Biomimetic Surface Engineering to Modulate the Coffee-Ring Effect for Amyloid-ß Detection in Rat Brains.

Surface engineering of nanoparticles has been widely used in biosensing and assays, where sensitivity was mainly limited by plasmonic colour change or electrochemical responses. Here, we report a novel biomimetic sensing strategy involving protein-modified gold nanoparticles (AuNPs), where the modulation strategy was inspired by gastropods in inhibition of coffee-ring effects in their trail-followings. The so-called coffee-ring effect presents the molecular behaviour of AuNPs to a macroscopic ring through aggregation, and thus greatly improves sensitivity. The assay relies upon the different assembly patterns of AuNPs against analytes, resulting in the formation or suppression of coffee-ring effects by the different surface engineering of AuNPs by proteins and peptides. The mechanism of the coffee-ring formation process is examined through experimental characterizations and computational simulations. A practical coffee-ring effect assay is developed for a proof-of-concept target, amyloid ß (1-42), which is a typical biomarker of Alzheimer's disease. A novel quasi-titrimetric protocol is constructed for quantitative determination of the target molecule. The assay shows excellent selectivity and sensitivity for the amyloid ß monomer, with a low detection limit of 20 pM. Combined with a fluorescent staining technique, the assay is designed as a smart sensor for amyloid ß detection and fibrillation evaluation in rat cerebrospinal fluids, which is a potential point-of-care test for Alzheimer's disease. Connections between amyloid fibrillation and different courses of brain ischaemia are also studied, with improved sensitivity, lower sample volumes that are required, convenience for rapid detection, and point-of-care testing.

ABPP-CoDEL: Activity-Based Proteome Profiling-Guided Discovery of Tyrosine-Targeting Covalent Inhibitors from DNA-Encoded Libraries.

DNA-encoded chemical library (DEL) has been extensively used for lead compound discovery for decades in academia and industry. Incorporating an electrophile warhead into DNA-encoded compounds recently permitted the discovery of covalent ligands that selectively react with a particular cysteine residue. However, noncysteine residues remain underexplored as modification sites of covalent DELs. Herein, we report the design and utility of tyrosine-targeting DELs of 67 million compounds. Proteome-wide reactivity analysis of tyrosine-reactive sulfonyl fluoride (SF) covalent probes suggested three enzymes (phosphoglycerate mutase 1, glutathione s-transferase 1, and dipeptidyl peptidase 3) as models of tyrosine-targetable proteins. Enrichment with SF-functionalized DELs led to the identification of a series of tyrosine-targeting covalent inhibitors of the model enzymes. In-depth mechanistic investigation revealed their novel modes of action and reactive ligand-accessible hotspots of the enzymes. Our strategy of combining activity-based proteome profiling and covalent DEL enrichment (ABPP-CoDEL), which generated selective covalent binders against a variety of target proteins, illustrates the potential use of this methodology in further covalent drug discovery.

Benzo[d]isoxazole Derivatives as Hypoxia-Inducible Factor (HIF)-1α Inhibitors.

Hypoxia-inducible factor, also known as HIF, is a transcriptional factor universally found in mammalian cells. HIF-1 is one of the HIF-families and acts as a heterodimer consisting of α and ß subunits. It is found to play significant roles in pathologic conditions such as tumor development and metastasis. Here, we first report benzo[d]isoxazole analogues as HIF-1α transcription inhibitors. Thereby, we designed and synthesized 26 benzo[d]isoxazole derivatives and evaluated their inhibitory activities against HIF-1α transcription in HEK293T cells by a dual-luciferase gene reporter assay. Among them, compounds 15 and 31 showed the best efficacy in a cell-based assay with an IC50 value of 24 nM and have potential antitumor effects for further development.

Modular Assembly of MXene Frameworks for Noninvasive Disease Diagnosis via Urinary Volatiles.

Volatile organic compounds (VOCs) in urine are valuable biomarkers for noninvasive disease diagnosis. Herein, a facile coordination-driven modular assembly strategy is used for developing a library of gas-sensing materials based on porous MXene frameworks (MFs). Taking advantage of modules with diverse composition and tunable structure, our MFs-based library can provide more choices to satisfy gas-sensing demands. Meanwhile, the laser-induced graphene interdigital electrodes array and microchamber are laser-engraved for the assembly of a microchamber-hosted MF (MHMF) e-nose. Our MHMF e-nose possesses high-discriminative pattern recognition for simultaneous sensing and distinguishing of complex VOCs. Furthermore, with the MHMF e-nose being a plug-and-play module, a point-of-care testing (POCT) platform is modularly assembled for wireless and real-time monitoring of urinary volatiles from clinical samples. By virtue of machine learning, our POCT platform achieves noninvasive diagnosis of multiple diseases with a high accuracy of 91.7%, providing a favorable opportunity for early disease diagnosis, disease course monitoring, and relevant research.

Tailoring Oxygen-Containing Groups on Graphene for Ratiometric Electrochemical Measurements of Ascorbic Acid in Living Subacute Parkinson's Disease Mouse Brains.

Ascorbic acid (AA), a major antioxidant in the central nervous system (CNS), is involved in withstanding oxidative stress that plays a significant role in the pathogenesis of Parkinson's disease (PD). Exploring the AA disturbance in the process of PD is of great value in understanding the molecular mechanism of PD. Herein, by virtue of a carbon fiber electrode (CFE) as a matric electrode, a three-step electrochemical process for tailoring oxygen-containing groups on graphene was well designed: potentiostatic deposition was carried out to fabricate graphene oxide on CFE, electrochemical reduction that assisted in removing the epoxy groups accelerated the electron transfer kinetics of AA oxidation, and electrochemical oxidation that increased the content of the carbonyl group (C═O) generated an inner-reference signal. The mechanism was solidified by ab initio calculations by comparing AA absorption on defected models of graphene functionalized with different oxygen groups including carboxyl, hydroxyl, epoxy, and carbonyl. It was found that epoxy groups would hinder the physical absorption of AA onto graphene, while other functional groups would be beneficial to it. Biocompatible polyethylenedioxythiophene (PEDOT) was further rationally assembled to improve the antifouling property of graphene. As a result, a new platform for ratiometric electrochemical measurements of AA with high sensitivity, excellent selectivity, and reproducibility was established. In vivo determination of AA levels in different regions of living mouse brains by the proposed method demonstrated that AA decreased remarkably in the hippocampus and cortex of a subacute PD mouse than those of a normal mouse.

Prescribing Silver Chirality with DNA Origami.

Metal nanostructures of chiral geometry interacting with light via surface plasmon resonances can produce tailorable optical activity with their structural alterations. However, bottom-up fabrication of arbitrary chiral metal nanostructures with precise size and morphology remains a synthetic challenge. Here we develop a DNA origami-enabled aqueous solution metallization strategy to prescribe the chirality of silver nanostructures in three dimensions. We find that diamine silver(I) complexes coordinate with the bases of prescribed single-stranded protruding clustered DNA (pcDNA) on DNA origami via synergetic interactions including coordination, hydrogen bonds, and ion-π interaction, which induce site-specific pcDNA condensation and local enrichment of silver precursors that lowers the activation energy for nucleation. Using tubular DNA origami-based metallization, we obtain helical silver patterns up to a micrometer in length with well-defined chirality and pitches. We further demonstrate tailorable plasmonic optical activity of metallized chiral silver nanostructures. This method opens new pathways to synthesize programmable inorganic materials with arbitrary morphology and chirality.

Metal-Bridged Graphene-Protein Supraparticles for Analog and Digital Nitric Oxide Sensing.

Self-limited nanoassemblies, such as supraparticles (SPs), can be made from virtually any nanoscale components, but SPs from nanocarbons including graphene quantum dots (GQDs), are hardly known because of the weak van der Waals attraction between them. Here it is shown that highly uniform SPs from GQDs can be successfully assembled when the components are bridged by Tb3+ ions supplementing van der Waals interactions. Furthermore, they can be coassembled with superoxide dismutase, which also has weak attraction to GQDs. Tight structural integration of multilevel components into SPs enables efficient transfer of excitonic energy from GQDs and protein to Tb3+ . This mechanism is activated when Cu2+ is reduced to Cu1+ by nitric oxide (NO)-an important biomarker for viral pulmonary infections and Alzheimer's disease. Due to multipronged fluorescence enhancement, the limit of NO detection improves 200 times reaching 10 × 10-12 m. Furthermore, the uniform size of SPs enables digitization of the NO detection using the single particle detection format resulting in confident registration of as few as 600 molecules mL-1 . The practicality of the SP-based assay is demonstrated by the successful monitoring of NO in human breath. The biocompatible SPs combining proteins, carbonaceous nanostructures, and ionic components provide a general path for engineering uniquely sensitive assays for noninvasive tracking of infections and other diseases.

Emergence of complexity in hierarchically organized chiral particles.

The structural complexity of composite biomaterials and biomineralized particles arises from the hierarchical ordering of inorganic building blocks over multiple scales. Although empirical observations of complex nanoassemblies are abundant, the physicochemical mechanisms leading to their geometrical complexity are still puzzling, especially for nonuniformly sized components. We report the self-assembly of hierarchically organized particles (HOPs) from polydisperse gold thiolate nanoplatelets with cysteine surface ligands. Graph theory methods indicate that these HOPs, which feature twisted spikes and other morphologies, display higher complexity than their biological counterparts. Their intricate organization emerges from competing chirality-dependent assembly restrictions that render assembly pathways primarily dependent on nanoparticle symmetry rather than size. These findings and HOP phase diagrams open a pathway to a large family of colloids with complex architectures and unusual chiroptical and chemical properties.

Diverse Nanoassemblies of Graphene Quantum Dots and Their Mineralogical Counterparts.

Complex structures from nanoparticles are found in rocks, soils, and sea sediments but the mechanisms of their formation are poorly understood, which causes controversial conclusions about their genesis. Here we show that graphene quantum dots (GQDs) can assemble into complex structures driven by coordination interactions with metal ions commonly present in environment and serve a special role in Earth's history, such as Fe3+ and Al3+ . GQDs self-assemble into mesoscale chains, sheets, supraparticles, nanoshells, and nanostars. Specific assembly patterns are determined by the effective symmetry of the GQDs when forming the coordination assemblies with the metal ions. As such, maximization of the electronic delocalization of π-orbitals of GQDs with Fe3+ leads to GQD-Fe-GQD units with D2 symmetry, dipolar bonding potential, and linear assemblies. Taking advantage of high electron microscopy contrast of carbonaceous nanostructures in respect to ceramic background, the mineralogical counterparts of GQD assemblies are found in mineraloid shungite. These findings provide insight into nanoparticle dynamics during the rock formation that can lead to mineralized structures of unexpectedly high complexity.

The Marriage of Protein and Lanthanide: Unveiling a Time-Resolved Fluorescence Sensor Array Regulated by pH toward High-Throughput Assay of Metal Ions in Biofluids.

A protein/lanthanide complex (BSA/Tb3+)-based sensor array in two different pH buffers has been designed for high-throughput recognition and time-resolved fluorescence (TRF) detection of metal ions in biofluids. BSA, which acted as an antenna ligand, can sensitize the fluorescence of Tb3+ (i.e., antenna effect), while the presence of metal ions would lead to the corresponding conformational change of BSA for altering the antenna effect accompanied by a substantial TRF performance of Tb3+. This principle has also been fully proved by both experimental characterizations and coarse-grained molecular dynamics (CG-MD) studies. By using Tris-HCl buffer with different pHs (at 7.4 and 8.5), 17 metal ions have been well-distinguished by using our proposed BSA/Tb3+ sensor array. Moreover, the sensor array has the potential to discriminate different concentrations of the same metal ions and a mixture of metal ions. Remarkably, the detection of metal ions in biofluids can be realized by utilizing the presented sensor array, verifying its practical applications. The platform avoids the synthesis of multiplex sensing receptors, providing a new method for the construction of convenient and feasible lanthanide complex-based TRF sensing arrays.

Colorimetric Detection of Carcinogenic Aromatic Amine Using Layer-by-Layer Graphene Oxide/Cytochrome c Composite.

Graphene and its derivatives were found to be efficient modulators of enzymes in various systems. However, the modulating mechanism was not well discussed for long time. Inspired by the artificial enzyme-enhancing property of graphene oxide (GO) toward cytochrome c (cyt. c), we have successfully fabricated a protein/GO hybrid structure via a layer-by-layer (LbL) strategy. The obtained LbL assemblies showed great enhancement in peroxidase activity of cyt. c, as well as excellent stability, resistance to extreme environment change, and also possibility for recycling by simple centrifugation without any obvious activity loss. The LbL cyt. c/GO hybrids were expanded to a colorimetric sensing system for the detection of carcinogenic aromatic amines. The probe showed high sensitivity and selectivity for aromatic amines over various competing soluble aromatic compounds and could be determined by the naked eye or portable devices. The working mechanism was well studied through kinetic evaluation, experimental characterization, and molecular dynamics simulations. This work does not only introduce a new graphene/protein hybrid material or a rapid and sensitive visualization of carcinogenic aromatic amines, but also spread the practical application of biomolecule-graphene interface strategy and further give a better understanding of the interaction of graphene and protein.

Chiral Ceramic Nanoparticles and Peptide Catalysis.

The chirality of nanoparticles (NPs) and their assemblies has been investigated predominantly for noble metals and II-VI semiconductors. However, ceramic NPs represent the majority of nanoscale materials in nature. The robustness and other innate properties of ceramics offer technological opportunities in catalysis, biomedical sciences, and optics. Here we report the preparation of chiral ceramic NPs, as represented by tungsten oxide hydrate, WO3-x·H2O, dispersed in ethanol. The chirality of the metal oxide core, with an average size of ca. 1.6 nm, is imparted by proline (Pro) and aspartic acid (Asp) ligands via bio-to-nano chirality transfer. The amino acids are attached to the NP surface through C-O-W linkages formed from dissociated carboxyl groups and through amino groups weakly coordinated to the NP surface. Surprisingly, the dominant circular dichroism bands for NPs coated by Pro and Asp are different despite the similarity in the geometry of the NPs; they are positioned at 400-700 nm and 500-1100 nm for Pro- and Asp-modified NPs, respectively. The differences in the spectral positions of the main chiroptical band for the two types of NPs are associated with the molecular binding of the two amino acids to the NP surface; Asp has one additional C-O-W linkage compared to Pro, resulting in stronger distortion of the inorganic crystal lattice and greater intensity of CD bands associated with the chirality of the inorganic core. The chirality of WO3-x·H2O atomic structure is confirmed by atomistic molecular dynamics simulations. The proximity of the amino acids to the mineral surface is associated with the catalytic abilities of WO3-x·H2O NPs. We found that NPs facilitate formation of peptide bonds, leading to Asp-Asp and Asp-Pro dipeptides. The chiroptical activity, chemical reactivity, and biocompatibility of tungsten oxide create a unique combination of properties relevant to chiral optics, chemical technologies, and biomedicine.

Nanomolar sensitive colorimetric assay for Mn2+ using cysteic acid-capped silver nanoparticles and theoretical investigation of its sensing mechanism.

A new facile, rapid, sensitive and selective colorimetric assay is proposed for the determination of manganese ions (Mn2+) utilizing cysteic acid (CA)-capped silver nanoparticles (CA-AgNPs) as colorimetric probes. The CA-AgNPs were prepared by reducing AgNO3 with NaBH4 in the presence of CA as the capping ligand. The presence of Mn2+ induces the quick aggregation of CA-AgNPs, associated with notable color changes of the CA-AgNPs solution from yellow to dark green. The Mn2+ can form a coordinated structure with CA capping on the AgNPs and leads to formation of large particles aggregation. We also used density functional theory (DFT) to calculate the change of the Gibbs free energy (ΔG) of the interactions between the CA-AgNPs and various metal ions, which shows that CA-AgNPs have high specificity for Mn2+. The high sensitivity and selectivity for Mn2+ were achieved and the detection limit is as low as 5 nM. Furthermore, the proposed method was successfully applied in detecting Mn2+ in a rat model of focal ischemia and the results indicate that our proposed method has great potential for practical applications.

Chiral Graphene Quantum Dots.

Chiral nanostructures from metals and semiconductors attract wide interest as components for polarization-enabled optoelectronic devices. Similarly to other fields of nanotechnology, graphene-based materials can greatly enrich physical and chemical phenomena associated with optical and electronic properties of chiral nanostructures and facilitate their applications in biology as well as other areas. Here, we report that covalent attachment of l/d-cysteine moieties to the edges of graphene quantum dots (GQDs) leads to their helical buckling due to chiral interactions at the "crowded" edges. Circular dichroism (CD) spectra of the GQDs revealed bands at ca. 210-220 and 250-265 nm that changed their signs for different chirality of the cysteine edge ligands. The high-energy chiroptical peaks at 210-220 nm correspond to the hybridized molecular orbitals involving the chiral center of amino acids and atoms of graphene edges. Diverse experimental and modeling data, including density functional theory calculations of CD spectra with probabilistic distribution of GQD isomers, indicate that the band at 250-265 nm originates from the three-dimensional twisting of the graphene sheet and can be attributed to the chiral excitonic transitions. The positive and negative low-energy CD bands correspond to the left and right helicity of GQDs, respectively. Exposure of liver HepG2 cells to L/D-GQDs reveals their general biocompatibility and a noticeable difference in the toxicity of the stereoisomers. Molecular dynamics simulations demonstrated that d-GQDs have a stronger tendency to accumulate within the cellular membrane than L-GQDs. Emergence of nanoscale chirality in GQDs decorated with biomolecules is expected to be a general stereochemical phenomenon for flexible sheets of nanomaterials.

A single-wavelength-emitting ratiometric probe based on phototriggered fluorescence switching of graphene quantum dots.

Ratiometric fluorescent probes are of great importance in research, because a built-in correction for environmental effects can be provided to reduce background interference. However, the traditional ratiometric fluorescent probes require two luminescent materials with different emission bands. Herein a novel ratiometric probe based on a single-wavelength-emitting material is reported. The probe works by regulating the luminescent property of graphene quantum dots with UV illumination as activator. The ratiometric sensor shows high sensitivity and specificity for iron ions. Moreover, the ratiometric sensor was successfully employed to monitor ferritin levels in Sprague Dawley rats with chemical-induced acute liver damage. The proposed single-wavelength ratiometric fluorescent probe may greatly broaden the applicability of ratiometric sensors in diagnostic devices, medical applications, and analytical chemistry.

Time-resolved probes and oxidase-based biosensors using terbium(III)-guanosine monophosphate-mercury(II) coordination polymer nanoparticles.

A novel lanthanide coordination polymer nanoparticle (LCPN)-based ternary complex was synthesized via the self-assembly of a terbium ion (Tb(3+)) with a nucleotide (GMP) and a mercury ion (Hg(2+)) in aqueous solution. The as-prepared LCPN-based ternary complex (Tb-GMP-Hg) can be applied to the development of time-resolved luminescence assays and oxidase-based biosensors.

DNA-based sensitization of Tb3+ luminescence regulated by Ag+ and cysteine: use as a logic gate and a H2O2 sensor.

A simple and facile strategy was developed for regulating the luminescence of Tb(3+) sensitized by DNA, in which Ag(+) and cysteine (Cys) act as activators. The Ag(+)/Cys-mediated reversible luminescence changes in the Tb(3+)-DNA sensing system enabled the design of a DNA INHIBIT logic gate and a H2O2 sensor in a time-resolved luminescence format.

A novel composite of graphene quantum dots and molecularly imprinted polymer for fluorescent detection of paranitrophenol.

A novel fluorescent sensor based on graphene quantum dots (GQDs) was synthesized for determination of paranitrophenol (4-NP) in water sample, where molecularly imprinted polymer (MIP) was incorporated in GQDs-based sensing system for the first time. A simple hydrothermal method was used to fabricate silica-coated GQDs. The final composite was developed by anchoring the MIP layer on the silica-coated GQDs using 3-aminopropyltriethoxysilane as functional monomer and tetraethoxysilane as crosslinker. The combination of GQDs and MIP endows the composite with stable fluorescent property and template selectivity. Due to resonance energy transfer from GQDs (donor) to 4-NP (acceptor), the fluorescence of the MIP-coated GQDs composite can be efficiently quenched when 4-NP molecules rebound to the binding sites. The composite was applied to the detection of the non-emissive 4-NP and exhibited a good linearity in range of 0.02-3.00 µg mL(-1) with the detection limit of 9.00 ng mL(-1) (S/N=3). This work may open a new possibility for developing GQDs-based composite with selective recognition, and it is desirable for chemical sensing application.

Hybrid nanotube-graphene junctions: spin degeneracy breaking and tunable electronic structure.

Hybrid carbon nanostructures have attracted enormous interest due to their structural stability and unique physical properties. Geometric and physical properties of a carbon nanotube (CNT)-graphene nanoribbon (GNR) hybrid system were investigated via first-principles density functional theory (DFT) calculations. The nanotube-graphene junction (NTGJ), where the GNR directly links to the CNT by covalent bonds, shows novel electronic dependence on the structural parameters of the building-blocks, such as chirality, nanotube diameter and width of the nanoribbon. For an armchair NTGJ, a small band gap opens up representing asymmetrical spin-up and spin-down bands. However, zig-zag NTGJ shows direct semi-conducting characteristics with a tunable band gap ranging from zero to 0.6 eV. Interestingly, the value of the band gap follows the specific width and diameter dependent oscillations, namely the 3p - 1 principle. Transition-state results reveal the formation of NTGJs is exothermic and has a low energy-barrier. In addition, nanotube-graphene-nanotube junctions or namely dumbbell NTGJs were also studied, which exhibits similar properties with single NTGJ.

Boronic acid functionalized graphene quantum dots as a fluorescent probe for selective and sensitive glucose determination in microdialysate.

3-Aminobenzeneboronic acid functionalized graphene quantum dots (APBA-GQDs) were synthesized and used as a selective and sensitive sensing system for glucose. Combined with microdialysis, glucose was monitored successfully in vivo in the striatum of rat.