Microarray‐Based Detection of Dye‐Labeled DNA by SERRS Using Particles Formed by Enzymatic Silver Deposition

The growing interest in DNA diagnostics is addressed today by microarrays with fluoresence detection. In our approach, we utilize spatially defined arrays of short oligonucleotides on a modified glass surface. Surface enhanced resonance Raman scattering (SERRS) is used to obtain molecularly specific spectra of the Raman‐active dye‐labeled DNA. Nanoparticles produced by enzymatic silver deposition are used as SERS‐active substrate. They grow directly on the modified oligonucleotides and only in the spatially defined areas on the chip. Furthermore, they potentially offer several advantages for SERS detection. The nanoparticles are characterized and their ability for use as SERS‐ and SERRS‐active substrate is estimated. Three different Raman‐active dyes are investigated for their potential for involvement in sequence specific DNA analysis.     

The Totally Nonnegative Part of G/P is a CW Complex

The totally nonnegative part of a partial ag variety G/P has been shown in [18], [17] to be a union of semialgebraic cells. Moreover, the closure of a cell was shown in [19] to be a union of smaller cells. In this paper we provide glueing maps for each of the cells to prove that (G/P)_?0 is a CW complex. This generalizes a result of Postnikov, Speyer and the second author [15] for Grassmannians.     

First principles analysis of H2O adsorption on the (110) surfaces of SnO2, TiO2 and their solid solutions

Both associative and dissociative H(2)O adsorption on SnO(2)(110), TiO(2)(110), and Ti-enriched Sn(1-x)Ti(x)O(2)(110) surfaces have been investigated at low ((1)/(12) monolayer (ML)) and high coverage (1 ML) by density functional theory calculations using the Gaussian and plane waves formalism. The use of a large supercell allowed the simulation at low symmetry levels. On SnO(2)(110), dissociative adsorption was favored at all coverages and was accompanied by stable associative H(2)O configurations. Increasing the coverage from (1)/(12) to 1 ML stabilized the (associatively or dissociatively) adsorbed H(2)O on SnO(2)(110) because of the formation of intermolecular H bonds. In contrast, on TiO(2)(110), the adsorption of isolated H(2)O groups ((1)/(12) ML) was more stable than at high coverage, and the favored adsorption changed from dissociative to associative with increasing coverage. For dissociative H(2)O adsorption on Ti-enriched Sn(1-x)Ti(x)O(2)(110) surfaces with Ti atoms preferably located on 6-fold-coordinated surface sites, the analysis of the Wannier centers showed a polarization of electrons surrounding bridging O atoms that were bound simultaneously to 6-fold-coordinated Sn and Ti surface atoms. This polarization suggested the formation of an additional bond between the 6-fold-coordinated Ti(6c) and bridging O atoms that had to be broken upon H(2)O adsorption. As a result, the H(2)O adsorption energy initially decreased, with increasing surface Ti content reaching a minimum at 25% Ti for (1)/(12) ML. This behavior was even more accentuated at high H(2)O coverage (1 ML) with the adsorption energy decreasing rapidly from 145.2 to 101.6 kJ/mol with the surface Ti content increasing from 0 to 33%. A global minimum of binding energies at both low and high coverage was found between 25 and 33% surface Ti content, which may explain the minimal cross-sensitivity to humidity previously reported for Sn(1-x)Ti(x)O(2) gas sensors. Above 12.5% surface Ti content, the binding energy decreased with increasing coverage, suggesting that the partial desorption of H(2)O is facilitated at a high fractional coverage.     

Discrimination of GalNAc (4S/6S) sulfation sites in chondroitin sulfate disaccharides by chip-based nanoelectrospray multistage mass spectrometry

Sulfation pattern within chondroitin sulfate (CS) glycosaminoglycan (GAG) chains is an important post-translational modification that regulates their interaction with proteins. In this context, development of highly efficient and reproducible analytical methods for the investigation of CS sulfation patterns is of high necessity. In this study we report a novel method for straightforward determination of N-acetylgalactosamine (GalNAc) sulfation sites in chondroitin sulfate disaccharides. Our protocol involves combining fully automated chip-based nanoelectrospray (nanoESI) for analyte infusion and ionization in negative ion mode with multistage (MSⁿ) collision-induced dissociation (CID) high capacity ion trap (HCT) mass spectrometry for generation of sequence ions diagnostic for identification of sulfate ester group position within GalNAc residues. The feasibility of this approach is here demonstrated on chondroitin 6-O-sulfate and chondroitin 4-O-sulfate disaccharides. Fragmentation patterns obtained by MS² and MS³ sequencing stages provided first mass spectrometric data from which sulfation site(s) within GalNAc monosaccharide ring could be unequivocally deciphered. Hence, the method allowed discriminating 4S/6S sulfation sites solely on the basis of MS and multistage MS evidence.      

StavroX—A Software for Analyzing Crosslinked Products in Protein Interaction Studies

Chemical crosslinking in combination with mass spectrometry has matured into an alternative approach to derive low-resolution structural information of proteins and protein complexes. Yet, one of the major drawbacks of this strategy remains the lack of software that is able to handle the large MS datasets that are created after chemical crosslinking and enzymatic digestion of the crosslinking reaction mixtures. Here, we describe a software, termed StavroX, which has been specifically designed for analyzing highly complex crosslinking datasets. The StavroX software was evaluated for three diverse biological systems: (1) the complex between calmodulin and a peptide derived from Munc13, (2) an N-terminal ß-laminin fragment, and (3) the complex between guanylyl cyclase activating protein-2 and a peptide derived from retinal guanylyl cyclase. We show that the StavroX software is advantageous for analyzing crosslinked products due to its easy-to-use graphical user interface and the highly automated analysis of mass spectrometry (MS) and tandem mass spectrometry (MS/MS) data resulting in short times for analysis. StavroX is expected to give a further push to the chemical crosslinking approach as a routine technique for protein interaction studies.     

Mechanical,thermomechanical, and thermal properties of polystyrene crosslinked with a multifunctional zirconium oxo cluster

Inorganic–organic hybrid materials were prepared by free radical polymerization of styrene in the presence of varying amounts of the cluster Zr₆O₄(OH)₄ (methacrylate)₁₂. Stepwise polymerization allowed the preparation of bubble‐ and crack‐free, transparent bulk samples on a 30 g scale with dimensions required for mechanical testing. Small‐angle X‐ray scattering investigations and transmission electron micrographs revealed that the clusters formed randomly distributed aggregates of random size. Solvent uptake in swelling experiments was related to the cluster proportion. Storage moduli in the glassy state were slightly increased when compared with neat polystyrene, but pronounced plateau moduli were observed above the glass transition temperature, which correlated to the cluster proportion. Plateau moduli were used to calculate network parameters such as network density. Onset temperatures of thermal decomposition and the glass transition temperatures of the cluster‐crosslinked polymers were higher than that of neat polystyrene. Thermal expansion coefficients were unaffected in the glassy state, but were gradually reduced above the glass transition temperature with increasing cluster proportion. Both the tensile moduli at room temperature and the yield points increased when polystyrene was doped with the cluster. The strain hardening moduli, as determined in compression tests at large deformations, increased linearly with the cluster proportion. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2215–2231, 2007     

Total Synthesis of 7‐ and 8‐Oxygenated Pyrano[3,2‐a]carbazole and Pyrano[2,3‐a]carbazole Alkaloids via Boronic Acid‐Catalyzed Annulation of the Pyran Ring

The boronic acid‐catalyzed annulation of citral opens up a short route to oxygenated cyclized monoterpenoid pyranocarbazole alkaloids. Thus, murrayamine‐D is available in only three steps and 55% overall yield from the corresponding carbazole precursor.