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.     

Synthese,Kristallstruktur und festkörper‐NMR‐spektroskopische Untersuchung neuer Oxonitridosilicate der Mischkristallreihe Ba4−xCaxSi6N10O

The new oxonitridosilicates Ba_4?xCa_xSi₆N₁₀O have been synthesized by means of high‐temperature synthesis in a radio‐frequency furnace, starting from calcium, barium, silicon diimide and amorphous silicon dioxide. The maximum reaction temperature was at about 1450 °C. The solid solution series Ba_4?xCa_xSi₆N₁₀O with a phase width 1.81 ≤ x ≤ 2.95 was obtained. The crystal structure of Ba_1.8Ca_2.2Si₆N₁₀O was determined by X‐ray single‐crystal structure determination (P2₁3, no. 198), a = 1040.2(1) pm, Z = 4, wR2 = 0.082). It can be described as a highly condensed network of corner‐sharing SiN₄ and SiON₃ tetrahedra, the voids of which are occupied by the alkaline earth ions. The structure is isotypic with that of BaEu(Ba_0.5Eu_0.5)YbSi₆N₁₁. In the ²⁹Si solid‐state MAS‐NMR spectrum two isotropic resonances at ?50.0 and ?53.6 ppm were observed.     

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.     

Structure and cooperativity of the hydrogen bonds in sodium dihydrogen triacetate

Geometry and energetics of low energy conformers of sodium dihydrogen triacetate (SDHTA) and its anion are studied using density functional theory (DFT) at the Becke, Lee‐Yang‐Parr hybrid functional (BLYP) and Becke, three‐parameter, Lee‐Yang‐Parr hybrid functional (B3LYP) levels. For both cases, two structures of comparable energy are found, which have different symmetry with respect to the two hydrogen bonds (HBs). DFT‐based Born–Oppenheimer molecular dynamics simulations are performed for SDHTA, which show that both structures are visited at room temperature conditions. The trajectory analysis further reveals that the two HBs behave anticooperative, that is, on average elongation of one HB is accompanied by a compression of the other one. This is in accord with nuclear magnetic resonance (NMR) experimental studies for a similar counter ion–dihydrogen triacetate complex. © 2012 Wiley Periodicals, Inc.     

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.     

Montecrinanes A–C: Triterpenes with an Unprecedented Rearranged Tetracyclic Skeleton from Celastrus vulcanicola. Insights into Triterpenoid Biosynthesis Based on DFT Calculations

Three new triterpenoids with an unprecedented 6/6/6/6‐fused tetracyclic carbon skeleton, montecrinanes A–C ( 1 – 3 ), were isolated from the root bark of Celastrus vulcanicola, along with known D:B‐friedobaccharanes ( 4 – 6 ), and lupane‐type triterpenes ( 7 – 12 ). The stereostructures of the new metabolites were elucidated based on spectroscopic (1D and 2D NMR) and spectrometric (HR‐EIMS and HR‐ESIMS) techniques. Their absolute configurations were determined by both NMR spectroscopy, with (R)‐(?)‐α‐methoxyphenylacetic acid as a chiral derivatizing agent, and biogenetic considerations. Biogenetic pathways for montecrinane and D:B‐friedobaccharane skeletons were proposed and studied by DFT methods. The theoretical results support the energetic feasibility of the putative biogenetic pathways, in which the 1,2‐methyl shift from the secondary baccharenyl cation represents a novel and key reaction step for a new montecrinane skeleton.     

Autonomously Propelled Motors for Value‐Added Product Synthesis and Purification

A proof‐of‐concept design for autonomous, self‐propelling motors towards value‐added product synthesis and separation is presented. The hybrid motor design consists of two distinct functional blocks. The first, a sodium borohydride (NaBH₄) granule, serves both as a reaction prerequisite for the reduction of vanillin and also as a localized solid‐state fuel in the reaction mixture. The second capping functional block consisting of a graphene–polymer composite serves as a hydrophobic matrix to attract the reaction product vanillyl alcohol (VA), resulting in facile separation of this edible value‐added product. These autonomously propelled motors were fabricated at a length scale down to 400 μm, and once introduced in the reaction environment showed rapid bubble‐propulsion followed by high‐purity separation of the reaction product (VA) by the virtue of the graphene–polymer cap acting as a mesoporous sponge. The concept has excellent potential towards the synthesis/isolation of industrially important compounds, affinity‐based product separation, pollutant remediation (such as heavy metal chelation/adsorption), as well as localized fuel‐gradients as an alternative to external fuel dependency.