Precise and Programmable Detection of Mutations Using Ultraspecific Riboregulators.

The ability to identify single-nucleotide mutations is critical for probing cell biology and for precise detection of disease. However, the small differences in hybridization energy provided by single-base changes makes identification of these mutations challenging in living cells and complex reaction environments. Here, we report a class of de novo-designed prokaryotic riboregulators that provide ultraspecific RNA detection capabilities in vivo and in cell-free transcription-translation reactions. These single-nucleotide-specific programmable riboregulators (SNIPRs) provide over 100-fold differences in gene expression in response to target RNAs differing by a single nucleotide in E. coli and resolve single epitranscriptomic marks in vitro. By exploiting the programmable SNIPR design, we implement an automated design algorithm to develop riboregulators for a range of mutations associated with cancer, drug resistance, and genetic disorders. Integrating SNIPRs with portable paper-based cell-free reactions enables convenient isothermal detection of cancer-associated mutations from clinical samples and identification of Zika strains through unambiguous colorimetric reactions.

Naphthalimide-based new architecture for fluorescence turn-on sensing of Cu2+ and colorimetric detection of F-/CN.

A new molecular structure 1 has been developed on naphthalimide motif. The amine and triazole binding groups have been employed at the 4-position of naphthalimide to explore the sensing behavior of molecule 1. Single crystal x-ray diffraction and other spectroscopic techniques confirm the identity of 1. Compound 1 exhibits high selectivity and sensitivity for Cu2+ ions in CH3CN. The binding of Cu2+ shows âˆ¼ 70-fold enhancement in emission at 520 nm. The binding follows 1:1 interaction and the detection limit is determined to be 6.49 × 10-7 M. The amine-triazole binding site in 1 also corroborates the detection of F- through a colour change in CH3CN. Initially H-bonding and then deprotonation of amine -NH- in the presence of F- are the sequential steps involved in F- recognition with a detection limit of 4.13 × 10-7 M. Compound 1 is also sensible to CN- like F- ion and they are distinguished by Fe3+ ion. Cu2+-ensemble of 1 fluorimetrically recognizes F- among the tested anions and vice-versa. The collaborative effect of amine and triazole motifs in the binding of both Cu2+ and F-/CN- has been explained by DFT calculation.

Synthesis of functionalized mesoporous silica nanoparticles for colorimetric and fluorescence sensing of selective metal (Fe3+) ions in aqueous solution.

The fabrication of red fluorescent hybrid mesoporous silica-based nanosensor materials has promised the bioimaging and selective detection of toxic pollutants in aqueous solutions. In this study, we present a hybrid mesoporous silica nanosensor in which the propidium iodide (PI) was used to conveniently integrate into the mesopore walls using bis(trimethoxysilylpropyl silane) precursors. Various characterization techniques including X-ray diffraction (XRD), Fourier-transform infrared (FTIR), N2 adsorption-desorption, zeta potential, particle size analysis, thermogravimetric, and UV-visible analysis were used to analyze the prepared materials. The prepared PI integrated mesoporous silica nanoparticles (PI-MSNs) selective metal ion sensing capabilities were tested with a variety of heavy metal ions (100 mM), including Ni2+, Cd2+, Co2+, Zn2+, Cr3+, Cu2+, Al3+, Mg2+, Hg2+ and Fe3+ ions. Among the investigated metal ions, the prepared PI-MSNs demonstrated selective monitoring of Fe3+ ions with a significant visible colorimetric pink color change into orange and quenching of pink fluorescence in an aqueous suspension. The selective sensing behavior of PI-MSNs might be due to the interaction of Fe3+ ions with the integrated PI functional fluorophore present in the mesopore walls. Therefore, we emphasize that the prepared PI-MSNs could be efficient for selective monitoring of Fe3+ ions in an aqueous solution and in the biological cellular microenvironment.

p-d Orbital Hybridization-Engineered PdSn Nanozymes for a Sensitive Immunoassay.

Nanozymes with peroxidase-like activity have been extensively studied for colorimetric biosensing. However, their catalytic activity and specificity still lag far behind those of natural enzymes, which significantly affects the accuracy and sensitivity of colorimetric biosensing. To address this issue, we design PdSn nanozymes with selectively enhanced peroxidase-like activity, which improves the sensitivity and accuracy of a colorimetric immunoassay. The peroxidase-like activity of PdSn nanozymes is significantly higher than that of Pd nanozymes. Theoretical calculations reveal that the p-d orbital hybridization of Pd and Sn not only results in an upward shift of the d-band center to enhance hydrogen peroxide (H2O2) adsorption but also regulates the O-O bonding strength of H2O2 to achieve selective H2O2 activation. Ultimately, the nanozyme-linked immunosorbent assay has been successfully developed to sensitively and accurately detect the prostate-specific antigen (PSA), achieving a low detection limit of 1.696 pg mL-1. This work demonstrates a promising approach for detecting PSA in a clinical diagnosis.

Colorimetric Pressure Sensing by Plasmonic Decoupling of Silver Nanoparticles Confined within Polymeric Nanoshells.

Employing a plasmonic decoupling mechanism, we report the design of a colorimetric pressure sensor that can respond to applied pressure with instant color changes. The sensor consists of a thin film of stacked uniform resorcinol-formaldehyde nanoshells with their inner surfaces functionalized with silver nanoparticles. Upon compression, the flexible polymer nanoshells expand laterally, inducing plasmonic decoupling between neighboring silver nanoparticles and a subsequent blue-shift. The initial color of the sensor is determined by the extent of plasmonic coupling, which can be controlled by tuning the interparticle distance through a seeded growth process. The sensing range can be conveniently customized by controlling the polymer shell thickness or incorporating hybrid nanoshells into various polymer matrices. The new colorimetric pressure sensors are easy to fabricate and highly versatile, allow for convenient tuning of the sensing range, and feature significant color shifts, holding great promise for a wide range of practical applications.

High-Throughput All-Optical Determination of Nanorod Size and Orientation.

As a single-particle characterization technique, optical microscopy has transformed our understanding of structure-function relationships of plasmonic nanoparticles, but the need for ex-situ-correlated electron microscopy to obtain structural information handicaps an otherwise exceptional high-throughput technique. Here, we present an all-optical alternative to electron microscopy to accurately and quickly extract structural information about single gold nanorods (Au NRs) using calcite-assisted localization and kinetics (CLocK) microscopy. Color CLocK images of single Au NRs allow scattering from the longitudinal and transverse plasmon modes to be imaged simultaneously, encoding spectral data in CLocK images that can then be extracted to obtain Au NR size and orientation. Moreover, through the use of convolutional neural networks, Au NR length, width, and aspect ratio can be predicted directly from color CLocK images within ∼10% of the true value measured by electron microscopy.

Ultrasensitive and fast detection of SARS-CoV-2 using RT-LAMP without pH-dependent dye.

This study investigates the performance of reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the colorimetric detection of SARS-CoV-2 using fluorometric dye, namely, calcein. The detection limit (LoD) with the N-ID1 primer set resulted in superior performance, corresponding to ~ 2 copies/reaction or ~ 0.1 copies/µL of the RNA sample. The color development can be observed by the naked eye, using an ultraviolet (UV) transilluminator or a hand-UV light without the requirement of expensive devices. The average time-to-reaction (TTR) value was 26.2 min in high-copy number samples, while it was about 50 min in rRT-PCR. A mobile application was proposed to quantify the positive and negative results based on the three-color spaces (RGB, Lab, and HSB). Compared to rRT-PCR (n = 67), this assay allows fast and sensitive visual detection of SARS-CoV-2, with high sensitivity (90.9%), selectivity (100%), and accuracy (94.03%). Besides, the assay was sensitive regardless of variants. Since this assay uses a fluorescent dye for visual observation, it can be easily adapted in RT-LAMP assays with high sensitivity. Thus, it can be utilized in low-source centers and field testing such as conferences, sports meetings, refugee camps, companies, and schools.

Colorimetric Detection of HER2-Overexpressing-Cancer-Derived Exosomes in Mouse Urine Using Magnetic-Polydiacetylene Nanoparticles.

Breast cancer (BC) is a major global health problem, with ≈20-25% of patients overexpressing human epidermal growth factor receptor 2 (HER2), an aggressive marker, yet access to early detection and treatment varies across countries. A low-cost, equipment-free, and easy-to-use polydiacetylene (PDA)-based colorimetric sensor is developed for HER2-overexpressing cancer detection, designed for use in low- and middle-income countries (LMICs). PDA nanoparticles are first prepared through thin-film hydration. Subsequently, hydrophilic magnetic nanoparticles and HER2 antibodies are sequentially conjugated to them. The synthesized HER2-MPDA can be concentrated and separated by a magnetic field while inheriting the optical characteristics of PDA. The specific binding of HER2 antibody in HER2-MPDA to HER2 receptor in HER2-overexpressing exosomes causes a blue-to-red color change by altering the molecular structure of the PDA backbone. This colorimetric sensor can simultaneously separate and detect HER2-overexpressing exosomes. HER2-MPDA can detect HER2-overexpressing exosomes in the culture medium of HER2-overexpressing BC cells and in mouse urine samples from a HER2-overexpressing BC mouse model. It can selectively isolate and detect only HER2-overexpressing exosomes through magnetic separation, and its detection limit is found to be 8.5 × 108 particles mL-1. This colorimetric sensor can be used for point-of-care diagnosis of HER2-overexpressing BC in LMICs.

Label-Free and Colorimetric Detection of Influenza A Virus via Receptor-Mediated Viral Fusion with Plasmonic Vesicles.

The rapid transmission and numerous re-emerging human influenza virus variants that spread via the respiratory system have led to severe global damage, emphasizing the need for detection tools that can recognize active and intact virions with infectivity. Here, this work presents a plasmonic vesicle-mediated fusogenic immunoassay (PVFIA) comprising gold nanoparticle (GNP) encapsulating fusogenic polymeric vesicles (plasmonic vesicles; PVs) for the label-free and colorimetric detection of influenza A virus (IAV). The PVFIA combines two sequential assays: a biochip-based immunoassay for target-specific capture and a PV-induced fusion assay for color change upon the IAV-PV fusion complex formation. The PVFIA demonstrates excellent specificity in capturing the target IAV, while the fusion conditions and GNP induce a significant color change, enabling visual detection. The integration of two consecutive assays results in a low detection limit (100.7919 EID50 mL-1 ) and good reliability (0.9901), indicating sensitivity that is 104.208 times higher than conventional immunoassay. Leveraging the PV viral membrane fusion activity renders the PVFIA promising for point-of-care diagnostics through colorimetric detection. The innovative approach addresses the critical need for detecting active and intact virions with infectivity, providing a valuable tool with which to combat the spread of the virus.

Pyridine-Bridged Covalent Organic Frameworks with Adjustable Band Gaps as Intelligent Artificial Enzymes for Light-Augmented Biocatalytic Sensing.

One of the biggest challenges in biotechnology and medical diagnostics is finding extremely sensitive and adaptable biosensors. Since metal-based enzyme-mimetic biocatalysts may lead to biosafety concerns on accumulative toxicity, it is essential to synthesize metal-free enzyme-mimics with optimal biocatalytic activity and superior selectivity. Here, the pyridine-bridged covalent organic frameworks (COFs) with specific oxidase-like (OXD-like) activities as intelligent artificial enzymes for light-augmented biocatalytic sensing of biomarkers are disclosed. Because of the adjustable bandgaps of pyridine structures on the photocatalytic properties of the pristine COF structures, the pyridine-bridged COF exhibit efficient, selective, and light-responsive OXD-like biocatalytic activity. Moreover, the pyridine-bridged COF structures show tunable and light-augmented biocatalytic detection capabilities, which outperform the recently reported state-of-the-art OXD-mimics regarding biosensing efficiency. Notably, the pyridine-bridged COF exhibits efficient and multifaceted diagnostic activity, including the extremely low limit of detection (LOD), which enables visual assays for abundant reducibility biomarkers. It is believed that this design will offer unique metal-free biocatalysts for high-sensitive and low-cost colorimetric detection and also provide new insights to create highly efficient enzyme-like COF materials via linkage-modulation strategies for future biocatalytic applications.

Dual-Track Multifunctional Bimetallic Metal-Organic Frameworks for Antibiotic Enrichment and Detection.

The improper use and overuse of antibiotics have led to significant burdens and detrimental effects on the environment, food supply, and human health. Herein, a magnetic solid-phase extraction program and an optical immunosensor based on bimetallic Ce/Zr-UiO 66 for the detection of antibiotics are developed. A magnetic Fe3O4@SiO2@Ce/Zr-UiO 66 metal-organic framework (MOF) is prepared to extract and enrich chloramphenicol from fish, wastewater, and urine samples, and a horseradish peroxidase (HRP)-Ce/Zr-UiO 66@bovine serum protein-chloramphenicol probe is used for the sensitive detection of chloramphenicol based on the dual-effect catalysis of Ce and HRP. In this manner, the application of Ce/Zr-UiO 66 in integrating sample pretreatment and antibiotic detection is systematically investigated and the associated mechanisms are explored. It is concluded that Ce/Zr-UiO 66 is a versatile dual-track material exhibiting high enrichment efficiency (6.37 mg g-1) and high sensitivity (limit of detection of 51.3 pg mL-1) for chloramphenicol detection and serving as a multifunctional MOF for safeguarding public health and hygiene.

The Identification of Oral Cariogenic Bacteria through Colorimetric Sensor Array Based on Single-Atom Nanozymes.

Effective identification of multiple cariogenic bacteria in saliva samples is important for oral disease prevention and treatment. Here, a simple colorimetric sensor array is developed for the identification of cariogenic bacteria using single-atom nanozymes (SANs) assisted by machine learning. Interestingly, cariogenic bacteria can increase oxidase-like activity of iron (Fe)─nitrogen (N)─carbon (C) SANs by accelerating electron transfer, and inversely reduce the activity of Fe─N─C further reconstruction with urea. Through machine-learning-assisted sensor array, colorimetric responses are developed as "fingerprints" of cariogenic bacteria. Multiple cariogenic bacteria can be well distinguished by linear discriminant analysis and bacteria at different genera can also be distinguished by hierarchical cluster analysis. Furthermore, colorimetric sensor array has demonstrated excellent performance for the identification of mixed cariogenic bacteria in artificial saliva samples. In view of convenience, precise, and high-throughput discrimination, the developed colorimetric sensor array based on SANs assisted by machine learning, has great potential for the identification of oral cariogenic bacteria so as to serve for oral disease prevention and treatment.

"Four-In-One" Multifunctional Dandelion-Like Gold@platinum Nanoparticles-Driven Multimodal Lateral Flow Immunoassay.

The traditional lateral flow immunoassay (LFIA) with a single signal output mode may encounter challenges such as low sensitivity, poor detection range, and susceptibility to external interferences. These limitations hinder its ability to meet the growing demand for advanced LFIA. To address these issues, the rational development of multifunctional labels for multimodal LFIA emerges as a promising strategy. Herein, this study reports a multimodal LFIA using "four-in-one" multifunctional dandelion-like gold@platinum nanoparticles (MDGP). The inherent properties of MDGP, such as the broad absorption spectrum, porous dandelion-like nanostructure, and bimetallic composition with gold and platinum, endow them with capacities in dual spectral-overlapped fluorescence quenching, optical readout, catalytic activity, and photothermal effect. Benefiting from their multifunctional properties, the MDGP-LFIA enables multimodal outputs including fluorescent, colorimetric, and photothermal signals. This multimodal MDGP-LFIA allows for the detection of acetamiprid at a range of 0.01-50 ng mL-1, with the lowest qualitative and quantitative detection results of 0.5 and 0.008 ng mL-1, respectively, significantly better than the traditional gold nanoparticles-based LFIA. The diversity, complementarity, and synergistic effect of integrated output signals in this multimodal MDGP-LFIA improve the flexibility, practicability, and accuracy of detection, holding great promise as a point-of-care testing platform in versatile application scenarios.

Capillary electrophoresis-mass spectrometry for creatinine analysis in residual clinical plasma samples and comparison with gold standard assay.

When hospitalized, infants, particularly preterm, are often subjected to multiple painful needle procedures to collect sufficient blood for metabolic screening or diagnostic purposes using standard clinical tests. For example, at least 100 µL of whole blood is required to perform one creatinine plasma measurement with enzymatic colorimetric assays. As capillary electrophoresis-mass spectrometry (CE-MS) utilizing a sheathless porous tip interface only requires limited amounts of sample for in-depth metabolic profiling studies, the aim of this work was to assess the utility of this method for the determination of creatinine in low amounts of plasma using residual blood samples from adults and infants. By using a starting amount of 5 µL of plasma and an injection volume of only 6.7 nL, a detection limit (S/N = 3) of 30 nM could be obtained for creatinine, and intra- and interday precisions (for peak area ratios) were below 3.2%. To shorten the electrophoretic separation time, a multi-segment injection (MSI) strategy was employed to analyze up to seven samples in one electrophoretic run. The findings obtained by CE-MS for creatinine in pretreated plasma were compared with the values acquired by an enzymatic colorimetric assay typically used in clinical laboratories for this purpose. The comparison revealed that CE-MS could be used in a reliable way for the determination of creatinine in residual plasma samples from infants and adults. Nevertheless, to underscore the clinical efficacy of this method, a subsequent investigation employing an expanded pool of plasma samples is imperative. This will not only enhance the method's diagnostic utility but also contribute to minimizing both the amount and frequency of blood collection required for diagnostic purposes.

Advances in high-throughput screening approaches for biosurfactants: current trends, bottlenecks and perspectives.

The market size of biosurfactants (BSs) has been expanding at an extremely fast pace due to their broad application scope. Therefore, the re-construction of cell factories with modified genomic and metabolic profiles for desired industrial performance has been an intriguing aspect. Typical mutagenesis approaches generate huge mutant libraries, whereas a battery of specific, robust, and cost-effective high-throughput screening (HTS) methods is requisite to screen target strains for desired phenotypes. So far, only a few specialized HTS assays have been developed for BSs that were successfully applied to obtain anticipated mutants. The most important milestones to reach, however, continue to be: specificity, sensitivity, throughput, and the potential for automation. Here, we discuss important colorimetric and fluorometric HTS approaches for possible intervention on automated HTS platforms. Moreover, we explain current bottlenecks in developing specialized HTS platforms for screening high-yielding producers and discuss possible perspectives for addressing such challenges.

Quantitation of oxidized and reduced albumin in mammals. An intriguing analytical question.

Oxidized albumin is considered a short-term biomarker of oxidative stress and its measurement in blood contributes to evaluate the impact of diseases, drugs, dialytic treatments, physical activity, environmental contaminants etc. on the red-ox balance of humans as well as of other mammalians. Nevertheless, the most common methods for quantifying the oxidized and reduced albumins are costly and time-consuming. Furthermore, there is a dearth of information regarding the proper ways to store human serum or plasma samples in order to prevent inaccurate quantification of these various albumin forms. This paper explores these aspects and proposes a few spectrophotometric assay procedures which make the quantitation of oxidized and reduced albumin very fast, precise and un-expensive in various mammals.

Smartphone-enabled colorimetric immunoassay for deoxynivalenol based on Mn2+-mediated aggregation of AuNPs.

Deoxynivalenol (DON) is a common mycotoxin in food that mainly pollutes grain crops and feeds, such as barley, wheat and corn. DON has caused widespread concern in the field of food and feed safety. In this study, a colorimetric immunoassay was proposed based on the aggregation of gold nanoparticles (AuNPs) due to the decomposition of Mn2+ from gold-coated manganese dioxide (AuNP@MnO2) nanosheets. In this study, 2-(dihydrogen phosphate)-l-ascorbic acid (AAP) was hydrolyzed by alkaline phosphatase (ALP) and converted to ascorbic acid (AA). Then, AuNP@MnO2 was reduced to Mn2+ and AuNPs aggregation occurred. Using the unique optical characteristics of AuNPs and AuNP@MnO2, visible color changes realized simple detection of DON with high sensitivity and portability. With increasing DON content, the color changed more obviously. To quantitatively detect DON, pictures can be taken and the blue value can be read by a smartphone. The detection limit (Ic10) of this method was 0.098 ng mL-1, which was 326 times higher than that of traditional competitive ELISA, and the detection range was 0.177-6.073 ng mL-1. This method exhibited high specificity with no cross-reaction in other structural analogs. The average recovery rate of DON in corn flour samples was 89.1 %-110.2 %, demonstrating the high accuracy and stability of this assay in actual sample detection. Therefore, the colorimetric immunoassay can be used for DON-related food safety monitoring.

Signal-off nanozyme-based colorimetric aptasensor for sensitive detection of ampicillin using MnO2 nanoflowers and gold nanoparticles.

The combination of nanomaterials possessing distinct characteristics and the precision of aptamers facilitates the creation of biosensors that exhibit exceptional selectivity and sensitivity. In this manuscript, we present a highly sensitive aptasensor that utilizes the distinctive characteristics of MnO2 nanoflowers and gold nanoparticles to selectively detect ampicillin (AMP). In this aptasensor, the mechanism of signal change is attributed to the difference in the oxidase-mimicking activity of MnO2 nanoflowers in the presence of a free sequence. The inclusion of AMP hindered the creation of a double-stranded DNA configuration through its binding to the aptamer, resulting in an observable alteration in absorbance. The relative absorbance varied linearly with the concentration of AMP in the range of 70 pM to 10 nM with a detection limit of 21.7 pM. In general, the colorimetric aptasensor that has been developed exhibits exceptional selectivity and remarkable stability. It also demonstrates favorable performance in human serum, making it a highly reliable diagnostic tool. Additionally, its versatility is noteworthy as it holds great potential for detecting various antibiotics present in complex samples by merely replacing the utilized sequences with new ones.

Pyrophosphate detection method using 5-Br-PAPS to detect nucleic acid amplification - Application to LAMP method.

Genetic testing has been increasingly used in several fields. In many applications, nucleic acid amplification technology is required. However, current methods to detect nucleic acid amplification require expensive reagents and special equipment or exhibit limited sensitivity, which hinders their use. To address this issue, this study reports an assay method for detecting occurrence of acid amplification in post-amplification samples using pyrophosphate, a highly sensitive byproduct of nucleic acid amplification. The method proposed requires two reagents and an automated analyzer. First, hydrogen peroxide is derived from pyrophosphate, an indicator of nucleic acid amplification, and the oxidizing power of hydrogen peroxide is used to produce Fe (III) from Fe (II). The specific metal chelator 5-Br-PAPS forms a complex with the trivalent iron produced, resulting in a highly sensitive coloration. The within-run reproducibility of our method (n = 20) was less than 3.67% at each concentration tested, and the detection limit was 0.075 µmol/L, sufficient for quantitative analysis. The technique described could detect pyrophosphate in a sample that was amplified using the loop-mediated isothermal amplification method after only 10 min. Therefore, the proposed method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.

Evaluation of AgNCs@PEI and their integrated hydrogel for colorimetric and fluorometric detection of ascorbic acid.

A dual-mode colorimetric and fluorometric sensor based on water soluble silver nanoclusters (AgNCs@PEI) is developed for quantitative and visual detection of ascorbic acid (Asc A). The detection method relies on the Asc A induced aggregation of AgNCs@PEI, which resulted in fluorecsence quenching of the sensor. The clusters exhibited a unique combination of static and collisional quenching with a wide range of dynamic detection (1-105 µM) Linear relationship was observed in the concentration range 102-103 µM using fluorescence and 0.2 × 102-5 × 103 µM using absorbance spectroscopy with respective detection limits of 10.65 µM and 2.49 µM. The corresponding colorimetric and fluorometric changes can be easily monitored by the naked eye with a visual detection limit of 103 µM. AgNCs@PEI were further integrated within a hydrogel for developing a solid-state visual detection platform. Notably, the sensing response of the clusters towards Asc A remained unaltered even after hydrogel integration. Additionally, digital image analysis was adopted, which improved the sensitivity of instrument-free fluorescence detection of Asc A. Analysis by the developed sensor showed excellent recovery percentages of Asc A in spiked urine samples, which further underscores the practical applicability of the sensor.