Design of specific nucleic acid‐based biosensors for protein binding activity

Nucleic acid-based biosensors for the detection of specific proteins combine the typical programmability of synthetic DNA systems with artificially controlled DNA-protein communication. The high-affinity interaction between a target protein and a specific ligand, such as an aptamer sequence, or a double stranded DNA domain, or a small peptide, is paired with a nature-mimicking molecular mechanism allowing for probing, processing, and translating protein binding activity into a measurable signal. In this Review, two main strategies developed in the context of protein-responsive nucleic acid-based biosensors are discussed. One is the design of proximity-based assays harnessing the spatial colocalization of functional probes within the volume of a multivalent protein. The other is the engineering of dynamic DNA structures that undergo a controlled conformational or structural change upon protein binding. Examples of applications from optical and electrochemical detection of antibodies in biofluids to fluorescence imaging of transcription factors in living cells are reported, and suggestions along with possible future directions in the field are discussed

The role of chain length in cucurbit[8]uril complexation of methyl alkyl viologens

Viologens are among the most studied guests for cucurbit[8]uril (CB[8]) and their complexation is usually driven by bipyridyl core inclusion inside the cavity to maximize both hydrophobic and cation-dipole interactions. The presence of alkyl substituents on the guest alters this complexation mode, switching to aliphatic chain inclusion in U-folded conformation. Here we report a thorough study of the influence of the alkyl chain length on the binding mode of methyl alkyl viologens. The chain length of the studied guests was increased by two methylene groups starting from methyl dodecyl viologen (MVC12) to the octadecyl analogue (MVC18). Complexation in water, investigated by NMR spectroscopy and ITC, revealed a clear switch from 1:1 to 2:1 stoichiometry moving from 12 to 16 carbon atoms, as a consequence of the chain folding of the major portion of the longer alkyl chain in one CB[8] cavity and the inclusion of the full viologen unit by another host molecule. The CB[8]2•MVC18 complex crystal structure evidences the unprecedented 2:1 stoichiometry and quantified in 12 the number of carbon atoms necessary to fill the CB[8] cavity in U-shaped conformation

Cavitand Decorated Silica as a Selective Preconcentrator for BTEX Sensing in Air

The monitoring of benzene and other carcinogenic aromatic volatile compounds at the ppb level requires boosting both the selectivity and sensitivity of the corresponding sensors. A workable solution is the introduction in the devices of preconcentrator units containing molecular receptors. In particular, quinoxaline cavitands (QxCav) resulted in very efficient preconcentrator materials for the BTEX in air to the point that they have been successfully implemented in a com- mercial sensor. In this work, we report a highly efficient quinoxaline-based preconcentrator mate- rial, in which the intrinsic adsorption capacity of the QxCav has been maximized. The new material consists of silica particles covalently coated with a suitable functionalized QxCav derivative (QxCav@SiO2). In this way, all the cavities are exposed to the analyte flux, boosting the performance of the resulting preconcentration cartridge well above that of the pure QxCav. It is noteworthy that the preconcentrator adsorption capacity is independent of the relative humidity of the incoming air

Is Near-Infrared Spectroscopy a Reliable Method to Evaluate Clamping Ischemia during Carotid Surgery?

Guidelines do not include cerebral oximetry among monitoring for carotid endarterectomy (CEA). The purpose of this study was to evaluate the reliability of near-infrared spectroscopy (NIRS) in the detection of clamping ischemia and in the prevention of clamping-related neurologic deficits using, as a cutoff for shunting, a 20% regional cerebral oxygen saturation (rSO2) decrease if persistent more than 4 minutes, otherwise a 25% rSO2 decrease. Bilateral rSO2 was monitored continuously in patients undergoing CEA under general anesthesia (GA). Data was recorded after clamping, declamping, during shunting and lowest values achieved. Preoperative neurologic, CT-scan, and vascular lesions were recorded. We reviewed 473 cases: 305 males (64.5%) mean age 73.3 ± 7.3. Three patients presented transient ischemic deficits at awakening, no perioperative stroke or death; 41 (8.7%) required shunting: 30 based on the initial rSO2 value and 11 due to a decrease during surgery. Using the ROC curve analysis we found, for a >25% reduction from baseline value, a sensitivity of 100% and a specificity of 90.6%. Reliability, PPV, and NPV were 95.38%, 9%, and 100%, respectively. In conclusion, this study indicates the potential reliability of NIRS monitoring during CEA under GA, using a cutoff of 25% or a cutoff of 20% for prolonged hypoperfusion

The Origin of Selectivity in the Complexation of N-Methyl Amino Acids by Tetraphosphonate Cavitands

We report on the eligibility of tetraphosphonate resorcinarene cavitands for the molecular recognition of amino acids. We determined the crystal structure of 13 complexes of the tetraphosphonate cavitand Tiiii[H, CH3, CH3] with amino acids. 1H NMR and 31P NMR experiments and ITC analysis were performed to probe the binding between cavitand Tiiii[C3H7, CH3, C2H5] or the water-soluble counterpart Tiiii[C3H6Py+Cl-, CH3, C2H5] and a selection of representative amino acids. The reported studies and results allowed us (i) to highlight the noncovalent interactions involved in the binding event in each case; (ii) to investigate the ability of tetraphosphonate cavitand receptors to discriminate between the different amino acids; (iii) to calculate the Ka values of the different complexes formed and evaluate the thermodynamic parameters of the complexation process, dissecting the entropic and enthalpic contributions; and (iv) to determine the solvent influence on the complexation selectivity. By moving from methanol to water, the complexation changed from entropy driven to entropy opposed, leading to a drop of almost three orders in the magnitude of the Ka. However, this reduction in binding affinity is associated with a dramatic increase in selectivity, since in aqueous solutions only N-methylated amino acids are effectively recognized. The thermodynamic profile of the binding does not change in PBS solution. The pivotal role played by cation 12\u3c0 interactions is demonstrated by the linear correlation found between the log\u202fKa in methanol solution and the depth of +N\u2013CH3 cavity inclusion in the molecular structures. These findings are relevant for the potential use of phosphonate cavitands as synthetic receptors for the detection of epigenetic modifications of histones in physiological media

Combined Approach of Mechanochemistry and Electron Crystallography for the Discovery of 1D and 2D Coordination Polymers

Mechanochemical synthesis is an attractive preparative method that combines a green approach with versatility, efficiency, and rapidity of reaction. However, it often yields microcrystalline materials, and their small crystal size is a major hindrance to structure elucidation with conventional single-crystal or powder X-ray diffraction methods. This work presents the novel approach of combining mechanochemistry with electron diffraction techniques to elucidate the crystal structure of metal−organic compounds of zinc(II) and copper(II) with 2,6-pyridinedicarboxylic acid and 4,4′-bipyridine

Phenoxy resin-based vinylogous urethane covalent adaptable networks

This work presents a post-polymerization approach to the preparation of vitrimers, exploiting the transamination of vinylogous urethane in linear phenoxy resins. Phenoxy vitrimers are obtained by a two-steps synthesis from a commercial phenoxy resin via partial conversion of hydroxyl groups to acetoacetates (AcAc), followed by network formation by reaction with m-xylylendiamine (XYDIA) as crosslinker. Three different vitrimers with variable crosslinking density are obtained by tuning the density of AcAc moieties along the phenoxy resin scaffold (5%, 10% and 15% conversion of hydroxyl groups). The conversion of linear polymers to dynamic crosslinked networks is confirmed by Dynamic Mechanical Thermal Analyzer (DMTA) and rheology measurements, followed by stress relaxation tests to investigate the kinetics of bond exchanges. Tensile tests as a function of reprocessing cycles reveal an increase of the maximum elongation and stress at break and prove the good recyclability of the vitrimers. Enhanced adhesive properties compared to pristine phenoxy resins are demonstrated, including the possibility to thermally re-join the assembly after its mechanical failure. Finally, the solvent-free preparation of vitrimer is explored for 5% crosslinked vitrimer via melt reactive blending, providing a valuable alternative to the less environmentally sustainable synthesis in solution

Encapsulation of trimethine cyanine in cucurbit[8]uril: solution versus solid-state inclusion behavior

Inclusion of polymethine cyanine dyes in the cavity of macrocyclic receptors is an effective strategy to alter their absorption and emission behavior in aqueous solution. In this paper, the effect of the host-guest interaction between cucurbit[8]uril (CB[8]) and a model trimethine indocyanine (Cy3) on dye spectral properties and aggregation in water is investigated. Solution studies, performed by a combination of spectroscopic and calorimetric techniques, indicate that the addition of CB[8] disrupts Cy3 aggregates leading to the formation of a 1:1 host-guest complex with an association constant of 1.5 × 10 6 M -1 . At concentrations suitable for NMR experiments, the slow formation of a supramolecular polymer was observed, followed by precipitation. Single crystals X-ray structure elucidation confirmed the formation of a polymer with 1:1 stoichiometry in the solid state

Population density, sex ratio and body size in a population of Salamandra atra atra on the Dolomites

Salamandra atra atra is the most widespread subspecies of the Alpine Salamander, both in Italy and in the other parts of the species distribution range. However, in particular for Italian populations, its ecology and demographic parameters are poorly known. We studied biometry (length, mass, body condition index) and demography (population density, sex ratio, proportion of gravid females) of this fully terrestrial salamander in the “Paneveggio-Pale di San Martino” Natural Park in the Dolomites. We used removal methods to estimate abundance on a surface of about 1000 m2. Density estimate of adults was 472 salamanders/ha, which falls within the density estimates that are available for this taxon. Sexes did not differ significantly in size and body mass. Body sizes of adults included the maximum sized salamander recorded in Italy. There was a high rate of gravid females (50%), which were comparable in size with non-gravid females. Males and non-gravid females did not show significant differences in their body condition index.

Reusable Cavitand‐Based Electrospun Membranes for the Removal of Polycyclic Aromatic Hydrocarbons from Water

The removal of toxic and carcinogenic polycyclic aromatic hydrocarbons (PAHs) from water is one of the most intractable environmental problems nowadays, because of their resistance to remediation. This work introduces a highly efficient, regenerable membrane for the removal of PAHs from water, featuring excellent filter performance and pH-driven release, thanks to the integration of a cavitand receptor in electrospun polyacrylonitrile (PAN) fibers. The role of the cavitand receptor is to act as molecular gripper for the uptake/ release of PAHs. To this purpose, the deep cavity cavitand BenzoQxCav is designed and synthetized and its molecular structure is elucidated via X-Ray diffraction. The removal efficiency of the new adsorbent material toward the 16 priority PAHs is demonstrated via GC-MS analyses at ng L−1 concentration. A removal efficiency in the 32%, to 99% range is obtained. The regeneration of the membrane is performed by exploiting the pH-driven conformational switching of the cavitand between the vase form, where the PAHs uptake takes place, to the kite one, where the PAHs release occurs. The absorbance and regeneration capability of the membrane are successfully tested in four uptake/release cycles and the morphological stability