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.     

Polymeric organosilicon systems. XVII. Synthesis and photochemical and conducting properties of poly[o-and m-(disilanylene)phenylene]s

Poly[o-(tetramethyldisilanylene)phenylene] ( 2a ), poly[o-(1,2-dimethyldiphenyldisilanylene)-phenylene] ( 2b ), poly[m-(tetramethyldisilanylene)phenylene] ( 2c ), and poly[m-(1,2-dimethyldiphenyldisilanylene)phenylene] ( 2d ) were prepared by the sodium condensation reaction of the corresponding 1,2-and 1,3-bis (chlorosilyl)benzenes in toluene. Irradiation of thin films of 2a-2d in air resulted in a rapid decrease of absorption maxima in the ultraviolet region. The photolysis of 2b and 2d in benzene afforded photodegradation products with low molecular weights. When thin films of 2b and 2d were doped with antimony pentafluoride vapor, films which have conductivities of semi-conductor level were obtained. © 1993 John Wiley & Sons, Inc.     

Sorption of ethanesulfonic acid by nylon-6 containing various numbers of end groups

From the analysis of the permeation of ³⁵S labeled ethanesulfonic acid, through nylon-6 films sorption isotherms were obtained. The films are characterized by their largely different content of carboxyl and amino end groups. It was found that the shape of the isotherm depends on the molar ratio of the two end groups: an S-shape curve for the film containing the carboxyl end group larger than the amino end group and a Langmuir-type curve for the film containing comparable numbers of end groups. These results were explained by the McGregor-Harris theory in which the acid dissociation constants of the two end groups in nylon were estimated experimentally.     

Photosensitized breakage and damage of DNA by CdSe-ZnS quantum dots

Strand breakages and nucleobase damages in plasmid DNA (pDNA) by CdSe-ZnS quantum dots (QDs) are investigated under different conditions of photoactivation. Here, streptavidin functionalized CdSe-ZnS QDs are conjugated to biotinylated pDNA, and photosensitized strand breakages and nucleobase damages in the conjugates are investigated using atomic force microscopy (AFM) imaging, gel electrophoreses analyses, and assay of reactive oxygen intermediates (ROI). Also, reactions of photoactivated pDNA-QD conjugates with base excision repair enzymes such as formamidopyrimidine glycosylase (Fpg) and endonuclease III (Endo III) show damages of purine and pyrimidine bases. The base excision repair enzymes recognize and remove the damaged bases. The base excision reactions of photoactivated pDNA-QD conjugates resulted in pDNA strand breakages, which appeared as sheared bands in agarose gel images. On the basis of AFM imaging, reactions of Fpg and Endo III with damaged pDNA, ROI assay, and literature reports, we attribute the breakage and damage of pDNA to its reactions with ROI. The production of ROI by photoactivated QDs is confirmed by nitroblue tetrazolium (NBT) assay. The current work shows that photoactivation of QD-conjugated nucleic acids for an extended period of time is not favorable for their stability. On the other hand, photoinduced production of ROI by QDs is an emerging research area with potential applications in the photodynamic therapy of cancer. In this regard, photosensitized damage of pDNA observed in the current work shows possibilities of QDs in nucleus-targeted photodynamic therapy.     

Effects of amino acids on the formation of hematite particles in a forced hydrolysis reaction

The influence of amino acids on the formation of hematite particles from a forced hydrolysis reaction of acidic FeCl3 solution was examined. The spherical particles were produced on the systems with L-phenylalanine (L-Phe), L-serine (L-Ser) and L-alanine (L-Ala), though L-glutamine (L-Gln) and L-glutamic acid (L-Glu) gave ellipsoidal hematite particles. This morphological change in hematite particles is consistent with the order of stability constant of amino acids against to Fe3+ ions (K). The hematite particles produced with L-Glu, L-Gln and L-Ser were highly porous because they are formed by aggregation of cluster particles. These particles exhibited microporous behavior by outgassing the particles below 200 degrees C while they changed to mesoporous after treating above 300 degrees C by elimination of amino acids molecules remained between the cluster particles within the hematite particles. The hematite particles strongly depended on the nature of amino acids such as alternation of solution pH and adsorption affinity to beta-FeOOH and/or polynuclear primary (PN) particles. The systems on L-Ala and L-Phe, showing very rapid phase transformation from beta-FeOOH to hematite, exhibited the Ostwald ripening. A rotational particle preparation procedure suggested that the morphology of hematite particle is governed by the mode and strength of amino acid adsorption onto beta-FeOOH and/or PN particles.     

Calorimetric study of molecular superconductor κ-(BEDT-TTF)<Subscript>2</Subscript>Ag(CN)<Subscript>2</Subscript>H<Subscript>2</Subscript>O which contains water in the anion layers

Thermodynamic investigation of an organic superconductor κ-(BEDT-TTF)₂Ag(CN)₂H₂O in which the BEDT-TTF dimers are arranged in the κ-type structure in the donor layers is performed by the relaxation calorimetric technique at low temperatures and under magnetic fields. A thermal anomaly related to the superconductive phase transition was observed at 5 K. The existence of residual γ^* in the superconductive state is about 18% of the normal state γ value, which is larger than those of κ-(BEDT-TTF)₂Cu(NCS)₂, and κ-(BEDT-TTF)₂Cu[N(CN)₂]Br salt. The lattice heat capacity reflected on the β-term in the low-temperature heat capacity was found to be affected by the cooling rate. The disorder produced in the network structure constructed by hydrogen bond in the insulating layer is considered to give low-energy phonon excitations reflected in the heat capacity.     

Liquid chromatographic analysis of cinchona alkaloids in beverages

A method for the determination of Cinchona extract (whose main components are the alkaloids cinchonine, cinchonidine, quinidine, and quinine) in beverages by liquid chromatography was developed. A beverage with an alcohol content of more than 10% was loaded onto an OASIS HLB solid-phase extraction cartridge, after it was adjusted to pH 10 with 28% ammonium hydroxide. Other beverages were centrifuged at 4000 rpm for 5 min, and the supernatant was loaded onto the cartridge. The cartridge was washed with water followed by 15% methanol, and the Cinchona alkaloids were eluted with methanol. The Cinchona alkaloids in the eluate were chromatographed on an L-column ODS (4.6 mm id x 150 mm) with methanol and 20 mmol/L potassium dihydrogen phosphate (3 + 7) as the mobile phase. Cinchona alkaloids were monitored with an ultraviolet (UV) detector at 230 nm, and with a fluorescence detector at 405 nm for cinchonine and cinchonidine and 450 nm for quinidine and quinine (excitation at 235 nm). The calibration curves for Cinchona alkaloids with the UV detector showed good linearity in the range of 2-400 microg/mL. The detection limit of each Cinchona alkaloid, taken to be the concentration at which the absorption spectrum could be identified, was 2 microg/mL. The recovery of Cinchona alkaloids added at a level of 100 microg/g to various kinds of beverages was 87.6-96.5%, and the coefficients of variation were less than 3.3%. A number of beverage samples, some labeled to contain bitter substances, were analyzed by the proposed method. Quinine was detected in 2 samples of carbonated beverage.     

Structural and electronic differences of copper(I) complexes with tris(pyrazolyl)methane and hydrotris(pyrazolyl)borate ligands

Copper(I) complexes with tripodal nitrogen-containing neutral ligands such as tris(3,5-diisopropyl-1-pyrazolyl)methane (L1') and tris(3-tertiary-butyl-5-isopropyl-1-pyrazolyl)methane (L3'), and with corresponding anionic ligands such as hydrotris(3,5-diisopropyl-1-pyrazolyl)borate (L1-) and hydrotris(3-tertiary-butyl-5-isopropyl-1-pyrazolyl)borate (L3-) were synthesized and structurally characterized. Copper(I) complexes [Cu(L1')Cl] (1), [Cu(L1')(OClO3)] (2), [Cu(L1')(NCMe)](PF6) (3a), [Cu(L1')(NCMe)](ClO4) (3b), [Cu(L1')(CO)](PF6) (4a), and [Cu(L1')(CO)](ClO4) (4b) were prepared using the ligand L1'. Copper(I) complexes [Cu(L3')Cl] (5) and [Cu(L3')(NCMe)](PF6) (6) with the ligand L3' were also synthesized. Copper(I) complexes [Cu(L1)(NCMe)] (7) and [Cu(L1)(CO)] (8) were prepared using the anionic ligand L1-. Finally, copper(I) complexes with anionic ligand L3- and acetonitrile (9) and carbon monoxide (10) were synthesized. The complexes obtained were fully characterized by IR, far-IR, 1H NMR, and 13C NMR spectroscopy. The structures of both ligands, L1' and L3', and of complexes 1, 2, 3a, 3b, 4a, 4b, 5, 6, 7, and 10 were determined by X-ray crystallography. The effects of the differences in (a) the fourth ligand and the counteranion, (b) the steric hindrance at the third position of the pyrazolyl rings, and most importantly, (c) the charge of the N3 type ligands, on the structures, spectroscopic properties, and reactivities of the copper(I) complexes are discussed. The observed differences in the reactivities toward O2 of the copper(I) acetonitrile complexes are traced back to differences in the oxidation potentials determined by cyclic voltammetry. A special focus is set on the carbonyl complexes, where the 13C NMR and vibrational data are presented. Density functional theory (DFT) calculations are used to shed light on the differences in CO bonding in the compounds with neutral and anionic N3 ligands. In correlation with the vibrational and electrochemical data of these complexes, it is demonstrated that the C-O stretching vibration is a sensitive probe for the "electron richness" of copper(I) in these compounds.     

Microgravity experiments on colloidal crystallization of silica spheres in the presence of sodium chloride

 Rate coefficients (k) in the colloidal crystallization of monodispersed silica spheres in the presence of sodium chloride are studied in microgravity achieved by parabolic flights of an aircraft. Time-resolved reflection spectroscopy is made with a continuous circulating-type stopped-flow cell system. The k values decrease as the salt concentration increases both at 0 and 1 G and those in microgravity are smaller than those in normal gravity by 16% (maximum), especially in water and in the presence of a small amount of the salt lower than 2 × 10⁻⁶ mol/l. The rates in flight at 1 G are larger by 15% (maximum) compared with those at 1 G on the ground. The k values obtained at 0 G, 1 G in flight and 1 G on the ground agree excellently with each other for the suspensions with 3 × 10⁻⁶ and 4 × 10⁻⁶ mol/l sodium chloride. Disappearance of the downward diffusion of spheres and no convection of the suspensions are important for retardation in microgravity. Received: 20 January 2000 Accepted: 9 March 2000     

XPS of oxygen atoms on Ag(111) and Ag(110) surfaces: Accurate study with SAC/SAC‐CI combined with dipped adcluster model

O1s core‐electron binding energies (CEBE) of the atomic oxygens on different Ag surfaces were investigated by the symmetry adapted cluster‐configuration interaction (SAC‐CI) method combined with the dipped adcluster model, in which the electron exchange between bulk metal and adsorbate is taken into account properly. Electrophilic and nucleophilic oxygens (O_elec and O_nuc) that might be important for olefin epoxidation in a low‐oxygen coverage condition were focused here. We consider the O1s CEBE as a key property to distinguish the surface oxygen states, and series of calculation was carried out by the Hartree–Fock, Density functional theory, and SAC/SAC‐CI methods. The experimental information and our SAC/SAC‐CI results indicate that O_elec is the atomic oxygen adsorbed on the fcc site of Ag(111) and that O_nuc is the one on the reconstructed added‐row site of Ag(110) and that one‐ and two‐electron transfers occur, respectively, to the O_elec and O_nuc adclusters from the silver surface. © 2013 Wiley Periodicals, Inc.