Characterization of single- and double-stranded DNA on gold surfaces

Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5'-C(6)H(12)SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation-infrared reflection absorption spectroscopy (PM-IRRAS). The formation of dsDNA on the surface was identified by PM-IRRAS by a dsDNA IR signature at approximately 1678 cm(-)(1) that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 degrees C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au-S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces.     

Determination of stability constants of some substituted 4-pyrazolone dyes containingo-methoxy,o-carboxy,ando-nitro groups with trivalent lanthanide ions

The relative stabilities of the metal derivatives of hydrazo pyrazolone dyes containingortho -OCH₃, -COOH, and -NO₂ groups have been measured potentiometrically in 75% (v/v) dioxane—water mixture at 30 °C and <0.1 ionic strength. The stability constant of their 1:1 and 1:2 chelates with twelve trivalent lanthanide ionsLn(III) have also been determined. The effects of substituents on the hydrazo-moiety of the ligand on the equilibria are discussed. The affinity of different ligands for complexation with lanthanide ions reaches its highest value withortho-carboxyphenylhydrazopyrazolone. The data were correlated and the results were used to explain the stabilization of such chelates by dative -bonding betweenLn(III) and the ligand.

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Bestimmung der Stabilitätskonstanten einigero-Methoxy-,o-Carboxy undo-Nitro-substituierter 4-Pyrazolon-Farbstoffe mit trivalenten Lanthanidenionen

Zusammenfassung Es wurden die relativen Stabilitäten der Metallderivate von Hydrazopyrazolon-Farbstoffen mitortho-OMe, -COOH und -NO₂ potentiometrisch in 75% (v/v) Dioxan—Wasser bei 30 °C und einer Ionenstärke <0.1 bestimmt. Die Stabilitätskonstanten der 1:1 und 1:2 Chelate mit zwölf trivalenten LanthanidenionenLn(III) wurden ebenfalls gemessen. Die Substituenteneffekte werden diskutiert. Dabei zeigeno-Carboxyphenylhydrazopyrazolone die höchste Affinität zu Lanthanidenionen. Die Daten werden miteinander korreliert und die Resultate auf der Basis einer dativen -Bindung zwischenLn(III)-Ion und dem Liganden diskutiert.

     

Absorbance Changes by Aromatic Amino Acid Side Chains in Early Rhodopsin Photointermediates

Abstract— Absorbance changes were monitored from 250 to 650 nm during the first microsecond after photolysis of detergent suspensions of bovine rhodopsin at 20°C. Global analysis of the resulting data produced difference spectra for bathorhodopsin, BSI and lumirhodopsin which give the change in absorbance of the aromatic amino acid side chains in these photointermediates relative to rhodopsin. These spectra show that the significant bleaching of absorbance near 280 nm, which has been seen previously for the lumirhodopsin, metarhodopsin I and metarhodopsin II intermediates, extends to times as early as bathorhodopsin. Because no corresponding absorbance increase is observed in the 250-275 nm region, the earliest bleaching of the 280 nm absorbance in rhodopsin is attributed to disruption of a hyperchromic interaction affecting Trp²⁶⁵. Partial decay of this 280 nm bleaching as bathorhodopsin converts to BSI takes place maximally near 290 nm, where Trp²⁶⁵ has been shown to absorb, and could be due to the ring of the retinylidene chromophore resuming a position at the BSI stage that reestablishes the hyperchromic interaction with Trp²⁶⁵. A subsequent change in the 250-300 nm region, which has no counterpart in the visible chromophore bands, indicates the possible presence of a protein-localized process as lumirhodopsin is formed.     

A Short Synthesis of (−)-Carbovir

(–)-Carbovir ((–)- 1 ) was synthesized via the cyclic carbonate 2 in four steps starting from enantiomerically enriched (–)-(S)-(cyclopent-2-enyl)methanol ((–)- 3 ).     

Two New Spermidine Alkaloids from Chisocheton weinlandii

The investigation of the MeOH extract of the leaves of Chisocheton weinlandii Harms (Meliaceae) revealed two new open‐chain spermidine alkaloids, chisitine 1 ( 1 ) and chisitine 2 ( 2 ). Their structures were elucidated by NMR spectroscopy, tandem‐mass spectrometry, and independant syntheses (Scheme 3). Detailed MS/MS fragmentation pathways are discussed for both compounds based on H/D exchange and ¹⁸O‐labeling experiments (Schemes 1 and 2).     

Phosphonio‐benzophospholide Zwitterions as Bridging 8e‐Donor Ligands: Synthetic and Mechanistic Studies

Reactions of the phosphonio‐benzophospholide π‐complexes 3a, b[Cr] with [M(CO)₅(olefin)] or of the σ‐complexes 2a, b[M] (M = Cr, Mo, W) with [M(CO)₃(aren)] lead to the first binuclear complexes 4a, b[CrM] featuring phosphonoio‐benzophospholides as μ‐bridging 8e‐donor ligands to two group 6 metal atoms. The constitution of the products was determined by spectroscopic and X‐ray diffraction studies. Mixed complexes with both group 6 and 7 metals were not accessible. Mechanistic studies showed that the reactions follow a complicated mechanism whose single steps may involve transfer of either M(CO)_n fragments or single CO ligands between complexes; the latter are associated with a σ/π‐coordination isomerization of the benzophospholide unit. Competition between both reaction channels can lead to the formation of product mixtures whose composition is controlled by the relative thermodynamic stabilities of the products. Computational studies suggest that in the more stable isomer of heterobimetallic complexes 4a, b[MM′] end‐on coordination to the heavier and side‐on coordination to the lighter metal atom is preferred.     

Reactivation pathway of the hydrogenase H‐cluster: Density functional theory study

This work puts forth a reaction pathway for the reactivation of exogenous ligand inhibited H‐cluster, the active site of Fe‐only hydrogenases. The H‐cluster is a dimetal complex, Fe–Fe, with the metal centers bridged by di(thiomethyl)amine. Exogenous ligands, H₂O, and OH^?, are bound to the distal iron (Fe_d). Density functional theory (DFT) calculations on the native and ruthenium‐modified H‐cluster have been performed using the B3LYP functional with 6‐31+G** and 6‐311+G** basis sets. We have ascertained that there is a thermodynamically favorable pathway for the reactivation of the OH^? inhibited H‐cluster, which proceeds by an initial protonation of the Fe_d–OH^? complex. The proposed reaction pathway has all its intermediate reactions ensue exothermically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Glycan side chains on naturally presented MHC class II ligands

The molecular characterization of unknown naturally presented major histocompatibility complex (MHC) class II glycopeptides carrying complex glycans has so far not been achieved, reflecting the different fragmentation characteristics of sugars and peptides in mass spectrometric analysis. Human leukocyte antigen (HLA)-DR-bound peptides were isolated by affinity purification, separated via high performance liquid chromatography and analyzed by matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry. We were able to identify two naturally processed MHC class II ligands, CD53(122-136) and CD53(121-136), carrying complex N-linked glycan side chains by a combination of in-source and collision-induced fragmentation on a quadrupole time-of-flight tandem mass spectrometer.     

Quantum yield of the iodide-iodate chemical actinometer: dependence on wavelength and concentrations

The quantum yield (QY) of the iodide-iodate chemical actinometer (0.6 M KI-0.1 M KIO3) was determined for irradiation between 214 and 330 nm. The photoproduct, triiodide, was determined from the increase in absorbance at 352 nm, which together with a concomitant measurement of the UV fluence enabled the QY to be calculated. The QY at 254 nm was determined to be 0.73 +/- 0.02 when calibration was carried out against a National Institute of Standards and Technology traceable radiometer or photometric device. At wavelengths below 254 nm the QY increased slightly, leveling off at -0.80 +/- 0.05, whereas above 254 nm the QY decreases linearly with wavelength, reaching a value of 0.30 at 284 nm. In addition, the QY was measured at different iodide concentrations. There is a slight decrease in QY going from 0.6 to 0.15 M KI, whereas below 0.15 M KI the QY drops off sharply, decreasing to 0.23 by 0.006 M KI. Calibration of the QY was also done using potassium ferrioxalate actinometry to measure the irradiance. These results showed a 20% reduction in QY between 240 and 280 nm as compared with radiometry. This discrepancy suggests that the QY of the ferrioxalate actinometer in this region of the spectrum needs reexamination.     

A novel MCR of isocyanates, aldehydes, and dienophiles

[reaction: see text] A novel one-pot procedure for the three-component coupling reaction of isocyanates, aldehydes, and dienophiles (IAD reaction) has been developed. Condensation of isocyanates and aldehydes and subsequent Diels-Alder reactions with electron-deficient dienophiles furnishes endo-selective amino-substituted cyclohexenes in good yield.