Cross-linking chemistry and biology: development of multifunctional photoaffinity probes

An efficient method of photoaffinity labeling has been developed based on rationally designed multifunctional photoprobes. Photoaffinity techniques have been used to elucidate the protein structure at the interface of biomolecules by the photochemical labeling of interacting sites. However, the identification of labeled sites within target proteins is often difficult. Novel biotinyl bioprobes bearing a diazirine photophore have contributed significantly to the rapid elucidation of ligand binding sites within proteins, thereby extending conventional photoaffinity methods. This article discusses the synthesis and applications of various photoprobes bearing a biotin, including strategies using cleavable linkages between photophores. The combination of photoaffinity methods with chip technology is also described as a novel entry to rapid affinity-based screening of inhibitors. This review focuses on a rapid and reliable photoaffinity method utilizing diazirine-based multifunctional photoprobes with numerous potential applications in functional proteomics of biomolecular interactions.     

On-line column preconcentration for the determination of cobalt in sea water by flow-injection chemiluminescence detection

A flow-injection method for the determination of dissolved cobalt(II) in sea water has been studied based on a combination of column preconcentration using 8-quinolinol immobilized on silica gel, fluoride containing metal alkoxide glass (8HQ-MAF) and chemiluminescence detection with a gallic acid-hydrogen peroxide system. Co(II) is selectively recovered from an acidified sample with 8-quinolinol immobilized on silica gel. After elution with dilute hydrochloric acid the resultant eluent is mixed with the reagent solutions, heated to 60^°C and then introduced into the CL cell. The analysis time including the 2-min sample load was 8 min per sea water sample with a corresponding detection limit of 0.62 ngl^-1 (3). The average standard deviation calculated for 10 replicate measurements of artificial sea water samples with a concentration of 10 ngl^-1 cobalt was ±2.1%. The method has been tested with the standard reference sea waters NASS and CASS.     

DNA sensor: A novel electrochemical gene detection method using carbon electrode immobilized DNA probes

Abstract

The authors have developed a novel, rapid, convenient, and specific gene detection method, named the ‘DNA sensor,’ using a graphite electrode loaded with DNA probes. Synthesized oligonucleotide (5-TGCAGTTCCGGTGGCTGATC-3′) complementary to oncogene v-myc was employed for a model probe. The oligonucleotide was chemically adsorbed on a basal plane pyrolytic graphite (BPPG) electrode. The sensor was able to be applied to a hybridization reaction (40°C) in a linearized pVM623 solution carrying the Pst I fragment of v-myc (1.5 kbp).

After the hybridization reaction, the sensor was immersed into an acridine orange solution (1 μM) and washed with a phosphate buffer (pH 7.0). Acridine orange intercalated between base pairs of the formed double stranded DNAs on the electrode. The anodic peak potential of acridine orange that interacted with the DNAs on the electrode was measured. The positive shift of the peak potential increased in proportional to the pVM623 concentration in the hybridization reaction. 10^?1 g/ml of pVM623 was able to be detected in the buffer solution using the sensor. This gene detection was completed within an hour.     

Use of tube radial distribution of ternary mixed carrier solvents for introduction of absorption reagent for metal ion separation and online detection into capillary

When ternary mixed solvents consisting of water-hydrophilic/hydrophobic organic solvents are fed into a micro-space under laminar flow conditions, the solvent molecules are radially distributed in the micro-space. The specific fluidic behavior of the solvents is called the "tube radial distribution phenomenon (TRDP)". A novel capillary chromatography method was developed based on the TRDP that creates the inner major and outer minor phases in a tube, where the outer phase acts as a pseudo-stationary phase. This is called "tube radial distribution chromatography (TRDC)". In this study, Chrome Azurol S as an absorption reagent was introduced into the TRDC system for metal ion separation and online detection. The fused-silica capillary tube (75 μm id and 110 cm length) and water-acetonitrile-ethyl acetate mixture (3:8:4 volume ratio) including 20 mM Chrome Azurol S as a carrier solution were used. Metal ions, i.e. Co(II), Cu(II), Ni(II), Al(III), and Fe(III), as models were injected into the present TRDC system. Characteristic individual absorption characteristics and elution times were obtained as the result of complex formation between the metal ions and Chrome Azurol S in the water-acetonitrile-ethyl acetate mixture solution. The elution times of the metal ions were examined based on their absorption behavior; Co(II), Ni(II), Al(III), Fe(III), and Cu(II) were eluted in this order over the elution times of 4.7-6.8 min. The elution orders were determined from the molar ratios of metal ion to Chrome Azurol S and Irving-Williams series for bivalent metal ions.     

Fully automated reagent peak‐free liquid chromatography fluorescence analysis of highly polar carboxylic acids using a column‐switching system and fluorous scavenging derivatization

In this study, we combined a column‐switching system with a fluorous scavenging derivatization method to develop a fully automated reagent peak‐free LC fluorescence detection protocol for the analysis of highly polar carboxylic acids. In this method, highly polar carboxylic acids were derivatized with fluorescent 1‐pyrenemethylamine in the presence of 1‐ethyl‐3‐(3‐dimethylaminopropyl)carbodiimide and 1‐hydroxy‐1H‐benzotriazole. Residual excess of the unreacted reagent was tagged with 2‐(perfluorooctyl)ethyl isocyanate and then removed selectively using a fluorous column‐switching system placed in front of an analytical reversed‐phase column. The signal of the fluorous‐tagged unreacted reagent was completely absent in the resulting chromatograms; therefore, it did not interfere with the quantification of each acid especially those eluted before 20 min. The detection limits (S/N = 3) for the examined acids were in the range from 4.0 to 22 fmol per injection. We have applied this method to comparative analysis of highly polar carboxylic acids in urine samples obtained from diabetes mellitus type‐II model mice and their control.     

Highly meso-Diastereoselective Pinacol Coupling of Aromatic Aldehydes Mediated by Al Powder/Copper Sulfate in Water

Pinacol-type coupling reaction products presenting a high meso-diastereoselectivity (the ratio dl/meso was 4/96 up to 1/99) were obtained in fair to good yields (24–69%) using several aromatic aldehydes as starting materials and aluminium powder/copper sulfate as catalysts, in water, under reflux conditions.     

Comparison in fractal dimension between those obtained from structure factor and viscoelasticity of gel networks of 1,3:2,4-bis-O-(p-methylbenzylidene)-D-sorbitol in polystyrene melt at gel point

We investigated time evolution of shear moduli in the physical gelation process of 1,3:2,4-bis-O-(p-methylbenzylidene)-D-sorbitol in polystyrene melt. At the gel point, storage and loss shear moduli, G' and G", were described by the power law of frequency omega, G' approximately G" approximately omegan, with the critical exponent n being nearly equal to 2/3, in agreement with the value predicted by the percolation theory. We also investigated the structure factor over two decades in length scale at gel point by using ultra-small-angle X-ray scattering, and small-angle X-ray scattering. We found the power-law behavior in low-q region, indicating that the gel network forms the self-similar structure with mass-fractal dimension. Comparison between the exponent of mass-fractal dimension from structure factor and that from viscoelasticity indicates that hydrodynamic interactions are completely screened out and the excluded volume effects are dominant in the gel. The gel strength was found to increase with the decrease in the lower limit length scale of fractality.     

Novel stereoselective entry to 2'-beta-carbon-substituted 2'-deoxy-4'-thionucleosides from 4-thiofuranoid glycals

2'-Beta-methyl- and 2'-beta-hydroxymethyl-2'-deoxy-4'-thionucleosides have been synthesized through PhSeCl-mediated electrophilic glycosidation using 4-thiofuranoid glycals having carbon substituents at the C2-position as a glycosyl donor. Preparation of these glycals were carried out by means of the C2 lithiation of 1-chloro-4-thiofuranoid glycal with LTMP followed by the Birch reduction of the chlorine atom. [reaction: see text]     

A large thermal hysteresis loop produced by a charge-transfer phase transition in a rubidium manganese hexacyanoferrate

In a rubidium manganese hexacyanoferrate, RbMn[Fe(CN)(6)], the magnetic susceptibility (chi(M)) decreased at 225 K (=T(1/2)decreasing) and abruptly increased at 300 K (=T(1/2)increasing) in the cooling and warming processes, respectively. X-ray photoelectron spectroscopy and infrared spectroscopy indicated that the high-temperature (HT) and low-temperature (LT) phases were composed of Mn(II)-NC-Fe(III) and Mn(III)-NC-Fe(II), respectively. A structural change from cubic (F43m, a = 10.533 A) to tetragonal (I4m2, a = b = 7.090 A, c = 10.520 A) accompanied the phase transition, and, on the basis of these results, the HT and LT phases were assigned to Mn(II)(t(2g)(3)e(g)(2), (6)A(1g); S = (5)/(2))-NC-Fe(III) (t(2g)(5), (2)T(2g); S = (1)/(2)) and Mn(III)(e(g)(2)b(2g)(1)a(1g)(1), (5)B(1g); S = 2)-NC-Fe(II) (b(2g)(2)e(g)(4), (1)A(1g); S = 0), respectively. This phenomenon is caused by a metal-to-metal charge transfer from Mn(II) to Fe(III) and a Jahn-Teller distortion of the produced Mn(III) ion. The reaction mechanism is discussed, considering the entropy difference between the HT and LT phases.