Label-free protein recognition using aptamer-based fluorescence assay

Assays to Estimate the Binding Affinity of Aptamers

Aptamers have become coming-of-age molecular recognition elements in both diagnostic and therapeutic applications. Generated by SELEX, the 'quality control' of aptamers, which involves the validation of their binding affinity against their respective targets is pivotal to ascertain their potency prior to use in any downstream assays or applications. Several aptamers have been isolated thus far, however, the usage of inappropriate validation assays renders some of these aptamers dubitable in terms of their binding capabilities. Driven by this need, we provide an up-to-date critical review of the various strategies used to determine the aptamer-target binding affinity with the aim of providing researchers a better comprehension of the different analytical approaches in respect to the molecular properties of aptamers and their intended targets. The techniques reported have been classified as label-based techniques such as fluorescence intensity, fluorescence anisotropy, filter-binding assays, gel shift assays, ELISA; and label-free techniques such as UV-Vis spectroscopy, circular dichroism, isothermal titration calorimetry, native electrospray ionization-mass spectrometry, quartz crystal microbalance, surface plasmon resonance, NECEEM, backscattering interferometry, capillary electrophoresis, HPLC, and nanoparticle aggregation assays. Hybrid strategies combining the characteristics of both categories such as microscale thermophoresis have been also additionally emphasized. The fundamental principles, complexity, benefits, and challenges under each technique are elaborated in detail.

G-Quadruplex-Based Fluorescent Turn-On Ligands and Aptamers: From Development to Applications

Guanine (G)-quadruplexes (G4s) are unique nucleic acid structures that are formed by stacked G-tetrads in G-rich DNA or RNA sequences. G4s have been reported to play significant roles in various cellular events in both macro- and micro-organisms. The identification and characterization of G4s can help to understand their different biological roles and potential applications in diagnosis and therapy. In addition to biophysical and biochemical methods to interrogate G4 formation, G4 fluorescent turn-on ligands can be used to target and visualize G4 formation both in vitro and in cells. Here, we review several representative classes of G4 fluorescent turn-on ligands in terms of their interaction mechanism and application perspectives. Interestingly, G4 structures are commonly identified in DNA and RNA aptamers against targets that include proteins and small molecules, which can be utilized as G4 tools for diverse applications. We therefore also summarize the recent development of G4-containing aptamers and highlight their applications in biosensing, bioimaging, and therapy. Moreover, we discuss the current challenges and future perspectives of G4 fluorescent turn-on ligands and G4-containing aptamers.

Aptamer-Modified Magnetic Beads in Biosensing

Magnetic beads (MBs) are versatile tools for the purification, detection, and quantitative analysis of analytes from complex matrices. The superparamagnetic property of magnetic beads qualifies them for various analytical applications. To provide specificity, MBs can be decorated with ligands like aptamers, antibodies and peptides. In this context, aptamers are emerging as particular promising ligands due to a number of advantages. Most importantly, the chemical synthesis of aptamers enables straightforward and controlled chemical modification with linker molecules and dyes. Moreover, aptamers facilitate novel sensing strategies based on their oligonucleotide nature that cannot be realized with conventional peptide-based ligands. Due to these benefits, the combination of aptamers and MBs was already used in various analytical applications which are summarized in this article.

Selection and characterization of a DNA aptamer to crystal violet

A shortened 42-mer aptamer with high affinity and good specificity for crystal violet, which showed higher fluorescence enhancement than G-quadruplexes was successfully selected.

An aptasensor based on heparin-mimicking hyperbranched polyester with anti-biofouling interface for sensitive thrombin detection

In this paper, novel heparin-mimicking hyperbranched polyester nanoparticles (HBPE-SO₃ NPs) with abundant of sulfonated acid functional groups were synthesized, and their antithrombogenicities were further evaluated. Further, a label-free electrochemical aptamer biosensor (aptasensor) based on HBPE-SO₃ NPs modified electrode was developed for thrombin (TB) detection in whole blood. Meanwhile, the anti-biofouling properties of different modified electrodes were studied by whole blood and platelet adhesion test, hemolysis assay and morphological changes of red blood cells in vitro. Besides, the thrombin-binding aptamer was selected as receptor for the proposed aptasensor, which has excellent binding affinity and selectivity for TB. When binding to TB, the electron transfer taking place at the modified electrode interface was inhibited that can attribute to the stereo-hindrance effect, resulting in the decreased current response. This aptasensor showed excellent electrochemical properties with a wide detection range and a low detection limit of 0.031pM (S/N = 3), and provided high selectivity, long-term stability and good reproducibility. Finally, the sensitively detection of TB in whole blood samples directly was achieved by this aptasensor we proposed, which suggested its great potential for TB detection in the clinic.

Magnetic Nanoparticles-based Aptasensor Using Gold Nanoparticles as Colorimetric Probes for the Detection of Salmonella typhimurium

This paper presents a sensitive and convenient visual methodology for Salmonella typhimurium detection using gold nanoparticles (AuNPs) as colorimetric probes and magnetic nanoparticles (MNPs) as concentration elements. In the protocol, the aptamers were first immobilized onto the surface of AuNPs and MNPs, respectively. Then, S. typhimurium were added into the above solution and incubated for 45 min. During the incubation, aptamer on the surface of nanoparticles could specifically bind to the target and form a MNPs-aptamer-S. typhimurium-aptamer-AuNPs sandwich structure complex. In a magnetic field, the formed complexes were easily separated from the solution, resulting in a fading of the AuNPs suspension and a decrease of the ultraviolet visible (UV/Vis) signal. The assay shows a linear response toward S. typhimurium concentration through a range of 25 to 10(5) cfu/mL, and the detection limit was improved to 10 cfu/mL. The applicability of the bioassay in real food samples was also investigated; the results were consistent with the experimental results obtained from plate-counting methods. It is believed that the developed aptasensor will broaden the application in bioassays.

A novel aptamer-based competition strategy for ultrasensitive electrochemical detection of leukemia cells

A robust, nanobiotechnology-based electrochemical cytosensing platform for the detection of acute leukemia cells was developed with high sensitivity, selectivity, acceptable rapidity and excellent extensibility. It utilized the competitive binding of cell-specific aptamers to acute leukemia cells and subsequent voltammetric quantification of the metal signature. Greatly enhanced sensitivity was achieved with dual signal amplification by using Fe3O4 magnetic nanoparticles (MNPs) as carriers to load a large amount of gold nanoparticles (AuNPs) and AuNP-catalyzed silver deposition. The proposed competitive cytosensor showed high sensitivity with a detection limit down to 10 cells. This simple and low-cost electrochemical cytosensing approach offers great promise to extend its application to early detection of human leukemia and possibly to other cancer cells.

Selection and characterization of a novel DNA aptamer for label-free fluorescence biosensing of ochratoxin A

Nucleic acid aptamers are emerging as useful molecular recognition tools for food safety monitoring. However, practical and technical challenges limit the number and diversity of available aptamer probes that can be incorporated into novel sensing schemes. This work describes the selection of novel DNA aptamers that bind to the important food contaminant ochratoxin A (OTA). Following 15 rounds of in vitro selection, sequences were analyzed for OTA binding. Two of the isolated aptamers demonstrated high affinity binding and selectivity to this mycotoxin compared to similar food adulterants. These sequences, as well as a truncated aptamer (minimal sequence required for binding), were incorporated into a SYBR® Green I fluorescence-based OTA biosensing scheme. This label-free detection platform is capable of rapid, selective, and sensitive OTA quantification with a limit of detection of 9 nM and linear quantification up to 100 nM.

Aptamer-directed lanthanide chelate self-assembly for rapid thrombin detection

We report a sensitive assay method for homogeneous thrombin detection. The method is based on lanthanide chelate complementation, where the luminescent complex is split into two separate label moieties, which are intrinsically non-luminescent. A luminescent mixed chelate complex is formed only when the label moieties are brought into close proximity directed by two separate binding events of aptamers to the analyte. This results in high specificity in signal generation while time-resolved fluorescence detection eliminates the short lifetime autofluorescence, which is inherent to many homogeneous assays and limits their applicability. The developed method is also very rapid as the maximum signal is obtained in just five minutes. Lanthanide chelate complementation can be applied for the detection of other proteins when two binders recognizing separate epitopes of the analyte are available.

Aptamer-functionalized hydrogel diffraction gratings for the human thrombin detection

The aptamer-functionalized hydrogel diffraction gratings were successfully fabricated by incorporating an aptamer and its complementary sequence as crosslinking junctions in the network structure. The gratings showed a sensitive response to human thrombin as read out from the diffracted light.

Label-free luminescent oligonucleotide-based probes

Breakthrough advances in chemistry and biology over the last two decades have vastly expanded the repertoire of nucleic acid structure and function with potential application in multiple areas of science and technology, including sensing and analytical applications. DNA oligonucleotides represent popular tools for the development of sensing platforms due to their low cost, rich structural polymorphism, and their ability to bind to cognate ligands with sensitivity and specificity rivaling those for protein enzymes and antibodies. In this review, we give an overview of the "label-free" approach that has been a particular focus of our group and others for the construction of luminescent DNA-based sensing platforms. The label-free strategy aims to overcome some of the drawbacks associated with the use of covalently-labeled oligonucleotides prevalent in electrochemical and optical platforms. Label-free DNA-based probes harness the selective interaction between luminescent dyes and functional oligonucleotides that exhibit a "structure-switching" response upon binding to analytes. Based on the numerous examples of label-free luminescent DNA-based probes reported recently, we envisage that this field would continue to thrive and mature in the years to come.

G-quadruplexes for luminescent sensing and logic gates

G-quadruplexes represent a versatile sensing platform for the construction of label-free molecular detection assays owing to their diverse structures that can be selectively recognized by G-quadruplex-specific luminescent probes. In this Survey and Summary, we highlight recent examples of the application of the label-free strategy for the development of G-quadruplex-based luminescent detection platforms with a view towards the potential application of tetraplex structures in the design of DNA logic gates.

Nucleic acid aptamers as high affinity ligands in biotechnology and biosensorics

Aptamers are small nucleic acid molecules capable of binding to a wide range of target molecules with high affinity and specificity. They have been developed and widely used not only as research tools, but also as biosensors, specific antagonists, and diagnostic markers and as protein purification platform for many pharmaceutical and clinical applications. Here, in this paper we will explore biochemical aspects of aptamer-target interactions and show why aptamers rival antibodies in target recognition and purification procedures. This review will focus on strategies of using aptamers as affinity ligands for molecules of therapeutic and pharmaceutical interest including applications in chromatography and capillary electrophoresis for protein and small molecule purification. Moreover, we will also discuss aptamers whose binding parameters can be controlled on demand for diagnostic approaches and used as sensitive receptors in biosensorics. Aptamers have opened up exciting fields in basic and applied research of pharmaceutical and biotechnological interest.

CuInS2 quantum dots as a near-infrared fluorescent probe for detecting thrombin in human serum

This paper describes a novel, simple method for the highly sensitive and selective detection of thrombin using fibrinogen (Fib) and CuInS(2) quantum dots (QDs) as biosensing probes. Water-soluble near-infrared CuInS(2) QDs capped by mercaptopropionic acid (MPA) were directly synthesized by a hydrothermal method. Addition of fibrinogen to the CuInS(2) QDs solution led to the formation of a Fib-CuInS(2) QDs complex through electrostatic interactions and hydrogen bonding, and resulting in the enhancement of photoluminescence (PL) intensity and a red shift of the PL peak. Once thrombin was introduced into the Fib-CuInS(2) QDs system, it catalyzed the polymerization of the free and conjugated fibrinogen species to form insoluble fibrillar fibrin-CuInS(2) QDs agglutinates. After centrifugation, the PL intensity of the supernatants decreased upon increasing the concentration of thrombin. This Fib-CuInS(2) QDs probe provided a highly specific selectivity and a linear detection of thrombin in the range of 6.7 × 10(-11) to 3.9 × 10(-7) mol L(-1) with a detection limit (LOD) of about 8.7 × 10(-12) mol L(-1), and realized the thrombin detection in human serum samples directly. Compared with those obtained by using other nanomaterials and aptamer-based detection methods, this approach provided a lower LOD for thrombin detection. The proposed approach provides a simple and fast-responding procedure, which might hold a promising potential for application in the diagnosis of diseases associated with coagulation abnormalities and cancers.

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.

A label-free electrochemiluminescence aptasensor for thrombin based on novel assembly strategy of oligonucleotide and luminol functionalized gold nanoparticles

In the work, a label-free electrochemiluminescence (ECL) aptasensor for the sensitive and selective detection of thrombin was constructed based on target-induced direct ECL signal change by virtue of a novel assembly strategy of oligonucleotide and luminol functionalized gold nanoparticles (luminol-AuNPs). It is the first label-free ECL biosensor based on luminol and its analogs functionalized AuNPs. Streptavidin AuNPs coated with biotinylated DNA capture probe 1 (AuNPs-probe 1) were firstly assembled onto an gold electrode through 1,3-propanedithiol. Then luminol-AuNPs co-loaded with thiolated DNA capture probe 2 and thiolated thrombin binding aptamer (TBA) (luminol-AuNPs-probe 2/TBA) were assembled onto AuNPs-probe 1 modified electrode through the hybridization between capture probes 1 and 2. The luminol-AuNPs-probe 2/TBA acted as both molecule recognition probe and sensing interface. An Au/AuNPs/ds-DNA/luminol-AuNPs/TBA multilayer architecture was obtained. In the presence of target thrombin, TBA on the luminol-AuNPs could capture the thrombin onto the electrode surface, which produced a barrier for electro-transfer and influenced the electro-oxidation reaction of luminol, leading to a decrease in ECL intensity. The change of ECL intensity indirectly reflected the concentration of thrombin. Thus, the approach showed a high sensitivity and a wider linearity for the detection of thrombin in the range of 0.005-50nM with a detection limit of 1.7pM. This work reveals that luminol-AuNPs are ideal platform for label-free ECL bioassays.

Label-free fluorescent assays based on aptamer-target recognition

Label-free fluorescent assays were developed based on the competition of intramolecular DNA hybridization and aptamer-target binding. Using small molecule adenosine triphosphate (ATP) and biomacro-molecule thrombin as model targets, our design was proved to be a general method with good sensitivity and high selectivity.

Label-free optical bifunctional oligonucleotide probe for homogeneous amplification detection of disease markers

Oligonucleotide-based detection schemes that avoid chemical modification possess significant advantages, including simplified design, intrinsic affinity for targets, low cost and ease to extend applications. In this contribution, we developed a label-free self-locked bifunctional oligonucleotide probe (signaling probe) for the detection of different disease markers in parallel. Two signal enhancement techniques based on isothermal circular strand-displacement polymerization reaction, cyclical nucleic acid strand-displacement polymerization (CNDP) and cyclical common (nonnucleic acid) target-displacement polymerization (CCDP), were employed to implement the amplification assay for p53 gene and PDGF-BB, respectively. The attractive assay properties confirmed the effectiveness of isothermal polymerization in common biosensing systems without evolving any chemical modification: PDGF could be detected down to 0.87ng/mL, and a dynamic response range of 8-5000ng/mL was achieved; The capability to screen the p53 gene was also considerably improved, including the detection limit, sensitivity, dynamic range and so on. Moreover, because no any chemical modification of the signaling probe was acquired and different targets were separately detected in homogeneous solution. This interrogating platform exhibits the design flexibility, convenience, simplicity and cost-effectiveness. The success achieved here is expected to serve as a significant step toward the development of robust label-free oligonucleotide probes in biomarker profiling and disease diagnostics.

Aptamer-functionalized magnetic nanoparticle-based bioassay for the detection of ochratoxin A using upconversion nanoparticles as labels

A sensitive luminescent bioassay for the detection of ochratoxin A (OTA), a small molecular mycotoxin, was developed using aptamer-conjugated magnetic nanoparticles (MNPs) as the recognition and concentration element and upconversion nanoparticles (UCNPs) as highly sensitive labels. The bioassay system was fabricated by immobilizing aptamer DNA 1 sequence onto the surface of Fe(3)O(4) MNPs, which were implemented to capture and concentrate OTA from bulk samples. The aptamer DNA 1 sequence then hybridized with UCNPs modified with DNA 2 sequence, which could dissociate from DNA 1 and result in a decreased luminescent signal when aptamer DNA 1 recognized and bound to target OTA. Under the optimal conditions, the decreased luminescent intensity (ΔI) is proportional to the concentration of OTA in the range of 1 × 10(-13) to 1 × 10(-9) g mL(-1) with a detection limit of 1 × 10(-13) g mL(-1). The proposed method then was successfully applied to measure OTA in naturally contaminated maize samples and validated by a commercially available enzyme-linked immunosorbent assay (ELISA) method. Benefiting from the magnetic separation and concentration effect of MNPs, the high sensitivity of UCNPs, as well as the selectivity and stability of the aptamer, the present upconversion luminescent bioassay offers a promising approach for the screening of small molecular mycotoxins because it is simple, rapid, highly sensitive, specific, does not require sample pre-concentration and lacks interference from autofluorescence of other biomolecules.

A simple assay to amplify the electrochemical signal by the aptamer based biosensor modified with CdS hollow nanospheres

A simple method to amplify the electrochemical signal by an aptamer with 22 bases modified with CdS hollow nanospheres (CdSHNs) was described. Using the thrombin as a model, the interaction between the aptamer and CdSHNs was characterized by cyclic voltammetry, electrochemical impedance spectroscopy and circular dichroism spectroscopy. CdSHNs promoted the electron transfer between the gold electrode and K(3)[Fe(CN)(6)] and facilitated the conformation conversion of the aptamer from hairpin to G-quadruplex after the aptamer interacted with thrombin. Under optimal conditions, the modified electrode could be used for the determination of thrombin from 0 to 33 μg mL(-1) and the sensitivity was 1.34 μA mL μg(-1)cm(-2), while the linear range of the modified electrode without the immobilization of CdSHNs was from 2.75 to 27.5 μg mL(-1) and the sensitivity was 0.062 μA mL μg(-1)cm(-2). This constructed biosensor also had a good stability, specificity, reproducibility and accuracy which could provide a promising platform for fabrication of aptamer based biosensors.