An aptamer-based fluorescence biosensor for multiplex detection using unmodified gold nanoparticles

Electrochemiluminescence Biosensor for Hyaluronidase Based on the Adjustable Electrostatic Interaction between the Surface-Charge-Controllable Nanoparticles and Negatively Charged Electrode

A novel electrochemiluminescence (ECL) biosensor for hyaluronidase (HAase) based on the adjustable electrostatic interaction between the surface-charge-controllable nanoparticles and negatively charged electrode has been devised. Hyaluronic acid (HA)-coated amino-modified ruthenium bipyridine-doped silica nanoparticles (Ru@SiO₂-NH₂@HA NPs) have been synthesized and act as ECL indicators, and the surface of this particle is negatively charged because HA contains a large amount of OH- and COO-. The strong electrostatic repulsion between the Ru@SiO₂-NH₂@HA NPs and negatively charged indium tin oxide (ITO) electrode surface leads to the detection of a low-intensity ECL signal. In the presence of HAase, the HA on the surface of the Ru@SiO₂-NH₂@HA NPs can be decomposed, and the particles can be transformed into positively charged amino-modified ruthenium bipyridine-doped silica nanoparticles (Ru@SiO₂-NH₂ NPs), which can be concentrated near the surface of the ITO electrode through electrostatic attraction, and result in the detection of an enhanced ECL signal. The ECL of the system has a good linear relationship with HAase concentration in the range of 2.0-60 U/mL, and the limit of detection was 0.37 U/mL. The designed biosensor had been applied to detect the target in real samples with satisfied results.

Nanoarchitectonics for Abused-Drug Biosensors

Rapid, accessible, and highly accurate biosensors for the detection of addictive and abused drugs are needed to reduce the adverse personal and societal impacts of addiction. Modern sensors that utilize next-generation technologies, e.g., nanobiotechnology and nanoarchitectonics, have triggered revolutionary progress in the field as they allow accurate detection and tracking of trace levels of major classes of drugs. This paper reviews advances in the field of biosensors for the detection of commonly abused drugs, both prescribed such as codeine and morphine, and illegal narcotics like cocaine.

Electrochemiluminescence Aptasensor for Charged Targets through the Direct Regulation of Charge Density in Microchannels

The change of surface charge density can cause many changes in physical or chemical properties and has been applied to design many sensitive sensors. Ochratoxin A (OTA) is a negatively charged target in neutral or alkaline solutions. In this work, a microchannel-based electrochemiluminescence (ECL) aptasensor for OTA detection based on this character had been designed. The charged target directly combined with functionalization layers of the microchannels, which caused surface charge density variation and therefore resulted in the change of ECL intensity of the (1,10-phenanthroline)ruthenium(II)/tripropylamine system. The decrease of ECL intensity is linearly dependent on OTA concentration ranging from 0.5 to 4 ng mL^-1 with a detection limit down to 0.17 ng mL^-1. This strategy has the advantages of simple interface chemistry design and universality, which offers a guiding significance for the charged target assay.

CRISPR/Cas-powered nanobiosensors for diagnostics

CRISPR diagnostics (CRISPR-Dx) offer a wide range of enhancements compared to traditional nanobiosensors by taking advantage of the excellent trans-cleavage activity of the CRISPR/Cas systems. However, the single-stranded DNA/RNA reporters of the current CRISPR-Dx suffer from poor stability and limited sensitivity, which make their application in complex biological environments difficult. In comparison, nanomaterials, especially metal nanoparticles, exhibits robust stability and desirable optical and electrocatalytical properties, which make them ideal as reporter molecules. Therefore, biosensing research is moving towards the use of the trans-cleavage activity of CRISPR/Cas effectors on metal nanoparticles and apply the new phenomenon to develop novel nanobiosensors to target various targets such as viral infections, genetic mutations and tumor biomarkers, by using different sensing methods, including, but not limited to fluorescence, luminescence resonance, colorimetric and electrochemical signal readout. In this review, we explore some of the most recent advances in the field of CRISPR-powered nanotechnological biosensors. Demonstrating high accuracy, sensitivity, selectivity and versatility, nanobiosensors along with CRISPR/Cas technology offer tremendous potential for next-generation diagnostics of multiple targets, especially at the point of care and without any target amplification.

Highly sensitive detection of cancer cells via split aptamer mediated proximity-induced hybridization chain reaction

Highly sensitive detection of cancer cells is of great importance for evaluating cancer development and improving survival rates. Here, we developed a split aptamer mediated proximity-induced hybridization chain reaction (HCR) strategy to meet this purpose. In this strategy, two split aptamer initiator probes, Sp-a and Sp-b, and two HCR hairpin probes, H1 and H2 were designed. The split aptamer initiator probes contained two components, split aptamer domains being responsible for target recognition, and the split initiator parts serving as the HCR promoter. In the presence of target cells, Sp-a and Sp-b would self-assemble on the cell surfaces, allowing the formation of an intact nicked initiator to activate the HCR reaction. Benefit from low background split aptamers and HCR amplification, this strategy presented high sensitivity in quantitative detection with a detection limit of 18 cells in 150 μL of binding buffer. Moreover, the approach exhibited excellent specificity to target cells in 10% fetal bovine serum and mixed cell samples, which was favorable for clinical diagnosis in complex biological environment. In addition, by changing the split aptamers attached to the split initiator, the proposed strategy can be expanded to detect various kinds of target cells. It may provide a novel and useful applicable platform for the sensitive detection of cancer cells in biomedicine and tumor-related studies.

Dopamine and Melamine Binding to Gold Nanoparticles Dominates Their Aptamer-Based Label-Free Colorimetric Sensing

Target-directed aptamer adsorption by gold nanoparticles (AuNPs) has been widely used to develop label-free colorimetric biosensors. However, the potential interactions between target molecules and AuNPs have not been considered, which may lead to misinterpretation of analytical results. In this work, the detection of dopamine, melamine, and K⁺ was studied as model systems to address this problem. First, dopamine and two control molecules all induced the aggregation of citrate-capped AuNPs with apparent K_d's of 5.8 μM dopamine, 51.6 μM norepinephrine, and 142 μM tyramine. Isothermal titration calorimetry measured the aptamer K_d to be 1.9 μM dopamine and 16.8 μM norepinephrine, whereas tyramine cannot bind. Surface enhanced Raman spectroscopy confirmed direct adsorption of dopamine, and the adsorbed dopamine inhibited the adsorption of DNA. Using a typical salt-induced colorimetric detection protocol, a similar color response was observed regardless of the sequence of DNA, indicating the observed color change reflected the adsorption of dopamine by the AuNPs instead of the binding of dopamine by the aptamer. For this label-free sensor to work, the interaction between the target molecule and AuNPs should be very weak, while dopamine represents an example of strong interactions. For the other two systems, the melamine detection did not reflect aptamer binding either but the K⁺ detection did, suggesting melamine also strongly interacted with AuNPs, whereas K⁺ had very weak interactions with AuNPs. Since each target molecule is different, such target/AuNP interactions need to be studied case-by-case to ensure the sensing mechanism.

Target-triggered aggregation of gold nanoparticles for photothermal quantitative detection of adenosine using a thermometer as readout

Colorimetric platform using the aggregation of gold nanoparticles (AuNPs) is a pretty simple method for biosensing, but advanced instruments such as specterophotometer is still needed to achieve accurately quantitative readout. Aggregated AuNPs exhibit excellent photothermal properties under near-infrared laser irradiation, which is significantly different from non-aggregated AuNPs. Herein, given the different photothermal effect, we translated the AuNPs-based colorimetric assay into a photothermal assay for the quantitative detection of adenosine using a thermometer as readout. Short single-stranded DNA (ssDNA, adenosine aptamer) was adsorbed on the surface of AuNPs and hence prevented the aggregation of AuNPs under high ionic concentration. The presence of adenosine caused the structural change of ssDNA and the AuNPs became aggregated. The enhanced temperature under NIR-laser irradiation has a linear response to the concentration of adenosine in the range of 2.0-50.0 μM. The detection limit was 1.7 μM. This proposed method is portable, easy and applicable to the quantitative assay of other targets by simply replacing of the sequence of ssDNA.

A ratiometric nanoprobe for biosensing based on green fluorescent graphitic carbon nitride nanosheets as an internal reference and quenching platform

The integrating of high fluorescent quenching capability of two-dimensional nanomaterials with dye-labelled ssDNA as nanoprobes has attracted increasing interest for biosensing applications. However, this absolute intensity-dependent single fluorescent signal may be influenced by target concentration-independent factors. To overcome this challenge, a ratiometric nanoprobe was developed by utilizing green fluorescent phenyl-doped carbon nitride (PDCN) nanosheets as an internal reference and quenching platform. 5-carboxy-X-rhodamine-labelled anti-adenosine aptamer was used as a signal probe. PDCN nanosheets quenched the fluorescence of the absorbed signal probe while kept their own fluorescence constantly. Upon addition of adenosine, the formation of adenosine-aptamer complexes led to desorption of the signal probe from the surface of PDCN nanosheets, resulted in the fluorescent recovery of the signal probe. The ratio of the fluorescent enhancement of the signal probe to the inherent fluorescence of PDCN nanosheets was used to quantitatively measure adenosine. The limit of detection for adenosine was 6.86 μM. Finally, the ratiometric nanoprobe was applied to determine adenosine in serum samples.

Photonic crystal enhanced fluorescence immunoassay on diatom biosilica

Fluorescence biosensing is one of the most established biosensing methods, particularly fluorescence spectroscopy and microscopy. These are two highly sensitive techniques but require high-grade electronics and optics to achieve the desired sensitivity. Efforts have been made to implement these methods using consumer grade electronics and simple optical setups for applications such as point-of-care diagnostics, but the sensitivity inherently suffers. Sensing substrates, capable of enhancing fluorescence are thus needed to achieve high sensitivity for such applications. In this paper, we demonstrate a photonic crystal-enhanced fluorescence immunoassay biosensor using diatom biosilica, which consists of silica frustules with sub-100 nm periodic pores. Utilizing the enhanced local optical field, the Purcell effect and increased surface area from the diatom photonic crystals, we create ultrasensitive immunoassay biosensors that can significantly enhance fluorescence spectroscopy as well as fluorescence imaging. Using standard antibody-antigen-labeled antibody immunoassay protocol, we experimentally achieved 100× and 10× better detection limit with fluorescence spectroscopy and fluorescence imaging respectively. The limit of detection of the mouse IgG goes down to 10^-16 M (14 fg/mL) and 10^-15 M (140 fg/mL) for the two respective detection modalities, virtually sensing a single mouse IgG molecule on each diatom frustule. The effectively enhanced fluorescence imaging in conjunction with the simple hot-spot counting analysis method used in this paper proves the great potential of diatom fluorescence immunoassay for point-of-care biosensing.

Aptamer-tagged DNA origami for spatially addressable detection of aflatoxin B1

A DNA origami-based platform for detecting aflatoxin B1 has been constructed with the assistance of aptamer probes and its complementary ssDNA-modified gold nanoparticles. This work may open new horizons for the application of DNA origami in the detection of a variety of small molecules.

A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers

Loop–loop (also known as kissing) interactions between RNA hairpins are involved in several mechanisms in both prokaryotes and eukaryotes such as the regulation of the plasmid copy number or the dimerization of retroviral genomes. The stability of kissing complexes relies on loop parameters (base composition, sequence and size) and base combination at the loop–loop helix - stem junctions. In order to identify kissing partners that could be used as regulatory elements or building blocks of RNA scaffolds, we analysed a pool of 5.2 × 10⁶ RNA hairpins with randomized loops. We identified more than 50 pairs of kissing RNA hairpins. Two kissing motifs, 5′CCNY and 5′RYRY, generate highly stable complexes with K_Ds in the low nanomolar range. Such motifs were introduced in the apical loop of hairpin aptamers that switch between unfolded and folded state upon binding to their cognate target molecule, hence their name aptaswitch. The aptaswitch–ligand complex is specifically recognized by a second RNA hairpin named aptakiss through loop–loop interaction. Taking advantage of our kissing motif repertoire we engineered aptaswitch–aptakiss modules for purine derivatives, namely adenosine, GTP and theophylline and demonstrated that these molecules can be specifically and simultaneously detected by surface plasmon resonance or by fluorescence anisotropy.

Three label-free thrombin aptasensors based on aptamers and [Ru(bpy)2(o-mopip)]2+

The label free aptasensor based on an aptamer pair and [Ru(bpy)₂(o-mopip)]²⁺–GO has been successfully applied to sandwich assays for thrombin detection.

Fluorometric detection of mutant DNA oligonucleotide based on toehold strand displacement-driving target recycling strategy and exonuclease III-assisted suppression

We describe here a fluorometric assay for sensitive detection of oligonucleotides, based on a target recycling amplification strategy driven by toehold-mediated strand displacement reaction and on exonuclease III (Exo Ш)-assisted fluorescence background suppression strategy. The network consists of a pair of partially complementary DNA hairpins (HP1 and HP2) with 3' overhang ends, between which the spontaneous hybridization is kinetically hindered by the stems. The target DNA is repeatedly used to trigger a recycling progress between the hairpins, generating numerous HP1-HP2 duplex complexes. Exo III was then employed to digest the double strand parts of the residual hairpins and the intermediate products. The fluorescent dye, SYBR Green I, binds to the double-strand DNA products and emits strong fluorescence to achieve sensitive detection of the target DNA with the detection limit of 5.34 pM. Moreover, this proposed strategy showed high discrimination efficiency towards target DNA against mismatched DNA and was successfully applied in the analysis of human serum sample.

Ultrasensitive colorimetric carcinoembryonic antigen biosensor based on hyperbranched rolling circle amplification

In this study, a hyperbranched rolling circle amplification (HRCA)-based colorimetric biosensor for carcinoembryonic antigen (CEA) is developed with high sensitivity and specificity. A CEA aptamer can bind with its target (CEA) to form a complex due to their high affinity, and the introduced CDNA cannot hybridize with the aptamer. Thus, free CDNA can propagate the HRCA reaction to form a large number of single-stranded DNA (ss-DNA). ss-DNA can be easily adsorbed onto AuNPs and prevent salt-induced AuNPs aggregation, which causes the change in the color of the system. It is found that the absorbance intensity ratio (A520/A660) has a linear relationship with the concentration of the target in the range of 5 pM-0.5 nM, and the detection limit is as low as 2 pM (S/N = 3).

Recent advances in nanoparticle based aptasensors for food contaminants

Food safety and hazard analysis is a prime concern of human life, thus quality assessment of food and water is the need of the day. Recent advances in nano-biotechnology play a significant role in providing possible solutions for developing highly sensitive and affordable detection tools for food analysis. Nanomaterials based aptasensors hold great potential to overcome the drawbacks of conventional analytical techniques. Aptamers comprise a novel class of highly specific bio-recognition elements which are produced by SELEX (systematic evolution of ligands by exponential enrichment) process. They bind to target molecules by folding into 3D structures that can discriminate different chiral compounds. The flexibility in making modifications in aptamers contribute to the design of biosensors, enabling the generation of bio-recognition elements for a wide variety of target molecules. Nanomaterials such as metal nanoparticles, metal nanoclusters, metal oxide nanoparticles, metal and carbon quantum dots, graphene, carbon nanotubes and nanocomposites enable higher sensitivity by signal amplification and introduce several novel transduction principles such as enhanced chemiluminescence, fluorescence, Raman signals, electrochemical signals, enhanced catalytic activity, and super-paramagnetic properties to the biosensor. Although there are a few reviews published recently which deal with the potential of aptamers in various fields, none are devoted exclusively to the potential of aptasensors based on nanomaterials for the analysis of food contaminants. Hence, the current review discusses several transduction systems and their principles used in aptamer based nanosensors which have been developed in the past five years, the challenges faced in their designing, along with their strengths and limitations.

A method for selecting structure-switching aptamers applied to a colorimetric gold nanoparticle assay

Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health and performance. Nucleic acid aptamers have been increasingly applied as recognition elements on biosensor platforms, but selecting aptamers toward small molecule targets requires special design considerations. This work describes modification and critical steps of a method designed to select structure-switching aptamers to small molecule targets. Binding sequences from a DNA library hybridized to complementary DNA capture probes on magnetic beads are separated from nonbinders via a target-induced change in conformation. This method is advantageous because sequences binding the support matrix (beads) will not be further amplified, and it does not require immobilization of the target molecule. However, the melting temperature of the capture probe and library is kept at or slightly above RT, such that sequences that dehybridize based on thermodynamics will also be present in the supernatant solution. This effectively limits the partitioning efficiency (ability to separate target binding sequences from nonbinders), and therefore many selection rounds will be required to remove background sequences. The reported method differs from previous structure-switching aptamer selections due to implementation of negative selection steps, simplified enrichment monitoring, and extension of the length of the capture probe following selection enrichment to provide enhanced stringency. The selected structure-switching aptamers are advantageous in a gold nanoparticle assay platform that reports the presence of a target molecule by the conformational change of the aptamer. The gold nanoparticle assay was applied because it provides a simple, rapid colorimetric readout that is beneficial in a clinical or deployed environment. Design and optimization considerations are presented for the assay as proof-of-principle work in buffer to provide a foundation for further extension of the work toward small molecule biosensing in physiological fluids.

A review of biosensing techniques for detection of trace carcinogen contamination in food products

Carcinogen contaminations in the food chain, for example heavy metal ions, pesticides, acrylamide, and mycotoxins, have caused serious health problems. A major objective of food-safety research is the identification and prevention of exposure to these carcinogens, because of their impossible-to-reverse tumorigenic effects. However, carcinogen detection is difficult because of their trace-level presence in food. Thus, reliable and accurate separation and determination methods are essential to protect food safety and human health. This paper summarizes the state of the art in separation and determination methods for analyzing carcinogen contamination, especially the advances in biosensing methods. Furthermore, the application of promising technology including nanomaterials, imprinted polymers, and microdevices is detailed. Challenges and perspectives are also discussed.

Tunable stringency aptamer selection and gold nanoparticle assay for detection of cortisol

The first-known aptamer for the stress biomarker cortisol was selected using a tunable stringency magnetic bead selection strategy. The capture DNA probe immobilized on the beads was systematically lengthened to increase the number of bases bound to the complementary pool primer regions following selection enrichment. This resulted in a single sequence (15-1) dominating the final round 15 pool, where the same sequence was the second-highest copy number candidate in the enriched pool with the shorter capture DNA probe (round 13). A thorough analysis of the next-generation sequencing results showed that a high copy number may only correlate with enhanced affinity under certain stringency and enrichment conditions, in contrast with prior published reports. Aptamer 15-1 demonstrated enhanced binding to cortisol (K(d) = 6.9 ± 2.8 μM by equilibrium dialysis; 16.1 ± 0.6 μM by microscale thermophoresis) when compared with the top sequence from round 13 and the negative control progesterone. Whereas most aptamer selections terminate at the selection round demonstrating the highest enrichment, this work shows that extending the selection with higher stringency conditions leads to lower amounts eluted by the target but higher copy numbers of a sequence with enhanced binding. The structure-switching aptamer was applied to a gold nanoparticle assay in buffer and was shown to discriminate between cortisol and two other stress biomarkers, norepinephrine and epinephrine, and a structurally analogous biomarker of liver dysfunction, cholic acid. We believe this approach enhances aptamer selection and serves as proof-of-principle work toward development of point-of-care diagnostics for medical, combat, or bioterrorism targets.

Exonuclease I aided enzyme-linked aptamer assay for small-molecule detection

A novel enzyme-linked aptamer assay (ELAA) with the aid of Exonuclease I (Exo I) for colorimetric detection of small molecules was developed. The fluorescein isothiocyanate (FITC)-labeled aptamer was integrated into a double-stranded DNA (dsDNA). In the presence of target, the binding of aptamer with target protected the aptamer from Exo I degradation, which resulted in the FITC tag remaining on the aptamer. Then, the anti-FITC-HRP conjugate was used to produce an optically observable signal. By monitoring the color change, we were able to detect two model molecules, ATP and L-argininamide, with high selectivity and high sensitivity even in the serum matrix. It is expected to be a simple and general ELAA method with wide applicability.

Homogeneous electrochemical aptamer-based ATP assay with signal amplification by exonuclease III assisted target recycling

A novel and homogeneous electrochemical aptamer-based adenosine triphosphate (ATP) assay was demonstrated with signal amplification by exonuclease III-assisted target recycling. A superior detection limit of 1 nM toward ATP with an excellent selectivity could be achieved.

Rational design of a thrombin electrochemical aptasensor by conjugating two DNA aptamers with G-quadruplex halves

A novel strategy for the fabrication of an electrochemical aptasensor is proposed; this strategy has been employed in this work to assay thrombin concentration. Two well-designed oligonucleotides were used as the core element. G-quadruplex-hemin complexes can be formed on the surface of the electrode to give a detectable signal only when thrombin is not bound to the aptamers. The detection limit of the biosensor has been lowered to 10nM. Moreover, since the electroactive probe is not required to be bound to the oligonucleotide, this strategy may integrate the advantages of being both label-free and cost-effective.

Characterization of structural changes in aptamer films for controlled release nanodevices

The dimension of the conformational changes of DNA-aptamers which can be used as stimulus-responsive gate-keepers in controlled delivery nanodevices has been determined by acoustic wave-based sensors upon molecular recognition of a small-sized target, adenosine-5'-monophosphate (AMP).