A versatile toolbox for variable DNA functionalization at high density

To broaden the applicability of chemically modified DNAs in nano- and biotechnology, material science, sensor development, and molecular recognition, strategies are required for introducing a large variety of different modifications into the same nucleic acid sequence at once. Here, we investigate the scope and limits for obtaining functionalized dsDNA by primer extension and PCR, using a broad variety of chemically modified deoxynucleotide triphosphates (dNTPs), DNA polymerases, and templates. All natural nucleobases in each strand were substituted with up to four different base-modified analogues. We studied the sequence dependence of enzymatic amplification to yield high-density functionalized DNA (fDNA) from modified dNTPs, and of fDNA templates, and found that GC-rich sequences are amplified with decreased efficiency as compared to AT-rich ones. There is also a strong dependence on the polymerase used. While family A polymerases generally performed poorly on "demanding" templates containing consecutive stretches of a particular base, family B polymerases were better suited for this purpose, in particular Pwo and Vent (exo-) DNA polymerase. A systematic analysis of fDNAs modified at increasing densities by CD spectroscopy revealed that single modified bases do not alter the overall B-type DNA structure, regardless of their chemical nature. A density of three modified bases induces conformational changes in the double helix, reflected by an inversion of the CD spectra. Our study provides a basis for establishing a generally applicable toolbox of enzymes, templates, and monomers for generating high-density functionalized DNAs for a broad range of applications.     

Biosynthetic Production of [N2,1,3,7,9-15N]Guanosine and [1,3,7,9-15N]inosine and conversion into [N6,1,3,7,9-15N]adenosine for structure elucidation of RNA by heteronuclear NMR

A procedure was developed for the biosynthetic preparation of ¹⁵N-labelled guanosine and inosine through the action of a mutant Bacillus subtilis strain. Crude [N²,1,3,7,9-¹⁵N]guanosine and [1,3,7,9-¹⁵N]inosine were isolated from the culture filtrate by precipitation and anion-exchange chromatography (Scheme 1). No cell lysis and no enzymatic degradation was necessary. The per-isobutyrylated derivatives 1 and 2 were isolated from a complex mixture, purified by virtue of their different lipophilicity, and separated in three steps involving normal-and reversed-phase silica-gel chromatography. One litre of complex nutrient medium yielded 8.44 mmol of guanosine derivative and 2.84 mmol of inosine derivative with high average ¹⁵N enrichment (83.5 and 91.9 atom-%, resp.). [N⁶,1,3,7,9-¹⁵N]Adenosine ( 4 ) was obtained from 2′,3′,5′-tri-O-isobutyryl[1,3,7,9-¹⁵N]inosine ( 1 ) through the ammonolysis of its 1,2,4-triazolyl derivative with aqueous ¹⁵NH₃ (Scheme 2).     

Stable Methods for Evaluating the Points cos(i{pi}/n)

A variety of alternative methods for evaluating cos(i/n) fori= 0, 1,...,n are compared theoretically and experimentally,and the best ones selected on the basis of accuracy and thecomputational efficiency. The error analysis involved demonstrateshow certain mathematically equivalent recurence relations canexhibit very different computational behaviour.     

Macrophage-targeting oligopeptides from Mortierella alpina

The realm of natural products of early diverging fungi such as Mortierella species is largely unexplored. Herein, the nonribosomal peptide synthetase (NRPS) MalA catalysing the biosynthesis of the surface-active biosurfactants, malpinins, has been identified and biochemically characterised. The investigation of the substrate specificity of respective adenylation (A) domains indicated a substrate-tolerant enzyme with an unusual, inactive C-terminal NRPS module. Specificity-based precursor-directed biosynthesis yielded 20 new congeners produced by a single enzyme. Moreover, MalA incorporates artificial, click-functionalised amino acids which allowed postbiosynthetic coupling to a fluorophore. The fluorescent malpinin conjugate penetrates mammalian cell membranes via an phagocytosis-mediated mechanism, suggesting Mortierella oligopeptides as carrier peptides for directed cell targeting. The current study demonstrates substrate-specificity testing as a powerful tool to identify flexible NRPS modules and highlights basal fungi as reservoir for chemically tractable compounds in pharmaceutical applications.

Specificity profiling of a nonribosomal peptide synthetase of an early diverging fungus revealed high substrate flexibility. Feeding studies with click-functionalised amino acids enabled the production of fluorescent peptides targeting macrophages.     

Screen Printable Sol-Gel Materials for High-Throughput Borosilicate Glass Film Production

The use of sol-gel materials can simplify the industrial fabrication of high-efficiency silicon solar cells if a suitable deposition method is established. In this work, we investigate the possibilities to adapt a borosilicate glass sol-gel to provide a stable screen printing process. This material has previously been used as a boron dopant source for silicon solar cells. We now use an adjusted synthesis process, with an increased gelling time and different additives. This changes the rheological properties (i.e., the elastic and viscous moduli G′ and G″) in a way that avoids the dripping of paste through the screen and that stabilizes the material transfer in subsequent printing steps. Using this synthesis process, we were able to show a printing process with long-term stability of more than 500 prints. When comparing the adjusted to the initial paste, we show that, after thermal treatment, the obtained thin films are very similar in terms of their constitution, with a refractive index between n = 1.47 (initial) and n = 1.55 (adjusted). We also show that they provide the same amount of doping under the tested conditions (950 °C, 30 min), resulting in sheet resistances of R_□ = (42.5 ± 2.6) Ω/□ (initial) and R_□ = (46.4 ± 3.6) Ω/□ (adjusted).     

Synthesis and Characterization of Ligand-Linked Pt Nanoparticles: Tunable,Three-Dimensional,Porous Networks for Catalytic Hydrogen Sensing

Porous networks of Pt nanoparticles interlinked by bifunctional organic ligands have shown high potential as catalysts in micro-machined hydrogen gas sensors. By varying the ligand among p-phenylenediamine, benzidine, 4,4‘‘-diamino-p-terphenyl, 1,5-diaminonaphthalene, and trans-1,4-diaminocyclohexane, new variants of such networks were synthesized. Inter-particle distances within the networks, determined via transmission electron microscopy tomography, varied from 0.8 to 1.4 nm in accordance with the nominal length of the respective ligand. While stable structures with intact and coordinatively bonded diamines were formed with all ligands, aromatic diamines showed superior thermal stability. The networks exhibited mesoporous structures depending on ligand and synthesis strategy and performed well as catalysts in hydrogen gas microsensors. They demonstrate the possibility of deliberately tuning micro- and mesoporosity and thereby transport properties and steric demands by choice of the right ligand also for other applications in heterogeneous catalysis.     

Synthesis of Stereochemically Flexible Cyclic Biphenylbisphosphinite Ligands: Control of the Dynamics and Selectivity

Novel l -tartaric acid based stereodynamic biphenylbisphosphinite ligands with anilino linkers were prepared as cyclic diamide compounds. The influence of the constitutional substitution pattern of the amino group at the aniline moiety on the diastereoselective formation of the ligand was investigated. While the meta-anilino bridged ligands showed a highly dynamic behavior and no discrimination between (R_ax) and (S_ax) configuration, l -tartaric acid substitution on ortho-anilino bridged ligands leads to diastereoselective self-alignment of the central biphenol axis, which controls the stereoselectivity of the ligand and catalyst. The experimental findings were corroborated by theoretical calculations. In the rhodium-catalyzed enantioselective hydrogenation of methyl 2-acetamidoacrylate (MAA), an enantiomeric ratio of 75 : 25 (R/S) was obtained for the ortho-substituted ligand.     

A Straightforward Synthesis of Polyketides via Ester Dienolate Matteson Homologation

Application of ester dienolates as nucleophiles in Matteson homologations allows for the stereoselective synthesis of highly substituted α,β-unsaturated δ-hydroxy carboxyl acids, structural motifs widespread found in polyketide natural products. The protocol is rather flexible and permits the introduction of substituents and functionalities also at those positions which are not accessible by the commonly used aldol reaction. Therefore, this ester dienolate Matteson approach is an interesting alternative to the “classical” polyketide syntheses.     

Eisen

Ohne Zusammenfassung     

Electron capture negative ion (ECNI) mass spectrometry of complex mixtures of chlorinated decanes and dodecanes: An approach to ECNI mass spectra of chlorinated paraffins in technical mixtures

The electron capture negative ion (ECNI) mass spectra of two complex mixtures of polychlorinated decanes (PCDe) and polychlorinated dodecanes (PCDo) are presented. The number of isomers in these mixtures is still high but is drastically reduced in comparison to technical products of chlorinated paraffins (CP), due to their fixed chain length. As a result, the mass spectra are simplified and less complex. Different modes of negative ion formation were observed in the spectra of the PCDe and PCDo. [M+Cl]^– adduct ions were the most abundant ions in the spectra of lower chlorinated molecules. Higher chlorinated isomers formed prominently [M-Cl]^– and [M-HCl]^– fragments besides [M+Cl]^–. Possible consequences for the determination of chlorinated paraffins by ECNI-MS that result from the variation in ion formation are addressed. Received: 18 August 1997 / Revised: 26 January 1998 / Accepted: 31 January 1998