Double helical oligoresorcinols specifically recognize oligosaccharides via heteroduplex formation through noncovalent interactions in water

We report on the oligosaccharide recognition through noncovalent interactions in water based on a unique supramolecular homoduplex-to-heteroduplex transformation of the oligoresorcinol nonamer as a fully artificial receptor. The oligoresorcinol forms a double helix in water, which unravels and entwines upon complexation with specific oligosaccharides with a particular chain length and glucosidic linkage pattern, thus generating the heteroduplex with an excess one-handed helical conformation that can be readily monitored and further quantified by absorption, circular dichroism, and NMR spectroscopies.     

Structure of the monoclinic-form misfit-layer compound, (Ca0.85OH)2alpha CoO2 (alpha approximately 0.57822)

The incommensurate modulated crystal structure of the new misfit-layer calcium cobalt oxide (Ca0.85OH)2alphaCoO2 was investigated using a superspace-group formalism with synchrotron X-ray diffraction data. The compound is a kind of composite crystal that consists of two interpenetrating subsystems, [CoO2]infinity layers containing triangular lattices formed by edge-sharing CoO6 octahedra, separated from each other by [2Ca0.85OH]infinity double-layered rock-salt-type slabs. Both the subsystems are monoclinic lattices with the unit cell parameters, a1 = 2.8180(4) A, b = 4.8938(6) A, c = 8.810(1) A, alpha0 = 95.75(3) degrees , and alpha(=|q|=a1/a2) = 0.57822(8), viz., a2 = 4.8736 A, with Z = 2. A possible superspace group is C2/m(alpha10)s0-C21/m(alpha(-1)10) for the respective subsystems. The atomic positions deviate from the average positions of the fundamental structure due to the incommensurable periodic interaction between the subsystems. A significant structural modulation was found in the [2Ca0.85OH] subsystem, whereas the modulation in the [CoO2] subsystem is less than in [2Ca0.85OH], due to the tight bonding of the close-packed CoO6 octahedra. The degree of modulation in the CoO2 layers, i.e., the potential modulation, is almost the same as those of other compounds of the misfit-layer cobalt oxides. Flattened CoO6 octahedra indicate hole doping into the CoO2 layers. The [2Ca0.85OH] blocks act as the charge reservoir layers, and the defect Ca ions are presumably the source of the holes.     

Massenspektren der von Aminosäuren bzw. Peptiden abgeleiteten Triazin-Derivate

A mass spectrometric study of about 30 triazine derivatives from amino acids and peptides is reported. These derivatives incorporated the C-terminal of amino acids and peptides in the ring. In contrast to the mass spectra of amino acids and peptide esters reported previously, they always showed characteristic fragments, denoting the presence of the terminal triazine ring. By using this peak as a marker, it is easy to estimate the C-terminal of peptides. In dipeptides, the N-terminal and C-terminal are determined simultaneously.     

Specific isolation of N-terminal fragments from proteins and their high-fidelity de novo sequencing

A new method to determine N-terminal amino acid sequences of multiple proteins at low pmol level by a parallel processing has been developed. The method contains the following five steps: (1) reduction, S-alkylation and guanidination for targeted proteins; (2) coupling with sulfosucccimidyl-2-(biotinamido)ethyl-1,3-dithiopropionate(sulfo-NHS-SS-biotin) to N(alpha)-amino groups of proteins; (3) digestion of the modified proteins by an appropriate protease; (4) specific isolation of N-terminal fragments of proteins by affinity capture using the biotin-avidin system; (5) de novo sequence analysis of peptides by MALDI-TOF-/MALDI-TOF-PSD mass spectrometry with effective utilization of the CAF (chemically assisted fragmentation) method.1 This method is also effective for N-terminal sequencing of each protein in a mixture of several proteins, and for sequencing components of a multiprotein complex. It is expected to become an essential proteomics tool for identifying proteins, especially when used in combination with a C-terminal sequencing method.     

Dynamic recording of a digital hologram with single exposure by a wave-splitting phase-shifting method

The wave-splitting phase-shifting digital holography using a pixelated microretarder array is proposed. By using four intensity images recorded by the pixelated microretarder array, Stokes parameters of the incident wave can be calculated. The fully complex amplitude distribution of the object wave can be obtained by using Stokes parameters, if the polarization states of the object and reference waves are linear and orthogonal. Two sets of experimental results are provided to verify the feasibility of the proposed method. One is the result for a movie recording using a CW laser and the other is the result for instant recording using a single pulsed laser.     

Circularly polarized luminescence (CPL) characteristics of hydrophobic pyrene derivatives/γ-cyclodextrin (γ-CD) complexes in aqueous solution dissolved by grinding

Circularly polarized luminescence (CPL) organic dyes are currently receiving a great interest, but there are still not many reported observations of CPL spectra of hydrophobic dyes from aqueous solution. We have prepared hydrophobic pyrene derivatives and dissolved them into aqueous solutions with γ-cyclodextrin (γ-CD) by using grinding technique. Among these derivatives, (pyrene-1-carbonyl)serine (PySer) forms a spatially restricted dimer in the hydrophobic chiral cavity of γ-CD and exhibits excimer emission with a high quantum yield of Φ_f?=?0.68. In addition, circular dichroism and CPL signals were induced for the complex. The strong g_CPL value of g_CPL?=?+?2.2?×?10^?3 was obtained, which may be attributed to the interaction between the hydroxyl groups in the side chain of PySer with those of γ-CD and it strengthens the chiral dimeric structure.

Graphic abstract

     

Topologically-Interlocked Minicircles as Probes of DNA Topology and DNA-Protein Interactions

DNA minicircles exist in biological contexts, such as kinetoplast DNA, and are promising components for creating functional nanodevices. They have been used to mimic the topological features of nucleosomal DNA and to probe DNA-protein interactions such as HIV-1 and PFV integrases, and DNA gyrase. Here, we synthesized the topologically-interlocked minicircle rotaxane and catenane inside a frame-shaped DNA origami. These minicircles are 183 bp in length, constitute six individual single-stranded DNAs that are ligated to realize duplex interlocking, and adopt temporary base pairing of single strands for interlocking. To probe the DNA-protein interactions, restriction reactions were carried out on DNAs with different topologies such as free linear duplex or duplex constrained inside origami and free or topologically-interlocked minicircles. Except the free linear duplex, all tested structures were resistant to restriction digestion, indicating that the topological features of DNA, such as flexibility, curvature, and groove orientation, play a major role in DNA-protein interactions.     

Reversible and Stepwise Single-Crystal-to-Single-Crystal Transformation of a Platinum(II) Complex with Vapochromic Luminescence

The vapochromic single-crystal-to-single-crystal (SCSC) transformation of a highly luminescent Pt^II complex bearing an N-heterocyclic carbene [Pt(CN)₂(tBu-impy)] (tBu-impyH⁺=1-tert-butyl-3-(2-pyridyl)-1H-imidazolium) is reported. The trihydrate form of the complex, which exhibits blue ³MMLCT emission owing to weak Pt⋅⋅⋅Pt interactions, changed its luminescence color from blue to yellowish-green upon the desorption of water molecules while keeping the high emission quantum yield of more than 0.45. Variable-temperature and continuous in-situ tracking of single-crystal X-ray diffraction measurements revealed that the SCSC transformation proceeds reversibly by the release and reabsorption of water molecules, thereby changing the stacked structure slightly. As a result, the dynamics of vapor-induced SCSC transformation were elucidated: that the anhydrous form returned to the original trihydrate form in a two-step process under a water vapor atmosphere. In addition, the Pt^II complex exhibited a similar SCSC response accompanied by a luminescence color change in the presence of methanol vapor, while being inactive toward ethanol vapor.     

Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation

Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.     

Construction of Helical Structures with Multiple Fused Anthracenes: Structures and Properties of Long Expanded Helicenes

Polycyclic aromatic compounds consisting of four or five fused anthracene units were synthesized by PtCl₂-catalyzed cycloisomerization as novel long expanded helicenes. These compounds have helical structures with significant stacking of the terminal anthracene moieties at 0.33 nm interlayer distance. In the UV-vis and fluorescence spectra, the absorption and emission bands were red-shifted as the number of fused anthracene units was increased. The characteristic broad and long-lived emission bands of the long analogues are explained by the excimer-like stabilization of the excited state. These photophysical data as well as their cyclic voltammetric data are discussed on the basis of the π-conjugation and interlayer π⋅⋅⋅π interactions in the molecular structures and the molecular orbitals. The barrier and mechanism of helical inversion are also reported.