Signal-on Protein Detection via Dye Translocation between Aptamer and Quantum Dot

Dual-signal fluorescence aptasensing system for adenosine triphosphate assisting by MoS2 nanosheets

Adenosine triphosphate (ATP) has an irreplaceable role in the maintenance of many physiological processes and biological functions, and can be employed as an indicator of many diseases. In this work, we constructed a simple and sensitive dual-signal fluorescence aptasensing system for ATP detection with berberine as the signal reporter, ATP-aptamer as the recognition unit and MoS2 nanosheets as the signal amplification. In the absence of ATP, berberine can bind to the single-stranded DNA (ssDNA) of ATP-aptamer and selectively assemble on the surface of MoS2 nanosheets, leading to the fluorescence quenching of bererbine based on the fluorescence resonance energy transfer, denoted by "OFF". Accordingly, the fluorescence anisotropy signal is enhanced due to restriction on rotate of the fluorescent probe and denoted as "ON". Conversely, in the presence of ATP, it specifically interacts with ATP-aptamer and switches the free-curled single-stranded of ATP-aptamer to the G-quadruplex structure of ATP-aptamer/ATP/berberine, causing the detachment from the surface of the MoS2 nanosheet. Accordingly, the fluorescence signal was reversed from "OFF" to "ON", and the fluorescence anisotropy signal was turned "ON" to "OFF". The developed aptasensing system achieved a desirable sensitivity of 40.0 nM with fluorescent mode, and of 20.8 nM with fluorescent anisotropic mode. The sensing system has demonstrated high quality detection performance in human serum sample, and obtained the satisfactory recovery results for fluorescent of 93.0-108.5%, fluorescent anisotropic of 96.4-106.7%.

Surface Functionalisation of Self-Assembled Quantum Dot Microlasers with a DNA Aptamer

The surface functionalisation of self-assembled colloidal quantum dot supraparticle lasers with a thrombin binding aptamer (TBA-15) has been demonstrated. The self-assembly of CdSSe/ZnS alloyed core/shell microsphere-shape CQD supraparticles emitting at 630 nm was carried out using an oil-in-water emulsion technique, yielding microspheres with an oleic acid surface and an average diameter of 7.3 ± 5.3 µm. Surface modification of the microspheres was achieved through a ligand exchange with mercaptopropionic acid and the subsequent attachment of TBA-15 using EDC/NHS coupling, confirmed by zeta potential and Fourier transform IR spectroscopy. Lasing functionality between 627 nm and 635 nm was retained post-functionalisation, with oleic acid- and TBA-coated microspheres exhibiting laser oscillation with thresholds as low as 4.10 ± 0.37 mJ·cm-2 and 7.23 ± 0.78 mJ·cm-2, respectively.

Recent advances in quantum dot-based fluorescence-linked immunosorbent assays

Fluorescence immunoassays have been given considerable attention among the quantitative detection methods in the clinical medicine and food safety testing fields. In particular, semiconductor quantum dots (QDs) have become ideal fluorescent probes for highly sensitive and multiplexed detection due to their unique photophysical properties, and the QD fluorescence-linked immunosorbent assay (FLISA) with high sensitivity, high accuracy, and high throughput has been greatly developed recently. In this manuscript, the advantages of applying QDs to FLISA platforms and some strategies for their application to in vitro diagnostics and food safety are discussed. Given the rapid development of this field, we classify these strategies based on the combination of QD types and detection targets, including traditional QDs or QD micro/nano-spheres-FLISA, and multiple FLISA platforms. In addition, some new sensors based on the QD-FLISA are introduced; this is one of the hot spots in this field. The current focus and future direction of QD-FLISA are also discussed, which provides important guidance for the further development of FLISA.

A novel biosensing platform for detection of glaucoma biomarker GDF15 via an integrated BLI-ELASA strategy

Glaucoma is a leading cause of irreversible blindness worldwide. Early discovery and prioritized intervention significantly impact its prognosis. Precise monitoring of the biomarker GDF15 contributes towards effective diagnosis and assessment of glaucoma. In this study, we demonstrate that GDF15 monitoring can also aid screening for glaucoma risk and early diagnosis. We obtained an aptamer (APT2TM) with high affinity, high specificity, and high stability for binding to both human-derived and rat-derived GDF15. Simulation results showed that the binding capabilities of APT2TM are mainly affected by the interplay between van der Waals forces and polar solvation energy, and that salt bridges and hydrogen bonds play critical roles. We then integrated an enzyme-linked aptamer sandwich assay (ELASA) into a biolayer interferometry (BLI) system to develop an automated, high-throughput, real-time monitoring BLI-ELASA biosensing platform. This platform exhibited a wide linear detection window (10-810 pg/mL range) and high sensitivity for GDF15 (detection limit of 5-6 pg/mL). Moreover, we confirmed its excellent performance when applied to GDF15 quantification in real samples from glaucomatous rats and clinical patients. We believe that this technology represents a robust, convenient, and cost-effective approach for risk screening, early diagnosis, and animal modeling evaluation of glaucoma in the near future.

A novel and sensitive ratiometric fluorescent quantum dot-based biosensor for alkaline phosphatase detection in biological samples via the inner-filter effect

Alkaline phosphatase (ALP) is an important biomarker whose abnormal level in activity is associated with hepatobiliary, skeletal, and renal diseases as well as cancer. Herein, we synthesized ZnSe@ZnS quantum dots (ZnSe@ZnS QDs) and Mn-doped ZnS quantum dots (Mn:ZnS QDs) as fluorophores to establish the ratiometric fluorescent assay for ALP activity detection in biological samples. p-Nitrophenyl phosphate (PNPP) was used as a substrate for ALP, and the overlaps between absorption spectra of PNPP and excitation spectra of QDs resulted in sharp fluorescence quenching. Under the catalysis of ALP, PNPP was hydrolyzed into p-nitrophenol (PNP), which caused a red shift of absorption band of PNPP and fluorescence recovery of Mn:ZnS QDs (585 nm). However, the overlaps between absorption spectra of PNP and emission spectra of ZnSe@ZnS QDs led a further quenching of ZnSe@ZnS QDs (405 nm). Therefore, the ratiometric fluorescent signals (F ₅₈₅/F ₄₀₅) were associated with activity of ALP based on bidirectional responses of QDs to the concentration of PNPP. Under the optimum conditions, the method exhibited a good linear relationship from 4 to 96 U per L (R ² = 0.9969) with the detection limit of 0.57 U per L. Moreover, the method was successfully applied for detecting the ALP activity in a complex biological matrix (human serum and HepG2 cells) with impressive specificity. In particular, the complicated chemical modifications of QDs and pretreatments of biological samples were not required in the whole detection procedures. Therefore, it not only provided a sensitive, specific and simple approach to clinical ALP activity detection, but it also provided support for early diagnosis of diseases.

Detection of Alpha-Fetoprotein Using Aptamer-Based Sensors

Alpha-fetoprotein (AFP) is widely-known as the most commonly used protein biomarker for liver cancer diagnosis at the early stage. Therefore, developing the highly sensitive and reliable method of AFP detection is of essential demand for practical applications. Herein, two types of aptamer-based AFP detection methods, i.e., optical and electrochemical biosensors, are reviewed in detail. The optical biosensors include Raman spectroscopy, dual-polarization interferometry, resonance light-scattering, fluorescence, and chemiluminescence. The electrochemical biosensors include cyclic voltammetry, electrochemical impedance spectroscopy, and giant magnetic impedance. Looking into the future, methods for AFP detection that are high sensitivity, long-term stability, low cost, and operation convenience will continue to be developed.

Target-induced activation of polymerase activity for recycling signal amplification cascades for sensitive aptamer-based detection of biomarkers

It is of great importance to develop biosensing methods for the sensitive and selective analysis of biomarkers at very low levels in biological samples. Using a new target-induced activation of the DNA polymerase activity for recycling amplification cascades, we describe an aptamer-based method for highly sensitive detection of platelet-derived growth factor BB (PDGF-BB) in human serums. The polymerase activity is initially inhibited by the binding of the polymerase to the enzyme aptamer sequence. PDGF-BB associates with and switches a PDGF-BB binding aptamer to trigger the release of an active polymerase, which further initiates the simultaneous recycling of the target PDGF-BB molecules and the enzyme aptamer sequence for the subsequent displacement of the fluorescently quenched probes to recover the fluorescence. Due to two recycling cascades, substantial fluorescence magnification is obtained for the highly sensitive detection of PDGF-BB with a low detection limit of 5.1 pM. Moreover, the potential applicability of this method for real samples was verified by determining PDGF-BB in diluted human serums, relying on the excellent specificity and selectivity of the aptamer. The demonstration of the PDGF-BB assay method here thus can be expanded for the construction of diverse sensing platforms for detecting different trace biomarkers with the integration of an elaborate design of the aptamer probes.

Fabrication of pH-Adjusted Boronic Acid-Aptamer Conjugate for Electrochemical Analysis of Conjugated N-Glycolylneuraminic Acid

In this work, the boronic acid-aptamer conjugate (BAAC) is elaborately designed and explored as a recognition unit. The admirable properties of the pH-dependent boronic acid ester are integrated with the specific capturing capability of the modified aptamer; thus, BAAC can efficiently and selectively bind with the target by adjusting the pH values. An electrochemical biosensor based on pH-adjusted BAAC has been further developed for the analysis of CNeu5Gc, an important biomarker of different kinds of cancer. The boronic acid moiety in BAAC can react with CNeu5Gc to form a BAAC-CNeu5Gc complex under acidic conditions, followed by the release of CNeu5Gc from the complex and subsequent capture by the aptamer moiety with the adjustment of the pH value to alkalinity. With simplicity, high specificity, and efficiency, the biosensor exhibits a wide linear range from 2.816 to 3603.960 ng/mL with a low detection limit of 1.224 ng/mL and can be applied to analyze CNeu5Gc in animal food samples. Besides, this work can also provide a kind of modified aptamer, i.e., the chemical capturing group-modified aptamer, to give a new viewpoint for the exploration of other functionalized aptamers.

Molecular Aptamer Beacons and Their Applications in Sensing, Imaging, and Diagnostics

The ability to monitor types, concentrations, and activities of different biomolecules is essential to obtain information about the molecular processes within cells. Successful monitoring requires a sensitive and selective tool that can respond to these molecular changes. Molecular aptamer beacon (MAB) is a molecular imaging and detection tool that enables visualization of small or large molecules by combining the selectivity and sensitivity of molecular beacon and aptamer technologies. MAB design leverages structure switching and specific recognition to yield an optical on/off switch in the presence of the target. Various donor-quencher pairs such as fluorescent dyes, quantum dots, carbon-based materials, and metallic nanoparticles have been employed in the design of MABs. In this work, the diverse biomedical applications of MAB technology are focused on. Different conjugation strategies for the energy donor-acceptor pairs are addressed, and the overall sensitivities of each detection system are discussed. The future potential of this technology in the fields of biomedical research and diagnostics is also highlighted.

Engineered Mesenchymal Stem Cell/Nanomedicine Spheroid as an Active Drug Delivery Platform for Combinational Glioblastoma Therapy

Mesenchymal stem cell (MSC) has been increasingly applied to cancer therapy because of its tumor-tropic capability. However, short retention at target tissue and limited payload option hinder the progress of MSC-based cancer therapy. Herein, we proposed a hybrid spheroid/nanomedicine system, comprising MSC spheroid entrapping drug-loaded nanocomposite, to address these limitations. Spheroid formulation enhanced MSC's tumor tropism and facilitated loading of different types of therapeutic payloads. This system acted as an active drug delivery platform seeking and specifically targeting glioblastoma cells. It enabled effective delivery of combinational protein and chemotherapeutic drugs by engineered MSC and nanocomposite, respectively. In an in vivo migration model, the hybrid spheroid showed higher nanocomposite retention in the tumor tissue compared with the single MSC approach, leading to enhanced tumor inhibition in a heterotopic glioblastoma murine model. Taken together, this system integrates the merits of cell- and nanoparticle- mediated drug delivery with the tumor-homing characteristics of MSC to advance targeted combinational cancer therapy.

An "off-on" phosphorescent aptasensor for the detection of thrombin based on PRET

Thrombin plays an important role in the blood coagulation cascade and it stimulates the process of platelet aggregation. Herein, we developed a highly efficient and sensitive phosphorescent aptasensor system for the quantitative analysis of thrombin. The phosphorescence of 3-mercaptopropionic acid capped Mn-doped ZnS quantum dots (MPA-Mn:ZnS QDs) was gradually quenched with the addition of thrombin binding aptamers-BHQ2 (TBA-BHQ2) based on phosphorescence resonance energy transfer (PRET). With the addition of the target analyte thrombin into the system, TBA-BHQ2 could change its spatial structure from a random coil to an antiparallel G-quadruplex which resulted from the combination of thrombin and TBA-BHQ2, leading to the phosphorescence recovery. Finally, the concentration of thrombin could be accurately determined by means of measuring the phosphorescence intensity change value (ΔP). The limit of detection (LOD) was obtained as low as 15.26 pM with wide linear ranges both from 60 to 2000 pM and from 2 to 900 nM. The proposed strategy was also successfully applied for thrombin detection in human serum samples and plasma samples with satisfactory recoveries from 96% to 99% and 95% to 104%, respectively. The long lifetime of phosphorescent QDs possessed a suitable time delay to eliminate autofluorescence and scattered light interference from biological matrices effectively. Thus, the signal to noise ratio of the phosphorescent aptasensor was improved visibly for the analysis of target analytes.

Chimeric Aptamers-Based and MoS2 Nanosheet-Enhanced Label-Free Fluorescence Polarization Strategy for Adenosine Triphosphate Detection

Adenosine triphosphate (ATP) as a primary energy source plays a unique role in the regulation of all cellular events. The necessity to detect ATP requires sensitive and accurate quantitative analytical strategies. Herein, we present our study of developing a MoS₂ nanosheet-enhanced aptasensor for fluorescence polarization-based ATP detection. A bifunctional DNA strand was designed to consist of chimeric aptamers that recognize and capture ATP and berberine, a fluorescence enhancer. In the absence of ATP, the DNA strand bound to berberine will be hydrolyzed when Exonuclease I (Exo I) is introduced, releasing berberine as a result. In contrast, when ATP is present, ATP aptamer folds into a G-quadruplex structure; thus, the complex can resist degradation by Exo I to maintain berberine for fluorescent detection purpose. In addition, to magnify the fluorescence polarization (FP) signal, MoS₂ nanosheets were also adopted in the system. This nanosheets-enhanced FP strategy is simple and facile which does not require traditional dye-labeled DNA strands and complex operation steps. The developed fluorescence polarization aptasensor showed high sensitivity for the quantification of ATP with a detection limit of 34.4 nM, performing well both in buffer solution and in biological samples.

Array-Based Protein Sensing Using an Aggregation-Induced Emission (AIE) Light-Up Probe

Protein detection and identification are important for the diagnosis of diseases; however, the development of facile sensing probes still remains challenging. Here, we present an array-based "turn on" protein-sensing platform capable of detecting and identifying proteins using aggregation-induced emission luminogens (AIEgens). The water-soluble AIEgens in which fluorescence was initially turned off showed strong fluorescence in the presence of nanomolar concentrations of proteins via restriction of the intramolecular rotation of the AIEgens. The binding affinities between the AIEgens and proteins were associated with various chemical functional groups on AIEgens, resulting in distinct fluorescent-signal outcomes for each protein. The combined fluorescence outputs provided sufficient information to detect and discriminate proteins of interest by linear discriminant analysis. Furthermore, the array-based sensor enabled classification of different concentrations of specific proteins. These results provide novel insight into the use of the AIEgens as a new type of sensing probe in array-based systems.

HPV Oncogene Manipulation Using Nonvirally Delivered CRISPR/Cas9 or Natronobacterium gregoryi Argonaute

CRISPR/Cas9 technology enables targeted gene editing; yet, the efficiency and specificity remain unsatisfactory, particularly for the nonvirally delivered, plasmid-based CRISPR/Cas9 system. To tackle this, a self-assembled micelle is developed and evaluated for human papillomavirus (HPV) E7 oncogene disruption. The optimized micelle enables effective delivery of Cas9 plasmid with a transient transgene expression profile, benefiting the specificity of Cas9 recognition. Furthermore, the feasibility of using the micelle is explored for another nucleic acid-guided nuclease system, Natronobacterium gregoryi Argonaute (NgAgo). Both systems are tested in vitro and in vivo to evaluate their therapeutic potential. Cas9-mediated E7 knockout leads to significant inhibition of HPV-induced cancerous activity both in vitro and in vivo, while NgAgo does not show significant E7 inhibition on the xenograft mouse model. Collectively, this micelle represents an efficient delivery system for nonviral gene editing, adding to the armamentarium of gene editing tools to advance safe and effective precision medicine-based therapeutics.

Binding-induced nicking site reconstruction strategy for quantitative detection of membrane protein on living cell

Here, a binding-induced nicking site reconstruction strategy has been fabricated for quantitative detection of membrane protein on living cell. Taking protein tyrosine kinase-7 (PTK7) as model analyst, first, an aptamer probe was designed with an aptamer sequence, a trigger sequence and a nicking site. In the absence of PTK7, the aptamer sequence could partially hybridize with the trigger sequence, forming a stem-loop structure. And the two complementary sequences of the nicking site were separated, which could not be recognized by nicking enzyme. In the presence of PTK7, the aptamer probe and PTK7 binding caused the reconstruction of the probe, leading to the hybridization of the two separated nicking site sequences. Then, the nicking site could be identified and nicked, yielding the release of the trigger sequence. Next, the trigger sequence could initiate the homogeneous cascade amplification, producing multiple G-quadruplex structures. By inserting the N-Methyl Mesoporphyrin IX (NMM), enhanced fluorescence signal could be acquired. Through the binding-induced nicking site reconstruction, the trigger sequence could be released on the surface of living cell and became more accessible. By combining the cascade rolling circle amplification (RCA) and hybridization chain reaction (HCR), high sensitivity was achieved with a detection limit of 0.3 fM. Moreover, Quantitative assay of PTK7 on living cancer cells and normal cells were performed, suggesting that the proposed method was sensitive enough to detect changes in PTK7 expression. Thus, this strategy provided a novel and reliable method for membrane protein expression assay on living cell.

Palladium Nanoparticles-Based Fluorescence Resonance Energy Transfer Aptasensor for Highly Sensitive Detection of Aflatoxin M₁ in Milk

A highly sensitive aptasensor for aflatoxin M₁ (AFM₁) detection was constructed based on fluorescence resonance energy transfer (FRET) between 5-carboxyfluorescein (FAM) and palladium nanoparticles (PdNPs). PdNPs (33 nm) were synthesized through a seed-mediated growth method and exhibited broad and strong absorption in the whole ultraviolet-visible (UV-Vis) range. The strong coordination interaction between nitrogen functional groups of the AFM₁ aptamer and PdNPs brought FAM and PdNPs in close proximity, which resulted in the fluorescence quenching of FAM to a maximum extent of 95%. The non-specific fluorescence quenching caused by PdNPs towards fluorescein was negligible. After the introduction of AFM₁ into the FAM-AFM₁ aptamer-PdNPs FRET system, the AFM₁ aptamer preferentially combined with AFM₁ accompanied by conformational change, which greatly weakened the coordination interaction between the AFM₁ aptamer and PdNPs. Thus, fluorescence recovery of FAM was observed and a linear relationship between the fluorescence recovery and the concentration of AFM₁ was obtained in the range of 5–150 pg/mL in aqueous buffer with the detection limit of 1.5 pg/mL. AFM₁ detection was also realized in milk samples with a linear detection range from 6 pg/mL to 150 pg/mL. The highly sensitive FRET aptasensor with simple configuration shows promising prospect in detecting a variety of food contaminants.

Quantum dots: from fluorescence to chemiluminescence, bioluminescence, electrochemiluminescence, and electrochemistry

During the past decade, nanotechnology has become one of the major forces driving basic and applied research. As a novel class of inorganic fluorochromes, research into quantum dots (QDs) has become one of the fastest growing fields of nanotechnology today. QDs are made of a semiconductor material with tunable physical dimensions as well as unique optoelectronic properties, and have attracted multidisciplinary research efforts to further their potential bioanalytical applications. Recently, numerous optical properties of QDs, such as narrow emission band peaks, broad absorption spectra, intense signals, and remarkable resistance to photobleaching, have made them biocompatible and sensitive for biological assays. In this review, we give an overview of these exciting materials and describe their potential, especially in biomolecules analysis, including fluorescence detection, chemiluminescence detection, bioluminescence detection, electrochemiluminescence detection, and electrochemical detection. Finally, conclusions are made, including highlighting some critical challenges remaining and a perspective of how this field can be expected to develop in the future.

How to make nanobiosensors: surface modification and characterisation of nanomaterials for biosensing applications

This report aims to provide the audience with a guideline for construction and characterisation of nanobiosensors that are based on widely used affinity probes including antibodies and aptamers.