Single Molecule Fluorescent Colocalization of Split Aptamers for Ultrasensitive Detection of Biomolecules

A dual-switch electrochemical aptasensor for label-free detection of thrombin and ATP based on split aptamers

BACKGROUND

Aptamers, consisting of specialized single-stranded nucleic acids, are engineered through the SELEX technique to recognize specific targets with strong affinity. Aptamers are exceptionally useful in various sensor technologies, such as fluorescence-based sensors, electrochemical sensors, and colorimetric detection systems. Due to its high sensitivity, specificity and fast response, electrochemical aptasensor shows great application prospects in analytical detection, food safety, and environmental monitoring. However, one aptasensor can usually detect only one type of target, limiting its universality in practical applications.

RESULTS

Here, we constructed a dual-switch and label-free electrochemical aptasensor based on split aptamer and nuclease. The feasibility, specificity, and sensitivity of the aptasensor were investigated by using thrombin and adenosine triphosphate (ATP) as targets. Split aptamer can not only capture target specifically but also form a stable sandwich structure with the target. In the presence of thrombin, it triggered a hydrolysis reaction of exonuclease I, leading to a decrease in the impedance signal. Differently, the presence of ATP could form a sandwich structure with split aptamers, leading to an increase in output signals. The aptasensor achieved sensitive and specific detection of thrombin and ATP, with low detection limits of 0.76 pM and 0.27 pM, respectively.

SIGNIFICANCE AND NOVELTY

The aptasensor realized the detection of two targets without replacing any reagents or equipment, which greatly saved time and cost. Furthermore, electrochemical impedance spectroscopy (EIS) uses impedance as an output signal, showing great application prospects in electrochemical aptasensors as label-free and simple methods. Because of its simplicity, label-free, and sensitivity in complex samples, the split aptamer-assisted aptasensor provides new ideas and methods in early diagnosis of diseases.

Recent Advance in Single-Molecule Fluorescent Biosensors for Tumor Biomarker Detection

The construction of biosensors for specific, sensitive, and rapid detection of tumor biomarkers significantly contributes to biomedical research and early cancer diagnosis. However, conventional assays often involve large sample consumption and poor sensitivity, limiting their further application in real samples. In recent years, single-molecule biosensing has emerged as a robust tool for detecting and characterizing biomarkers due to its unique advantages including simplicity, low sample consumption, ultra-high sensitivity, and rapid assay time. This review summarizes the recent advances in the construction of single-molecule biosensors for the measurement of various tumor biomarkers, including DNAs, DNA modifications, RNAs, and enzymes. We give a comprehensive review about the working principles and practical applications of these single-molecule biosensors. Additionally, we discuss the challenges and limitations of current single-molecule biosensors, and highlight the future directions.

A molecularly imprinted sensor for single-molecule detection of pesticide metabolite at the amol/L level sensitized by water-soluble luminol derivative encapsulated liposome via click reaction

A novel luminol derivative, 4-[(1,4-dioxo-1,2,3,4-tetrahydrophthalazin-5-yl)amino]-4-oxobut-2-enoic acid (ALD) with electrochemiluminescence intensity and stability characteristics similar to luminol, but higher solubility in near neutral solution, was designed and synthesized in this study. Using this derivative, a molecular imprinted electrochemiluminescence sensor (MIECLS) was prepared for the sensitive and selective determination of 2-amino-5-mercapto-1,3,4-thiadiazole (AMT), a metabolite of bismerthiazol, thiediazole copper, thiazole zinc, and other pesticides. The ALD probes encapsulated in liposomes are immobilized on the molecularly imprinted film by light-triggered click reaction, and the concurrent release of multiple probes allows for highly sensitive detection. In the AMT concentration range of 1.00 × 10-18 - 5.00 × 10-13 mol/L, the relation between ECL response and log AMT concentration is linear. With a detection limit of 5.25 × 10-19 mol/L (about 4 - 6 molecules in 10 μL of the sample), the sensor allows for high sensitivity analysis of ultra-trace amounts of small organic compounds. In general, the ECL-based single-molecule detection technique proposed herein might be a promising alternative to fluorescence single-molecule detection.

The Thermodynamic Fingerprints of Ultra-Tight Nanobody-Antigen Binding Probed via Two-Color Single-Molecule Coincidence Detection

Life on the molecular scale is based on a versatile interplay of biomolecules, a feature that is relevant for the formation of macromolecular complexes. Fluorescence-based two-color coincidence detection is widely used to characterize molecular binding and was recently improved by a brightness-gated version which gives more accurate results. We developed and established protocols which make use of coincidence detection to quantify binding fractions between interaction partners labeled with fluorescence dyes of different colors. Since the applied technique is intrinsically related to single-molecule detection, the concentration of diffusing molecules for confocal detection is typically in the low picomolar regime. This makes the approach a powerful tool for determining bi-molecular binding affinities, in terms of KD values, in this regime. We demonstrated the reliability of our approach by analyzing very strong nanobody-EGFP binding. By measuring the affinity at different temperatures, we were able to determine the thermodynamic parameters of the binding interaction. The results show that the ultra-tight binding is dominated by entropic contributions.

Surface modification for improving immunoassay sensitivity

Immunoassays are widely performed in many fields such as biomarker discovery, proteomics, drug development, and clinical diagnosis. There is a growing need for high sensitivity of immunoassays to detect low abundance analytes. As a result, great effort has been made to improve the quality of surfaces, on which the immunoassay is performed. In this review article, we summarize the recent progress in surface modification strategies for improving the sensitivity of immunoassays. The surface modification strategies can be categorized into two groups: antifouling coatings to reduce background noise and nanostructured surfaces to amplify the signals. The first part of the review summarizes the common antifouling coating techniques to prevent nonspecific binding and reduce background noise. The techniques include hydrophilic polymer based self-assembled monomers, polymer brushes, and surface attached hydrogels, and omniphobicity based perfluorinated surfaces. In the second part, some common nanostructured surfaces to amplify the specific detection signals are introduced, including nanoparticle functionalized surfaces, two dimensional (2D) nanoarrays, and 2D nanomaterial coatings. The third part discusses the surface modification techniques for digital immunoassays. In the end, the challenges and the future perspectives of the surface modification techniques for immunoassays are presented.

Nanoconfinement-Enhanced Electrochemiluminescence for in Situ Imaging of Single Biomolecules

Direct imaging of electrochemical reactions at the single-molecule level is of potential interest in materials, diagnostic, and catalysis applications. Electrochemiluminescence (ECL) offers the opportunity to convert redox events into photons. However, it is challenging to capture single photons emitted from a single-molecule ECL reaction at a specific location, thus limiting high-quality imaging applications. We developed the nanoreactors based on Ru(bpy)₃²⁺-doped nanoporous zeolite nanoparticles (Ru@zeolite) for direct visualization of nanoconfinement-enhanced ECL reactions. Each nanoreactor not only acts as a matrix to host Ru(bpy)₃²⁺ molecules but also provides a nanoconfined environment for the collision reactions of Ru(bpy)₃²⁺ and co-reactant radicals to realize efficient in situ ECL reactions. The nanoscale confinement resulted in enhanced ECL. Using such nanoreactors as ECL probes, a dual-signal sensing protocol for visual tracking of a single biomolecule was performed. High-resolution imaging of single membrane proteins on heterogeneous cells was effectively addressed with near-zero backgrounds. This could provide a more sensitive tool for imaging individual biomolecules and significantly advance ECL imaging in biological applications.

Improved immunoassay sensitivity and specificity using single-molecule colocalization

Enzyme-linked immunosorbent assays (ELISAs) are a cornerstone of modern molecular detection, but the technique still faces notable challenges. One of the biggest problems is discriminating true signal generated by target molecules versus non-specific background. Here, we developed a Single-Molecule Colocalization Assay (SiMCA) that overcomes this problem by employing total internal reflection fluorescence microscopy to quantify target proteins based on the colocalization of fluorescent signal from orthogonally labeled capture and detection antibodies. By specifically counting colocalized signals, we can eliminate the effects of background produced by non-specific binding of detection antibodies. Using TNF-α, we show that SiMCA achieves a three-fold lower limit of detection compared to conventional single-color assays and exhibits consistent performance for assays performed in complex specimens such as serum and blood. Our results help define the pernicious effects of non-specific background in immunoassays and demonstrate the diagnostic gains that can be achieved by eliminating those effects.

Applications of Smartphone-Based Aptasensor for Diverse Targets Detection

Aptamers are a particular class of functional recognition ligands with high specificity and affinity to their targets. As the candidate recognition layer of biosensors, aptamers can be used to sense biomolecules. Aptasensors, aptamer-based biosensors, have been demonstrated to be specific, sensitive, and cost-effective. Furthermore, smartphone-based devices have shown their advantages in binding to aptasensors for point-of-care testing (POCT), which offers an immediate or spontaneous responding time for biological testing. This review describes smartphone-based aptasensors to detect various targets such as metal ions, nucleic acids, proteins, and cells. Additionally, the focus is also on aptasensors-related technologies and configurations.

Split aptamer acquisition mechanisms and current application in antibiotics detection: a short review

Antibiotic contamination is becoming a prominent global issue. Therefore, sensitive, specific and simple technology is desirable the demand for antibiotics detection. Biosensors based on split aptamer has gradually attracted extensive attention for antibiotic detection due to its higher sensitivity, lower cost, false positive/negative avoidance and flexibility in sensor design. Although many of the reported split aptamers are antibiotics aptamers, the acquisition and mechanism of splitting is still unknow. In this review, six reported split aptamers in antibiotics are outlined, including Enrofloxacin, Kanamycin, Tetracycline, Tobramycin, Neomycin, Streptomycin, which have contributed to promote interest, awareness and thoughts into this emerging research field. The study introduced the pros and cons of split aptamers, summarized the assembly principle of split aptamer and discussed the intermolecular binding of antibiotic-aptamer complexes. In addition, the recent application of split aptamers in antibiotic detection are introduced. Split aptamers have a promising future in the design and development of biosensors for antibiotic detection in food and other field. The development of the antibiotic split aptamer meets many challenges including mechanism discovery, stability improvement and new biosensor development. It is believed that split aptamer could be a powerful molecular probe and plays an important role in aptamer biosensor.

In Situ Single-Molecule Imaging of MicroRNAs in Switchable Migrating Cells under Biomimetic Confinement

Spatial imaging of RNAs in single cells is extremely charming for deciphering of regulatory mechanisms in multiple migration modes during tumor metastasis. Herein, enzyme-free-mediated cascade amplified nanoprobes were designed for in situ single-molecule imaging of dual-microRNAs (miRNAs) in switchable migrating cells. Differential expression and localization of dual-miRNAs were clearly exhibited in multiple cell lines attributed to enhanced sensitivity via the cascade signal amplification strategy. Significantly, in situ three-dimensional (3D) imaging of dual-miRNAs in transition of cell migration phenotypes was successfully reconstructed in both non-confined and confined microenvironments in vitro, of which differential spatial distribution was observed in a single cell. This is very promising for exploring key roles of spatial RNA distribution in migrating cells at the single-molecule level, which will advance revealing the molecular mechanism and physical principle in 3D cell migration in vivo.

Recent progress in fluorescent aptasensors for the detection of aflatoxin B1 in food

Aflatoxin B1 pollution is one of the most critical issues of food safety and has been categorized as a group I carcinogen by the International Agency for Research on Cancer. Aflatoxin B1 exists in various foods and feedstuff products and can be produced and contaminate food products in all processes, including growth, harvest, storage, or processing. Therefore, it is of great value for detecting and on-site monitoring aflatoxin B1. Aptamers are short single-stranded DNA or RNA obtained from the nucleic acid molecular library through SELEX. With advantages of high specificity, large affinity, and easy modification, aptasensors have become popular in a wide range of promising applications. This review focuses on recent advances on fluorescent aptamer sensors for the detection of aflatoxin B1, including their design strategies, working mechanisms, and applications to on-site detection. Finally, the current challenges and prospects are discussed.

Single Biomolecule Imaging by Electrochemiluminescence

Herein, a single biomolecule is imaged by electrochemiluminescence (ECL) using Ru(bpy)₃²⁺-doped silica/Au nanoparticles (RuDSNs/AuNPs) as the ECL nanoemitters. The ECL emission is confined to the local surface of RuDSNs leading to a significant enhancement in the intensity. To prove the concept, a single protein molecule at the electrode is initially visualized using the as-prepared RuDSN/AuNPs nanoemitters. Furthermore, the nanoemitter-labeled antibody is linked at the cellular membrane to image a single membrane protein at one cell, without the interference of current and optical background. The success in single-biomolecule ECL imaging solves the long-lasting task in the ultrasensitive ECL analysis, which should be able to provide more elegant information about the protein in cellular biology.

Proximity-induced exponential amplification reaction triggered by proteins and small molecules

We proposed a method to regulate nucleic acid polymerization by proximity and designed an ultrasensitive biosensor based on proximity-induced exponential amplification reaction for proximity assay of proteins (streptavidin) and small molecules (adenosine triphosphate), which allows us to detect a variety of interesting targets by simply changing the binding sites of DNA.

Target-Triggered Assembly in a Nanopipette for Electrochemical Single-Cell Analysis

Engineered nanopipette tools have recently emerged as a powerful approach for electrochemical nanosensing, which has major implications in both fundamental biological research and biomedical applications. Herein, we describe a generic method of target-triggered assembly of aptamers in a nanopipette for nanosensing, which is exemplified by sensitive and rapid electrochemical single-cell analysis of adenosine triphosphate (ATP), a ubiquitous energy source in life and important signaling molecules in many physiological processes. Specifically, a layer of thiolated aptamers is immobilized onto a Au-coated interior wall of a nanopipette tip. With backfilled pairing aptamers, the engineered nanopipette is then used for probing intracellular ATP via the ATP-dependent linkage of the split aptamers. Due to the higher surface charge density from the aptamer assembly, the nanosensor would exhibit an enhanced rectification signal. Besides, this ATP-responsive nanopipette tool possesses excellent selectivity and stability as well as high recyclability. This work provides a practical single-cell nanosensor capable of intracellular ATP analysis. More generally, integrated with other split recognition elements, the proposed mechanism could serve as a viable basis for addressing many other important biological species.

Construction of Dual-Color Probes with Target-Triggered Signal Amplification for In Situ Single-Molecule Imaging of MicroRNA

The in vitro detection of low abundance biomolecules via nonenzymatic signal amplification is an attractive strategy. However, it remains a challenge to monitor targets of interest in situ in living cells by low-background interference and visualized enzyme-free signal amplification strategies. Taking advantage of the single-molecule imaging and dynamic DNA nanotechnologies, we have achieved the target-triggered self-assembly of nanostructure-based dual-color fluorescent probes (NDFPs) by an enzyme-free toehold-mediated strand displacement cascade. NDFPs will facilitate the simple and visualized monitoring of microRNA (miRNA) at the femtomolar level. The recycled miRNA can be considered as the catalyst for the assembly of multiple H1/H2 duplexes. This generated the fluorescence signal of the enhanced target expression, indicating both in vitro and in vivo signal-amplified imaging. Moreover, the NDFPs improved the measurement accuracy by dual-color colocalization imaging to greatly avoid false-positive signals and enabled the successful in situ imaging of miRNA in living cells in real time. This work provides a strategy to visually monitor and study the integration of signal amplification detection and single-molecule imaging. NDFPs may be an important step toward the enzyme-free amplified monitoring and imaging of various biomolecules in living cells at the single-molecule level.

Advances in Optical Single-Molecule Detection: En Route to Supersensitive Bioaffinity Assays

The ability to detect low concentrations of analytes and in particular low-abundance biomarkers is of fundamental importance, e.g., for early-stage disease diagnosis. The prospect of reaching the ultimate limit of detection has driven the development of single-molecule bioaffinity assays. While many review articles have highlighted the potentials of single-molecule technologies for analytical and diagnostic applications, these technologies are not as widespread in real-world applications as one should expect. This Review provides a theoretical background on single-molecule-or better digital-assays to critically assess their potential compared to traditional analog assays. Selected examples from the literature include bioaffinity assays for the detection of biomolecules such as proteins, nucleic acids, and viruses. The structure of the Review highlights the versatility of optical single-molecule labeling techniques, including enzymatic amplification, molecular labels, and innovative nanomaterials.

Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors

In analogy to split-protein systems, which rely on the appropriate fragmentation of protein domains, split aptamers made of two or more short nucleic acid strands have emerged as novel tools in biosensor set-ups. The concept relies on dissecting an aptamer into a series of two or more independent fragments, able to assemble in the presence of a specific target. The stability of the assembled structure can further be enhanced by functionalities that upon folding would lead to covalent end-joining of the fragments. To date, only a few aptamers have been split successfully, and application of split aptamers in biosensing approaches remains as promising as it is challenging. Further improving the stability of split aptamer target complexes and with that the sensitivity as well as efficient working modes are important tasks. Here we review functional nucleic acid assemblies that are derived from aptamers and ribozymes/DNAzymes. We focus on the thrombin, the adenosine/ATP and the cocaine split aptamers as the three most studied DNA split systems and on split DNAzyme assemblies. Furthermore, we extend the subject into split light up RNA aptamers used as mimics of the green fluorescent protein (GFP), and split ribozymes.

Simultaneous and ultrasensitive detection of multiple microRNAs by single-molecule fluorescence imaging

Cell status changes are typically accompanied by the simultaneous changes of multiple microRNA (miRNA) levels. Thus, simultaneous and ultrasensitive detection of multiple miRNA biomarkers shows great promise in early cancer diagnosis. Herein, a facile single-molecule fluorescence imaging assay was proposed for the simultaneous and ultrasensitive detection of multiple miRNAs using only one capture anti-DNA/RNA antibody (S9.6 antibody). Two complementary DNAs (cDNAs) designed to hybridize with miRNA-21 and miRNA-122 were labelled with Cy3 (cDNA1) and Cy5 (cDNA2) dyes at their 5'-ends, respectively. After hybridization, both miRNA-21/cDNA1 and miRNA-122/cDNA2 complexes were captured by S9.6 antibodies pre-modified on a coverslip surface. Subsequently, the Cy3 and Cy5 dyes on the coverslip surface were imaged by the single-molecule fluorescence setup. The amount of miRNA-21 and miRNA-122 was quantified by counting the image spots from the Cy3 and Cy5 dye molecules in the green and red channels, respectively. The proposed assay displayed high specificity and sensitivity for singlet miRNA detection both with a detection limit of 5 fM and for multiple miRNA detection both with a detection limit of 20 fM. Moreover, it was also demonstrated that the assay could be used to detect multiple miRNAs simultaneously in human hepatocellular cancer cells (HepG2 cells). The proposed assay provides a novel biosensing platform for the ultrasensitive and simple detection of multiple miRNA expressions and shows great prospects for early cancer diagnosis.

Colocalized Particle Counting Platform for Zeptomole Level Multiplexed Quantification

For multiplexed detection, it is important yet challenging to simultaneously meet the requirement of sensitivity, throughput, and implementation convenience for practical applications. Using the detection of DNAs and miRNAs for illustration, we present a colocalized particle counting platform that can realize the separation-free multiplexed detection of 6 nucleic acid targets with a zeptomole sensitivity and a dynamic range of up to 5 orders of magnitude. The presence of target induces the formation of a sandwich nanostructure via hybridization; thus, there is an occurrence of colocalization of two microbeads with two different colors. The sequence specific coding is realized by an arbitrary combination of two fluorescence channels with different emitting colors. The platform presents robustness in detecting multiple nucleic acid targets with a minimal cross talk and matrix effect as well as the ability to distinguish the specific miRNA from members of the same family. The results of simultaneous detection of 3 miRNAs in 3 different cell lines present straight consistency with that of the standard qRT-PCR. This platform can be adapted to other multiplexing designs such as the "turn-off" mode, in which the proportion of colocalized microbeads is decreased due to the strand-displacement reaction initiated by the specific target. This separation-free platform offers the possibility to achieve the on-site multiplexed detection with compatibility to different experimental designs and extensibility to other signal sources for enumeration.

A portable oligonucleotide-based microfluidic device for the detection of VEGF165 in a three-step suspended-droplet mode

Vascular endothelial growth factor (VEGF165), an important glycosylated protein from the VEGF family, is a type of signal protein highly associated with the development and progression of cancers. In this work, we designed a G-quadruplex-based aptasensing platform for the sensitive and selective detection of VEGF165 in aqueous solution and red blood cell solution. A long-lived phosphorescence iridium(iii) complex (1) with promising photophysical properties and a large Stokes shift was chosen as a selective G-quadruplex probe. The platform could achieve a limit of detection (LOD) down to the picomolar level using a conventional fluorometer. Furthermore, we successfully applied the platform to a three-step suspended droplet (SD)-based microfluidic device for the monitoring of VEGF165. In contrast to the channel-based and digital microfluidic chips, SD-based chips allow easy introduction of liquid samples, valve-free manipulation of multiple reaction steps and flexible volume range. Importantly, polypropylene (PP), a hydrophobic and thermally stable material, was chosen as a substrate to fabricate the chip for the SD-based microfluidic device. The PP-based chip allows the combination of superhydrophobic force, gravity and surface tension for effective driving of the suspended droplet throughout the channel without reverse migration. After assembling all the major components, including a UV lamp, a rotatable chip holder, a filter and a camera into the portable device, we successfully demonstrated the applicability of the device to detect VEGF165 in aqueous solution with a LOD of 0.33 nM at a signal-to-noise ratio (S/N) of 3 and a linear range of 1-100 nM.