Detection Of Molecules Research Articles

Programming ADAR-recruiting hairpin RNA sensor to detect endogenous molecules.

RNA editing leveraging ADARs (adenosine deaminases acting on RNA) shows promising potential for in vivo biosensing beyond gene therapy. However, current ADAR sensors sense only a single target of RNA transcripts, thus limiting their use in different biosensing scenarios. Here, we report a hairpin RNA sensor that exploits new mechanisms to generate intramolecular duplex substrates for efficient ADAR recruitment and editing and apply it to detection of various intracellular molecules, including messenger RNA, small molecules and proteins. We utilize the base pairing interactions between neighbouring bases for enhanced stability, as well as the reverse effects to sense RNA transcripts and single-nucleotide variants with high sensitivity and specificity, irrespective of sequence requirement for complementarity to an UAG stop codon. In addition, we integrate RNA aptamers into the hairpin RNA sensor to realize the detection of the primary energy-supplying molecule, ATP, and a transcription factor, nuclear factor-kappa B(NF-κB), in live cells via a simple conformational change for programming the activation of hairpin RNA. This sensor not only broadens the detection of applicable molecules, but also offers potential for diverse cell manipulation.

Super signal-enhancement biosensing platform for precise target recognition based on rolling circle-hybridization chain dual linear cascade amplification technology

This paper presents a self-powered biosensing platform based on graphdiyne@Au (2D GDY@Au) nanoparticles and rolling circle-hybridization chain (RC-HC) dual linear cascade amplification technology, which significantly enhances target recognition and signal amplification efficiency for miRNA-141. Specifically, the target on bioanode outputs a large amount of single-stranded DNA (T1) through the strand displacement amplification (SDA) mechanism. This efficient target recycling process triggers RC-HC dual linear cascade reaction. The RCA product and H2 form the L-Liner/H2 hybridized chain through a hybridization chain reaction, and then are immobilized on a flexible electrode using a Y-DNA capture handle. [Ru(NH3)6]3+ is precisely anchored in the grooves of the DNA double helix. The 2D GDY@Au enhances the electron mobility of the system to form a rich electron-donating center. The [Ru(NH3)6]3+ on the biocathode receives electrons and is reduced to [Ru(NH3)6]2+, producing a significantly amplified open-circuit voltage signal. Dual linear cascade amplification technology realizes precise target recognition, exponential amplification, and efficient conversion of biological signals. This technique displays an extensive linear range (0.0001–10000 pM) with a detection limit of 25.9 aM (S/N = 3), and it provides an innovative method for developing sensors based on nucleic acid amplification and presents a promising novel approach for the sensitive and precise detection of low-abundance target molecules, highlighting a new tactic for the creation of compact and portable analytical devices.

Sample-to-answer point-of-care testing platform for quantitative detection of small molecules in blood using a smartphone-and microfluidic-based nanoplasmonic biosensor

Rapid and ultrasensitive detection of small molecules is of great significance in point-of-care testing (POCT) for health management and biomarker detection for many diseases. In this study, a novel POCT device integrated with a metasurface plasmon resonance (MetaSPR) chip with diffusion film enhancement was designed and controlled by a smartphone app for small molecule ultrasensitive detection based on competitive immunoassays. In this method, the sample competes with the antigen immobilized on the chip, and labeled antibodies are pumped from the sample pad to the chip for multiplexed and sample-to-answer analysis of blood. The entire process of detection is 14.3-fold less time (210 s in total) compared to an enzyme-linked immunosorbent assay (ELISA). For this assay, the limit of detection was 0.36 ppt and 1.05 ppt for testosterone and 25-hydroxyvitamin D3, respectively, and showed 100- to 1000-fold greater sensitivity than that of ELISA. Collectively, the data suggest that this novel POCT platform, based on a MetaSPR biosensor, provides ultrasensitive, rapid, regenerable, versatile, and real-time quantitative analysis for applications in health management and early diagnosis.

RNA-Protein Interaction Prediction without High-Throughput Data: An Overview and Benchmark of in silico Tools

RNA-protein interactions (RPIs) are crucial for accurately operating various processes in and between organisms across kingdoms of life. Mutual detection of RPI partner molecules depends on distinct sequential, structural, or thermodynamic features, which can be determined via experimental and bioinformatic methods. Still, the underlying molecular mechanisms of many RPIs are poorly understood. It is further hypothesized that many RPIs are not even described yet. Computational RPI prediction is continuously challenged by the lack of data and detailed research of very specific examples. With the discovery of novel RPI complexes in all kingdoms of life, adaptations of existing RPI prediction methods are necessary. Continuously improving computational RPI prediction is key in advancing the understanding of RPIs in detail and supplementing experimental RPI determination. The growing amount of data covering more species and detailed mechanisms support the accuracy of prediction tools, which in turn support specific experimental research on RPIs. Here, we give an overview of RPI prediction tools that do not use high-throughput data as the user's input. We review the tools according to their input, usability, and output. We then apply the tools to known RPI examples across different kingdoms of life. Our comparison shows that the investigated prediction tools do not favor a certain species and equip the user with results varying in degree of information, from an overall RPI score to detailed interacting residues. Furthermore, we provide a guide tree to assist users which RPI prediction tool is appropriate for their available input data and desired output.

Interfacial effects of gold on PEDOT nanotubes modified electrodes employed for the adsorption of micropollutants

In this work poly(3,4-ethylenedioxythiophene) nanotubes (PEDOT-NTs) containing gold nanoparticles (AuNPs) were electrochemically synthesized and characterized in detail by using in situ Raman spectroelectrochemistry. Combining conducting polymers and metallic nanoparticles (AuNPs) enhanced conductivity and superficial area of PEDOT-NTs, key factors for electrochemical sensors. In order, to better understand the modified electrodes behavior, two different micropollutants, butylparaben and triclosan, were added onto the electrode surface and the spectroelectrochemical characterization was done. The Raman imaging showed that micropollutants adsorption increases the presence of partially oxidized segments in PEDOT nanotubes, showing that PEDOT-NTs/AuNPs modified electrodes has sensitivity to micropollutants presence. In this regard the electrochemical impedance spectroscopy characterization was performed and agrees with the spectroelectrochemical characterization results, in which the charge-transfer resistance increase proportionally with the micropollutants concentration. Therefore, the present work shows the potentiality of combining the unique characteristics of the PEDOT nanotubes decorated with AuNPs nanoparticles to develop devices for detection of organic molecules of environmental interest.

Uniformly aligned Ag NPs/graphene paper for enhanced SERS detection of pesticide residue

The surface-enhanced Raman scattering (SERS) technique provides a quick and reliable method for detecting pesticide residues. In this study, flexible substrates, composed of orderly arranged silver nanospheres (Ag NPs) films on graphene paper, were fabricated through a simple, low-cost Ag NP self-assembly process at a liquid–liquid interface, followed by transfer of the films onto the graphene paper. The SERS performance of the fabricated substrates was evaluated using a portable Raman spectrometer, with rhodamine 6G (R6G) serving as the probe molecule. The results indicate that the bilayer Ag NP films-covered graphene paper exhibits optimal overall performance, characterized by high sensitivity and high uniformity. The limit of detection (LOD) for the R6G molecule is as low as 8.73 × 10−9 M, demonstrating the strong signal amplification capability of the SERS substrate. Moreover, the relative standard deviation (RSD) of the Raman intensity at 1508 cm−1 for different selected points on the substrate is 5.018 %, indicating high uniformity of the SERS substrate. Finally, the performance of the SERS substrate was further evaluated by detecting thiram in fresh orange juice, demonstrating the capability to detect concentrations as low as 10−6 M. This result highlights the significant potential of the developed SERS substrate for practical applications in food safety and quality control.

A hydrogel film microarray stabilizes very short structure switching aptamer duplexes to achieve enhanced sensing of small molecules

The reduction of affinity associated with the modifications required to create FRET- aptamer constructs represents a key challenge hindering the practical adaptation of such systems for small molecule detection. While the use of shorter and rationally positioned quencher stems is desirable to enhance target-induced fluorescence recovery, the weak hybridization potential of such stems results in high levels of background fluorescence and poor sensitivity. Herein, we introduce a hydrogel microarray sensor able to thermally stabilize very short aptamer duplexes (i.e., quencher stems ≤10-bp), resulting in improved FRET efficiency and reduced background levels across a broad range of conditions. The optimal hydrogel microarray can physically entrap >75 % of loaded aptamer reporters while maintaining high accessibility to the target molecules, enabling accurate quantification of dose-responsive affinity interactions. Using an ATP aptamer reporter, the hydrogel sensor can achieve a binding affinity as low as 14.7 µm − comparable to the native aptamer – and very low limits of detection (LOD) of 1.2 µm in a pure buffer and 4.6 µm in 50 % serum. Moreover, the developed hydrogel microarray is reusable, amenable to printing fabrication, and provides protection against nuclease-based degradation. This simple approach thus holds promise for advancing microarray aptamer technology in critical biosensing applications.

On the Ionization Tolerance of C20 Fullerene in Ground and Excited Electronic States in Planetary Nebulae

As the smallest member of the fullerene family, C20 is yet to be discovered in planetary nebulae. In this work, we present a quantum chemical study via density functional theory (DFT) and partially by the MP2 on the ionization tolerance of this molecule in the space environment. Considering that the ionization and excitation phenomena play key roles in demonstrating the lifetime of a molecule, we examined both ground and excited electronic-state potential energy surfaces (PES) of C20 and its cations C20q+. Our theoretical results indicate that the C20 cage tolerates a positive charge as high as 13+ by characterizing local minimum geometries on both the abovementioned electronic states. The results are backed by characterizing both C2012+ and C2013+ as local minimum geometries at the MP2 level of computations. We also explored, theoretically and systematically, scenarios in which the electronic structure of neutral C20 is excited to very high spin multiplicity (beyond triplet state), and local minimum molecular geometries with cage structures are well characterized. We anticipate that such structural resistance to excitation and ionization delivers a prolonged lifetime necessary for the spectroscopic detection of this interesting molecule and its cations in space and potentially in planetary nebulae (PN).

Assessment of microbial antagonistic activity and Quorum Sensing Signal Molecule (Cyclopeptides-DKPs and N-Acyl Homoserine Lactones) detection in bacterial strains obtained from avocado thrips (Thysanoptera: Thripidae)

The control of avocado pests and diseases heavily relies on the use of several types of pesticides, some of which are strictly monitored or not internationally accepted. New sources of bioactive molecules produced by phytopathogen-inhibiting microorganisms offer an excellent alternative for the control of pests and diseases. This study explores the potential antagonistic action against phytopathogenic microorganisms, using bacterial strains obtained from avocado thrips. In addition, we detected and identified quorum sensing (QS) signaling molecules that are related to virulence factors and antibiotic production. The results showed that Bacillus, Pantoea, and Serratia strains exhibited antagonism against five fungal phytopathogens. Additionally, some bacteria also produce specific signaling molecules like N-3-(oxododecanoyl)-l-homoserine lactone (OdDHL), N-(3-oxo)-hexanoyl l-HL (OHHL), 4‑hydroxy-2-heptylquinoline (HHQ) or 2-heptyl-3,4-dihydroxyquinoline (PQS, Pseudomonas quinolone signal), cyclo(L-Phe-l-Pro), and cyclo(L-Pro-l-Tyr, which might give them antimicrobial properties. This research explores the biotechnological potential of these bacteria in fighting the diseases affecting avocados in Colombia.

Integration of MOF/COF core-shell composite material with wrinkled supramolecular hydrogel: A portable electrochemical sensing platform for noradrenaline bitartrate detection

Predictably integration of rigid powder nanocrystals with flexible soft materials for rapid, accurate and portable detection of biological small molecules is an ongoing goal of researchers. In this research, the MOF/COF core-shell composite material (MIL-88B(FeCu)/COF) was constructed via monomer-mediated solvothermal approach. Subsequently, the MIL-88B(FeCu)/COF was effectively combined with chitosan-acrylamide based wrinkled supramolecular hydrogel to form a unique rigid-flexible composite material (MIL(FeCu)/COF@Hy). Next, the noradrenaline bitartrate (NB) was selected as a target molecule for electrochemical behavioral assessment. Of note, the portable electrochemical sensing platform constructed in this study does not require the use of solutions (chitosan or Nafion) to seal the electrode materials, and the portable device provides sufficient convenience for NB detection. And the excellent linear window (0.06–10 and 10–1600 μmol/L), sensitivity (0.0645 and 0.0729 μA μM cm−2), detection limit (0.02 μmol/L) and anti-interference stability can be achieved. The outstanding electrochemical behaviors may be ascribed to: 1) hydrogel matrix significantly improves the dispersion of MOF/COF composite materials and avoids its agglomeration; 2) there are abundant diffusion paths in the hydrogel nanocomposite; 3) the synergistic catalytic effect of MOF/COF and hydrogel. In short, the combination of this heterostructured MOF/COF composite materials and hydrogel soft materials will provide a valuable reference for the rapid detection of biomolecules.

Magnetically-assembled multifunctional Fe3O4@SiO2@Au particles for SERS detection of low-concentration dye molecules

Abstract Surface-enhanced Raman scattering (SERS) is a sensitive spectroscopic method to detect low concentration-low volume analytes. Owing to this, there has been a rising interest in developing improved as well as novel nanostructured substrates for SERS applications. For SERS applications, it is desirable to have large-scale assemblies of such nanostructures that can sustain multiple electromagnetic ‘hotspots’ for improved sensitivity. In this work, we use magnetic-field aided large-scale assembly of multifunctional magnetic-plasmonic particles to generate a large area SERS substrate. The particles, composed of a Fe3O4 core with a thin silica coating followed by Au nanoparticles (Fe3O4@SiO2@Au), were synthesized by simple chemical methods. The multifunctional particles were characterized using powder x-ray diffraction, transmission electron microscopy, Raman spectroscopy, and SQUID magnetometer. Magnetic assembly of the composite particles, carried out using a bi-electromagnet setup, was used for SERS detection of organic dyes such as rhodamine B and methylene blue. Using this scheme, it was possible to detect ultra-low concentrations (up to 1fM) of the dye molecules. This method is promising for applications such as chemical sensors, biomolecular detection, cancer detection, and hyperthermia treatment, forensic investigations, and drug delivery.

Exploring aptamer-aTF sandwich and CRISPR-Cas12a methods for sensitive L-lactate biosensing in human serum and saliva

In this study, a novel transcription factor and aptamer-based sandwich assay is proposed to detect L-lactate in biofluids with excellent selectivity and sensitivity. The assay employs an L-lactate-specific allosteric transcription factor (aTF) fused with a cellulose-binding domain (CBD) and immobilized on cellulose nanocrystals (CNCs). The aTF-CBD/L-lactate complex is coupled with a fluorescently labeled aptamer (fAPTlac), generating a quantifiable fluorescence signal. Remarkably, the proposed assay demonstrated a dynamic detection range from 1 nM to 50 mM, a limit of detection of 28.2 pM, and high selectivity against potentially interfering molecules. Moreover, the proposed method exhibited better performance compared to the CRISPR-Cas12a/aTF-based (CaT) method without compromising the sensitivity or specificity. Furthermore, the assay accurately quantified L-lactate in human serum and saliva samples, with recovery rates between 98 % and 104 %. The proposed method offers a simple, cost-effective, and highly sensitive platform for L-lactate detection in clinical settings, addressing the limitations of existing biosensors for small molecule detection such as matrix interference, low sensitivity, and poor selectivity.

High‐Gain, High‐Order Vortex Air Lasing Generated by Plasma Amplification

AbstractVortex air lasing opens exciting perspectives for remote generation, amplification, and control of vortex beams in ambient air. By combining the advantages of air lasing and vortex beams, it holds great potential in some specific applications such as standoff detection of chiral molecules and rotating objects. However, it remains challenging to produce high‐order vortex air lasing and flexibly control its orbital angular momentum, hindered by the inhomogeneous distribution and instability of laser‐induced plasma. Herein, vortex lasing with a tunable vortex order from the first up to the tenth order is achieved through vortex seed amplification in plasma. The helical phase structure of the seed is well conserved in the amplification process. Each order vortex air lasing shows the same topological charge as the seed and a doughnut‐shaped profile. Moreover, the amplification factor is up to 104. Generation of high‐order, high‐gain vortex air lasing is attributed to the choice of an appropriate population‐inversion system, as well as the optimal control over spatial matching of pump and seed beams, gas pressures, and focusing conditions. This work facilitates the understanding of the gain mechanism of lasing and promises to extend the application scenarios of air‐lasing‐based spectroscopy.

PlQC based highly sensitive and reproducible novel SERS active substrate for biomolecule detection with high specificity

Surface-enhanced Raman spectroscopy (SERS) is a powerful tool for biomolecule sensing. When combined with a broadband plasmonic structure, label-free, highly sensitive detection of specific molecules is possible. It is non-invasive, sensitive, fast, and can be used for in-situ analysis, unlike enzyme-linked immunosorbent assay, fluorescence immunoassay, and radioimmunoassay. However, one of the challenges is to have an active SERS substrate that is uniform, sensitive, and specific to molecules of interest. In this work, we report plasmonic quasicrystal (PlQC) as a highly sensitive (enhancement factor ≈ 1014), uniform, reproducible, and stable (concerning time and ambient conditions) SERS active substrate. Herein, we present the label-free sensing of standard cotinine (up to 1 ng/mL), the ideal biomarker for nicotine exposure due to its long lifetime compared to nicotine. In addition, up to 1 nanogram level of cotinine has also been detected in synthetic urine and saliva employing PlQC as a SERS-active substrate. Our results on the principal component analysis of Rhodamine 6G and Cotinine demonstrate that broadband, dispersionless PlQC is suitable for label-free detection of single biomolecules.

Molecular adsorption of chloromethane and vinyl chloride on square lattice net phosphorene – A first-principles study

The advancement of two-dimensional (2D) materials after the discovery of graphene leads to the path of various 2D materials. One such 2D material is square lattice (sql) net phosphorene. Initially, the structural and dynamic stability of sql phosphorene is confirmed with regard to the formation energy and phonon-band-spectrum. The electronic properties of sql phosphorene are explored using band structure and projected density of states spectrum. Besides, the calculated band gap value of sql phosphorene is 3.174 eV which shows the semiconducting nature of the material. Owing to the structural firmness and semiconducting nature of sql phosphorene material, it is used as a sensing element for chloromethane and vinyl chloride molecules. Evidently, the adsorption of chloromethane and vinyl chloride on sql phosphorene leads to modulating the energy band gap, electron difference density, and charge transfer, which infers changes in the electronic properties of sql phosphorene. The adsorption energy range is recorded to be −0.152 eV to −0.608 eV which confirms that the chloromethane and vinyl chloride are physisorbed on sql phosphorene. The findings ensure that sql phosphorene is a proper sensing element for the detection of chloromethane and vinyl chloride molecules.

A novel all-in-one target-powered entropy-driven dynamic DNA networks to regulate the activity of CRISPR/AsCas12a for enhanced DNA detection

BackgroundThe non-enzyme autonomous DNA nanodevices have been developed to detect various analytes through the programmability of Watson-Crick base pairing. Nevertheless, by comparison with enzymatic biosensors, the usage of enzyme-free DNA networks to create biosensors for testing low amounts of targets is still subject to the finite number of cycles. Besides, these biosensors still require the incorporation of other amplification strategies to improve the sensitivity, which complicates the detection workflow and lacks of a uniform compatible system to respond to the target in one pot. ResultsHere, we put forward a novel way for rapid and sensitive DNA diagnostic via EDN (entropy-driven dynamic network) coupling with CRISPR/AsCas12a-powered amplification. In the absence of the target, the autonomous hybridization among the substrate and crRNA is kinetically hindered by enclosing complementary regions, which leads to the loss of the activation function of Cas12a. On the contrary, the target initiates the EDN, reconfiguring the activator strand from a duplex to branch construction, which provides a valid means to adjust the hybridization with crRNA, thereby controlling the indiscriminate collateral cleavage activities of the CRISPR/AsCas12a. Compared with the traditional EDN, synergistic activation between the EDN and the CRISPR catalyst could dramatically enhance the detection signal of the target in one pot. Furthermore, the proposed approach provides universal platforms through the rational functional and structural design of DNA assembly modules. Significance and noveltyOverall, this target-triggered EDN switches the activator strand to regulate the activity of AsCas12a (called TERA), which showed nearly one orders of magnitude sensitivity than the conventional Cas12a alone assay, resulting in a devisable universal CRISPR sensing platform that favours the fast, robust and one-pot detection of nucleic molecules.

Study of Protein Hydration Water with the V4S Structural Index: Focus on Binding Site Description.

V4S, a new structural indicator for water specially designed to be suitable for hydration and nanoconfined contexts, has been recently introduced and preliminarily applied for water in contact with self-assembled monolayers and graphene-like systems. This index enabled an accurate detection of defective high local density water molecules (called HDA-like given their structural resemblance with the high-density amorphous ice, HDA). In the present work, we shall apply this new metric to characterize protein hydration water with particular interest in protein binding sites. As a first result, we shall find that protein hydration water has a higher concentration of HDA-like molecular arrangements compared to the bulk. Significantly, we shall show that the concentration of HDA-like molecules sharply decreases beyond the first hydration layer. Finally, we shall also reveal a highly nonuniform spatial distribution of the V4S values for the first hydration shell on the protein surface, where the higher hydrophobicity inherent to the ligand binding site will be evident from an enrichment in HDA-like molecules as compared to the population exhibited by the global protein surface.

Aun nanocluster decorated arsenene heterostructures as effective sensing platform for caffeine and nicotine molecules detection: a DFT study

Aun nanocluster decorated arsenene heterostructures as effective sensing platform for caffeine and nicotine molecules detection: a DFT study

Functional Organic Electrochemical Transistor-Based Biosensors for Biomedical Applications

Organic electrochemical transistors (OECTs), as an emerging device for the development of novel biosensors, have attracted more and more attention in recent years, demonstrating their promising prospects and commercial potential. Functional OECTs have been widely applied in the field of biosensors due to their decisive advantages, such as high transconductance, easy functionalization, and high integration capability. Therefore, this review aims to provide a comprehensive summary of the most recent advances in the application of functional OECT-based biosensors in biomedicine, especially focusing on those biosensors for the detection of physiological and biochemical parameters that are critical for the health of human beings. First, the main components and basic working principles of OECTs will be briefly introduced. In the following, the strategies and key technologies for the preparation of functional OECT-based biosensors will be outlined and discussed with regard to the applications of the detection of various targets, including metabolites, ions, neurotransmitters, electrophysiological parameters, and immunological molecules. Finally, the current main issues and future development trends of functional OECT-based biosensors will be proposed and discussed. The breakthrough in functional OECT-based biosensors is believed to enable such devices to achieve higher performance, and thus, this technology could provide new insight into the future field of medical and life sciences.

SERS-Encoded Nanoprobes Based on Silver-Coated Gold Nanorods for Cell Sorting.

Optically-encoded probes have great potential for applications in the fields of biosensing and imaging. By employing specific encoding methods, these probes enable the detection of multiple target molecules and high-resolution imaging within the same sample. Among the various encoding methods, surface-enhanced Raman scattering (SERS) spectral encoding stands out due to its extremely narrow linewidth. Compared to fluorescence spectral encoding, SERS encoding significantly reduces crosstalk between adjacent peaks, thereby achieving a larger encoding capacity and enabling multi-channel parallel analysis. This article presents the design and construction of two novel sets of SERS-encoded probes based on noble metal core-shell nanostructures. Two different encoding strategies are successfully applied to encode the SERS spectra of the probes: 1D encoding based on the wavenumber of characteristic peaks in the SERS spectrum, and 2D encoding combining both wavenumber and intensity of characteristic peaks in the SERS spectrum. In addition, this study also demonstrates the potential application of 1D encoded probes in cell sorting. These studies verify the feasibility of applying these two encoding methods to SERS core-shell probes and provide new insights into the construction of optically encoded probes.