Synthesis of fluorescently labeled alkylated DNA adduct standards and separation by capillary electrophoresis

DNA adducts are regarded as individual internal dosimeters for the exposure to chemical carcinogens. To date, the most sensitive method for DNA adduct analysis is the radioactive 32P-postlabeling method, which allows the detection of one adduct in 10(10) unmodified nucleotides in microg amounts of DNA. However, this technique suffers from disadvantages such as working with radioactive phosphorus and time-consuming chromatographic separation procedures. In addition, the simultaneous detection of adducts from different classes of carcinogens in a DNA sample is difficult. In order to overcome these drawbacks, we are developing a new detection method, comprising fluorescence labeling of DNA adducts, capillary electrophoretic (CE) separation, and on-line detection by monitoring laser-induced fluorescence (LIF). So far, we have evaluated the separation power and the detection limit of CE with fluorescently labeled standard compounds such as unmodified nucleotides or alkylated thymidines. For this purpose, we developed a universal method for labeling 5'-OH-mononucleosid-3'-dicyanoethyl-phosphates with fluorescent dyes based on the phosphoramidite technology for DNA synthesis. The separation of N3-methylated, N3-, O2- and O4-butylated thymidines from the unmodified nucleotide within a few minutes recommends CE-LIF as a powerful method for DNA adduct 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.     

Immunosensor for estrone with an equal limit of detection as common analytical methods

Immunoanalytical methods at a very low limit of detection (LOD) and a low limit of quantification (LOQ) are becoming more and more important for environmental analysis and especially for monitoring drinking water quality. Biosensors have suitable characteristics such as efficiency in allowing very fast, sensitive, and cost-effective detection. Here we describe a fully automated immunoassay for estrone with a LOD below 0.20 ng L^–1 and a LOQ below 1.40 ng L^–1. In contrast to common analytical methods such as GC-MS or HPLC-MS, the biosensor used requires no sample pre-treatment and pre-concentration. The basis of our sensitive assay is the antibody with a high affinity constant towards estrone. The very low amount of antibody per sample results in low validation parameters (LOD, LOQ, and IC50), but this assay for estrone represents the current device-related limitation of the River Analyser (RIANA).     

An improved catalyst for the asymmetric arylation of ketone enolates

A new catalyst system for the enantioselective alpha-arylation of ketones is reported. This catalyst, prepared from Pd(2)(dba)(3) and a bulky dialkylphosphino-binaphthyl ligand, is able to effect the asymmetric arylation of ketone enolates with aryl bromides utilizing NaO(t)()Bu as base. These new catalysts enjoy much higher reactivity than previous systems; arylation reactions could be effected at room temperature with only 2 mol % of the Pd catalyst. The coupling of alpha-alkyl-alpha'-protected cyclopentanones proceeded in high yield, and the resulting quaternary stereogenic center was installed in up to 94% ee.     

Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA:RNA hybrids

Locked nucleic acids (LNAs) containing one or more 2'-O,4'-C-methylene-linked bicyclic ribonucleoside monomers possess a number of the prerequisites of an effective antisense oligonucleotide, e.g. unprecedented helical thermostability when hybridized with cognate RNA and DNA. To acquire a detailed understanding of the structural features of LNA giving rise to its remarkable properties, we have conducted structural studies by use of NMR spectroscopy and now report high-resolution structures of two LNA:RNA hybrids, the LNA strands being d(5'-CTGAT(L)ATGC-3') and d(5'-CT(L)GAT(L)AT(L)GC-3'), respectively, T(L) denoting a modified LNA monomer with a thymine base, along with the unmodified DNA:RNA hybrid. In the structures, the LNA nucleotides are positioned as to partake in base stacking and Watson-Crick base pairing, and with the inclusion of LNA nucleotides, we observe a progressive change in duplex geometry toward an A-like duplex structure. As such, with the inclusion of three LNA nucleotides, the hybrid adopts an almost canonical A-type duplex geometry, and thus it appears that the number of modifications has reached a saturation level with respect to structural changes, and that further incorporations would furnish only minute changes in the duplex structure. We attempt to rationalize the conformational steering induced by the LNA nucleotides by suggesting that the change in electronic density at the brim of the minor groove, introduced by the LNA modification, is causing an alteration of the pseudorotational profile of the 3'-flanking nucleotide, thus shifting this sugar equilibrium toward N-type conformation.     

<!?tlsb=‐0.06pt>Zigzag polymer chains in catena‐poly[[[triaqua(isobutyrato‐κO)magnesium(II)]‐μ‐isobutyrato‐κ2O:O′] monohydrate]

The structure of the title compound, {[Mg(C₄H₇O₂)₂(H₂O)₃]·H₂O}_n, features one‐dimensional ...(μ₂‐ib)Mg(μ₂‐ib)Mg... zigzag chains (ib is isobutyrate) parallel to the c axis. The octahedral Mg environment is completed by three fac‐oriented terminal water ligands, as well as one further monodentate end‐on coordinated ib ligand. In the crystal structure, the hydrophobic ib groups are all oriented within one half of the coordination perimeter of each chain, whereas the water ligands, together with hydrogen‐bonded noncoordinated solvent water molecules, define the other half. Along the a axis, neighbouring strands are oriented so that both the hydrophilic and hydrophobic sides are adjacent to each other. This results in an extensive hydrogen‐bonding network within the hydrophilic areas, also involving an additional solvent water molecule per formula unit. There are van der Waals contacts between the aliphatic isopropyl groups of the hydrophobic areas.     

Free Path Lengths in Quasicrystals

Previous studies of kinetic transport in the Lorentz gas have been limited to cases where the scatterers are distributed at random (e.g., at the points of a spatial Poisson process) or at the vertices of a Euclidean lattice. In the present paper we investigate quasicrystalline scatterer configurations, which are non-periodic, yet strongly correlated. A famous example is the vertex set of a Penrose tiling. Our main result proves the existence of a limit distribution for the free path length, which answers a question of Wennberg. The limit distribution is characterised by a certain random variable on the space of higher dimensional lattices, and is distinctly different from the exponential distribution observed for random scatterer configurations. The key ingredients in the proofs are equidistribution theorems on homogeneous spaces, which follow from Ratner’s measure classification.