Experimental Validation of a Fundamental Model for PCR Efficiency

Recently a theoretical analysis of PCR efficiency has been published by Booth et al. (2010). The PCR yield is the product of three efficiencies: (i) the annealing efficiency is the fraction of templates that form binary complexes with primers during annealing, (ii) the polymerase binding efficiency is the fraction of binary complexes that bind to polymerase to form ternary complexes and (iii) the elongation efficiency is the fraction of ternary complexes that extend fully. Yield is controlled by the smallest of the three efficiencies and control could shift from one type of efficiency to another over the course of a PCR experiment. Experiments have been designed that are specifically controlled by each one of the efficiencies and the results are consistent with the mathematical model. The experimental data has also been used to quantify six key parameters of the theoretical model. An important application of the fully characterized model is to calculate initial template concentration from real-time PCR data. Given the PCR protocol, the midpoint cycle number (where the template concentration is half that of the final concentration) can be theoretically determined and graphed for a variety of initial DNA concentrations. Real-time results can be used to calculate the midpoint cycle number and consequently the initial DNA concentration, using this graph. The application becomes particularly simple if a conservative PCR protocol is followed where only the annealing efficiency is controlling.     

Biocatalytic Synthesis of Nitriles through Dehydration of Aldoximes: The Substrate Scope of Aldoxime Dehydratases

Nitriles, which are mostly needed and produced by the chemical industry, play a major role in various industry segments, ranging from high‐volume, low‐price sectors, such as polymers, to low‐volume, high‐price sectors, such as chiral pharma drugs. A common industrial technology for nitrile production is ammoxidation as a gas‐phase reaction at high temperature. Further popular approaches are substitution or addition reactions with hydrogen cyanide or derivatives thereof. A major drawback, however, is the very high toxicity of cyanide. Recently, as a synthetic alternative, a novel enzymatic approach towards nitriles has been developed with aldoxime dehydratases, which are capable of converting an aldoxime in one step through dehydration into nitriles. Because the aldoxime substrates are easily accessible, this route is of high interest for synthetic purposes. However, whenever a novel method is developed for organic synthesis, it raises the question of substrate scope as one of the key criteria for application as a “synthetic platform technology”. Thus, the scope of this review is to give an overview of the current state of the substrate scope of this enzymatic method for synthesizing nitriles with aldoxime dehydratases. As a recently emerging enzyme class, a range of substrates has already been studied so far, comprising nonchiral and chiral aldoximes. This enzyme class of aldoxime dehydratases shows a broad substrate tolerance and accepts aliphatic and aromatic aldoximes, as well as arylaliphatic aldoximes. Furthermore, aldoximes with a stereogenic center are also recognized and high enantioselectivities are found for 2‐arylpropylaldoximes, in particular. It is further noteworthy that the enantiopreference depends on the E and Z isomers. Thus, opposite enantiomers are accessible from the same racemic aldehyde and the same enzyme.     

Supramolecular Capsules Derived from Resorcin[4]arenes by H-Bonding and Metal Coordination: Synthesis,Characterization, and Single-Molecule Force Spectroscopy

Self-assembly by H-bonding and by metal-coordination of functionalized calix[4]arenes and cavitands to large supramolecular capsules is described. In addition, a new method of analyzing supramolecular recognition processes at the single molecule level is discussed. By measuring interaction forces in a hydrogen-bonded assembly using single-molecule force spectroscopy (SMFS), the dynamics of the self-assembly process can be evaluated. In the future, consequent application of this new technique will influence supramolecular design principles and the use of non-covalent interactions as construction elements in the field of nanotechnology.     

Chemoenzymatic Total Synthesis of Sorbicatechol Structural Analogues and Evaluation of Their Antiviral Potential

Sorbicillinoids are fungal polyketides characterized by highly complex and diverse molecular structures, with considerable stereochemical intricacy combined with a high degree of oxygenation. Many sorbicillinoids possess promising biological activities. An interesting member of this natural product family is sorbicatechol A, which is reported to have antiviral activity, particularly against influenza A virus (H1N1). Through a straightforward, one-pot chemoenzymatic approach with recently developed oxidoreductase SorbC, the characteristic bicyclo[2.2.2]octane core of sorbicatechol is structurally diversified by variation of its natural 2-methoxyphenol substituent. This facilitates the preparation of a focused library of structural analogues bearing substituted aromatic systems, alkanes, heterocycles, and ethers. Fast access to this structural diversity provides an opportunity to explore the antiviral potential of the sorbicatechol family.     

Two‐Step Protein Labeling by Using Lipoic Acid Ligase with Norbornene Substrates and Subsequent Inverse‐Electron Demand Diels–Alder Reaction

Inverse‐electron‐demand Diels–Alder cycloaddition (DA_inv) between strained alkenes and tetrazines is a highly bio‐orthogonal reaction that has been applied in the specific labeling of biomolecules. In this work we present a two‐step labeling protocol for the site‐specific labeling of proteins based on attachment of a highly stable norbornene derivative to a specific peptide sequence by using a mutant of the enzyme lipoic acid ligase A (LplA^W37V), followed by the covalent attachment of tetrazine‐modified fluorophores to the norbornene moiety through the bio‐orthogonal DA_inv . We investigated 15 different norbornene derivatives for their selective enzymatic attachment to a 13‐residue lipoic acid acceptor peptide (LAP) by using a standardized HPLC protocol. Finally, we used this two‐step labeling strategy to label proteins in cell lysates in a site‐specific manner and performed cell‐surface labeling on living cells.     

Processing behavior and mechanical properties of autopolymerizing hypoallergenic denture base polymers

Driven by the phenomenon of increasing irritations and allergic reactions of dental prosthesis carriers preferably due to residual methyl methacrylate monomer in conventional dental materials, autopolymerizing hypoallergenic denture base polymers were prepared as two‐component materials in the shape of paste/paste‐ or powder/liquid systems. The processing behavior of these materials was investigated regarding the processing and solidification times also in dependence on the polymerization catalyst concentration, whereas the whole processing and curing characteristics and the final polymer properties were evaluated by dynamic mechanical analysis in shear mode in the temperature range from ?145°C to 200°C. The mechanical properties of the hypoallergenic denture base polymers were validated regarding stiffness (flexural modulus E') and fracture toughness (maximum factor of loading intensity , total work of fracture ) and the effects of monomer composition, kind of resin powder, impact modification by the liquid component, and water immersion on these properties were investigated. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015 , 132, 41378.     

Carrot cropping on organic soil is a hotspot for nitrous oxide emissions

The emissions of the greenhouse gas nitrous oxide (N₂O) were measured from a non nitrogen fertilized carrot (Daucus carota ssp. sativa) field on an organic soil in Sweden during one cropping and post-harvest season. The cumulative emission during the measuring period of 149?days was 41 (±2.8) kg N₂O ha^?1. Dividing the measuring period into a cropping and a post-harvest period revealed that the presence of carrots strongly stimulated N₂O emissions, as the emission during the cropping period was one order of magnitude higher compared to the post-harvest period. The N₂O emission from the carrot field were higher than fluxes reported from cereal crop and grass production, but in the same order as reported fluxes from vegetable cropping on organic soils. In conclusion, our results indicate that the cultivation of root vegetable, such as carrots, on organic soil can be a high point source for N₂O emissions.     

Cyclohexa‐3,5‐diene‐1,2‐trans‐diols – Synthesis and Application in Target‐Oriented Syntheses

An exhaustive overview of the field of cyclohexa‐3,5‐diene‐1,2‐trans‐diols is given. Early and recent methods for the formation of the compounds are reviewed and the various syntheses in which the title compounds have been applied are presented. Special emphasis is given to naturally occurring epoxides, which have been the dominant target molecules since the 1970s. Finally, recent advances in biotechnology are highlighted; with the increased availability of the enantiomerically pure cyclohexa‐3,5‐diene‐1,2‐trans‐diols, new synthetic endeavours were initiated.     

Contribution of the Internal and External Oxygen to the Oxidation of Microencapsulated Fish Oil

Microencapsulation aims to protect polyunsaturated fatty acids against oxidation by embedding oil droplets in a solid matrix. In such a system the internal (dissolved and entrapped) and external (in the environment) oxygen can be differentiated. The study aims to quantify the impact of both oxygen sources on the oxidation of microencapsulated fish oil. The impact of the solubilized oxygen in bulk fish oil is investigated by saturating the oil with nitrogen, synthetic air, and pure oxygen. Even though more dissolved oxygen results in more oxidation products, the difference between the oxidation of the nitrogen and air saturated oil is significant but low. For encapsulated fish oil powders, the internal oxygen is modified by preparing oil‐in‐water emulsions under atmospheric and inert conditions. The feed is atomized and spray dried with either nitrogen or air. Powders are stored under vacuum and in vials and the hydroperoxides and anisidine value are determined in the total‐ and encapsulated oil. The internal oxygen has a minor impact, whereas the external oxygen is the main determinant for autoxidation. Apart from oxidizing the non‐encapsulated oil, the external O₂ penetrates into the particle and reacts with the encapsulated oil. Practical Applications: Comparing the contribution of the internal and external oxygen to the oxidative stability shows that the internal O₂ plays a minor role and can be neglected. This means that the emulsion preparation as well as the spray drying process can be conducted under ambient conditions. An inert production is not extending the shelf life significantly as long as the external O₂ determines oxidation. The focus should be on optimizing the diffusion barrier properties of the wall matrix to reduce the penetration of the external oxygen into the particle system. Alternatively, packaging solution reducing the external O₂ will extend the shelf life of the microencapsulated oil.     

DNA block copolymers: functional materials for nanoscience and biomedicine

We live in a world full of synthetic materials, and the development of new technologies builds on the design and synthesis of new chemical structures, such as polymers. Synthetic macromolecules have changed the world and currently play a major role in all aspects of daily life. Due to their tailorable properties, these materials have fueled the invention of new techniques and goods, from the yogurt cup to the car seat belts. To fulfill the requirements of modern life, polymers and their composites have become increasingly complex. One strategy for altering polymer properties is to combine different polymer segments within one polymer, known as block copolymers. The microphase separation of the individual polymer components and the resulting formation of well defined nanosized domains provide a broad range of new materials with various properties. Block copolymers facilitated the development of innovative concepts in the fields of drug delivery, nanomedicine, organic electronics, and nanoscience. Block copolymers consist exclusively of organic polymers, but researchers are increasingly interested in materials that combine synthetic materials and biomacromolecules. Although many researchers have explored the combination of proteins with organic polymers, far fewer investigations have explored nucleic acid/polymer hybrids, known as DNA block copolymers (DBCs). DNA as a polymer block provides several advantages over other biopolymers. The availability of automated synthesis offers DNA segments with nucleotide precision, which facilitates the fabrication of hybrid materials with monodisperse biopolymer blocks. The directed functionalization of modified single-stranded DNA by Watson-Crick base-pairing is another key feature of DNA block copolymers. Furthermore, the appropriate selection of DNA sequence and organic polymer gives control over the material properties and their self-assembly into supramolecular structures. The introduction of a hydrophobic polymer into DBCs in aqueous solution leads to amphiphilic micellar structures with a hydrophobic polymer core and a DNA corona. In this Account, we discuss selected examples of recent developments in the synthesis, structure manipulation and applications of DBCs. We present achievements in synthesis of DBCs and their amplification based on molecular biology techniques. We also focus on concepts involving supramolecular assemblies and the change of morphological properties by mild stimuli. Finally, we discuss future applications of DBCs. DBC micelles have served as drug-delivery vehicles, as scaffolds for chemical reactions, and as templates for the self-assembly of virus capsids. In nanoelectronics, DNA polymer hybrids can facilitate size selection and directed deposition of single-walled carbon nanotubes in field effect transistor (FET) devices.