Multiplexed protein detection using an affinity aptamer amplification assay

Affinity probe capillary electrophoresis (APCE) is potentially one of the most versatile technologies for protein diagnostics, offering an excellent balance between robustness, analysis speed and sensitivity. Combining the immunosensing and separating strength of capillary electrophoresis with the signal enhancement power of nucleic acid amplification, aptamers can further push the analytical limits of APCE to offer ultrasensitive, multiplexed detection of protein biomarkers, even when differences in electrophoretic mobility between the different aptamer-target complexes are limited. It is demonstrated how, through careful selection of experimental parameters, simultaneous detection of picomolar levels of three target proteins can be achieved even with aptamers that were initially selected under very different conditions and further taking into account that the aptamers need to be modified to allow successful PCR amplification. Aptamer-enhanced APCE offers limits of detection that are orders of magnitude lower than those that can be achieved through traditional capillary electrophoresis-based immunosensing. With recent developments in aptamer selection that for the first time realise the promise of aptamers as easily accessible, high affinity recognition molecules, it can therefore be envisioned that aptamer-enhanced APCE on parallel microfluidic platforms can be the basis for a truly high-throughput multiplexed proteomics platform, rivalling genetic screening for the first time.     

Exploiting Complex Fluorophore Interactions to Monitor Virus Capsid Disassembly

Supramolecular protein complexes are the corner stone of biological processes; they are essential for many biological functions. Unraveling the interactions responsible for the (dis)assembly of these complexes is required to understand nature and to exploit such systems in future applications. Virus capsids are well-defined assemblies of hundreds of proteins and form the outer shell of non-enveloped viruses. Due to their potential as a drug carriers or nano-reactors and the need for virus inactivation strategies, assessing the intactness of virus capsids is of great interest. Current methods to evaluate the (dis)assembly of these protein assemblies are experimentally demanding in terms of instrumentation, expertise and time. Here we investigate a new strategy to monitor the disassembly of fluorescently labeled virus capsids. To monitor surfactant-induced capsid disassembly, we exploit the complex photophysical interplay between multiple fluorophores conjugated to capsid proteins. The disassembly of the capsid changes the photophysical interactions between the fluorophores, and this can be spectrally monitored. The presented data show that this low complexity method can be used to study and monitor the disassembly of supramolecular protein complexes like virus capsids. However, the range of labeling densities that is suitable for this assay is surprisingly narrow.     

Fast polarisation-insensitive optical shutter supported by backflow in dichroic dye-doped dual-frequency liquid crystal

This paper describes a novel implementation of a dual-frequency liquid crystal optical shutter of the guest–host type. The transmissive state of the filter is obtained by applying a low-frequency electric field that brings the dichroic dye in a homeotropic orientation. The light-absorbing state is realised by a twisted planar configuration for which the absorption is quasi-independent of the polarisation. Switching between the two states occurs in about 1 ms and the devices show no scattering for wavelengths inside or outside the absorption band of the dichroic dye. Simulations and experiments reveal how a twisted state is obtained through the backflow phenomenon.     

Factors affecting gas-phase deuterium scrambling in peptide ions and their implications for protein structure determination

In this report, we evaluate the validity of using hydrogen/deuterium exchange in combination with collision-induced dissociation mass spectrometry (CID MS) for the detailed structural and conformational investigation of peptides and proteins. This methodology, in which partly deuterated peptide ions are subjected to collision-induced dissociation in the vacuum of a mass spectrometer, has emerged as a useful tool in structural biology. It may potentially provide quantitatively the extent of deuterium incorporation per individual amino acid in peptides and proteins, thus providing detailed structural information related to protein structure and folding. We report that this general methodology has limitations caused by the fact that the incorporated deuterium atoms migrate prior or during the CID MS analysis. Our data are focused on a variety of transmembrane peptides, incorporated in a lipid bilayer, in which the near-terminal amino acids that anchor at the lipid-water interface are systematically varied. Our findings suggest that, under the experimental conditions we use, the extent of intramolecular hydrogen scrambling is strongly influenced by experimental factors, such as the exact amino acid sequence of the peptide, the nature of the charge carrier, and therefore most likely by the gas-phase structure of the peptide ion. Moreover, the observed scrambling seems to be independent of the nature of the peptide fragment ions (i.e., protonated B and Y' ' ions, and sodiated A and Y' ions). Our results strongly suggest that scrambling may be reduced by using alkali metal cationization instead of protonation in the ionization process.     

Methane Oxidation over Cu2+/[CuOH]+ Pairs and Site-Specific Kinetics in Copper Mordenite Revealed by Operando Electron Paramagnetic Resonance and UV/Visible Spectroscopy

Cu-exchanged mordenite (MOR) is a promising material for partial CH₄ oxidation. The structural diversity of Cu species within MOR makes it difficult to identify the active Cu sites and to determine their redox and kinetic properties. In this study, the Cu speciation in Cu-MOR materials with different Cu loadings has been determined using operando electron paramagnetic resonance (EPR) and operando ultraviolet-visible (UV/Vis) spectroscopy as well as in situ photoluminescence (PL) and Fourier-transform infrared (FTIR) spectroscopy. A novel pathway for CH₄ oxidation involving paired [CuOH]⁺ and bare Cu²⁺ species has been identified. The reduction of bare Cu²⁺ ions facilitated by adjacent [CuOH]⁺ demonstrates that the frequently reported assumption of redox-inert Cu²⁺ centers does not generally apply. The measured site-specific reaction kinetics show that dimeric Cu species exhibit a faster reaction rate and a higher apparent activation energy than monomeric Cu²⁺ active sites highlighting their difference in the CH₄ oxidation potential.     

Bicyclic Guanidine Promoted Mechanistically Divergent Depolymerization and Recycling of a Biobased Polycarbonate

We here report the organocatalytic and temperature-controlled depolymerization of biobased poly(limonene carbonate) providing access to its trans-configured cyclic carbonate as the major product. The base TBD (1,5,7-triazabicyclo[4.4.0]dec-5-ene) offers a unique opportunity to break down polycarbonates via end-group activation or main chain scission pathways as supported by various controls and computational analysis. These energetically competitive processes represent an unprecedented divergent approach to polycarbonate recycling. The trans limonene carbonate can be converted back to its polycarbonate via ring-opening polymerization using the same organocatalyst in the presence of an alcohol initiator, offering thus a potential circular and practical route for polycarbonate recycling.     

Investigations of a highly crowded phosphino-substituted biphenyl: A precursor for a λ3, λ5-diphosphaphenanthrene

The synthesis of 2,2′-bis(bis(dimethylamino)-phosphino)-3,3′5,5′-tetra-tert-butylbiphennyl ( 5 ) is described. It was extensively studied by ¹H, ¹³C, and ³¹P NMR spectroscopy. Furthermore, the X-ray analysis of 5 is reported. Crystals of 5 are tetragonal, space group P¯42₁c, a = b = 24.770 (3) Å, c = 12.658 (4) Å, Z = 8. The surprising reaction of 5 with proton acids leading to the formation of various phosphorus containing five- and six-membered ring compounds is discussed. On reaction of one of the six-membered ring compounds ( 9 ) with magnesium in THF, a λ³, λ⁵-diphosphaphenanthrene ( 19 ) was obtained.     

Furanosyl Oxocarbenium Ion Conformational Energy Landscape Maps as a Tool to Study the Glycosylation Stereoselectivity of 2-Azidofuranoses, 2-Fluorofuranoses and Methyl Furanosyl Uronates

The 3D shape of glycosyl oxocarbenium ions determines their stability and reactivity and the stereochemical course of S_N1 reactions taking place on these reactive intermediates is dictated by the conformation of these species. The nature and configuration of functional groups on the carbohydrate ring affect the stability of glycosyl oxocarbenium ions and control the overall shape of the cations. We herein map the stereoelectronic substituent effects of the C2-azide, C2-fluoride and C4-carboxylic acid ester on the stability and reactivity of the complete suite of diastereoisomeric furanoses by using a combined computational and experimental approach. Surprisingly, all furanosyl donors studied react in a highly stereoselective manner to provide the 1,2-cis products, except for the reactions in the xylose series. The 1,2-cis selectivity for the ribo-, arabino- and lyxo-configured furanosides can be traced back to the lowest-energy ³E or E₃ conformers of the intermediate oxocarbenium ions. The lack of selectivity for the xylosyl donors is related to the occurrence of oxocarbenium ions adopting other conformations.