties, single-walled carbon nanotube thin-film transistors (SWCNT-TFTs) are expected to be used in various flexible electronics applications. To fabricate SWCNT channel layers for TFTs, solution-based film formation on a self-assembled monolayer (SAM) covered with amino groups is commonly used. However, this method uses highly oxidized surfaces, which is not suitable for flexible polymeric substrates. In this work, a solution-based SWCNT film fabrication using methoxycarbonyl polyallylamine (Moc-PAA) is reported. The NH₂-terminated surface of the cross-linked Moc-PAA layer enables the formation of highly dense and uniform SWCNT networks on both rigid and flexible substrates. TFTs that use the fabricated SWCNT thin film exhibited excellent performance with small variations. The presented simple method to access SWCNT thin film accelerates the realization of flexible nanoelectronics.     

Electronically Excited States in Model Complexes of Noble Metal Clusters with Carbon Nanodots

Russian Physics Journal - Theoretical calculations of excited states in the complexes of gold and silver three-atom nanoclusters with carbon quantum nanodots are performed using the M062X...     

Saccharide Recognition by a Three-Arm-Shaped Host Having Preorganized Three-Dimensional Hydrogen-Bonding Sites

Generally, cage-shaped hosts for saccharides can bind strongly to guest molecules because of the three-dimensional preorganized hydrogen-bonding sites. However, the preparation of cage molecules is often difficult because of the low yield of the macrocyclization step. Here, we report a three-arm-shaped molecule possessing pyridine-acetylene-phenol units as a new kind of host having a preorganized three-dimensional hydrogen-bonding site. This three-arm-shaped host was readily prepared compared to a cage-shaped analogue. This host associated with lipophilic glycosides to form chiral complexes, and the association constants were sufficiently high as to be comparable to those of the cage-shaped analogue. Furthermore, this host extracted native monosaccharides into a lipophilic solvent.     

Reactions of Selenobenzophenones with Olefins

Reactions of selenobenzophenones with methyl propiolate afforded two types of cycloadducts regioselectively. The reaction with tetracyanoethylene gave selenophene derivatives. Mechanisms of these reactions were discussed.     

Improving Resolution of Isomeric Flavonoids and Their Glycosides Using Two-Dimensional Liquid Chromatography Coupled With High-Resolution Mass Spectrometry

Chromatographia - The separation of isomers is one of the key issues in analysing complex natural matrices, thus commanding a higher separating power from the applied analytical system. In this...     

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

The nucleosides of adenine and cytosine have pKa values of 3.50 and 4.08, respectively, and are assumed to be unprotonated under physiological conditions. However, evidence from recent NMR and X-Ray crystallography studies has revealed the prevalence of protonated adenine and cytosine in RNA macromolecules. Such nucleotides with elevated pKa values may play a role in stabilizing RNA structure and participate in the mechanism of ribozyme catalysis. With the work presented here, we establish the framework and demonstrate the first constant pH MD simulations (CPHMD) for nucleic acids in explicit solvent in which the protonation state is coupled to the dynamical evolution of the RNA system via λ-dynamics. We adopt the new functional form λ(Nexp) for λ that was recently developed for Multi-Site λ-Dynamics (MSλD) and demonstrate good sampling characteristics in which rapid and frequent transitions between the protonated and unprotonated states at pH = pKa are achieved. Our calculated pKa values of simple nucleotides are in a good agreement with experimentally measured values, with a mean absolute error of 0.24 pKa units. This work demonstrates that CPHMD can be used as a powerful tool to investigate pH-dependent biological properties of RNA macromolecules.