Detection and identification of proteins using nanoparticle-fluorescent polymer 'chemical nose' sensors

Surface-Engineered Nanomaterials for Optical Array Based Sensing

Array based sensing governed by optical methods provides fast and economic way for detection of wide variety of analytes where the ideality of detection processes depends on the sensor element's versatile mode of interaction with multiple analytes in an unbiased manner. This can be achieved by either the receptor unit having multiple recognition moiety, or their surface property should possess tuning ability upon fabrication called surface engineering. Nanomaterials have a high surface to volume ratio, making them viable candidates for molecule recognition through surface adsorption phenomena, which makes it ideal to meet the above requirements. Most crucially, by engineering a nanomaterial's surface, one may produce cross-reactive responses for a variety of analytes while focusing solely on a single nanomaterial. Depending on the nature of receptor elements, in the last decade the array-based sensing has been considering as multimodal detection platform which operates through various pathway including single channel, multichannel, binding and indicator displacement assay, sequential ON-OFF sensing, enzyme amplified and nanozyme based sensing etc. In this review we will deliver the working principle for Array-based sensing by using various nanomaterials like nanoparticles, nanosheets, nanodots and self-assembled nanomaterials and their surface functionality for suitable molecular recognition.

Development of Optical Differential Sensing Based on Nanomaterials for Biological Analysis

The discrimination and recognition of biological targets, such as proteins, cells, and bacteria, are of utmost importance in various fields of biological research and production. These include areas like biological medicine, clinical diagnosis, and microbiology analysis. In order to efficiently and cost-effectively identify a specific target from a wide range of possibilities, researchers have developed a technique called differential sensing. Unlike traditional "lock-and-key" sensors that rely on specific interactions between receptors and analytes, differential sensing makes use of cross-reactive receptors. These sensors offer less specificity but can cross-react with a wide range of analytes to produce a large amount of data. Many pattern recognition strategies have been developed and have shown promising results in identifying complex analytes. To create advanced sensor arrays for higher analysis efficiency and larger recognizing range, various nanomaterials have been utilized as sensing probes. These nanomaterials possess distinct molecular affinities, optical/electrical properties, and biological compatibility, and are conveniently functionalized. In this review, our focus is on recently reported optical sensor arrays that utilize nanomaterials to discriminate bioanalytes, including proteins, cells, and bacteria.

Enhanced "Electronic Tongue" for Dental Bacterial Discrimination and Elimination Based on a DNA-Encoded Nanozyme Sensor Array

Bacterial infections are the second leading cause of death around the world, especially those caused by delayed treatment and misdiagnosis. Therefore, rapid discrimination and effective elimination of multiple bacteria are of great importance for improving the survival rate in clinic. Herein, a novel colorimetric sensor array for bacterial discrimination and elimination is constructed using programmable DNA-encoded iron oxide nanoparticles (IONPs) as sensing elements. Utilizing differential interactions of bacteria on DNA-encoded IONPs, 11 kinds of dental bacteria and 6 kinds of proteins have been successfully identified by linear discriminant analysis (LDA). Moreover, the developed sensing system also performs well in the quantitative determination of individual bacteria and identification of bacterial mixtures. More importantly, the practicability of this sensing strategy is further verified by precise differentiation of blind and artificial saliva samples. Furthermore, the sensor array is used for efficiently killing multiple bacteria, demonstrating great potential in clinical prophylaxis and therapy.

Identification of Water-Soluble Polymers through Machine Learning of Fluorescence Signals from Multiple Peptide Sensors

Recently, there has been growing concern about the discharge of water-soluble polymers (especially synthetic polymers) into the environment. Therefore, the identification of water-soluble polymers in water samples is becoming increasingly crucial. In this study, a chemical tongue system to simply and precisely identify water-soluble polymers using multiple fluorescently responsive peptide sensors was demonstrated. Fluorescence spectra obtained from the mixture of each peptide sensor and water-soluble polymer were changed depending on the combination of the polymer species and peptide sensors. Water-soluble polymers were successfully identified through the supervised or unsupervised machine learning of multidimensional fluorescence signals from the peptide sensors.

Supramolecular Click Chemistry for Surface Modification of Quantum Dots Mediated by Cucurbit[7]uril

Cucurbiturils (CBs), barrel-shaped macrocyclic molecules, are capable of self-assembling at the surface of nanomaterials in their native state, via their carbonyl-ringed portals. However, the symmetrical two-portal structure typically leads to aggregated nanomaterials. We demonstrate that fluorescent quantum dot (QD) aggregates linked with CBs can be broken-up, retaining CBs adsorbed at their surface, via inclusion of guests in the CB cavity. Simultaneously, the QD surface is modified by a functional tail on the guest, thus the high affinity host-guest binding (logKa > 9) enables a non-covalent, click-like modification of the nanoparticles in aqueous solution. We achieved excellent modification efficiency in several functional QD conjugates as protein labels. Inclusion of weaker-binding guests (logKa = 4-6) enables subsequent displacement with stronger binders, realising modular switchable surface chemistries. Our general "hook-and-eye" approach to host-guest chemistry at nanomaterial interfaces will lead to divergent routes for nano-architectures with rich functionalities for theranostics and photonics in aqueous systems.

Interfacing Nanomaterials with Biology through Ligand Engineering

Nanoparticles (NPs) have incredible potential in biology and biomedicine. Gold nanoparticles (AuNPs) have become a cornerstone of the nanomedicine revolution due to their ease of synthesis, inertness, and versatility. The widespread use of AuNPs can be traced to the development of accessible, bottom-up wet synthesis methods that emphasized the role of ligands in controlling the size, dispersity, and stability of colloids in solution. Decoration of AuNPs with organic ligands can be used to dictate the interactions of these nanomaterials with biosystems on multiple scales. The tunability of the AuNP ligand monolayer via covalent and noncovalent approaches allows the use of AuNPs in a broad range of biomedical fields.In this Account, we describe our use of AuNPs to answer a central question in the ligand engineering of colloidal nanoparticles: can we fabricate NPs that are nontoxic, modular, and functional in biological environments? We explored spherical AuNPs of different sizes and ligand structures, empirically exploring the AuNP-biomolecule interaction. We show here how the atom-by-atom control provided by organic synthesis can be used to create engineered ligands. Presenting these ligands on the surface of AuNPs creates multivalent constructs with unique and useful properties. Ligand design is a key feature of these AuNPs. We have developed ligands that have three distinct structural segments: 1) a hydrophobic alkanethiol interior that imparts stability; 2) a tetra(ethylene glycol) segment that creates a noninteracting tabula rasa surface; and 3) ligand headgroups that dictate how the AuNP interacts with the outside world. Our research into the design principles of ligands on AuNPs and their interactions with biological systems can be translated to other nanoparticle systems.This Account also summarizes the trajectory of ligand engineering in our laboratory and further afield. At the outset, experimental and theoretical fundamental studies were focused on the interactions between AuNPs and cellular components, such as proteins and lipid membranes. Understanding these behaviors provided the direction for investigating how ligands mediate the interface of AuNPs with mammalian and bacterial cells. In these experiments, it was particularly noteworthy that the ligand hydrophobicity and charge play a significant role in the uptake and toxicity of AuNPs. These revelations formed a basis for translating AuNPs to physiological environments. We present how we have integrated our synthetic abilities to construct AuNPs for biomedical applications, including delivery, bioorthogonal catalysis, antimicrobial and antitumor therapeutics, and biosensing.Overall, we hope that this Account will give the reader insight into how our research has evolved, changing AuNPs from synthetic curiosities into functional nanoplatforms for nanomedicine, all through the power of ligand design and synthesis.

An enzymatic activity regulation-based clusterzyme sensor array for high-throughput identification of heavy metal ions

The accurate identification and sensitive quantification of heavy metal ions are of great significance, considering that pose a serious threat to environment and human health. Most array-based sensing platforms, to date, utilize nanozymes as sensing elements, but few studies have explored the application of the peroxidase-like activity of clusterzymes in identification of multiple analytes. Herein, for the first time, we developed a clusterzyme sensor array utilizing gold nanoclusters (AuNCs) as sensing elements for five heavy metal ions identification including Hg²⁺, Pb²⁺, Cu²⁺, Cd²⁺ and Co²⁺. The heavy metal ions can differentially regulate the peroxidase-like activity of AuNCs, and that can be converted into colorimetric signals with 3,3',5,5'-tetramethylbenzidine (TMB) as the chromogenic substrate. Subsequently, the generated composite responses can be interpreted by combining pattern recognition algorithms. The developed clusterzyme sensor array can identify five heavy metal ions at concentrations as low as 0.5 μM and their multi-component mixtures. Especially, we demonstrated the successful identification of multiple heavy metal ions in tap water and traditional Chinese medicine, with an accuracy of 100% in blind test. This study provided a simple and effective method for identification and quantification of heavy metal ions, rendering a promising technique for environmental monitoring and drug safety assurance.

Recent Advances in the Pharmaceutical and Biomedical Applications of Cyclodextrin-Capped Gold Nanoparticles

The real problem in pharmaceutical preparation is drugs' poor aqueous solubility, low permeability through biological membranes, and short biological t_1/2. Conventional drug delivery systems are not able to overcome these problems. However, cyclodextrins (CDs) and their derivatives can solve these challenges. This article aims to summarize and review the history, properties, and different applications of cyclodextrins, especially the ability of inclusion complex formation. It also refers to the effects of cyclodextrin on drug solubility, bioavailability, and stability. Moreover, it focuses on preparing and applying gold nanoparticles (AuNPs) as novel drug delivery systems. It also studies the uses and effects of cyclodextrins in this field as novel drug carriers and targeting devices. The system formulated from AuNPs linked with CD molecules combines the advantages of both CD and AuNPs. Cyclodextrins benefit in increasing aqueous drug solubility, loading capacity, stability, and size control of gold NPs. Also, AuNPs are applied as diagnostic and therapeutic agents because of their unique chemical properties. Plus, AuNPs possess several advantages such as ease of detection, targeted and selective drug delivery, greater surface area, high loading efficiency, and higher stability than microparticles. In the present article, we tried to present the potential pharmaceutical applications of CD-derived AuNPs in biomedical applications including antibacterial, anticancer, gene-drug delivery, and various targeted drug delivery applications. Also, the article highlighted the role of CDs in the preparation and improvement of catalytic enzymes, the formation of self-assembling molecular print boards, the fabrication of supramolecular functionalized electrodes, and biosensors formation.

An Insight Into the Physicochemical Properties of Gold Nanoparticles in Relation to Their Clinical and Diagnostic Applications

The ease of formulation and surface modification of gold nanoparticles (AuNPs) by ligands, greater biocompatibility, non-cytotoxicity, and excellent optical properties are the characteristics that necessitate their application in clinical and genomic research. Not only that, but the extensive synthetic chemistry of AuNPs also offers precise control over physicochemical and optical properties owing to the inert, biocompatible, and non-toxic nature of the inner gold core. Another important property of AuNPs involves their incorporation into larger structures, including liposomes or polymeric materials, thereby increasing their capability of drug delivery in concurrent therapy and imaging labels for enhanced diagnostic applications. AuNPs are endowed with physical properties that suggest their use as adjuvants for radiotherapy and bio-imaging and in computed tomography (CT) scans, diagnostic systems, and therapy. Thus, these features strongly endorse the AuNPs in thrust areas of biomedical fields. The diverse properties of gold nanoparticles (AuNPs) have made them promising candidates in biomedical fields, including in the development of theranostics, which encompasses using these gold nanoparticles for both diagnosis and therapy simultaneously. To appreciate these and related applications, a need arises to review the basic principles and multifunctional attributes of AuNPs in relation to their advances in imaging, therapy, and diagnostics.

Recent Progress in Sensor Arrays: From Construction Principles of Sensing Elements to Applications

The traditional sensors are designed based on the "lock-and-key" strategy with high selectivity and specificity for detecting specific analytes, which however are not suitable for detecting multiple analytes simultaneously. With the help of pattern recognition technologies, the sensor arrays excel in distinguishing subtle changes caused by multitarget analytes with similar structures in a complex system. To construct a sensor array, the multiple sensing elements are undoubtedly indispensable units that will selectively interact with targets to generate the unique "fingerprints" based on the distinct responses, enabling the identification among various analytes through pattern recognition methods. This comprehensive review mainly focuses on the construction strategies and principles of sensing elements, as well as the applications of sensor array for identification and detection of target analytes in a wide range of fields. Furthermore, the present challenges and further perspectives of sensor arrays are discussed in detail.

Mass spectrometry-based targeted proteomics for analysis of protein mutations

Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.

An ion-coordination hydrogel based sensor array for point-of-care identification and removal of multiple tetracyclines

Misuse and overuse of tetracycline antibiotics (TCs) brings serious issues to ecological environment, food safety and human health. It is urgent to develop unique platform for high efficient identification and removal of TCs. In the present investigation, an effective and simple fluorescence sensor array was constructed based on the interaction between metal ions (Eu³⁺ and Al³⁺) and antibiotics. Benefiting from the different affinities between the ions and TCs, the sensor array can identify TCs from other antibiotics, which also can further differentiating four kinds of TCs (OTC, CTC, TC and DOX) from each other via linear discriminant analysis (LDA) technique. Meanwhile, the sensor array performed well in quantitative analysis of single TC antibiotic and differentiation of TCs mixtures. More interestingly, Eu³⁺ and Al³⁺-doped sodium alginate/polyvinyl alcohol hydrogel beads (SA/Eu/PVA and SA/Al/PVA) were further constructed, which can not only identify the TCs but simultaneously remove the antibiotics with high efficiency. The investigation provided an instructive way for rapid detection and environment protection.

Giving Gold Wings: Ultrabright and Fragmentation Free Mass Spectrometry Reporters for Barcoding, Bioconjugation Monitoring, and Data Storage

The widespread application of laser desorption/ionization mass spectrometry (LDI-MS) highlights the need for a bright and multiplexable labeling platform. While ligand-capped Au nanoparticles (AuNPs) have emerged as a promising LDI-MS contrast agent, the predominant thiol ligands suffer from low ion yields and extensive fragmentation. In this work, we develop a N-heterocyclic carbene (NHC) ligand platform that enhances AuNP LDI-MS performance. NHC scaffolds are tuned to generate barcoded AuNPs which, when benchmarked against thiol-AuNPs, are bright mass tags and form unfragmented ions in high yield. To illustrate the transformative potential of NHC ligands, the mass tags were employed in three orthogonal applications: monitoring a bioconjugation reaction, performing multiplexed imaging, and storing and reading encoded information. These results demonstrate that NHC-nanoparticle systems are an ideal platform for LDI-MS and greatly broaden the scope of nanoparticle contrast agents.

Peroxidase-Mimicking DNAzymes as Receptors for Label-Free Discriminating Heavy Metal Ions by Chemiluminescence Sensor Arrays

Receptors are crucial to the analytical performance of sensor arrays. Different from the previous receptors in sensor arrays, herein, peroxidase-mimicking DNAzymes were innovatively used as receptors to develop a label-free chemiluminescence sensor array for discriminating various heavy metal ions in complex samples. The peroxidase-mimicking DNAzymes are composed of functional oligonucleotides and hemin, including G-triplex-hemin DNAzyme (G3-DNAzyme), G-quadruplex-hemin DNAzyme (G4-DNAzyme), and the dimer of G-quadruplex-hemin DNAzyme (dG4-DNAzyme). Circular dichroism (CD) spectroscopy demonstrated that different metal ions diversely affect the conformation of G-quadruplex and G-triplex, resulting in a change in the activity of peroxidase-mimicking DNAzyme. Thus, the unique fingerprints formed to easily discriminate seven kinds of heavy metal ions by principal component analysis (PCA) within 20 min. The discrimination of unknown metal ions in tap water further confirmed its ability for discriminating multiple heavy metal ions. Moreover, it will not bring water pollution due to the good biocompatibility of DNA. Therefore, it not only merely offers a label-free, rapid, environment-friendly, and cheap (1.49 $) sensor assay for discriminating metal ions but also comes up with an innovative way for developing sensor arrays.

A Metal Nanoparticle Thermistor with the Beta Value of 10 000 K

The thermistor, typically made from metallic oxides, is a type of resistor whose electrical resistance is dependent on its temperature. Despite the wide usage, the limitations of ceramic thermistors become increasingly apparent as devices with improved performances are sought and as new applications emerge. Herein, a thermistor that is showed with a beta (B) value of 10 000 K can be made exclusively from metal nanoparticles functionalized with charged organic ligands. This B value is hard to achieve for ceramic devices, which is due to the increase of effective counterion concentration and its mobility upon thermal activation. Importantly, the performance of the nanoparticle thermistor is maintained when it is fabricated on a flexible substrate and experiences reversible bending. Demos of thermistor arrays for heat transfer, distribution, and comparison of their performance with commercial products are also demonstrated. Owing to the low temperature and simple casting process, conformably flexible characteristics, stable solid states, and ultra-high sensitivities, this device is expected to be practically used soon.

Preparation and Evaluation of 64Cu-Radiolabled Dual-Ligand Multifunctional Gold Nanoparticles for Tumor Theragnosis

Gold nanoparticles (AuNPs) are cutting-edge platforms for combined diagnostic and therapeutic approaches due to their exquisite physicochemical and optical properties. Using the AuNPs physically produced by femtosecond pulsed laser ablation of bulk Au in deionized water, with a capping agent-free surface, the conjugation of functional ligands onto the AuNPs can be tunable between 0% and 100% coverage. By taking advantage of this property, AuNPs functionalized by two different types of active targeting ligands with predetermined ratios were fabricated. The quantitatively controllable conjugation to construct a mixed monolayer of multiple biological molecules at a certain ratio onto the surface of AuNPs was achieved and a chelator-free ⁶⁴Cu-labeling method was developed. We report here the manufacture, radiosynthesis and bioevaluation of three different types of dual-ligand AuNPs functionalized with two distinct ligands selected from glucose, arginine-glycine-aspartate (RGD) peptide, and methotrexate (MTX) for tumor theragnosis. The preclinical evaluation demonstrated that tumor uptakes and retention of two components AuNP conjugates were higher than that of single-component AuNP conjugates. Notably, the glucose/MT- modified dual-ligand AuNP conjugates showed significant improvement in tumor uptake and retention. The novel nanoconjugates prepared in this study make it possible to integrate several modalities with a single AuNP for multimodality imaging and therapy, combining the power of chemo-, thermal- and radiation therapies together.

Ensemble Modified Aptamer Based Pattern Recognition for Adaptive Target Identification

The difficulty of the molecular design and chemical synthesis of artificial sensing receptors restricts their diagnostic and proteomic applications. Herein, we report a concept of "ensemble modified aptamers" (EMAmers) that exploits the collective recognition abilities of a small set of protein-like side-chain-modified nucleic acid ligands for discriminative identification of molecular or cellular targets. Different types and numbers of hydrophobic functional groups were incorporated at designated positions on nucleic acid scaffolds to mimic amino acid side chains. We successfully assayed 18 EMAmer probes with differential binding affinities to seven proteins. We constructed an EMAmer-based chemical nose sensor and demonstrated its application in blinded unknown protein identification, giving a 92.9% accuracy. Additionally, the sensor is generalizable to the detection of blinded unknown bacterial and cellular samples, which enabled identification accuracies of 96.3% and 94.8%, respectively. This sensing platform offers a discriminative means for adaptive target identification and holds great potential for diverse applications.

Fluorescent copper conjugated curcumin cysteine nanoprobe for selective determination of Fe3+ and G-quadruplex DNA

The synthesis of fluorescent copper-curcumin-cysteine (Cu-CC) as a sensing platform is reported. The synthesized probe has been confirmed by UV-visible spectroscopy, FT-IR, XRD, SEM, and TEM characterization techniques, respectively. The mechanistic aspects of selective sensing of Fe³⁺ and detection of different G-quadruplex DNA have been illustrated based on the "turn-off-on" concept of a regeneratable fluorescence sensing probe at λ_ex 450 nm. Interestingly, we have noticed a high selectivity to Fe³⁺ ion by the developed Cu-CC sensing probe in comparison with other metal ions. Furthermore, the restoration of fluorescence of the sensing probe in the presence of different DNA sequences is illustrating a cost-effective, convenient, and reliable detection methodology of DNA detection. It is highly sensitive for the determination of Pu27, promoter c-MYC quadruplex DNA in a wide linear range of 100-700 nM having a detection limit of 13.1 nM (RSD: 0.15%) and sensitivity of 37.2 cps/nM. Whereas, the Pu18 and H-telo telomeric DNA sequences are showing a narrow linear range, i.e., 10 nM-200 nM and 10 nM-180 nM, respectively. The real-world sample analysis performance of the regeneratable sensing probe for Pu27 DNA detection in fresh human blood serum samples is showing a satisfactory result.

A facile way to construct sensor array library via supramolecular chemistry for discriminating complex systems

Differential sensing, which discriminates analytes via pattern recognition by sensor arrays, plays an important role in our understanding of many chemical and biological systems. However, it remains challenging to develop new methods to build a sensor unit library without incurring a high workload of synthesis. Herein, we propose a supramolecular approach to construct a sensor unit library by taking full advantage of recognition and assembly. Ten sensor arrays are developed by replacing the building block combinations, adjusting the ratio between system components, and changing the environment. Using proteins as model analytes, we examine the discriminative abilities of these supramolecular sensor arrays. Then the practical applicability for discriminating complex analytes is further demonstrated using honey as an example. This sensor array construction strategy is simple, tunable, and capable of developing many sensor units with as few syntheses as possible.

Aggregation and Binding-Directed FRET Modulation of Conjugated Polymer Materials for Selective and Point-of-Care Monitoring of Serum Albumins

Nonspecific interactions of conjugated polymers (CPs) with various proteins prove to be a major impediment for researchers when designing a suitable CP-based probe for the amplified and selective recognition of particular proteins in complex body fluids. Herein, a new strategy is presented for the precise and specific monitoring of clinically important serum albumin (SA) proteins at the nanomolar level using fluorescence resonance energy transfer (FRET)-modulated CP-surfactant ensembles as superior sensing materials. In brief, the newly designed color-tunable CP PF-DBT-Im undergoes intense aggregation with the surfactant sodium dodecyl sulfate (SDS), enabling drastic change in the emission color from violet to deep red due to intermolecular FRET. The emission of PF-DBT-Im/SDS ensembles then changed from deep red to magenta specifically on addition of SAs owing to the exclusive reverse FRET facilitated by synergistic effects of electrostatic interactions, hydrophobic forces, and the comparatively high intrinsic quantum yield of SAs. Interestingly, PF-DBT-Im itself could not differentiate SAs from other proteins, demonstrating the superiority of the PF-DBT-Im/SDS self-assembly over PF-DBT-Im. Finally, an affordable smartphone-integrated point-of-care (PoC) device is also fabricated as a proof-of-concept for the on-site and rapid monitoring of SAs, validating the potential of the system in long-term clinical applications.

Multiple-Aptamer-Integrated DNA-Origami-Based Chemical Nose Sensors for Accurate Identification of Cancer Cells

Developing simple, rapid, and accurate methods for cancer cell identification could facilitate early cancer diagnosis and tumor metastasis research. Herein, we develop a novel chemical nose sensor that employs the collective recognition abilities of a set of multiple-aptamer-integrated DNA origami (MADO) probes for discriminative identification of cancer cells. By controlling the types and/or copies of aptamers assembled on the DNA origami nanostructure, we constructed five MADO probes with differential binding affinities (ranging from 3.08 to 78.92 nM) to five types of cells (HeLa, MDA-MB-468, MCF-7, HepG2, and MCF-10A). We demonstrate the utility of the MADO-based chemical nose sensor in the identification of blinded unknown cell samples with a 95% accuracy. This sensing platform holds great potential for applications in medical diagnostics.

Flower-like Gold Nanoparticles for In Situ Tailoring Luminescent Molecules for Synergistic Enhanced Chemiluminescence

In recent years, gold nanoparticles (AuNPs) have attracted much attention due to their ease of surface modification, excellent biocompatibility, and extraordinary optoelectronic and catalytic activities. Herein, based on a AuNP-catalyzed reaction, a strategy for tailoring luminescent molecules in situ is proposed to trigger an ultrastrong chemiluminescence (CL). In the strategy, flower-like AuNPs are prepared using CL molecular probes (Probe-OH for NaClO/ONOO^-) via one-pot synthesis and subsequently act as a tailor for Probe-OH to generate novel CL molecules, allowing a synergistic CL enhancement about 4 times that of initial Probe-OH. Furthermore, by modification with poly(vinylpyrrolidone) (PVP) on the surface, the CL signals (only for NaClO) are amplified by 100 times based on an intermolecular chemically initiated electron exchange luminescence (CIEEL) mechanism. Given the improved sensitivity and selectivity over Probe-OH, the thus-formed CIEEL nanoplatform (PVP-Au) is successfully developed for detecting NaClO in a wide range of 2.5-100 μM, and the detection limit is 10.68 nM. This work provides unprecedented perspectives for expanding this facile and effective strategy for CL amplification based on AuNP catalysis.

A Gold Nanoparticle-Based Molecular Self-Assembled Colorimetric Chemosensor Array for Monitoring Multiple Organic Oxyanions

Determination of oxyanions is of paramount importance because of the essential role they play in metabolic processes involved in various aquatic environmental problems. In this investigation, a novel chemical sensor array has been developed by using gold nanoparticles modified with different chain lengths of aminothiols (AET-AuNPs) as sensing elements. The proposed sensor array provides a fingerprint-like response pattern originating from cross-reactive binding events and capable of targeting various anions, including the herbicide glyphosate. In addition, chemometric techniques, linear discrimination analysis (LDA) and the support vector machine (SVM) algorithm were employed for analyte classification and regression/prediction. The obtained sensor array demonstrates a remarkable ability to determine multiple oxyanions in both qualitative and quantitative analysis. The described methodology could be used as a simple, sensitive and fast routine analysis for oxyanions in both laboratory and field settings.

Carbon Quantum Dots Based Chemosensor Array for Monitoring Multiple Metal Ions

The simultaneous identification of multiple metal ions in water has attracted enormous research interest in the past few decades. We herein describe a novel method for multiple metal ion detection using a carbon quantum dots (CQDs)-based chemosensor array and the CQDs are functionalized with different amino acids (glutamine, histidine, arginine, lysine and proline), which act as sensing elements in the sensor array. Eleven metal ions are successfully identified by the designed chemosensor array, with 100% classification accuracy. Importantly, the proposed method allowed the quantitative prediction of the concentration of individual metal ions in the mixture with the aid of a support vector machine (SVM). The sensor array also enables the qualitative detection of unknown metal ions under the interference of tap water and local river water. Thus, the strategy provides a novel high-throughput approach for the identification of various analytes in complex systems.

One metal-ion-regulated AgTNPs etching sensor array for visual discrimination of multiple organic acids

The detection and discrimination of organic acids (OAs) is of great importance in the early diagnosis of specific diseases. In this study, we established an effective visual sensor array for the identification of OA. This is the first time, to our best knowledge, that metal ions were used to regulate the etching of silver triangular nanoprisms (AgTNPs) in an OA discrimination sensor array. The sensor array was based on the oxidation etching of AgTNPs by three metal ions (Mn²⁺, Pb²⁺, and Cr³⁺) and accelerated etching of AgTNPs by OA. The introduction of metal ions alone led to a slight wavelength shift of the AgTNPs colloid solution, signifying the incomplete etching of the AgTNPs. Nevertheless, when metal ions and OA were introduced simultaneously to the solution, a significant blueshift of the localized surface plasmon resonance peak was detected, and a color change of the AgTNPs was observed, which were the consequences of morphological transitions of the AgTNPs. The addition of different OA accelerated AgTNPs etching in varying degrees, generating diverse colorimetric response patterns (i.e., RGB variations) as "fingerprints" associated with each specific organic acid. Pattern recognition algorithms and neural network simulation were employed to further data analysis, indicating the outstanding discrimination capability of the provided array for eight OA at the 33 µM level. Moreover, excellent results of selective experiments as well as real samples tests demonstrate that our proposed method possesses great potential for practical applications.

Metabolism-Triggered Colorimetric Sensor Array for Fingerprinting and Antibiotic Susceptibility Testing of Bacteria

The rapid identification and antibiotic susceptibility testing (AST) of bacteria would help us to accurately identify the infectious sources as well as guide the use of antibiotics, which are crucial for improving the survival rate and antimicrobial resistance. Herein, a colorimetric sensor array for bacteria fingerprinting was constructed with d-amino acid (d-AA)-modified gold nanoparticles (AuNPs) as probes (Au/d-AA). Bacteria can metabolize the d-AA, triggering the aggregation of AuNPs. Making use of different metabolic capabilities of bacteria toward different d-AA, eight kinds of bacteria including antibiotic-resistant bacteria and strains of the same bacterial species are successfully differentiated via learning the response patterns. Meanwhile, the sensor array also performs well in quantitative analysis of single bacterium and differentiation of bacteria mixtures. More interestingly, a rapid colorimetric AST approach has been developed based on the Au/d-AA nanoprobes by monitoring the d-AA metabolic activity of bacteria toward various antibiotic treatments. In this regard, the outlined work here would promote clinical practicability and facilitate antibiotic stewardship.

Peptide-Induced Fractal Assembly of Silver Nanoparticles for Visual Detection of Disease Biomarkers

We report the peptide-programmed fractal assembly of silver nanoparticles (AgNPs) in a diffusion-limited aggregation (DLA) mode, and this change in morphology generates a significant color change. We show that peptides with specific repetitions of defined amino acids (i.e., arginine, histidine, or phenylalanine) can induce assembly and coalescence of the AgNPs (20 nm) into a hyperbranched structure (AgFSs) (∼2 μm). The dynamic process of this assembly was systematically investigated, and the extinction of the nanostructures can be modulated from 400 to 600 nm by varying the peptide sequences and molar ratio. According to this rationale, two strategies of SARS-CoV-2 detection were investigated. The activity of the main protease (Mpro) involved in SARS-CoV-2 was validated with a peptide substrate that can bridge the AgNPs after the proteolytic cleavage. A sub-nanomolar limit of detection (0.5 nM) and the capacity to distinguish by the naked eye in a wide concentration range (1.25-30 nM) were achieved. Next, a multichannel sensor-array based on multiplex peptides that can visually distinguish SARS-CoV-2 proteases from influenza proteases in doped human samples was investigated.

CsPbBr3 and CsPbBr3/SiO2 Nanocrystals as a Fluorescence Sensing Platform for High-Throughput Identification of Multiple Thiophene Sulfides

Air pollution is a serious problem. Refractory thiophene sulfides, which cause air pollution, bring great challenges to their rapid and accurate identification. In this work, we propose a fluorescent sensor array based on two perovskite nanocrystals (CsPbBr₃ NCs and CsPbBr₃/SiO₂ NCs) to distinguish different thiophene sulfides. The hydrogen bonding force between the thiophenics of thiophene sulfides and the amino groups of the perovskite NCs results in the weakening of the fluorescence signals of the perovskite NCs. The diverse interactions between thiophene sulfides and two perovskite NCs provide rich information, which can be obtained on the sensor array and identified by linear discriminant analysis. Five thiophene sulfides (i.e., benzothiophene, dibenzothiophene, 2-methylbenzothiophene, 3-methylthiophene, and thiophene) were discriminated by the sensor array at concentrations of 10-50 ppm. The effectiveness of the sensor array was further verified in the discrimination of blinded samples, in which all 10 samples were correctly identified. In addition, it is gratifying that even binary mixtures of thiophene sulfides could be distinguished by the proposed sensor array.

Construction of a colorimetric sensor array based on the coupling reaction to identify phenols

Phenols are harmful to the human body and the environment. Since there are a variety of phenols in actual samples, this requires a sensor which possesses the ability to simultaneously distinguish them. Herein, we report a colorimetric sensor array, which uses two nanozymes (Fe-N-C nanozymes and Cu-N-C nanozymes) as electronic tongues for fingerprint identification of six phenols (2,4,6-trichlorophenol (2,4,6-Tri), 4-nitrophenol (P-np), phenol (Phe), 3-chlorophenol (3-CP), 4-chlorophenol (4-CP), and o-nitrophenol (O-np)) in the environment. Nanozymes catalyzed the reaction of hydrogen peroxide, different phenols and 4-aminoantipyrine (4-AAP) to produce different color variations. These signal changes as fingerprints encouraged us to develop a pattern recognition method for the identification of phenols by linear discriminant analysis (LDA). The six phenols at 50 nM have their own response patterns, respectively. Surprisingly, this sensor array had distinguished the six phenols in actual samples successfully.

Multiplexing the Quantitation of MAP Kinase Activities Using Differential Sensing

Protein kinases are therapeutic targets for many human diseases, but the lack of user-friendly quantitative assays limits the ability to follow the activities of numerous kinases at once (multiplexing). To develop such an assay, we report an array of sulfonamido-oxine (SOX)-labeled peptides showing cross-reactivity to different mitogen-activated protein kinases (MAPKs) for use in a differential sensing scheme. We first verified using linear discriminant analysis that the array could differentiate MAPK isoforms. Then, using principal component analysis, the array was optimized based on the discrimination imparted by each SOX-peptide. Next, the activity of individual MAPK families in ternary mixtures was quantified by support vector machine regression. Finally, we multiplexed the quantification of three MAPK families using partial least squares regression in A549 cell lysates, which has possible interference from other kinase classes. Thus, our method simultaneously quantifies the activity of multiple kinases. The technique could be applied to other protein kinase families and the monitoring of diseases.

Single Probe-Based Chemical-Tongue Sensor Array for Multiple Bacterial Identification and Photothermal Sterilization in Real Time

Simple and efficient identification of multiple bacteria and sterilization in real time is of considerable significance for clinical diagnostics and quality control in food. Herein, a novel chemical-tongue sensor array with 3,3',5,5'-tetramethylbenzidine (TMB) as a single probe was developed for bacterial identification and photothermal elimination. The synthesized bimetallic palladium/platinum nanoparticles (Pd/Pt_NPs) present excellent catalytic capability that can catalyze TMB into oxidized TMB (oxTMB) with four feature absorption peaks. Bacteria have different ability on inhibiting the reaction between TMB and Pd/Pt_NPs. With the absorbance intensity of oxTMB at the four feature peaks as readout, nine kinds of bacteria including two drug-resistant bacteria can be successfully distinguished via linear discriminant analysis. Remarkably, oxTMB exhibits excellent photothermal properties and can effectively kill bacteria in real time under near-infrared laser irradiation. The strategy of selecting TMB as a single probe simplifies the experimental operation and reduces the time cost. Furthermore, the developed sensing system was used to promote the wound healing process of MRSA-infected mice in vivo. The investigation provides a promising simple and efficient strategy for bacterial identification and sterilization with a universal platform, which has great potential application in clinical diagnosis and therapy.

Designing Functional Bionanoconstructs for Effective In Vivo Targeting

The progress achieved over the last three decades in the field of bioconjugation has enabled the preparation of sophisticated nanomaterial–biomolecule conjugates, referred to herein as bionanoconstructs, for a multitude of applications including biosensing, diagnostics, and therapeutics. However, the development of bionanoconstructs for the active targeting of cells and cellular compartments, both in vitro and in vivo, is challenged by the lack of understanding of the mechanisms governing nanoscale recognition. In this review, we highlight fundamental obstacles in designing a successful bionanoconstruct, considering findings in the field of bionanointeractions. We argue that the biological recognition of bionanoconstructs is modulated not only by their molecular composition but also by the collective architecture presented upon their surface, and we discuss fundamental aspects of this surface architecture that are central to successful recognition, such as the mode of biomolecule conjugation and nanomaterial passivation. We also emphasize the need for thorough characterization of engineered bionanoconstructs and highlight the significance of population heterogeneity, which too presents a significant challenge in the interpretation of in vitro and in vivo results. Consideration of such issues together will better define the arena in which bioconjugation, in the future, will deliver functional and clinically relevant bionanoconstructs.

High affinity protein surface binding through co-engineering of nanoparticles and proteins

Control over supramolecular recognition between proteins and nanoparticles (NPs) is of fundamental importance in therapeutic applications and sensor development. Most NP-protein binding approaches use 'tags' such as biotin or His-tags to provide high affinity; protein surface recognition provides a versatile alternative strategy. Generating high affinity NP-protein interactions is challenging however, due to dielectric screening at physiological ionic strengths. We report here the co-engineering of nanoparticles and protein to provide high affinity binding. In this strategy, 'supercharged' proteins provide enhanced interfacial electrostatic interactions with complementarily charged nanoparticles, generating high affinity complexes. Significantly, the co-engineered protein-nanoparticle assemblies feature high binding affinity even at physiologically relevant ionic strength conditions. Computational studies identify both hydrophobic and electrostatic interactions as drivers for these high affinity NP-protein complexes.

Detection and separation of proteins using micro/nanofluidics devices

Microfluidics is the technology or system wherein the behavior of fluids' is studied onto a miniaturized device composed of chambers and tunnels. In biological and biomedical sciences, microfluidic technology/system or device serves as an ultra-high-output approach capable of detecting and separating the biomolecules present even in trace quantities. Given the essential role of protein, the identification and quantification of proteins help understand the various living systems' biological function regulation. Microfluidics has enormous potential to enable biological investigation at the cellular and molecular level and maybe a fair substitution of the sophisticated instruments/equipment used for proteomics, genomics, and metabolomics analysis. The current advancement in microfluidic systems' development is achieving momentum and opening new avenues in developing innovative and hybrid methodologies/technologies. This chapter attempts to expound the micro/nanofluidic systems/devices for their wide-ranging application to detect and separate protein. It covers microfluidic chip electrophoresis, microchip gel electrophoresis, and nanofluidic systems as protein separation systems, while methods such as spectrophotometric, mass spectrometry, electrochemical detection, magneto-resistive sensors and dynamic light scattering (DLS) are discussed as proteins' detection system.

Spectral image contrast-based flow digital nanoplasmon-metry for ultrasensitive antibody detection

Background

Gold nanoparticles (AuNPs) have been widely used in local surface plasmon resonance (LSPR) immunoassays for biomolecule sensing, which is primarily based on two conventional methods: absorption spectra analysis and colorimetry. The low figure of merit (FoM) of the LSPR and high-concentration AuNP requirement restrict their limit of detection (LOD), which is approximately ng to μg mL⁻¹ in antibody detection if there is no other signal or analyte amplification. Improvements in sensitivity have been slow in recent for a long time, and pushing the boundary of the current LOD is a great challenge of current LSPR immunoassays in biosensing.

Results

In this work, we developed spectral image contrast-based flow digital nanoplasmon-metry (Flow DiNM) to push the LOD boundary. Comparing the scattering image brightness of AuNPs in two neighboring wavelength bands near the LSPR peak, the peak shift signal is strongly amplified and quickly detected. Introducing digital analysis, the Flow DiNM provides an ultrahigh signal-to-noise ratio and has a lower sample volume requirement. Compared to the conventional analog LSPR immunoassay, Flow DiNM for anti-BSA detection in pure samples has an LOD as low as 1 pg mL⁻¹ within only a 15-min detection time and 500 μL sample volume. Antibody assays against spike proteins of SARS-CoV-2 in artificial saliva that contained various proteins were also conducted to validate the detection of Flow DiNM in complicated samples. Flow DiNM shows significant discrimination in detection with an LOD of 10 pg mL⁻¹ and a broad dynamic detection range of five orders of magnitude.

Conclusion

Together with the quick readout time and simple operation, this work clearly demonstrated the high sensitivity and selectivity of the developed Flow DiNM in rapid antibody detection. Spectral image contrast and digital analysis further provide a new generation of LSPR immunoassay with AuNPs.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-021-01188-6.

A sensor array based on DNA-wrapped bimetallic zeolitic imidazolate frameworks for detection of ATP hydrolysis products

Most current biosensors were designed for the detection of individual analytes, or a group of chemically similar analytes. We reason that sensors designed to track both reactants and products might be useful for following chemical reactions. Adenosine triphosphate (ATP) is a key biomolecule that participates in various biochemical reactions, and its hydrolysis plays a fundamental role in life. ATP can be converted to adenosine diphosphate (ADP) and inorganic phosphate (Pi) via the dephosphorylation process. ATP can also be hydrolyzed to adenosine monophosphate (AMP) and pyrophosphate (PPi) through depyrophosphorylation, depending on where the bond is cleaved. The detection of ATP-related hydrolysates would enable a better understanding of the different reaction pathways with a high level of robustness and confidence. Herein, we prepared a fluorescent sensor array based on a series of bimetallic zeolite imidazole frameworks M/ZIF-8 (M = Ni, Mn, Cu) and ZIF-67 to discriminate ATP hydrolysis and detect ATP hydrolysis related analytes. A fluorescently-labeled DNA oligonucleotide was used for signaling. Interestingly, Cu/ZIF-8 exhibited an ultrahigh selectivity for recognizing pyrophosphate with a detection limit of 2.5 μM. Moreover, the practicality of this sensor array was demonstrated in fetal bovine serum, clearly discriminating ATP hydrolysis products.

Nanogold-based materials in medicine: from their origins to their future

The properties of gold-based materials have been explored for centuries in several research fields, including medicine. Multiple published production methods for gold nanoparticles (AuNPs) have shown that the physicochemical and optical properties of AuNPs depend on the production method used. These different AuNP properties have allowed exploration of their usefulness in countless distinct biomedical applications over the last few years. Here we present an extensive overview of the most commonly used AuNP production methods, the resulting distinct properties of the AuNPs and the potential application of these AuNPs in diagnostic and therapeutic approaches in biomedicine.

Multiplexed Profiling of Extracellular Vesicles for Biomarker Development

Extracellular vesicles (EVs) are cell-derived membranous particles that play a crucial role in molecular trafficking, intercellular transport and the egress of unwanted proteins. They have been implicated in many diseases including cancer and neurodegeneration. EVs are detected in all bodily fluids, and their protein and nucleic acid content offers a means of assessing the status of the cells from which they originated. As such, they provide opportunities in biomarker discovery for diagnosis, prognosis or the stratification of diseases as well as an objective monitoring of therapies. The simultaneous assaying of multiple EV-derived markers will be required for an impactful practical application, and multiplexing platforms have evolved with the potential to achieve this. Herein, we provide a comprehensive overview of the currently available multiplexing platforms for EV analysis, with a primary focus on miniaturized and integrated devices that offer potential step changes in analytical power, throughput and consistency.

Histopathological evaluation of amino acid capped silver nanoconjugates in albino mice

Various molecules may modify the surface chemistry of commonly used nanomaterials (NMs), resulting in the synthesis of novel and safer NMs. The current study was delineated to evaluate the in vivo toxicity profiling of the silver nanoconjugates (AgNCs) conjugated with different amino acids. The L-glycine capped-AgNCs exhibited toxicity and caused tissue damage, while L-cystine- and L-tyrosine-capped AgNCs showed protective effects against cadmium-induced toxicity. L-cystine-capped AgNCs performed well as compared to other amino-acid AgNCs. The level of serum creatinine, alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase and blood urea increased (p < 0.05) in G2, G3 and G5 in comparison to G1 (control group), while an increase in bilirubin for G2 was statistically non-significant (p > 0.05). The ALT and AST elevated (p < 0.05) in G4; however, other serological parameters in G4 and G6 did not show any noticeable change in their values. Histological analysis showed disturbed and deformed cellular structures in liver and kidney tissues of G2, G3 and G5. However, G4 and G6 samples demonstrated minute changes in comparison to G1. It is concluded that L-cystine- and L-tyrosine-capped AgNCs exhibited protective effects and should be tested further for developing safer nanoconjugates for biomedical uses.

Identification of Water-Soluble Polymers through Discrimination of Multiple Optical Signals from a Single Peptide Sensor

The pollution of water environments is a worldwide concern. Not only marine pollution by plastic litter, including microplastics, but also the spillage of water-soluble synthetic polymers in wastewater have recently gained increasing attention due to their potential risks to soil and water environments. However, conventional methods to identify polymers dissolved in water are laborious and time-consuming. Here, we propose a simple approach to identify synthetic polymers dissolved in water using a peptide-based molecular sensor with a fluorophore unit. Supervised machine learning of multiple fluorescence signals from the sensor, which specifically or nonspecifically interacted with the polymers, was applied for polymer classification as a proof of principle demonstration. Aqueous solutions containing different polymers or multiple polymer species with different mixture ratios were identified successfully. We found that fluorophore-introduced biomolecular sensors have great potential to provide discriminative information regarding water-soluble polymers. Our approach based on the discrimination of multiple optical signals of water-soluble polymers from peptide-based molecular sensors through machine learning will be applicable to next-generation sensing systems for polymers in wastewater or natural environments.

Role of nanotechnology in animal production and veterinary medicine

Nanotechnology is the discipline and technology of small and specific things that are < 100 nm in size. Because of their extremely miniscule size, any changes in their chemical and physical structure may show higher reactivity and solubility than larger particles. Nanotechnology plays a vital role in every field of life. It is considered one of the most bleeding edge field of scientific research. It has already several applications in a myriad of disciplines while its application in the field of animal production and veterinary medicine is still experimental in nature. But, in recent years, the role of nanotechnology in the aforementioned fields of scientific inquiry has shown great progress. These days, nanotechnology has been employed to revolutionize drug delivery systems and diagnose atypical diseases. Applications of nanoparticle technology in the field of animal reproduction and development of efficacious vaccines have been at the forefront of scientific endeavors. Additionally, their impacts on meat and milk quality are also being judiciously inquired in recent decades. Veterinary nanotechnology has great potential to improve diagnosis and treatment, and provide new tools to this field. This review focuses on some noteworthy applications of nanoparticles in the field of animal production and their future perspectives.

Transition-Metal Dichalcogenide Artificial Antibodies with Multivalent Polymeric Recognition Phases for Rapid Detection and Inactivation of Pathogens

Antibodies are recognition molecules that can bind to diverse targets ranging from pathogens to small analytes with high binding affinity and specificity, making them widely employed for sensing and therapy. However, antibodies have limitations of low stability, long production time, short shelf life, and high cost. Here, we report a facile approach for the design of luminescent artificial antibodies with nonbiological polymeric recognition phases for the sensitive detection, rapid identification, and effective inactivation of pathogenic bacteria. Transition-metal dichalcogenide (TMD) nanosheets with a neutral dextran phase at the interfaces selectively recognized S. aureus, whereas the nanosheets bearing a carboxymethylated dextran phase selectively recognized E. coli O157:H7 with high binding affinity. The bacterial binding sites recognized by the artificial antibodies were thoroughly identified by experiments and molecular dynamics simulations, revealing the significance of their multivalent interactions with the bacterial membrane components for selective recognition. The luminescent WS₂ artificial antibodies could rapidly detect the bacteria at a single copy from human serum without any purification and amplification. Moreover, the MoSe₂ artificial antibodies selectively killed the pathogenic bacteria in the wounds of infected mice under light irradiation, leading to effective wound healing. This work demonstrates the potential of TMD artificial antibodies as an alternative to antibodies for sensing and therapy.

Development of pattern recognition based on nanosheet-DNA probes and an extendable DNA library

Pattern recognition, also called "array sensing," is a recognition strategy with a wide and expandable analysis range, based on high-throughput analysis data. In this work, we constructed a sensor array for the identification of targets including bacterial pathogens and proteins by using FAM-labeled DNA probes and 2D nanosheet materials. We designed an ordered and extendible DNA library for the collection of recognition probes. Unlike traditional DNA probes with random and massive sequences, our DNA library was constructed following a 5-digit binary number (00000-11111, 0 = CCC, and 1 = TTT), and especially, 8 special symmetry sequences were chosen from the library. Two different nanosheet materials were used as the quencher. When targets were added, the interaction between DNA and the nanosheets was competitively affected, and as a result, the fluorescence signal changed accordingly. Finally, by using our fluorescent sensor array, 17 bacteria and 8 proteins were precisely recognized. We believe that our work has provided a simple and valuable strategy for the improvement of the recognition range and discrimination precision for the development of pattern recognition.