Time-resolved fluorescence aptamer-based sandwich assay for thrombin detection

Highly-Efficient Selection of Aptamers for Quantitative Fluorescence Detecting Multiple IAV Subtypes

Influenza A virus (IAV) can cause infectious respiratory diseases in humans and animals. IAVs mutate rapidly through antigenic drift and shift, resulting in the emergence of numerous IAV subtypes and significant challenges for IAV detection. Therefore, achieving the simultaneous detection of multiple IAVs is crucial. In this work, three specific aptamers targeting the hemagglutination (HA) protein of the influenza A H5N1, H7N9, and H9N2 viruses were screened using a multichannel magnetic microfluidic chip. The aptamers exhibit nanomolar affinity and excellent specificity for the HA protein of H5N1, H7N9, and H9N2 viruses. Furthermore, three specific aptamers were truncated and labeled with different fluorescence markers to realize fluorescence quantitative detection of influenza A H5N1, H7N9, and H9N2 viruses through an aptamer sandwich assay in 1 h. The limit of detection (LOD) of the developed method is 0.38 TCID50/mL for the H5N1 virus, 0.75 TCID50/mL for the H7N9 virus, and 1.14 TCID50/mL for the H9N2 virus. The detection method has excellent specificity, strong anti-interference ability, and good reproducibility. This work provides a sensitive quantitative detection method for the H5N1, H7N9, and H9N2 viruses, enabling quantitative fluorescence detection for multiple IAV subtypes.

Time-resolved Fluorescence DNA-based Sensors for Reducing Background Fluorescence of Environment

The fluorescence assay is one of the popular methods that is applied for detection of different targets. However, this method may show low sensitivity and high background in biological samples due to the natural fluorescence of different compounds in complicated samples. In addition, it inevitably affects the detection results accuracy. A fundamental solution to this problem is the use of the time-resolved fluorescence technique (TRF). The main component of this technique is the use of long fluorescence lifetime reagents. In this review, various time-resolved fluorescent reagents such as complexes of lanthanide ions, lanthanide-doped inorganic nanoparticles; Mn-doped ZnS quantum dots (QDs) and pyrene excimer are introduced. Moreover, TRF sensors, especially TRF aptasensors (DNA-based sensors) are discussed. This review will give new ideas for researchers to develop novel high-sensitive TRF sensors that can remove or decrease background fluorescence and use them for the detection of various targets in complicated samples without treatment.

Electrochemical dual-aptamer biosensors based on nanostructured multielectrode arrays for the detection of neuronal biomarkers

Multielectrode arrays (MEAs) have been increasingly used for the development of biosensors due to their capability to record signals from multiple channels, fast mass transfer rates, and high spatial resolution. Alzheimer's disease (AD) is often associated with mitochondrial dysfunction, which is closely related to reduced levels of adenosine triphosphate (ATP). Therefore, simultaneous detection of ATP together with amyloid-β oligomers (AβO), a reliable biomarker for AD, can potentially advance the early detection of Alzheimer's disease. In this work, a dual-aptamer modified MEA chip was developed that consists of microelectrodes modified with electrodeposited 3D nanostructures (3D-GMEs). Electrodeposition methods, deposition potential, and deposition time were systematically altered and the active surface areas as well as the electrode morphologies were characterized by cyclic voltammetry and scanning electron microscopy. The nanostructured microelectrodes were sequentially modified with AβO and ATP specific aptamer receptors. To achieve the modification of different aptamer receptors at different 3D-GMEs of the same MEA chip, electrochemical cleaning was applied to individual 3D-GMEs. Ferrocene labels were attached to the aptamer receptors to enable amperometric signaling after target-aptamer binding. The developed aptasensor showed a linear detection range from 1 pM to 200 nM for the detection of AβO and from 0.01 nM to 1000 nM for the detection of ATP. Finally, ATP and AβO were detected simultaneously in the same analyte solution by the same sensor chip, which could support the early detection of AD, provide comprehensive information about the health status of the patient, and be helpful for pathological studies of neurodegenerative diseases.

Hydrogel based aptasensor for thrombin sensing by Resonance Rayleigh Scattering

In this research, a novel Resonance Rayleigh Scattering (RRS) aptasensor was developed for thrombin monitoring using in-situ synthesized and embedded Au nanoparticles (AuNPs) into poly vinyl alcohol -borax hydrogel (PBH). Thiolated-thrombin binding aptamer (thiolated-TBA) was attached to the surface of AuNPs embedded into PBH to design the PBH-aptasensor for thrombin detection (thiolated-TBA@AuNPs-PBH). To verify the characteristic and morphology of PBH nanocomposite, energy dispersive X-ray analysis, TEM, average particle size analizer and UV-Vis spectra were performed. The difference in RRS intensities in the absence and presence of thrombin was calculated and selected as the monitoring signal. Effect of different parameters on the RRS signal was investigated at excitation wavelength of 500 nm. Under the approved conditions, the linear detection range was validated over the concentration of 0.70 pM- 0.02 μM. The limit of detection based on 3S_b was 0.10 pM. The relative standard deviation for 5.6 pM and 3.6 nM were 4.0 and 2.7% (n = 10), respectively. The proposed aptasensor was successfully applied as an experimental model for thrombin detection in serum samples of healthy volunteers with acceptable results.

Pyrophosphate ion-triggered competitive displacement of ssDNA from a metal-organic framework and its application in fluorescent sensing of alkaline phosphatase

Nanomaterial/aptamer assembly has been extensively explored in the detection of various targets, but some limitations still exist in its practical applications, especially time consumption and low-efficient detachment of the aptamer from the nanomaterial surface. In this work, we demonstrated the ligand role of pyrophosphate ion (PPi) in the competitive displacement of ssDNA from the nanoscaffold surface. For this purpose, a fluorescein-labeled ssDNA (F-DNA) and a mixed valence state cerium (Ce³⁺/Ce⁴⁺)-based MOF (MVCM) were employed as the signal response unit and nanoscaffold, respectively. Benefiting from the existence of Ce⁴⁺, the MVCM exhibits an ultrahigh quenching efficiency (more than 90%) to F-DNA fluorescence, which is 3-fold higher than that of the MOF with Ce³⁺ only. However, it was found that PPi can effectively suppress the quenching effect of the MVCM by competitive coordination with the MVCM to displace F-DNA. Different from the conventional target-induced conformational change of aptamers, the PPi-triggered displacement assay is independent of the ssDNA sequence and can be rapidly completed in just 2 min. The displacement assay is also highly sensitive, even at a PPi concentration as low as 55 nM. In contrast to PPi, however, the phosphate ions and other anions cannot displace F-DNA from the MVCM surface to switch on the F-DNA fluorescence. Inspired by this fact, the PPi-triggered displacement assay was further applied in the detection of alkaline phosphatase (ALP). The detection limit toward ALP was obtained at 0.18 mU mL^-1. Moreover, the accurate determination of ALP concentration in serum samples indicates the applicability of this sensing system in detecting real samples.

Development of a SPR aptasensor containing oriented aptamer for direct capture and detection of tetracycline in multiple honey samples

Although surface plasmon resonance (SPR) technique and aptamer technology shows great potential in analytical and biological chemistry, direct capture and analysis of small molecules using SPR remains tough. Detection sensitivity of aptasensor and recognition ability of aptamer is limited, because direct immobilization of aptamer causes large steric hindrance and strand entanglement. Herein, we chose a typical small molecule-tetracycline (Mw. 444.4 g/mol) as a model, and combined aptamer technology, DNA nanostructure, and commercial Biacore T200 SPR instrument to develop a straightforward format SPR aptasensor. Anti-tetracycline aptamer (Apt76) was fabricated on the top of a tetrahedron nanostructure to provide a better accessibility to tetracycline than the single-stranded Apt76 (ss-Apt76), and thus to improve sensitivity of the SPR aptasensor. The aptasensor was then validated in real world application for tetracycline screening in multiple honey samples, achieving good recovery rates of 80.20-114.3%, intuitive sensorgrams indicating the binding kinetic properties, and high specificity towards tetracycline. LOD of the tetrahedron-based SPR aptasensor was obtained using the real honey sample and calculated to be 0.0069 μg/kg, which was 10-fold range lower than that of the ss-Apt76-based aptasensor. The proof-of-concept demonstrated that aptamers of small molecules can be oriented immobilized on the SPR surface in a uniform nanoscale distance in both lateral and vertical direction, so as to achieve better conformational folding and better accessibility to small molecules. The concept is promising to be a universal and powerful tool for other ligand immobilization and SPR studies for both real world detection and molecular interaction.

Polystyrene latex particles containing europium complexes prepared by miniemulsion polymerization using bovine serum albumin as a surfactant for biochemical diagnosis

Luminescent particles have been attracting significant attention because they can be used in biochemical applications, such as detecting and imaging biomolecules. In this study, luminescent polystyrene latex particles were prepared through miniemulsion polymerization of styrene with dissolved europium complexes in the presence of bovine serum albumin (BSA) and poly(ethylene glycol) monomethoxy methacrylate as surfactants. The solubility of the europium complex in styrene has a strong effect on the yield of the particle. Europium tris(2-thenoyl trifluoroacetonate) di(tri-n-octyl phosphine oxide), which has a high solubility in styrene, was sufficiently incorporated into the polystyrene particles compared to europium tris(2-thenoyl trifluoroacetonate), which has a low solubility in styrene. The luminescence property of the europium complex could remain intact even after its incorporation through the miniemulsion polymerization. In the aqueous dispersion, the resulting particles could emit strong luminescence, which is a characteristic of the europium complex. The antibody fragments were covalently attached to BSA-covered particles after a reaction with a bifunctional linker, N-(6-maleimidocaproyloxy)succinimide. The time-resolved fluoroimmunoassay technique showed that 3.3pg/mL of human α-fetoproteins (AFP) can be detected by using the resulting luminescent particles. An immunochromatographic assay using the resulting particles was also performed as a convenient method to qualitatively detect biomolecules. The detection limit of AFP measured by the immunochromatographic assay was determined to be 2000pg/mL. These results revealed that the luminescent particles obtained in this study can be utilized for the highly sensitive detection of biomolecules and in vitro biochemical diagnosis.

[Atomic force microscopy fishing of gp120 on immobilized aptamer and its mass spectrometry identification]

A method of atomic force microscopy-based fishing (AFM fishing) has been developed for protein detection in the analyte solution using a chip with an immobilized aptamer. This method is based on the biospecific fishing of a target protein from a bulk solution onto the small AFM chip area with the immobilized aptamer to this protein used as the molecular probe. Such aptamer-based approach allows to increase an AFM image contrast compared to the antibody-based approach. Mass spectrometry analysis used after the biospecific fishing to identify the target protein on the AFM chip has proved complex formation. Use of the AFM chip with the immobilized aptamer avoids interference of the antibody and target protein peaks in a mass spectrum.

A molecular recognition assisted colorimetric aptasensor for tetracycline

Based on the study of intrinsic conformational structure-dependent molecular recognition between tetracycline (TC) and anti-TC aptamers, herein, we focus on the classic gold nanoparticle (AuNPs)-based colorimetric aptasensor.

A time-resolved luminescent competitive assay to detect L-selectin using aptamers as recognition elements

L-selectin is a protein with potential importance for numerous diseases and clinical disorders. In this paper, we present a new aptamer-based luminescent assay developed to detect L-selectin. The sensing system working principle is based on Förster Resonance Energy Transfer (FRET) from a donor terbium complex (TbC) to an acceptor cyanine dye (Cy5). In the present approach, the biotinylated aptamer is combined with Cy5-labelled streptavidin (Cy5-Strep) to yield an aptamer-based acceptor construct (Apta-Cy5-Strep), while L-selectin is conjugated using luminescent TbC. Upon aptamer binding to the TbC-labelled L-selectin (L-selectin-TbC), permanent donor-acceptor proximity is established which allows for radiationless energy transfer to occur. However, when unlabelled L-selectin is added, it competes with the L-selectin-TbC and the FRET signal decreases as the L-selectin concentration increases. FRET from the TbC to Cy5 was observed with time-gated time-resolved luminescence spectroscopy. A significant change in the corrected luminescence signal was observed in the dynamic range of 10-500 ng/mL L-selectin, the concentration range relevant for accelerated cognitive decline of Alzheimer's disease, with a limit of detection (LOD) equal to 10 ng/mL. The aptasensor-based assay is homogeneous and can be realized within one hour. Therefore, this method has the potential to become an alternative to tedious heterogeneous analytical methods, e.g. based on enzyme-linked immunosorbent assay (ELISA).

A novel label-free and enzyme-free electrochemical aptasensor based on DNA in situ metallization

In this work, we presented a novel label-free and enzyme-free electrochemical aptasensor based on DNA in situ silver metallization as effective electrochemical label. Molecular beacon 2 (MB2, Peptide nucleic acid) was first immobilized on the gold electrode (AuE) through Au-S bond. In the presence of thrombin, the thrombin binding aptamer (MB1) preferred to form thrombin/aptamer complex in lieu of aptamer-DNA duplex, resulting in the 8-17 DNAzyme liberating from the caged structure and hybridization with the MB2, the MB2 will replace and free the target thrombin when it hybridizes with MB1. The released target thrombin can participate in the next hybridization process with MB1. Eventually, each target thrombin went through many cycles, resulting in numerous MB1 confining close to the AuE, which leaded to the surface became negatively charged and allowed the absorption of silver ions on the DNA skeleton. After chemical reduction by hydroquinone, the formed silver nanoparticles could be afforded a signal trace for electrochemical stripping analysis of target thrombin. Through introducing a hybridization chain reaction to increase the DNA length, the current signal was further amplified, achieved the detection of thrombin with a linear range from 1.0×10(-16) to 1.0×10(-11) M and a detection limit of 37 aM. In addition, the signal amplification is realized without using any enzymes or sophisticated label process, and the sensing strategy is completely non-labeled. The success in the present biosensor served as a significant step towards the development of monitoring ultratrace thrombin in clinical detection.

Combining a loop-stem aptamer sequence with methylene blue: a simple assay for thrombin detection by resonance light scattering technique

Schematic illustration of the RLS aptasensor for selective detection of human thrombin.

An electrochemical aptasensor for thrombin detection based on the recycling of exonuclease III and double-stranded DNA-templated copper nanoparticles assisted signal amplification

In this paper, we report an improved electrochemical aptasensor based on exonuclease III and double-stranded DNA (dsDNA)-templated copper nanoparticles (CuNPs) assisted signal amplification. In this sensor, duplex DNA from the hybridization of ligated thrombin-binding aptamer (TBA) subunits and probe DNA can act as an effective template for the formation of CuNPs on the electrode surface, so copper ions released from acid-dissolution of CuNPs may catalyze the oxidation of ο-phenylenediamine to produce an amplified electrochemical response. In the presence of thrombin, a short duplex domain with four complementary base pairs can be stabilized by the binding of TBA subunits with thrombin, in which TBA subunit 2 can be partially digested from 3' terminal with the cycle of exonuclease III, so the ligation of TBA subunits and the subsequent formation of CuNPs can be inhibited. By electrochemical characterization of dsDNA-templated CuNPs on the electrode surface, our aptasensor can display excellent performances for the detection of thrombin in a broad linear range from 100 fM to 1 nM with a low detection limit of 20.3 fM, which can also specially distinguish thrombin in both PBS and serum samples. Therefore, our aptasensor might have great potential for clinical diagnosis of biomarkers in the future.

Atomic force microscopy fishing and mass spectrometry identification of gp120 on immobilized aptamers

Atomic force microscopy (AFM) was applied to carry out direct and label-free detection of gp120 human immunodeficiency virus type 1 envelope glycoprotein as a target protein. This approach was based on the AFM fishing of gp120 from the analyte solution using anti-gp120 aptamers immobilized on the AFM chip to count gp120/aptamer complexes that were formed on the chip surface. The comparison of image contrasts of fished gp120 against the background of immobilized aptamers and anti-gp120 antibodies on the AFM images was conducted. It was shown that an image contrast of the protein/aptamer complexes was two-fold higher than the contrast of the protein/antibody complexes. Mass spectrometry identification provided an additional confirmation of the target protein presence on the AFM chips after biospecific fishing to avoid any artifacts.

In vitro selection of a single-stranded DNA molecular recognition element against atrazine

Widespread use of the chlorotriazine herbicide, atrazine, has led to serious environmental and human health consequences. Current methods of detecting atrazine contamination are neither rapid nor cost-effective. In this work, atrazine-specific single-stranded DNA (ssDNA) molecular recognition elements (MRE) were isolated. We utilized a stringent Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology that placed the greatest emphasis on what the MRE should not bind to. After twelve rounds of SELEX, an atrazine-specific MRE with high affinity was obtained. The equilibrium dissociation constant (Kd) of the ssDNA sequence is 0.62 ± 0.21 nM. It also has significant selectivity for atrazine over atrazine metabolites and other pesticides found in environmentally similar locations and concentrations. Furthermore, we have detected environmentally relevant atrazine concentrations in river water using this MRE. The strong affinity and selectivity of the selected atrazine-specific ssDNA validated the stringent SELEX methodology and identified a MRE that will be useful for rapid atrazine detection in environmental samples.

Planar Hall magnetoresistive aptasensor for thrombin detection

The use of aptamer-based assays is an emerging and attractive approach in disease research and clinical diagnostics. A sensitive aptamer-based sandwich-type sensor is presented to detect human thrombin using a planar Hall magnetoresistive (PHR) sensor in cooperation with superparamagnetic labels. A PHR sensor has the great advantages of a high signal-to-noise ratio, a small offset voltage and linear response in the low-field region, allowing it to act as a high-resolution biosensor. In the system presented here, the sensor has an active area of 50 µm × 50 µm with a 10-nm gold layer deposited onto the sensor surface prior to the binding of thiolated DNA primary aptamer. A polydimethylsiloxane well of 600-µm radius and 1-mm height was prepared around the sensor surface to maintain the same specific area and volume for each sensor. The sensor response was traced in real time upon the addition of streptavidin-functionalized magnetic labels on the sensor. A linear response to the thrombin concentration in the range of 86 pM-8.6 µM and a lower detection limit down to 86 pM was achieved by the proposed present method with a sample volume consumption of 2 µl. The proposed aptasensor has a strong potential for application in clinical diagnosis.

Development of an indirect competitive assay-based aptasensor for highly sensitive detection of tetracycline residue in honey

Tetracycline (TC) is widely used for prevention and control of animal diseases for its broad spectrum antimicrobial activity and low cost, but its abuse can seriously affect human health and may result in trade loss. Thus there is an imperative need to develop high-performing analytical technique for TC detection. In this study, we developed a biosensor based on an indirect competitive enzyme-linked aptamer assay (ic-ELAA). A 76mer single-stranded DNA (ssDNA) aptamer, selected by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), was applied for the recognition and detection of TC in honey. The limit of detection was 9.6×10(-3) ng/mL with a linear working range from 0.01 to 100 ng/mL toward TC in honey, and a mean recovery rate of 93.23% in TC-spiked honey was obtained. This aptasensor can be applied to detect TC residue in food with high sensitivity and simplicity, and it is prospective to develop useful ELAA Kits for TC determination in food.

Aptamer-based luminescence energy transfer from near-infrared-to-near-infrared upconverting nanoparticles to gold nanorods and its application for the detection of thrombin

A new luminescence energy transfer (LET) system has been designed for the detection of thrombin in the near-infrared (NIR) region by utilizing NIR-to-NIR upconversion lanthanide nanophosphors (UCNPs) as the donor and gold nanorods (Au NRs) as the acceptor. The use of upconverting NaYF4 :Yb(3+) ,Tm(3+) nanoparticles with sharp NIR emission peaks upon NIR excitation by an inexpensive infrared continuous wave laser diode provided large spectral overlap between the donor and the acceptor. Both the Au NRs and carboxyl-terminated NaYF4 :Yb(3+) ,Tm(3+) UCNPs were first modified with different thrombin aptamers. When thrombin was added, a LET system was then formed because of the specific recognition between the thrombin aptamers and thrombin. The LET system was used to monitor thrombin concentrations in aqueous buffer and human blood samples. The limits of detection for thrombin are as low as 0.118 nM in buffer solution and 0.129 nM in human serum. The method was also successfully applied to thrombin detection in blood samples.

A colorimetric aptamer biosensor based on cationic polymer and gold nanoparticles for the ultrasensitive detection of thrombin

A colorimetric assay for the ultrasensitive determination of thrombin based on cationic polymer and gold nanoparticles was presented, in which unmodified gold nanoparticles (AuNPs) was used as probes and 21-mer thrombin-binding aptamer (TBA) as sensing elements. Upon the addition of thrombin, TBA interacted specifically with thrombin to form a G-quadruplex structure. As a result, the conformation change facilitated the cationic polymer, poly(diallyldimethylammonium chloride) (PDDA)-induced AuNP aggregation. Thus, the visible change in color from wine-red to blue-purple was readily seen by the naked eye. The colorimetric sensor could detect thrombin down to 1 pM with high selectivity in the presence of other interferring proteins. Furthermore, the assay was successfully employed to determine thrombin in human serum sample, which suggested its great potential for diagnostic purposes.

Patterned biochemical functionalization improves aptamer-based detection of unlabeled thrombin in a sandwich assay

Here we propose a platform for the detection of unlabeled human α-thrombin down to the picomolar range in a fluorescence-based aptamer assay. In this concept, thrombin is captured between two different thrombin binding aptamers, TBA1 (15mer) and TBA2 (29mer), each labeled with a specific fluorescent dye. One aptamer is attached to the surface, the second one is in solution and recognizes surface-captured thrombin. To improve the limit of detection and the comparability of measurements, we employed and compared two approaches to pattern the chip substrate-microcontact printing of organosilanes onto bare glass slides, and controlled printing of the capture aptamer TBA1 in arrays onto functionalized glass substrates using a nanoplotter device. The parallel presence of functionalized and control areas acts as an internal reference. We demonstrate that both techniques enable the detection of thrombin concentrations in a wide range from 0.02 to 200 nM with a detection limit at 20 pM. Finally, the developed method could be transferred to any substrate to probe different targets that have two distinct possible receptors without the need for direct target labeling.

An indirect competitive assay-based aptasensor for detection of oxytetracycline in milk

Oxytetracycline (OTC) is a common antibacterial agent used for the control of animal diseases. OTC abuse can seriously affect human health; therefore, we developed a biosensor using single-stranded DNA (ssDNA) aptamers for the detection of OTC. The binding probe aptamers for OTC were selected by a Systematic Evolution of Ligands by the exponential enrichment (SELEX) process and identified by the enzyme-linked aptamer assay (ELAA). Among the selected 5 aptamers, aptamer OTC3 showed the strongest affinity (Kd=4.7 nM) and highest specificity for OTC compared to structurally similar antibiotics, tetracycline and chlortetracycline. OTC was detected using indirect competitive ELAA. The limit of detection and quantitation with aptamer OTC3 were 12.3 and 49.8 µg/L, respectively, in milk and showed recovery rates of more than 90% in OTC-spiked milk. This biosensor method with high sensitivity and specificity based on indirect competitive ELAA can be applied to OTC detection in food products on-site because of the simplicity of detection.

Aptamer/thrombin/aptamer-AuNPs sandwich enhanced surface plasmon resonance sensor for the detection of subnanomolar thrombin

A sensitive and selective aptamer/thrombin/aptamer-AuNPs sandwich enhanced surface plasmon resonance (SPR) sensor has been developed for real-time detection of subnanomolar thrombin. In this protocol, one thiol-modified thrombin aptamer (TBA29) was immobilized on gold nanoparticles (AuNPs) via Au-S bonding. The other biotinylated thrombin aptamer (TBA15) was grafted onto streptavidin pretreated SPR gold film through biotin-streptavidin recognition. The presence of thrombin would then induce the formation of a double aptamer sandwich structure on the SPR gold film and results in obvious enhancement of SPR signal, which was proportional to the concentration of thrombin. This proposed assay took advantage of sandwich binding of two affinity aptamers for increased specificity, AuNPs for signal enhancement, as well as SPR signal readout for real-time detection. The SPR signal had a good linear relationship with thrombin concentration in the range of 0.1-75nM, and the detection limit for thrombin was determined to be as low as 0.1nM. It was found that aptamer functionalized AuNPs enhanced the signal of SPR response and thus increased the limit of detection 4-fold and 5-fold compared to direct detection format without AuNPs. This sensor also showed good selectivity for thrombin without being affected by some other proteins, such as BSA and lysozyme. Furthermore, this proposed SPR sensing platform was successfully applied to thrombin analysis in diluted human serum samples.

Label-free sensing of thrombin based on quantum dots and thrombin binding aptamer

A facile and sensitive label-free approach for detection of thrombin based on CdTe quantum dots (QDs) and thrombin binding aptamer (TBA) is presented. The crude QDs can be "activated" with fluorescence enhancement by adding extra Cd(2+) to the solution in basic medium. As a result, the positively charged Cd(2+)-activating CdTe QDs could interact with the negatively charged TBA, leading to fluorescence quenching. When thrombin was added, TBA was induced to form a G-quadruplex structure and combined specifically with its target, releasing the QDs with a recovery of the fluorescence intensity. The sensing approach is based on the strongly specific interactions between TBA and thrombin over the electrostatic interactions between TBA and positively charged QDs. Based on the fluorescence enhancement of QDs, selective detection of thrombin was successfully achieved. A linear response for thrombin was observed in the range from 1.4 nM to 21 nM with a detection limit of 0.70 nM.

A sensitive strategy for label-free and time-resolved fluorescence assay of thrombin using Tb-complex and unmodified gold nanoparticles

Gold nanoparticles (GNPs) can effectively differentiate the unfolded and folded aptamer, and quench the fluorescence of terbium ternary complexes (Tb-complexes), thus the authors herein report a sensitive strategy for protein detection, using label-free aptamer, Tb-complexes and GNPs. In the presence of thrombin, the aptamer is inclined to form G-quartet, and the folded aptamer cannot adsorb on the surface of GNPs, inducing the GNPs aggregation in the presence of 0.5 mol L(-1) salt. After centrifugation at low speed to remove the aggregated GNPs, the quenching capability of the supernatant for Tb-complexes is decreased. The fluorescence intensity of Tb-complexes increases as the concentration of thrombin increases. Due to the highly specific recognition ability of the aptamer for thrombin and the strong quenching property of GNPs for Tb-complexes, the proposed protocol has good selectivity and high sensitivity for thrombin. Under the optimum conditions, a linear range from 1.0 × 10(-9) M to 1.0 × 10(-8) M is obtained with a detection limit of 0.14 nM, which is much lower than those commonly obtained for colorimetric sensors and some fluorescent sensors. The signal of Tb-complexes can be measured by time-resolved manner which made most of the unspecific fluorescent background signals be eliminated. The proposed sensor has been successfully applied in complicated biological samples for thrombin detection, and it can provide a promising potential for label-free aptamer-based protein detection.

Highly sensitive optical biosensor for thrombin based on structure switching aptamer-luminescent silica nanoparticles

We describe here the construction of a sensitive and selective optical sensor system for the detection of human α-thrombin. The surface functionalized luminescent [Ru(dpsphen)(3)](4-) (dpsphen-4,7-diphenyl-1,10-phenanthroline disulfonate) ion doped silica nanoparticles (SiNPs) with a size ~70 nm have been prepared. The DABCYL (2-(4-dimethylaminophenyl)diazenyl-benzoic acid) quencher labeled thrombin binding aptamer is conjugated to the surface of SiNPs using BS(3) (bis(sulfosuccinimidyl) suberate) as a cross-linker, resulting in the conformational change of aptamer to form G-quadruplex structure upon the addition of thrombin. The binding event is translated into a change in the luminescence intensity of Ru(II) complex via FRET mechanism, due to the close proximity of DABCYL quencher with SiNPs. The selective detection of thrombin using the SiNPs-aptamer system up to 4 nM is confirmed by comparing its sensitivity towards other proteins. This work demonstrates the application of simple aptamer-SiNPs conjugate as a highly sensitive system for the detection of thrombin and also it is highly sensitive towards thrombin in the presence of other proteins and complex medium such as BSA.

Aptamer-based silver nanosensor for multiple protein detection

In the present work we design a novel aptamer-based silver nanosensor for one-spot simultaneously detection of multiple proteins. SS-DNA modified AgNPs were immobilized on the aldehyde coated glass slide to form an AgNP array. Then dye-labeled aptamer sequences were allowed to hybridize with their complementary strands assembled on the surface of AgNPs. The target proteins were introduced to associate with the corresponding aptamers to form the aptamer-target complexes. The removal of the aptamer-target complexes resulted in a remarkable decrease in fluorescent signals. This nanosensor is found to be highly sensitive for the detection of proteins. When thrombin was employed as a sample model, the limit of detection of the optimized nanosenor was 0.4 fmol with a linear response of 0.8 fmol to 0.5 pmol. We further demonstrated the multiple protein detection of IgE and thrombin using multicolor silver nanoprobes, which shows effective recognition of the relative protein individually or simultaneously. This silver nanosensor offers a unique heterogeneous approach for protein detection with several advantages, such as high sensitivity, rapidity, high throughput, and miniaturization.

Development and Optimization of a Thrombin Sandwich Aptamer Microarray

A sandwich microarray employing two distinct aptamers for human thrombin has been optimized for the detection of subnanomolar concentrations of the protein. The aptamer microarray demonstrates high specificity for thrombin, proving that a two-site binding assay with the TBA1 aptamer as capture layer and the TBA2 aptamer as detection layer can ensure great specificity at times and conditions compatible with standard routine analysis of biological samples. Aptamer microarray sensitivity was evaluated directly by fluorescent analysis employing Cy5-labeled TBA2 and indirectly by the use of TBA2-biotin followed by detection with fluorescent streptavidin. Sub-nanomolar LODs were reached in all cases and in the presence of serum, demonstrating that the optimized aptamer microarray can identify thrombin by a low-cost, sensitive and specific method.

Label-free impedimetric thrombin sensor based on poly(pyrrole-nitrilotriacetic acid)-aptamer film

A label-free and highly sensitive impedimetric aptasensor was developed based on electropolymerized film for the determination of thrombin. The first step is the electrogeneration of a poly(pyrrole-nitrilotriacetic acid) (poly(pyrrole-NTA)) film onto the surface of electrodes followed by complexation of Cu(2+) ions. Then, the histidine labeled thrombin aptamer was immobilized onto the electrode through coordination of the histidine groups on the NTA-Cu(2+) complex. The aptamer sensor was applied for the detection and quantification of thrombin via impedimetric detection without a labeling step. A linear quantification of thrombin was obtained in the range 4.7×10(-12)-5.0×10(-10) mol L(-1) with a sensitivity of 2838 Ω/log unit (R(2)=0.9984). The impedance modulus at 0.3 Hz as a function of thrombin concentration was used to elaborate a similar linear relationship from 4.7×10(-12) to 5×10(-10) mol L(-1). In addition, aptamer-poly(pyrrole-NTA) electrodes incubated for 40 min in aqueous solutions of bovine serum albumin (BSA), lysozyme and IgG (5×10(-7) mol L(-1)) did not exhibit non-specific adsorption of proteins. Moreover, it has been demonstrated that the selective sensor can be regenerated several times with a good reproducibility.

Sensitive and homogeneous protein detection based on target-triggered aptamer hairpin switch and nicking enzyme assisted fluorescence signal amplification

Specific and sensitive detection of proteins in biotechnological applications and medical diagnostics is one of the most important goals for the scientific community. In this study, a new protein assay is developed on the basis of hairpin probe and nicking enzyme assisted signal amplification strategy. The metastable state hairpin probe with short loop and long stem is designed to contain a protein aptamer for target recognition. A short Black Hole Quencher (BHQ)-quenching fluorescence DNA probe (BQF probe) carrying the recognition sequence and cleavage site for the nicking enzyme is employed for fluorescence detection. Introduction of target protein into the assay leads to the formation change of hairpin probe from hairpin shape to open form, thus faciliating the hybridization between the hairpin probe and BQF probe. The fluorescence signal is amplified through continuous enzyme cleavage. Thrombin is used as model analyte in the current proof-of-concept experiments. This method can detect thrombin specifically with a detection limit as low as 100 pM. Additionally, the proposed protein detection strategy can achieve separation-free measurement, thus eliminating the washing steps. Moreover, it is potentially universal because hairpin probe can be easily designed for other proteins by changing the corresponding aptamer sequence.

Sensitivity and selectivity on aptamer-based assay: the determination of tetracycline residue in bovine milk

A competitive enzyme-linked aptamer assay (ELAA) to detect tetracycline in milk was performed by using two different aptamers individually; one is 76 mer-DNA aptamer and the other is 57 mer-RNA aptamer. The best optimum condition was obtained without monovalent ion, Na⁺ and also by adding no Mg²⁺ ion in the assay buffer, along with RT incubation. The optimized ELAA showed a good sensitivity (LOD of 2.10 × 10⁻⁸ M) with a wide dynamic range (3.16 × 10⁻⁸ M ~ 3.16 × 10⁻⁴ M). In addition, the average R.S.D. across all data points of the curve was less than 2.5% with good recoveries (~101.8%) from the milk media. Thus, this method provides a good tool to monitor tetracycline in milk from MRLs' point of view. However, this ELAA method was not superior to the ELISA method in terms of specificity. This paper describes that it does not always give better sensitivity and specificity in assays even though aptamers have several advantages over antibodies and have been known to be good binders for binding assays.

Assays for aptamer-based platforms

Aptamers are single stranded DNA or RNA oligonucleotides that have high affinity and specificity towards a wide range of target molecules. Aptamers have low molecular weight, amenable to chemical modifications and exhibit stability undeterred by repetitive denaturation and renaturation. Owing to these indispensable advantages, aptamers have been implemented as molecular recognition element as alternative to antibodies in various assays for diagnostics. By amalgamating with a number of methods that can provide information on the aptamer-target complex formation, aptamers have become the elemental tool for numerous biosensor developments. In this review, administration of aptamers in applications involving assays of fluorescence, electrochemistry, nano-label and nano-constructs are discussed. Although detection strategies are different for various aptamer-based assays, the core of the design strategies is similar towards reporting the presence of specific target binding to the corresponding aptamers. It is prognosticated that aptamers will find even broader applications with the development of new methods of transducing aptamer target binding.

Highly sensitive thrombin detection by matrix assisted laser desorption ionization-time of flight mass spectrometry with aptamer functionalized core-shell Fe₃O₄@C@Au magnetic microspheres

Here, we describe a sensitive and specific method for thrombin detection with aptamer functionalized core-shell Fe(3)O(4)@C@Au magnetic microspheres (Au-MMPs). Firstly, Au-MMPs were synthesized through surface adsorption of gold nanoparticles onto PDDA functionalized Fe(3)O(4)@C magnetic microspheres. Then, the as-synthesized Au-MMPs were developed as new substrate for immobilization of thrombin binding aptamer (TBA) through easy formation of Au-S bond. After that, the prepared aptamer functionalized Au-MMPs (TBA@Au-MMPs) were used as effective magnetic absorbent to extract trace level of thrombin from dilute solutions. Finally, enriched thrombin was digested by trypsin and analyzed by matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Taking advantage of the efficient affinity extraction ability of our TBA@Au-MMPs and the sensitive mass readout of MALDI-TOF, highly sensitive detection of thrombin was achieved. The limit of detection was as low as 18 fmol, corresponding to 0.36 nM thrombin in 50 μL original solution. Linear relation was observed within a concentration range from 0.5 nM to 10nM with linear correlation R(2)=0.998. Other proteins including human serum albumin (HSA), Ig G, transferrin, oval albumin (OVA) and fetal calf serum did not interfere with thrombin detection. This simple method holds great potential for analyzing, sensing, purification and preconcentration of proteins in biological fluids.

Human thrombin detection through a sandwich aptamer microarray: interaction analysis in solution and in solid phase

We have developed an aptamer-based microarray for human thrombin detection exploiting two non-overlapping DNA thrombin aptamers recognizing different exosites of the target protein. The 15-mer aptamer (TBA1) binds the fibrinogen-binding site, whereas the 29-mer aptamer (TBA2) binds the heparin binding domain. Extensive analysis on the complex formation between human thrombin and modified aptamers was performed by Electrophoresis Mobility Shift Assay (EMSA), in order to verify in solution whether the chemical modifications introduced would affect aptamers/protein recognition. The validated system was then applied to the aptamer microarray, using the solid phase system devised by the solution studies. Finally, the best procedure for Sandwich Aptamer Microarray (SAM) and the specificity of the sandwich formation for the developed aptasensor for human thrombin were optimized.

Aptamer biosensor based on fluorescence resonance energy transfer from upconverting phosphors to carbon nanoparticles for thrombin detection in human plasma

We presented a new aptamer biosensor for thrombin in this work, which was based on fluorescence resonance energy transfer (FRET) from upconverting phosphors (UCPs) to carbon nanoparticles (CNPs). The poly(acrylic acid) (PAA) functionalized UCPs were covalently tagged with a thrombin aptamer (5'-NH(2)- GGTTGGTGTGGTTGG-3'), which bound to the surface of CNPs through π-π stacking interaction. As a result, the energy donor and acceptor were taken into close proximity, leading to the quenching of fluorescence of UCPs. A maximum fluorescence quenching rate of 89% was acquired under optimized conditions. In the presence of thrombin, which induced the aptamer to form quadruplex structure, the π-π interaction was weakened, and thus, the acceptor was separated from the donor blocking the FRET process. The fluorescence of UCPs was therefore restored in a thrombin concentration-dependent manner, which built the foundation of thrombin quantification. The sensor provided a linear range from 0.5 to 20 nM for thrombin with a detection limit of 0.18 nM in an aqueous buffer. The same linear range was obtained in spiked human serum samples with a slightly higher detection limit (0.25 nM), demonstrating high robustness of the sensor in a complex biological sample matrix. As a practical application, the sensor was used to monitor thrombin level in human plasma with satisfactory results obtained. This is the first time that UCPs and CNPs were employed as a donor-acceptor pair to construct FRET-based biosensors, which utilized both the photophysical merits of UCPs and the superquenching ability of CNPs and thus afforded favorable analytical performances. This work also opened the opportunity to develop biosensors for other targets using this UCPs-CNPs system.