Investigation of Al diffusion in different oxide thin-film layers by SNMS/HFM method

Depth profiles of Ga₂O₃/a-SiO₂/Al₂O₃- substrate, Ga₂O₃/a-Si₃N₄/Al₂O₃- substrate, and Ga₂O₃/Al₂O₃ substrate thin layers were determined by the SNMS/HFM method. Al diffusion from the Al₂O₃ substrate was investigated after 50, and in some cases after 600 hours of heat treatment time at different temperatures (600 °C,850 °C,950 °C,1050 °C and 1150 °C). The diffusion coefficient of Al at 850 °C was found to be D _Al=8.7 * 10^–18 cm²/s in amorphous SiO₂; D _Al=1.5*10^–17 cm²/s in amorphous Si₃N₄ and D _Al=5.5* 10^–16 cm²/s in Ga₂O₃ at 600 °C, respectively. The possible diffusion mechanism is explained in terms of the metal-oxygen bond-strengths. Although the studied materials have high resistivity at room temperature, the applied SNMS/HFM method has proven to be an efficient surface analytical tool even in these cases.Dedicated to Professor Dr. rer. nat. Dr. h.c. Hubertus Nickel on the occasion of his 65th birthday     

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

Stochastic detection of motor protein-RNA complexes by single-channel current recording.

A label- and immobilization-free approach to detecting the reversible formation of complexes between nucleic acids and proteins at the single-molecule level is described. The voltage-driven translocation of individual oligoribonucleotides through a nanoscale protein pore is observed by single-channel current recordings. The oligoribonucleotide 5'-C25A(25)-3' gives rise to current blockades with an average duration of approximately 0.5 ms. In the presence of the RNA-binding ATPase P4, a viral packaging motor from bacteriophage phi8, longer events of tens to hundreds of milliseconds are observed. Upon addition of ATP the long events disappear, indicating the dissociation of the P4RNA complex. The frequency of events also depends on the concentration of P4 and the length of the oligoribonucleotide, thereby confirming the specificity of the P4RNA events. This study shows that single-channel current recordings can be used to monitor RNA-protein complex formation, thus opening up a new means to examine the motor activity of RNA- or DNA-processing enzymes.     

A generic approach to the impurity profiling of drugs using standardised and independent capillary zone electrophoresis methods coupled to electrospray ionisation mass spectrometry

Three standardised, capillary zone electrophoresis-electrospray ionisation mass spectrometry (CZE-ESI-MS) methods were developed for the analysis of six drug candidates and their respective process-related impurities comprising a total of 22 analytes with a range of functional groups and lipophilicities. The selected background electrolyte conditions were found to be: 60/40 v/v 10 mM ammonium formate pH 3.5/organic, 60/40 v/v 10 mM ammonium acetate pH 7.0/organic and 10 mM piperidine, pH 10.5, where the organic solvent is 50/50 v/v methanol/acetonitrile. The coaxial sheath flow consisted of either 0.1% v/v formic acid in 50/50 v/v methanol/water, or 10 mM ammonium acetate in 50/50 v/v methanol/water, depending on the mixture being analysed. Factor analysis and informational theory were used to quantify the orthogonality of the methods and predict their complementarities. The three selected CZE-ESI-MS methods allowed the identification of 21 out of 22 of all the drug candidates and their process-related impurities and provided orthogonality with four established high-performance liquid chromatography-mass spectrometry (HPLC-MS) methods. These methodologies therefore form the basis of a generic approach to impurity profiling of pharmaceutical drug candidates and can be applied with little or no analytical method development, thereby offering significant resource and time savings.     

Detection and recognition of cancer cells in vivo

A fundamentally new recognition method of bio-objects (e.g., cancer cells as the most important case of them) that escape the immune system supervision control is suggested. It is proposed to use a unified complex consisting of several molecular groups (e.g., antibodies or their fragments) bound with each other. Binding targets are localized on the surface of this bio-object. The choice of the targets is determined by antigen profiling being expressed on the surface of these bio-objects. The recognition efficiency appears to be notably higher than in a situation when molecular groups do not form a unified complex and act separately.     

Vesicle formation between single-chained cationic surfactants and ribo-oligonucleotides

Recently,we reported that deoxyribo-oligonucleotides could induce single chained cationic surfactant aggregation to form vesicles.In this paper,we will present that ribo-oligonucleotides can also induce vesicle formation,and compared with deoxyribo-oligonucleotides,ribo-oligonucleotides exhibit a higher inductive efficiency.     

Optical characterization of high speed microscanners based on static slit profiling method

Optical characterization of high-speed microscanners is a challenging task that usually requires special high speed, extremely expensive camera systems. This paper presents a novel simple method to characterize the scanned beam spot profile and size in high-speed optical scanners under operation. It allows measuring the beam profile and the spot sizes at different scanning angles. The method is analyzed theoretically and applied experimentally on the characterization of a Micro Electro Mechanical MEMS scanner operating at 2.6 kHz. The variation of the spot size versus the scanning angle, up to ±15°, is extracted and the dynamic bending curvature effect of the micromirror is predicted.