Radiation damage to alkyl chain monolayers on semiconductor substrates investigated by electron spectroscopy

Monolayers of alkyl chains, attached through direct Si-C bonds to Si(111), via phosphonates to GaAs(100) surfaces, or deposited as alkyl-silane monolayers on SiO2, are investigated by ultraviolet and inverse photoemission spectroscopy and X-ray absorption spectroscopy. Exposure to ultraviolet radiation from a He discharge lamp, or to a beam of energetic electrons, leads to significant damage, presumably associated with radiation- or electron-induced H-abstraction leading to carbon-carbon double-bond formation in the alkyl monolayer. The damage results in an overall distortion of the valence spectrum, in the appearance of (occupied) states above the highest occupied molecular orbital of the alkyl molecule, and in a characteristic (unoccupied state) pi resonance at the edge of the carbon absorption peak. These distortions present a serious challenge for the interpretation of the electronic structure of the monolayer system. We show that extrapolation to zero damage at short exposure times eliminates extrinsic features and allows a meaningful extraction of the density of state of the pristine monolayer from spectroscopy measurements.     

Lipid domain specific recruitment of lipophilic nucleic acids: a key for switchable functionalization of membranes

Lipid domains in mammalian plasma membranes serve as platforms for specific recruitment or separation of proteins involved in various functions. Here, we have applied this natural strategy of lateral separation to functionalize lipid membranes at micrometer scale in a switchable and reversible manner. Membrane-anchored peptide nucleic acid and DNA, differing in their lipophilic moieties, partition into different lipid domains in model and biological membranes. Separation was visualized by hybridization with the respective complementary fluorescently labeled DNA strands. Upon heating, domains vanished, and both lipophilic nucleic acid structures intermixed with each other. Reformation of the lipid domains by cooling led again to separation of membrane-anchored nucleic acids. By linking appropriate structures/functions to complementary strands, this approach offers a reversible tool for triggering interactions among the structures and for the arrangement of reactions and signaling cascades on biomimetic surfaces.     

Bisoxazolines with one and two sidearms: stereodirecting ligands for copper-catalysed asymmetric allylic oxidations of alkenes

A series of sidearm functionalized bisoxazoline ligands has been synthesized by reaction of the monolithiated methyl{bis(oxazolinyl)}methane with the appropriate electrophiles, and tested in the copper catalyzed asymmetric allylic oxidation of cyclohexene ("Kharasch-Sosnovski" reaction). The observed enantioselectivities were higher (up to 85% ee) than for the unfunctionalized bisoxazoline ("BOX") derivatives (ca. 60% ee). Regardless of the functional groups incorporated into the sidearm unit, the ee's obtained for the different derivatives were essentially indistinguishable. This implies that the sidearms do not interfere directly in this reaction and only play an indirect role by virtue of their steric demand. Three of the copper complexes have been characterized by X-ray diffraction, establishing a distorted octahedral coordination geometry around the copper atom in all three cases. In the elongated distorted CuN(2)O(4) octahedra, the two nitrogen atoms of the oxazolines and one oxygen atom of each acetate ligand occupy the 'equatorial' positions whereas the sidearms do not interact with the metal centres.     

Applications of 2,5-bis(trimethylstannyl)thiophene. Synthesis of 3-methoxy-17α,-(5-iodothien-2-yl)-estra-1,3,5(10)trien-17β-ol

Monotransmetallation of 2,5-bis(trimethylstannyl)thiophene followed by the addition of estrone 3-methyl ether and iodine yields 3-methoxy-17α,-(5-iodothien-2-yl)estra-1,3,5(10)trien-17β-ol.     

A clear,amine-containing poly(vinyl chloride) membrane for in situ optical detection of 2,4,6-trinitrotoluene

A membrane has been developed for the direct determination of 2,4,6-trinitrotoluene (TNT) in natural waters at levels as low as 10 ng ml^?1. A typical membrane is prepared by dissolving the following in tetrahydrofuran: 0.5 g of poly(vinyl chloride) (PVC), 0.2 ml of dioctyl phthalate to serve as a plasticizer and 0.12 ml of Jeffamine T403, a polyoxyethyleneamine which reacts with TNT to produce a colored product. The membrane is formed by casting the solution into a glass Petri dish with a diameter of 8 cm and allowing the solvent to evaporate slowly. Trace amounts of 1,3,5-trinitrobenzene (TNB), 2,4,5-trinitrotoluene (2,4,5-TNT) and N-picryl-N-methylnitramine (tetryl) also react with the membrane to produce a reddish brown color, but their visible absorption spectra differ from that of TNT. The membranes remain clear indefinitely in water. After storage for 80 days in air in a sealed container, over 80% of the amine remains in the membranes. After exposure to water for 10 days, over 40% of the amine remains in the membranes, which continue to respond to TNT. The membrane can be used to determine TNT in untreated water samples of pH 6–9. Recoveries of 0.1–4.0 mg l^?1 of TNT from spiked groundwater ranged from 95 to 105%. Results by direct analysis of turbid water samples agreed with those obtained by high-performance liquid chromatography.     

Single-nucleotide-specific PNA-peptide ligation on synthetic and PCR DNA templates

DNA-directed chemical synthesis has matured into a useful tool with applications such as fabrication of defined (nano)molecular architectures, evolution of amplifiable small-molecule libraries, and nucleic acid detection. Most commonly, chemical methods were used to join oligonucleotides under the control of a DNA or RNA template. The full potential of chemical ligation reactions can be uncovered when nonnatural oligonucleotide analogues that can provide new opportunities such as increased stability, DNA affinity, hybridization selectivity, and/or ease and accuracy of detection are employed. It is shown that peptide nucleic acid (PNA) conjugates, nonionic biostable DNA analogues, allowed the fashioning of highly chemoselective and sequence-selective peptide ligation methods. In particular, PNA-mediated native chemical ligations proceed with sequence selectivities and ligation rates that reach those of ligase-catalyzed oligodeoxynucleotide reactions. Usually, sequence-specific ligations can only be achieved by employing short-length probes, which show DNA affinities that are too low to allow stable binding to target segments in large, double-stranded DNA. It is demonstrated that the PNA-based ligation chemistry allowed the development of a homogeneous system in which rapid single-base mutation analyses can be performed even on double-stranded PCR DNA templates.     

Convergent strategies for the attachment of fluorescing reporter groups to peptide nucleic acids in solution and on solid phase

The site-selective conjugation of peptide nucleic acids (PNA) with fluorescent reporter groups is essential for the construction of hybridisation probes that can report the presence of a particular DNA sequence. This paper describes convergent methods for the solution- and solid-phase synthesis of multiply labelled PNA oligomers. The solid-phase synthesis of protected PNA enabled the selective attachment of fluorescent labels at the C-terminal end (3' in DNA) which demonstrated that further manipulations on protected PNA fragments are feasible. For the conjugation to internal sites, a method is introduced that allows for the on-resin assembly of modified monomers thereby omitting the need to synthesise an entire monomer in solution. Furthermore, it is shown that the application of a highly orthogonal protecting group strategy in combination with chemoselective conjugation reactions provides access to a rapid and automatable solid-phase synthesis of dual labelled PNA probes. Real-time measurements of nucleic acid hybridisation were possible by taking advantage of the fluorescence resonance energy transfer (FRET) between suitably appended fluorophoric groups. Analogously to DNA-based molecular beacons, the dual labelled PNA probes were only weakly fluorescing in the single-stranded state. Hybridisation to a complementary oligonucleotide, however, induced a structural reorganisation and conferred a vivid fluorescence enhancement.     

Analytical studies using iodine-luminol chemiluminescence

Trace amounts of substances have been related to iodine consumption monitored by chemiluminescence from the iodine-luminol system. Iodine titrations of sulphite and arsenic(III) have been carried out at levels of 1.0 x 10(-7) and 5.0 x 10(-8)M with a precision and error of better than 1% on a day-to-day basis. A calibrated standard of 1.8 ppm SO(2) in air was analysed with a precision of +/-1.2%, and an error of 0.9%. A rate method has been developed based on the reaction between iodine and penicillin G; a linear range from 10(-8) to 10(-7)M was found, the precision being +/-9%.