Probing lysine mono-methylation in histone H3 tail peptides with an abiotic receptor coupled to a non-plasmonic resonator

Enrichment of histone tail methylated lysine residues via cavitand-decorated magnetic nanoparticles for ultra-sensitive proteomics

Nearly every protein in the human body is modified with post-translational modifications (PTMs). PTMs affect proteins on many levels, including their function, interaction, half-life, and localization. Specifically, for histone proteins, PTMs such as lysine methylation and acetylation play essential roles in chromatin dynamic regulations. For this reason, methods to accurately detect and quantify PTMs are of paramount importance in cell biology, biochemistry, and disease biology. Most protein modifications are sub-stoichiometric, so, to be analyzed, they need methods of enrichment, which are mostly based on antibodies. Antibodies are produced using animals, resulting in high costs, ecological concerns, significant batch variations, and ethical implications. We propose using ferromagnetic nanoparticles functionalized with synthetic receptors, namely tetraphosphonate cavitands, as a tool for selective enrichment of methylated lysines present on histone tails. Before the enrichment step, histone proteins from calf thymus were digested to facilitate the recognition process and to obtain small peptides suitable for mass analyses. Cavitands were anchored on ferromagnetic nanoparticles to easily separate the PTM-peptides of interest from the rest of the proteolytic peptides. Our approach detects more modified peptides with higher signal intensity, rivaling commercial antibodies. This chemical strategy offers a cost-effective and efficient alternative for PTM detection, potentially advancing proteomic research.

Recent advances in non-plasmonic surface-enhanced Raman spectroscopy nanostructures for biomedical applications

Surface-enhanced Raman spectroscopy (SERS) is an emerging powerful vibrational technique offering unprecedented opportunities in biomedical science for the sensitive detection of biomarkers and the imaging and tracking of biological samples. Conventional SERS detection is based on the use of plasmonic substrates (e.g., Au and Ag nanostructures), which exhibit very high enhancement factors (EF = 1010 -1011 ) but suffers from serious limitations, including light-induced local heating effect due to ohmic loss and expensive price. These drawbacks may limit detection accuracy and large-scaled practical applications. In this review, we focus on alternative approaches based on plasmon-free SERS detection on low-cost nanostructures, such as carbons, oxides, chalcogenides, polymers, silicons, and so forth. The mechanism of non-plasmonic SERS detection has been attributed to interfacial charge transfer between the substrate and the adsorbed molecules, with no photothermal side-effects but usually less EF compared with plasmonic nanostructures. The strategies to improve Raman signal detection, through the tailoring of substrate composition, structure, and surface chemistry, is reviewed and discussed. The biomedical applications, for example, SERS cell characterization, biosensing, and bioimaging are also presented, highlighting the importance of substrate surface functionalization to achieve sensitive, accurate analysis, and excellent biocompatibility. This article is categorized under: Diagnostic Tools > Diagnostic Nanodevices Diagnostic Tools > Biosensing Diagnostic Tools > In Vivo Nanodiagnostics and Imaging.

Combining Excellent Selectivity with Broad Target Scope: Biosensing with Arrayed Deep Cavitand Hosts

Simple macrocyclic water-soluble hosts such as cucurbiturils, cyclophanes, and calixarenes have long been used for biosensing via indicator displacement assays. Using multiple hosts and dyes in an arrayed format allows pattern recognition-based "chemical nose" sensing, which confers exquisite selectivity, even rivaling the abilities of biological recognition tools such as antibodies. However, a challenge in indicator displacement-based biosensing with macrocyclic hosts is that selectivity and scope are often inversely correlated: strong selectivity for a specific target can limit wide application, and broad scope sensing can suffer from a lack of selectivity between similar targets. This problem can be addressed by using water-soluble, self-folding deep cavitands as hosts. These flexible bowl-shaped receptors can be easily functionalized with different motifs at the upper and lower rim, and the large cavities can bind many different fluorescent dyes, causing either fluorescence enhancement or quenching upon binding.Cavity-based affinity is strongest for NMe₃⁺ groups such as trimethyl-lysine, and we have exploited this for the site-selective recognition of post-translational lysine methylations in oligopeptides. The host recognizes the NMe₃⁺ group, and by applying differently functionalized hosts in an arrayed format, discrimination between identical modifications at different positions on the oligopeptide is possible. Multiple recognition elements can be exploited for selectivity, including a defined, yet "breathable" cavity, and variable upper rim functions oriented toward the target.While the performance of the host/guest sensing system is impressive for lysine methylations, the most important advance is the use of multiple different sensing mechanisms that can target a broad range of different biorelevant species. The amphiphilic deep cavitands can both bind fluorescent dyes and interact with charged biomolecules. These non-cavity-based interactions, when paired with additives such as heavy metal ions, modulate fluorescence response in an indirect manner, and these different mechanisms allow selective recognition of serine phosphorylation, lysine acetylation, and arginine citrullination. Other targets include heavy metals, drugs of abuse, and protein isoforms. Furthermore, the hosts can be applied in supramolecular tandem assays of enzyme function: the broad scope allows analysis of such different enzymes as chromatin writers/erasers, kinases, and phosphatases, all from a single host scaffold. Finally, the indirect sensing concept allows application in sensing different oligonucleotide secondary structures, including G-quadruplexes, hairpins, triplexes, and i-motifs. Discrimination between DNA strands with highly similar structures such as G-quadruplex strands with bulges and vacancies can be achieved. Instead of relying on a single highly specific fluorescent probe, the synthetic hosts tune the fluorophore-DNA interaction, introducing multiple recognition equilibria that modulate the fluorescence signal. By applying machine learning algorithms, a classification model can be established that can accurately predict the folding state of unknown sequences. Overall, the unique recognition profile of self-folded deep cavitands provides a powerful, yet simple sensing platform, one that can be easily tuned for a wide scope of biorelevant targets, in complex biological media, without sacrificing selectivity in the recognition.

Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors

To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.

Cationic Pillar[6]arene Induces Cell Apoptosis by Inhibiting Protein Tyrosine Phosphorylation Via Host-Guest Recognition

We reported for the first time that cationic pillar[6]arene (cPA6) could tightly bind to peptide polymer (MW~20–50 kDa), an artificial substrate for tyrosine (Tyr) phosphorylation, and efficiently inhibit Tyr protein phosphorylation through host–guest recognition. We synthesized a nanocomposite of black phosphorus nanosheets loaded with cPA6 (BPNS@cPA6) to explore the effect of cPA6 on cells. BPNS@cPA6 was able to enter HepG2 cells, induced apoptosis, and inhibited cell proliferation by reducing the level of Tyr phosphorylation. Furthermore, BPNS@cPA6 showed a stronger ability of inhibiting cell proliferation in tumor cells than in normal cells. Our results revealed the supramolecular modulation of enzymatic Tyr phosphorylation by the host–guest recognition of cPA6.

Ultratrace Nitroaromatic Vapor Detection via Surface-Enhanced Fluorescence on Carbazole-Terminated Black Silicon

Detection of nitroaromatic compounds (NACs) is an important applied task for environmental monitoring, medical diagnostics, and forensic analysis. However, detection of NAC vapors is challenging owing to their low vapor pressure and relatively weak sensitivity of the existing detection techniques. Here, we propose a novel concept to design fluorescence (FL) detection platforms based on chemical functionalization of nanotextured dielectric surfaces exhibiting resonant light absorption, trapping, and localization effects. We demonstrate highly-efficient NAC vapor sensor with selective FL-quenching response from monolayers of carbazole moieties covalently bonded to a spiky silicon surface, "black" silicon, produced over the centimeter-scale area using simple reactive ion etching. The sensor is shown to provide unprecedented ppt (10^-12) range limits of detection for several NAC vapors. Easy-to-implement scalable fabrication procedure combined with simple and versatile functionalization techniques applicable to all-dielectric surfaces make the suggested concept promising for realization of various gas sensing systems for social and environmental safety applications.

Ag@TiO2 nanogranular films by gas phase synthesis as hybrid SERS platforms

The synthesis of hybrid metallic-dielectric substrates as reliable SERS platforms relies on core-shell nanoparticles, obtained by wet chemistry, with an outer dielectric shell composed of SiO₂ or TiO₂. Apart from the shell composition, the nanoparticle density and aggregation type strongly affect the surface-enhanced SERS. Going beyond a single layer by building random aggregates of hybrid NPs would result in a step forward in the production of reliable hybrid SERS platforms. Here we achieve the fabrication of a 3D nanogranular film of Ag metallic cores not fully enclosed in a TiO₂ capping layer, defined as a Ag@TiO₂ quasi-shell-isolated Raman substrate (Ag@TiO₂ QuaSIRS) by an environmentally friendly gas phase synthesis technique (SCBD). The Ag core drives the electromagnetic enhancement with plasmonic hotspots while the TiO₂ shell passivates it and leads to different possible surface functionalization. The SERS capabilities of the Ag@TiO₂ QuaSIRS peak at a film thickness of 60 nm providing a detection limit of 10^-9 M concentration for Methylene Blue at 632.81 nm. The importance of the nanogranular 3D morphology is evidenced by the very good detection of analytes dispersed in aqueous solutions, since the liquid can penetrate the pores hence exploiting most of the plasmonic hotspots present in the film. The versatility of SCBD to deposit such reliable hybrid SERS platforms by a single step at room temperature over different substrates provides an opportunity to design a new generation of hybrid SERS-active substrates based on hybrid nanoparticles.

Velcrand Functionalized Polyethylene

Velcrands are a specific class of cavitands whose complementary surfaces induce self-dimerization. The insertion of a velcrand as physical cross-linking unit into a polymer is reported. To this purpose, the velcrand was functionalized at the lower rim with an isocyanate group. The functional velcrand was reacted with poly (ethylene-co-(2-hydroxethylmethacrylate)) (PE-HEMA), a polymer equipped with free hydroxyl groups suitable for reaction with the isocyanate group. The obtained functionalized polymer was characterized by nuclear magnetic resonance (NMR), differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR), proving the introduction of velcraplexes in the polymer. Films with varying amounts of velcrands were obtained by solution casting and slow evaporation, testifying the processability of the functionalized polymers. The obtained films were used to measure the oxygen barrier properties of the functionalized material.

Fluorinated Tetraphosphonate Cavitands

Two synthetic protocols for the introduction of fluorine atoms into resorcinarene-based cavitands, at the lower and upper rim, respectively, are reported. Cavitand 1, bearing four fluorocarbon tails, and cavitand 2, which presents a fluorine atom on the para position of a diester phosphonate phenyl substituent, were synthesized and their complexation abilities toward the model guest sarcosine methyl ester hydrochloride were evaluated via NMR titration experiments. The effect of complexation on the ¹⁹F NMR resonance of the probe is evident only in the case of cavitand 2, where the inset of the cation-dipole and H-bonding interactions between the P=O bridges and the guest is reflected in a sizable downfield shift of the fluorine probe.

Biochemical sensing with macrocyclic receptors

Preventive healthcare asks for the development of cheap, precise and non-invasive sensor devices for the early detection of diseases and continuous population screening. The actual techniques used for diagnosis, e.g. MRI and PET, or for biochemical marker sensing, e.g. immunoassays, are not suitable for continuous monitoring since they are expensive and prone to false positive responses. Synthetic supramolecular receptors offer new opportunities for the creation of specific, selective and cheap sensor devices for biological sensing of specific target molecules in complex mixtures of organic substances. The fundamental challenges faced in developing such devices are the precise transfer of the molecular recognition events at the solid-liquid interface and its transduction into a readable signal. In this review we present the progress made so far in turning synthetic macrocyclic hosts, namely cyclodextrins, calixarenes, cucurbiturils and cavitands, into effective biochemical sensors and the strategies utilized to solve the above mentioned issues. The performances of the developed sensing devices based on these receptors in detecting specific biological molecules, drugs and proteins are critically discussed.

Chemically non-perturbing SERS detection of a catalytic reaction with black silicon

All-dielectric resonant micro- and nano-structures made of high-index dielectrics have recently emerged as a promising surface-enhanced Raman scattering (SERS) platform which can complement or potentially replace the metal-based counterparts in routine sensing measurements. These unique structures combine the highly-tunable optical response and high field enhancement with the non-invasiveness, i.e. chemically non-perturbing the analyte, simple chemical modification and recyclability. Meanwhile, commercially competitive fabrication technologies for mass production of such structures are still missing. Here, we attest a chemically inert black silicon (b-Si) substrate consisting of randomly-arranged spiky Mie resonators for a true non-invasive (chemically non-perturbing) SERS identification of the molecular fingerprints at low concentrations. Based on the comparative in situ SERS tracking of the para-aminothiophenol (PATP)-to-4,4'-dimercaptoazobenzene (DMAB) catalytic conversion on the bare and metal-coated b-Si, we justify the applicability of the metal-free b-Si for ultra-sensitive non-invasive SERS detection at a concentration level as low as 10-6 M. We performed supporting finite-difference time-domain (FDTD) calculations to reveal the electromagnetic enhancement provided by an isolated spiky Si resonator in the visible spectral range. Additional comparative SERS studies of the PATP-to-DMAB conversion performed with a chemically active bare black copper oxide (b-CuO) substrate as well as SERS detection of the slow daylight-driven PATP-to-DMAB catalytic conversion in the aqueous methanol solution loaded with colloidal silver nanoparticles (Ag NPs) confirm the non-invasive SERS performance of the all-dielectric crystalline b-Si substrate. A proposed SERS substrate can be fabricated using the easy-to-implement scalable technology of plasma etching amenable on substrate areas over 10 × 10 cm2 making such inexpensive all-dielectric substrates promising for routine SERS applications, where the non-invasiveness is of high importance.

Donor-acceptor interaction-driven self-assembly of amphiphilic rod-coil molecules into supramolecular nanoassemblies

Rigid-flexible amphiphilic molecules consisting of an aromatic segment based on pyrene and biphenyl units and hydrophilic polyethylene oxide chains self-assemble into lamellar, hexagonal columnar, and two-dimensional columnar nanostructures in the bulk state. In aqueous solution, these molecules self-assemble into nanofibers, spherical micelles, and multilayer nanotubes, depending on the chain or rod length of the molecules. Notably, ordered nanostructures of supramolecular polymers, such as single-layer curving fragments, nanofibers, and nanosheets, were constructed through charge-transfer interactions between the nanoobjects and an electron-acceptor molecule, 2,4,5,7-tetranitrofluorenone. These experimental results reveal that diverse supramolecular morphologies can be controlled by tuning rod-coil molecular interactions or charge-transfer interactions between the donor and acceptor molecules.

Selectivity/Specificity Improvement Strategies in Surface-Enhanced Raman Spectroscopy Analysis

Surface-enhanced Raman spectroscopy (SERS) is a powerful technique for the discrimination, identification, and potential quantification of certain compounds/organisms. However, its real application is challenging due to the multiple interference from the complicated detection matrix. Therefore, selective/specific detection is crucial for the real application of SERS technique. We summarize in this review five selective/specific detection techniques (chemical reaction, antibody, aptamer, molecularly imprinted polymers and microfluidics), which can be applied for the rapid and reliable selective/specific detection when coupled with SERS technique.

Site-Selective Sensing of Histone Methylation Enzyme Activity via an Arrayed Supramolecular Tandem Assay

Arrayed deep cavitands can be coupled to a fluorescence-based supramolecular tandem assay that allows site-selective in situ monitoring of post-translational modifications catalyzed by the lysine methyltransferase PRDM9 or the lysine demethylase JMJD2E. An arrayed sensor system containing only three cavitand components can detect the specific substrates of enzyme modification, in the presence of other histone peptides in the enzyme assay, enabling investigation of cross-reactivity over multiple methylation sites and interference from nonsubstrate peptides.