Binding sites of the viral RNA element TAR and of TAR mutants for various peptide ligands, probed with LILBID: A new laser mass spectrometry

A new laser-based mass spectrometry method, called laser induced liquid bead ion desorption (LILBID), was applied to investigate RNA:ligand interactions. As model system the HIV Tat:TAR transactivation complex and its binding behavior were analyzed. TARwt of HIV Type 1 and Type 2 and different artificial mutants were compared regarding their binding to Tat and different peptide ligands. Specific and nonspecific association to TAR was deduced, with the bulge being the well known specific binding site of TAR. In the case of triple arginine (RRR) as a nonspecific ligand, multiple electrostatic binding to TAR was found at higher concentration of RRR. This contrasted with the formation of only ternary complexes in competitive binding studies with TAR, Tat, and potential inhibitors. The fact that the stoichiometries of the complexes can be determined is a major advantage of MS methods over the widely applied fluorimetric methods. A quantitative evaluation of the spectra by a numeric model for ternary complex formation allows conclusions about the role and strength of the binding sites of the RNAs, the specificity and affinity of different ligands, the determination of apparent IC50 and KD values, and a comparison of the binding efficiencies of potential inhibitors.     

Solubilisation of different medium chain esters in zwitterionic surfactant solutions--effects on phase behaviour and structure

We studied the effect of solubilisation of methyl esters with different chains of medium length into the binary surfactant system tetradecyldimethylamine oxide/water at constant surfactant concentration of 200 mM. As esters we employed valeric, capronic, enanthic, and pelargonic methyl ester, thereby decreasing the polarity. Always a phase sequence L(1)-L(α)-L(1) is observed with increasing ester concentration, where the L(α)-phase increases in extent and goes to much lower temperatures with increasing chain length of the ester. Viscosity measurements show a maximum at intermediate concentrations of additive that is independent of the type of ester. From SANS measurements detailed information about the structural changes occurring during the rod-to-sphere transition in the system of the shortest additive is deduced, which proceeds first through a pronounced rod growth. Interestingly, for the different esters an almost constant value of the volumic solubilisation capacity is observed, in agreement with the relatively constant interfacial tension. For the different esters no effect on the radius and the area requirement at the amphiphilic interface is observed at the solubilisation boundary. The microemulsions present here are spherical aggregates where the ester is partitioned between core and shell. From the SANS and interfacial tension data the effective bending constants of the surfactant monolayers were deduced and they show that the extension of the L(α)-phase is directly related to a corresponding increase in the bending constants of the surfactant/ester monolayers.     

Magnetic circular dichroism studies 23. 1. Magnetic circular dichroism spectra of indole alkaloids

The magnetic circular dichroism spectra of a number of indole alkaloids show two B-terms of opposite sign in the 250–330 nm wavelength region associated with the ¹L_b and ¹L_a electronic transitions, the long wavelength, ¹L^b, band being of positive sign, whereas both bands strongly overlap in absorption. Various substituents in different positions of the indole ring cause a red shift of both bands and a broadening of the long wavelength B-term. The sign pattern, howver, remains unchanged in all examples thus far investigated. Dihydroindole and oxindole, on the other hand, exhibit MCD. bands with the opposite sign sequence as compared to the indole chromophore. This observation allows identification of the indole chromophore in alkaloids from the sign pattern of the MCD. bands.     

Focused ion beam sectioning and lift-out method for copper and resist vias in organic low-k dielectrics.

The focused ion beam lift-out technique for scanning electron microscope (SEM) and transmission electron microscope (TEM) sample preparation was shown to be applicable to copper/low-k dielectric semiconductor technology. High resolution SEM, TEM, and scanning transmission electron microscope analyses were performed on metal contacts and resist vias with no evidence of the interface damage or metal smearing commonly observed with mechanical polishing. Ion milling of the sample ex situ to the substrate provided decoration and adjustment of the exposed plane of the section when necessary for SEM analysis.     

Stereochemical effects in supramolecular self-assembly at surfaces: 1-D versus 2-D enantiomorphic ordering for PVBA and PEBA on Ag(111)

We present investigations on noncovalent bonding and supramolecular self-assembly of two related molecular building blocks at a noble metal surface: 4-[trans-2-(pyrid-4-yl-vinyl)]benzoic acid (PVBA) and 4-[(pyrid-4-yl-ethynyl)]benzoic acid (PEBA). These rigid, rodlike molecules comprising the same complementary moieties for hydrogen bond formation are comparable in shape and size. For PVBA, the ethenylene moiety accounts for two-dimensional (2-D) chirality upon confinement to a surface; PEBA is linear and thus 2-D achiral. Molecular films were deposited on a Ag(111) surface by organic molecular beam epitaxy and characterized by scanning tunneling microscopy. At low temperatures (around 150 K), both species form irregular networks of flat lying molecules linked via their endgroups in a diffusion-limited aggregation process. In the absence of kinetic limitations (adsorption or annealing at room temperature), hydrogen-bonded supramolecular assemblies form which are markedly different. With PVBA, enantiomorphic twin chains in two mirror-symmetric species running along a high-symmetry direction of the substrate lattice form by diastereoselective self-assembly of one enantiomer. The chirality signature is strictly correlated between neighboring twin chains. Enantiopure one-dimensional (1-D) supramolecular nanogratings with tunable periodicity evolve at intermediate coverages, reflecting chiral resolution in micrometer domains. In contrast, PEBA assembles in 2-D hydrogen-bonded islands, which are enantiomorphic because of the orientation of the supramolecular arrangements along low-symmetry directions of the substrate. Thus, for PVBA, chiral molecules form 1-D enantiomorphic supramolecular structures because of mesoscopic resolution of a 2-D chiral species, whereas with PEBA, the packing of an achiral species causes 2-D enantiomorphic arrangements. Model simulations of supramolecular ordering provide a deeper understanding of the stability of these systems.     

Mesoscopic chiral reshaping of the Ag(110) surface induced by the organic molecule PVBA

We report scanning tunneling microscopy observations on the restructuring of a Ag(110) surface induced by the molecule 4-[trans-2-(pyrid-4-yl-vinyl)]benzoic acid (PVBA). Our data reveal that the surface undergoes a mesoscopic step faceting following exposure to submonolayer coverages and thermal activation. A sawtooth arrangement evolves implying long-range mass transport of substrate atoms and forming a regular arrangement of kink sites. Its formation is associated with the molecules' functional headgroups forming carboxylates with [100] Ag microfacets at step edges, and eventually operating to reshape the surface morphology. Interestingly, the resulting microfacets act as chiral templates for the growth of supramolecular PVBA structures. Theoretical modeling based on ab initio results indicates that chiral recognition processes discriminating between the two enantiomers of adsorbed PVBA molecules occur in this process.     

Deuterium-labelled N-acyl-L-homoserine lactones (AHLs)--inter-kingdom signalling molecules--synthesis, structural studies, and interactions with model lipid membranes

N-Acyl-l-homoserine lactones (AHLs) are synthesized by Gram-negative bacteria. These quorum-sensing molecules play an important role in the context of bacterial infection and biofilm formation. They also allow communication between microorganisms and eukaryotic cells (inter-kingdom signalling). However, very little is known about the entire mechanism of those interactions. Precise structural studies are required to analyse the different AHL isomers as only one form is biologically most active. Theoretical studies combined with experimental infrared and Raman spectroscopic data are therefore undertaken to characterise the obtained compounds. To mimic interactions between AHL and cell membranes, we studied the insertion of AHL in supported lipid bilayers, using vibrational sum-frequency-generation spectroscopy. Deuterium-labelled AHLs were thus synthesized. Starting from readily available deuterated fatty acids, a two-step procedure towards deuterated N-acyl-l-homoserine lactones with varying chain lengths is described. This included the acylation of Meldrum’s acid followed by amidation. Additionally, the detailed analytical evaluation of the products is presented herein.     

Introduction of Primary Amino Groups on Poly(ethylene terephthalate) Surfaces by Ammonia and a Mix of Nitrogen and Hydrogen Plasma

With the aim of introducing primary amino groups on the surface of poly(ethylene terephthalate) (PET), two methods were compared—the use of ammonia or a combination of nitrogen and hydrogen low-pressure microwave plasma. Several plasma parameters were optimized on the reactor to increase the –NH₂ surface density, which was estimated by colorimetric titration and X-ray photoelectron spectroscopy (XPS). These techniques show that whatever the plasma treatment, almost 2 –NH₂/nm2 are incorporated on PET films. Emission spectroscopy highlighted a correlation between the density of primary amino groups and the ratio between an NH peak intensity and an Ar peak intensity (I_NH/I_Ar). Variation in surface hydrophilicity with aging in air after plasma treatment was monitored with contact angle measurements and showed a hydrophobic recovery. This was confirmed by XPS, which suggests also that surfaces treated by NH₃ plasma are more stable than surfaces treated by N₂/H₂.     

The probable conformation of substrates recognized by dipeptidyl-peptidase IV and some aspects of the catalytic mechanism derived from theoretical investigations

Summary By theoretical conformational investigations of substrates and nonsubstrates of the enzyme dipeptidyl-peptidase IV (DP IV) as well as dipeptide-esters using the ECEPP83 method we determined the structure of peptides recognized and cleaved by the enzyme. From a comparison of all possible structures for the substrates with conformations not possible in nonsubstrates we concluded that a single conformation explains substrate specificities of DP IV. This conformation is characterized by the following dihedral angles: {ie159-1}, {ie159-2}, {ie159-3}, {ie159-4}, and {ie159-5}. The conclusions were supported by comparisons of molecular electrostatic potentials calculated with the molecular graphics program HAMOG.     

Measuring site-specific cluster-surface bond formation

Recent advances in dynamic force microscopy show that it is possible to measure the forces between atomically sharp tips and particular atomic positions on surfaces as a function of distance. However, on most ionic surfaces, the positive and negative ions can so far not be distinguished. In this paper, we use the CaF2(111) surface, where atomic resolution force microscopy has allowed identification of the positions of the Ca2+ and F- ions in the obtained images, to demonstrate that short-range interaction forces can be measured selectively above chemically identified surface sites. Combining experimental and theoretical results allows a quantification of the strength and distance dependence of the interaction of a tip-terminating cluster with particular surface ions and reveals details of cluster and surface relaxation. Further development of this approach will provide new insight into mechanisms of chemical bond formation between clusters, cluster deposition at surfaces, processes in adhesion and tribology, and single atom manipulation with the force microscope.