Development of aptamer-conjugated magnetic graphene/gold nanoparticle hybrid nanocomposites for specific enrichment and rapid analysis of thrombin by MALDI-TOF MS

A review of aptamer-conjugated nanomaterials for analytical sample preparation: Classification according to the utilized nanomaterials

BACKGROUND

Sample extraction before detection is a critical step in analysis. Since targets of interest are often found in complex matrices, the sample can not be directly introduced to the analytical instrument. Nanomaterials with unique physical-chemical properties are excellent supports for use in sorbent-based extraction. However, they lack selectivity and thus need to be functionalized with target-capturing molecules. Antibodies and molecularly imprinted polymers (MIPs) can be used for this purpose, but they have some problems that limit their practical applications. Hence, functionalization of nanomaterials for selectivity remains a problem.

RESULTS

Nucleic acid aptamers are affinity reagents that can provide superiority to antibodies since they can be selected in vitro and at a lower cost. Moreover, aptamers can be chemically synthesized and easily modified with different functional groups. Hence, aptamers are good candidates to impart selectivity to the nanomaterials. Recent studies focus on the integration of aptamers with magnetic nanoparticles, carbon-based nanomaterials, metal-organic frameworks, gold nanoparticles, gold nanorods, silica nanomaterials, and nanofibers. The unique properties of nanomaterials and aptamers make the aptamer-conjugated nanomaterials attractive for use in sample preparation. Aptamer-functionalized nanomaterials have been successfully used for selective extraction of proteins, small molecules, and cells from different types of complex samples such as serum, urine, and milk. In particular, magnetic nanoparticles have a wider use due to the rapid extraction of the sample under magnetic field.

SIGNIFICANCE

In this review, we aim to emphasize how beneficial features of nanomaterials and aptamers could be combined for extraction or enrichment of the analytes from complex samples. We aim to highlight that the benefits are twofold in terms of selectivity and efficiency when employing nanomaterials and aptamers together as a single platform.

Aptamer functionalized and reduced graphene oxide hybridized porous polymers SPE coupled with LC-MS for adsorption and detection of human α-thrombin

In this study, reduced graphene oxide (rGO) hybridized high internal phase emulsions were developed and polymerized as porous carriers for aptamer (5'/5AmMC6/-AGT CCG TGG TAG GGC AGG TTG GGG TGA CT-3') modification to enrich human α-thrombin from serum. The structure and properties of the materials were confirmed by scanning electron microscope (SEM), Fourier transform infrared spectroscope (FT-IR), and X-ray photoelectron spectra (XPS). The adsorption ability and selectivity were studied and the thrombin was detected with liquid chromatography-mass spectrometry (LC-MS). The adsorption of thrombin onto the sorbent was achieved within 30 min and the desorption was realized using 5.0 mL of acetonitrile/water (80/20, v/v). The thrombin was quantified by LC-MS according to its characteristic peptide sequence of ELLESYIDGR.

Biosensors based on aptamer-conjugated gold nanoparticles: A review

Simply synthetized gold nanoparticles have been highly used in medicine and biotechnology as a result of their biocompatibility, conductivity, and being easily functionalized with biomolecules such as aptamer. Aptamer-conjugated gold nanoparticle structures synergically possess characteristics of both aptamer and gold nanoparticles including high binding affinity, high biocompatibility, enhanced target selectivity, and long circulatory half-life. Aptamer-conjugated gold nanoparticles have extensively gained considerable attention for designing of biosensing systems due to their interesting optical and electrochemical features. Moreover, biosensors based on aptamer-gold nanoparticles are easy to use, with fast response, and inexpensive which make them ideal in individualized medicine, disease markers detection, food safety, and so forth. Moreover, due to high selectivity and biocompatibility of aptamer-gold nanoparticles, these biosensing platforms are ideal tools for targeted drug delivery systems. The application of this nanostructure as diagnostic and therapeutic tool has been developed for detection of cancer in the early stage by detecting cancer biomarkers, pathogens, proteins, toxins, antibiotics, adenosine triphosphate, and other small molecules. This review obviously demonstrates that this nanostructure effectively is applicable in the field of biomedicine and possesses potential of commercialization aims.

An ultrasensitive, homogeneous fluorescence quenching immunoassay integrating separation and detection of aflatoxin M1 based on magnetic graphene composites

A homogeneous fluorescence quenching immunoassay is described for simultaneous separation and detection of aflatoxin M₁ (AFM₁) in milk. The novel assay relies on monoclonal antibody (mAb) functionalized Fe₃O₄ decorated reduced-graphene oxide (rGO-Fe₃O₄-mAb) as both capture probe and energy acceptor, combined with tetramethylrhodamine cadaverine-labeled aflatoxin B₁ (AFB₁-TRCA) as the energy donor. In the assay, AFB₁-TRCA binds to rGO-Fe₃O₄-mAb in the absence of AFM₁, quenching the fluorescence of TRCA by resonance energy transfer. Significantly, the immunoassay integrates sample preparation and detection into a single step, by using magnetic graphene composites to avoid washing and centrifugation steps, and the assay can be completed within 10 min. Under optimized conditions, the visual and quantitative detection limits of the assay for AFM₁ were 50 and 3.8 ng L^-1, respectively, which were significantly lower than those obtained by fluorescence polarization immunoassay using the same immunoreagents. Owing to its operation and highly sensitivity, the proposed assay provides a powerful tool for the detection of AFM₁.

Evaluation of Aptamers as Affinity Reagents for an Enhancement of SRM-Based Detection of Low-Abundance Proteins in Blood Plasma

Selected reaction monitoring (SRM) is a mass spectrometric technique characterized by the exceptionally high selectivity and sensitivity of protein detection. However, even with this technique, the quantitative detection of low- and ultralow-abundance proteins in blood plasma, which is of great importance for the search and verification of novel protein disease markers, is a challenging task due to the immense dynamic range of protein abundance levels. One approach used to overcome this problem is the immunoaffinity enrichment of target proteins for SRM analysis, employing monoclonal antibodies. Aptamers appear as a promising alternative to antibodies for affinity enrichment. Here, using recombinant protein SMAD4 as a model target added at known concentrations to human blood plasma and SRM as a detection method, we investigated a relationship between the initial amount of the target protein and its amount in the fraction enriched with SMAD4 by an anti-SMAD4 DNA-aptamer immobilized on magnetic beads. It was found that the aptamer-based enrichment provided a 30-fold increase in the sensitivity of SRM detection of SMAD4. These results indicate that the aptamer-based affinity enrichment of target proteins can be successfully employed to improve quantitative detection of low-abundance proteins by SRM in undepleted human blood plasma.

An LC-MS/MS method for protein detection based on a mass barcode and dual-target recognition strategy

A mass barcode mediated signal amplification strategy was developed and applied to the determination of protein. A new compound, N'-((2-aminopyridin-3-yl)methylene)-5-(1,2-dithiolan-3-yl)pentanehydrazide (TAPA), was synthesized from the linker and the signal barcode, and used as the bonding barcode. For the realization of signal transduction, TAPAs and the target catcher aptamers, were both modified on gold nanoparticles (AuNPs) to establish the relationship between TAPAs and the target. Owing to the fact that the amount of TAPAs was much greater than the target, the signal of the target was not only transduced to the signal of the mass barcodes, but also amplified greatly. Thrombin, an important biomarker for coagulation abnormality diseases, was selected as a model analyte. Two kinds of thrombin recognition aptamers, aptamer 29 (apt29) and aptamer 15 (apt15), were modified onto the magnetic beads (MBs) and AuNPs, respectively. The modified AuNPs were further functionalized with lots of TAPA and formed apt15-AuNPs-TAPA. MBs-apt29 and apt15-AuNPs-TAPA could both recognize the target thrombin and form the sandwich complex (MBs-apt29/thrombin/apt15-AuNPs-TAPA). After the complex was separated by an extra magnetic field, NaClO oxidant solution was added to release the signal barcodes, 2-Amino-3-pyridinecarboxaldehyde (APA), which were then collected after centrifuging and analyzed by LC-MS/MS. Under optimized conditions, the mass response intensity was proportional to thrombin concentration in the range of 0.05-10 nM, with a 0.007 nM detection limit. This method was applied to the determination of thrombin in spiked serum samples, and the average recoveries ranged from 89.6% to 110.4%, which confirmed the applicability of this method.

Functionalized gold nanoparticles for sample preparation: A review

Sample preparation is a crucial step for the reliable and accurate analysis of both small molecule and biopolymers which often involves processes such as isolation, pre-concentration, removal of interferences (purification), and pre-processing (e.g., enzymatic digestion) of targets from a complex matrix. Gold nanoparticle (GNP)-assisted sample preparation and pre-concentration has been extensively applied in many analytical procedures in recent years due to the favorable and unique properties of GNPs such as size-controlled synthesis, large surface-to-volume ratio, surface inertness, straightforward surface modification, easy separation requiring minimal manipulation of samples. This review article primarily focuses on applications of GNPs in sample preparation, in particular for bioaffinity capture and biocatalysis. In addition, their most common synthesis, surface modification and characterization methods are briefly summarized. Proper surface modification for GNPs designed in accordance to their target application directly influence their functionalities, e.g., extraction efficiencies, and catalytic efficiencies. Characterization of GNPs after synthesis and modification is worthwhile for monitoring and controlling the fabrication process to ensure proper quality and functionality. Parameters such as morphology, colloidal stability, and physical/chemical properties can be assessed by methods such as surface plasmon resonance, dynamic light scattering, ζ-potential determinations, transmission electron microscopy, Taylor dispersion analysis, and resonant mass measurement, among others. The accurate determination of the surface coverage appears to be also mandatory for the quality control of functionality of the nanoparticles. Some promising applications of (functionalized) GNPs for bioanalysis and sample preparation are described herein.

[Use of DNA-aptamers for enrichment of low abundant proteins in cellular extracts for quntitative detection by selected reaction monitoring]

The relationship between the amount of a target protein in a complex biological sample and its amount measured by selected reaction monitoring (SRM) mass spectrometry upon the affinity enrichment of target protein with aptamers immobilized on a solid phase was studied. Human thrombin added in known concentrations to cellular extracts derived from bacterial cells was used as model target protein. It has been demonstrated that the affinity enrichment of thrombin in cellular extracts by means of the thrombin-binding aptamer immobilized on the surface of magnetic microbeads results in an approximately 10-fold increase of the concentration of target protein and a 100-fold decrease of the low limit of a target protein concentration range where its quantitative detection by SRM is possible without an interference from other peptides present in a tryptic digest.

One-Step Facile Synthesis of Aptamer-Modified Graphene Oxide for Highly Specific Enrichment of Human A-Thrombin in Plasma

The enrichment of low-abundance proteins in complex biological samples plays an important role in clinical diagnostics and biomedical research. This work reports a novel one-step method for the synthesis of aptamer-modified graphene oxide (GO/Apt) nanocomposites, without introducing the use of gold, for the rapid and specific separation and enrichment of human α-thrombin from buffer solutions with highly concentrated interferences. The obtained GO/Apt nanocomposites had remarkable aptamer immobilization, up to 44.8 nmol/mg. Furthermore, GO/Apt nanocomposites exhibited significant specific enrichment efficiency for human α-thrombin (>90%), even under the presence of 3000-fold interference proteins, which was better than the performance of other nanomaterials. Finally, the GO/Apt nanocomposites were applied in the specific capturing of human α-thrombin in highly concentrated human plasma solutions with negligible nonspecific binding of other proteins, which demonstrated their prospects in rare protein analysis and biosensing applications.

Electrogenerated Chemiluminescence Resonance Energy Transfer between Ru(bpy)3(2+) Electrogenerated Chemiluminescence and Gold Nanoparticles/Graphene Oxide Nanocomposites with Graphene Oxide as Coreactant and Its Sensing Application

In the present work, strong anodic electrogenerated chemiluminescence (ECL) of Ru(bpy)3(2+) was observed at a graphene oxide modified glassy carbon electrode (GO/GCE) in the absence of coreactants. The electrocatalytical effect of GO on the oxidation of Ru(bpy)3(2+) suggested that GO itself can act as the coreactant of Ru(bpy)3(2+) ECL, which can be used to fabricate the ECL biosensor. Thiol group terminated adenosine triphosphate (ATP) aptamer was immobilized on the GO film via DNA hybridization. When gold nanoparticles/graphene oxide (AuNPs/GO) nanocomposites were modified on the aptamer through the S-Au bond to form a sandwich-like structure, the ECL resonance energy transfer (ECL-RET) could occur between Ru(bpy)3(2+) and AuNPs/GO nanocomposites, resulting in an apparent decrease of ECL signal. After the ECL sensor was incubated in ATP solution, the AuNPs/GO nanocomposites were released from the electrode due to the specific interaction between aptamer and ATP, leading to the increased ECL signal. On the basis of these results, an ECL aptasensor was fabricated and could be used in the sensitive and selective detection of ATP in the range of 0.02-200 pM with a detection limit of 6.7 fM (S/N = 3). The proposed ECL aptasensor can be applied in the detection of ATP in real samples with satisfactory results.

Graphene/graphene oxide and their derivatives in the separation/isolation and preconcentration of protein species: A review

The distinctive/unique electrical, chemical and optical properties make graphene/graphene oxide-based materials popular in the field of analytical chemistry. Its large surface offers excellent capacity to anchor target analyte, making it an powerful sorbent in the adsorption and preconcentration of trace level analyte of interest in the field of sample preparation. The large delocalized π-electron system of graphene framework provides strong affinity to species containing aromatic rings, such as proteins, and the abundant active sites on its surface offers the chance to modulate adsorption tendency towards specific protein via functional modification/decoration. This review provides an overview of the current research on graphene/graphene oxide-based materials as attractive and powerful adsorption media in the separation/isolation and preconcentration of protein species from biological sample matrixes. These practices are aiming at providing protein sample of high purity for further investigations and applications, or to achieve certain extent of enrichment prior to quantitative assay. In addition, the challenges and future perspectives in the related research fields have been discussed.

Graphene-based nanoprobes for molecular diagnostics

In recent years, graphene has received widespread attention owing to its extraordinary electrical, chemical, optical, mechanical and structural properties. Lately, considerable interest has been focused on exploring the potential applications of graphene in life sciences, particularly in disease-related molecular diagnostics. In particular, the coupling of functional molecules with graphene as a nanoprobe offers an excellent platform to realize the detection of biomarkers, such as nucleic acids, proteins and other bioactive molecules, with high performance. This article reviews emerging graphene-based nanoprobes in electrical, optical and other assay methods and their application in various strategies of molecular diagnostics. In particular, this review focuses on the construction of graphene-based nanoprobes and their special advantages for the detection of various bioactive molecules. Properties of graphene-based materials and their functionalization are also comprehensively discussed in view of the development of nanoprobes. Finally, future challenges and perspectives of graphene-based nanoprobes are discussed.

Designed synthesis of aptamer-immobilized magnetic mesoporous silica/Au nanocomposites for highly selective enrichment and detection of insulin

We designed and synthesized aptamer-immobilized magnetic mesoporous silica/Au nanocomposites (MMANs) for highly selective detection of unlabeled insulin in complex biological media using MALDI-TOF MS. The aptamer was easily anchored onto the gold nanoparticles in the mesochannels of MMANs with high capacity for highly efficient and specific enrichment of insulin. With the benefit from the size-exclusion effect of the mesoporous silica shell with a narrow pore size distribution (∼2.9 nm), insulin could be selectively detected despite interference from seven untargeted proteins with different size dimensions. This method exhibited an excellent response for insulin in the range 2-1000 ng mL(-1). Moreover, good recoveries in the detection of insulin in 20-fold diluted human serum were achieved. We anticipate that this novel method could be extended to other biomarkers of interest and potentially applied in disease diagnostics.

Biomarker Characterization by MALDI-TOF/MS

Mass spectrometric techniques frequently used in clinical diagnosis, such as gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, ambient ionization mass spectrometry, and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF/MS), are discussed. Due to its ability to rapidly detect large biomolecules in trace amounts, MALDI-TOF/MS is an ideal tool for characterizing disease biomarkers in biologic samples. Clinical applications of MS for the identification and characterization of microorganisms, DNA fragments, tissues, and biofluids are introduced. Approaches for using MALDI-TOF/MS to detect various disease biomarkers including peptides, proteins, and lipids in biological fluids are further discussed. Finally, various sample pretreatment methods which improve the detection efficiency of disease biomarkers are introduced.

An exonuclease-assisted amplification electrochemical aptasensor of thrombin coupling "signal on/off" strategy

In this work, a dual-signaling electrochemical aptasensor based on exonuclease-catalyzed target recycling was developed for thrombin detection. The proposed aptasensor coupled "signal-on" and "signal-off" strategies. As to the construction of the aptasensor, ferrocene (Fc) labeled thrombin binding aptamer (TBA) could perfectly hybridize with the methylene blue (MB) modified thiolated capture DNA to form double-stranded structure, hence emerged two different electrochemical signals. In the presence of thrombin, TBA could form a G-quadruplex structure with thrombin, leading to the dissociation of TBA from the duplex DNA and capture DNA formed hairpin structure. Exonuclease could selectively digest single-stranded TBA in G-quadruplex structure and released thrombin to realize target recycling. As a consequence, the electrochemical signal of MB enhanced significantly, which realized "signal on" strategy, meanwhile, the deoxidization peak current of Fc decreased distinctly, which realized "signal off" strategy. The employment of exonuclease and superposition of two signals significantly improved the sensitivity of the aptasensor. In this way, an aptasensor with high sensitivity, good stability and selectivity for quantitative detection of thrombin was constructed, which exhibited a good linear range from 5 pM to 50 nM with a detection limit of 0.9 pM (defined as S/N=3). In addition, this design strategy could be applied to the detection of other proteins and small molecules.