Molecularly imprinted aptamers of gold nanoparticles for the enzymatic inhibition and detection of thrombin

Molecular imprinted based microcryogels for thrombin purification

In addition to understanding and explaining the functions of proteins, the need for low-cost, easy and efficient purification methods has been increasing in the field of protein purification, which is also important for enzyme production. In this context, an alternative approach has been developed for the purification of thrombin, which has a crucial role in the hemostatic process, via thrombin imprinted microcryogels that allow reuse and have high selectivity. The characterization studies of the microcryogels were accomplished with micro-computed tomography (µCT), scanning electron microscopy (SEM), optical microscope, surface area measurements (BET analyses) and swelling test measurements. By scanning various parameters affecting thrombin adsorption, the maximum thrombin adsorption capacity (Qmax) was found to be 55.86 mg/g. Also, the selectivity of microcryogels was investigated with the competitive agents and reusability studies were performed. The purity of thrombin was evaluated by Fast Performance Liquid Chromatography (FPLC) method. Experimental results indicated that adsorption of thrombin by the developed microcryogels fit the Langmuir isotherm model (Qmax: 55.86 mg/g, R2: 0.9505) and pseudo-second order for three different thrombin concentrations (R2: 0.9978, R2: 0.9998, R2: 0.9999).

Molecularly Imprinting–Aptamer Techniques and Their Applications in Molecular Recognition

Molecular imprinting–aptamer techniques exhibit the advantages of molecular imprinting and aptamer technology. Hybrids of molecularly imprinted polymer–aptamer (MIP–aptamer) prepared by this technique have higher stability, binding affinity and superior selectivity than conventional molecularly imprinted polymers or aptamers. In recent years, molecular imprinting–aptamer technologies have attracted considerable interest for the selective recognition of target molecules in complex sample matrices and have been used in molecular recognition such as antibiotics, proteins, viruses and pesticides. This review introduced the development of molecular imprinting–aptamer-combining technologies and summarized the mechanism of MIP–aptamer formation. Meanwhile, we discussed the challenges in preparing MIP–aptamer. Finally, we summarized the application of MIP–aptamer to the molecular recognition in disease diagnosis, environmental analysis, food safety and other fields.

Molecular imprinted polymer combined with aptamer (MIP-aptamer) as a hybrid dual recognition element for bio(chemical) sensing applications. Review

The development of diagnostic devices based on memetic molecular recognitions are becoming highly promising due to high specificity, sensitivity, stability, and low-cost comparing to natural molecular recognition. During the last decade, molecular imprinted polymers (MIPs) and aptamer have shown dramatic enhancement in the molecular recognition characteristics for bio(chemical) sensing applications. Recently, MIP-aptamer, as an emerging hybrid recognition element, merged the advantages of the both recognition components. This dual recognition-based sensor has shown improved properties and desirable features, such as high sensitivity, low limit of detection, high stability under harsh environmental conditions, high binding affinity, and superior selectivity. Hybrid MIP-aptamer as dual recognition element, was used in the real sample analysis, such as detection of proteins, neurotransmitters, environmental pollutants, biogenic compounds, small ions, explosives, virus detections and pharmaceuticals. This review focuses on a comprehensive overview of the preparation strategies of various MIP-aptamer recognition elements, mechanism of formation of MIP-aptamer, and detection of various target molecules in different matrices.

Modulation of Acetylcholinesterase Activity Using Molecularly Imprinted Polymer Nanoparticles

Modulation of enzyme activity allows for control over many biological pathways and while strategies for the pharmaceutical design of inhibitors are well established; methods for promoting activation, that is an...

Platelet activation by charged ligands and nanoparticles: platelet glycoprotein receptors as pattern recognition receptors

Charge interactions play a critical role in the activation of the innate immune system by damage- and pathogen-associated molecular pattern receptors. The ability of these receptors to recognize a wide spectrum of ligands through a common mechanism is critical in host defense. In this article, we argue that platelet glycoprotein receptors that signal through conserved tyrosine-based motifs function as pattern recognition receptors (PRRs) for charged endogenous and exogenous ligands, including sulfated polysaccharides, charged proteins and nanoparticles. This is exemplified by GPVI, CLEC-2 and PEAR1 which are activated by a wide spectrum of endogenous and exogenous ligands, including diesel exhaust particles, sulfated polysaccharides and charged surfaces. We propose that this mechanism has evolved to drive rapid activation of platelets at sites of injury, but that under some conditions it can drive occlusive thrombosis, for example, when blood comes into contact with infectious agents or toxins. In this Opinion Article, we discuss mechanisms behind charge-mediated platelet activation and opportunities for designing nanoparticles and related agents such as dendrimers as novel antithrombotics.

Oriented Immobilization of Protein Templates: A New Trend in Surface Imprinting

In this Review, we have summarized recent trends in protein template imprinting. We emphasized a new trend in surface imprinting, namely, oriented protein immobilization. Site-directed proteins were assembled through specially selected functionalities. These efforts resulted in a preferably oriented homogeneous protein construct with decreased protein conformation changes during imprinting. Moreover, the maximum functionality for protein recognition was utilized. Various strategies were exploited for oriented protein immobilization, including covalent immobilization through a boronic acid group, metal coordinating center, and aptamer-based immobilization. Moreover, we have discussed the involvement of semicovalent as well as covalent imprinting. Interestingly, these approaches provided additional recognition sites in the molecular cavities imprinted. Therefore, these molecular cavities were highly selective, and the binding kinetics was improved.

Synthesis of a molecularly imprinted polymer using MOF-74(Ni) as matrix for selective recognition of lysozyme

A molecularly imprinted polymer and metal organic framework were combined to prepare protein imprinted material. MOF-74(Ni) was used as a matrix to prepare surface-imprinted material with lysozyme as a template and polydopamine as an imprinting polymer. MOF-74(Ni) not only provides a large surface area (150.0 m²/g) to modify the polymer layer with more recognition sites (Wt (Ni) = 42.24%), but also facilitates the immobilization of lysozyme by using the chelation between Ni²⁺ of the MOF-74(Ni) and protein. The thin polydopamine layer (10 nm) of the molecularly imprinted material (named MOF@PDA-MIP) enables surface imprinting. Benefiting from the thin polymer layer, MOF@PDA-MIP reached adsorption equilibrium within 10 min. The maximum adsorption capacity reaches 313.5 mg/g with the highest imprinting factor (IF) of 7.8. The specific recognition sites can distinguish target lysozyme from other proteins such as egg albumin (OVA), bovine serum albumin (BSA) and ribonuclease A (RNase A). The material was successfully applied to separation of lysozyme from egg white. Graphical abstract.

Nanoparticles for hematologic diseases detection and treatment

Nanotechnology, as an interdisciplinary science, combines engineering, physics, material sciences, and chemistry with the biomedicine knowhow, trying the management of a wide range of diseases. Nanoparticle-based devices holding tumor imaging, targeting and therapy capabilities are formerly under study. Since conventional hematological therapies are sometimes defined by reduced selectivity, low therapeutic efficacy and many side effects, in this review we discuss the potential advantages of the NPs' use in alternative/combined strategies. In the introduction the basic notion of nanomedicine and nanoparticles' classification are described, while in the main text nanodiagnostics, nanotherapeutics and theranostics solutions coming out from the use of a wide-ranging NPs availability are listed and discussed.

Efficient Mass Spectrometric Dissection of Glycans via Gold Nanoparticle-Assisted in-Source Cation Adduction Dissociation

Structural identification of glycans is important but remains challenging, for which tandem mass spectrometry has evolved as an indispensable tool. However, it requires additional complex hardware and extra time for ion extraction. Herein, we report a straightforward approach called gold nanoparticles (AuNPs)-assisted in-source cation adduction dissociation (isCAD) for efficient mass spectrometry (MS) dissection of glycans. Although AuNPs have been employed as an inorganic matrix for MALDI MS, this is the first report of AuNP-induced fragmentation. In this approach, AuNPs were employed as an energy absorber for laser ionization as well as a trigger for fragmentation, while residual or deliberately added sodium ions acted as a cationizing agent. The addition of sodium ions induced intensive fragmentation, but the addition of protons suppressed the fragmentation, allowing for facile tuning of the degree of fragmentation. In addition, it was found that larger oligosaccharides and glycans were much easier to fragment as compared with their smaller counterparts, and the use of high-concentration AuNPs effectively suppressed the degree of fragmentation and thereby provided abundant molecular ions. Without any extra hardware and ion extraction, this approach provides a straightforward, cost-efficient and tunable fragmentation for efficient MS dissection of saccharides, including monosaccharides, oligosaccharides, and glycans. Thus, it opens new access to efficient MS dissection of glycans.

Molecular Imprinting with Functional DNA

Molecular imprinting refers to templated polymerization with rationally designed monomers, and this is a general method to prepare stable and cost-effective ligands. This attractive concept however suffers from low affinity, low specificity, and limited signaling mechanisms for binding. Acrydite-modified DNA oligonucleotides can be readily copolymerized into acrylic polymers. With molecular recognition and catalytic functions, such functional DNAs are recently shown to enhance the performance of molecularly imprinted polymers (MIPs) in a few ways. First, DNA aptamers are used as macromonomers to enhance binding affinity and specificity of MIPs. Second, DNA can help produce optical signals to follow binding events. Third, imprinting can also improve the performance of catalytic DNA by enhancing its activity and specificity toward the template substrate. Finally, MIP is shown to help aptamer selection. Bulk imprinting, nanoparticle imprinting, and surface imprinting are all demonstrated with DNA. Since both DNA and synthetic polymers are cost effective and stable, their hybrid materials still possess such properties while enhancing the function of each component. This review covers recent developments on the abovementioned aspects of DNA-containing MIPs, a field just emerged in the last five years, and future research directions are discussed toward the end.

Controllably Prepared Aptamer-Molecularly Imprinted Polymer Hybrid for High-Specificity and High-Affinity Recognition of Target Proteins

Molecularly imprinted polymers (MIPs) and aptamers, as effective mimics of antibodies, can overcome only some drawbacks of antibodies. Since they have their own advantages and disadvantages, the combination of MIPs with aptamers could be an ideal solution to produce hybrid alternatives with improved properties and desirable features. Although quite a few attempts have been made in this direction, a facile and controllable approach for the preparation of aptamer-MIP hybrids still remains lacking. Herein, we present a new approach for facile and controllable preparation of aptamer-MIP hybrids for high-specificity and high-affinity recognition toward proteins. An aptamer that can bind the glycoprotein alkaline phosphatase (ALP) with relative weak affinity and specificity was used as a ligand, and controllable oriented surface imprinting was carried out with an in-water self-polymerization system of dopamine. A thin layer of polydopamine was formed to cover the template to an appropriate thickness. After removing the template from the polymer, an aptamer-MIP hybrid with apparently improved affinity and specificity toward ALP was obtained, giving cross-reactivity of 3.2-5.6% and a dissociation constant of 1.5 nM. With this aptamer-MIP hybrid, a plasmonic immunosandwich assay (PISA) was developed. Reliable detection of ALP in human serum by the PISA was demonstrated.

Molecularly Imprinted Plasmonic Substrates for Specific and Ultrasensitive Immunoassay of Trace Glycoproteins in Biological Samples

Assays of glycoproteins hold significant biological importance and clinical values, for which immunoassay has been the workhorse tool. As immunoassays are associated with disadvantages such as poor availability of high-specificity antibodies, limited stability of biological reagents, and tedious procedure, innovative alternatives that can overcome these drawbacks are highly desirable. Plasmonic immunosandwich assay (PISA) has emerged as an appealing alternative to immunoassay for fast and sensitive determination of trace glycoproteins in biosamples. Plasmonic substrates play key roles in PISA, not only in determining the specificity but also in greatly influencing the detection sensitivity. Herein, we report a new type of molecularly imprinted plasmonic substrates for rapid and ultrasensitive PISA assay of trace glycoproteins in complex real samples. The substrates were fabricated from glass slides, first coated with self-assembled monolayer (SAM) of gold nanoparticles (AuNPs) and then molecularly imprinted with organo-siloxane polymer in the presence of template glycoproteins. The prepared molecularly imprinted substrates exhibited not only a significant plasmonic effect but also excellent binding properties, ensuring the sensitivity as well as the specificity of the assay. Alkaline phosphatase (ALP) and α-fetoprotein (AFP), glycoproteins that are routinely used as disease markers in clinical diagnosis, were used as representative targets. The limit of detection (LOD) was 3.1 × 10^-12 M for ALP and 1.5 × 10^-14 M for AFP, which is the best among the PISA approaches reported. The sample volume required was only 5 μL, and the total time required was within 30 min for each assay. Specific and ultrasensitive determination of ALP and AFP in human serum was demonstrated. Because many disease biomarkers are glycoproteins, the developed PISA approach holds great promise in disease diagnostics.

Plastic antibody based surface plasmon resonance nanosensors for selective atrazine detection

This study reports a surface plasmon resonance (SPR) based affinity sensor system with the use of molecular imprinted nanoparticles (plastic antibodies) to enhance the pesticide detection. Molecular imprinting based affinity sensor is prepared by the attachment of atrazine (chosen as model pesticide) imprinted nanoparticles onto the gold surface of SPR chip. Recognition element of the affinity sensor is polymerizable form of aspartic acid. The imprinted nanoparticles were characterized via FTIR and zeta-sizer measurements. SPR sensors are characterized with atomic force microscopy (AFM), scanning electron microscopy (SEM), Fourier transform infrared spectrophotometry (FTIR) and contact angle measurements. The imprinted nanoparticles showed more sensitivity to atrazine than the non-imprinted ones. Different concentrations of atrazine solutions are applied to SPR system to determine the adsorption kinetics. Langmuir adsorption model is found as the most suitable model for this affinity nanosensor system. In order to show the selectivity of the atrazine-imprinted nanoparticles, competitive adsorption of atrazine, simazine and amitrole is investigated. The results showed that the imprinted nanosensor has high selectivity and sensitivity for atrazine.

Biomedical Applications of DNA-Conjugated Gold Nanoparticles

Gold nanoparticles (AuNPs) are useful for diagnostic and biomedical applications, mainly because of their ease in preparation and conjugation, biocompatibility, and size-dependent optical properties. However, bare AuNPs do not possess specificity for targets. AuNPs conjugated with DNA aptamers offer specificity for various analytes, such as proteins and small molecules/ions. Although DNA aptamers themselves have therapeutic and target-recognizing properties, they are susceptible to degradation in vivo. When DNA aptamers are conjugated to AuNPs, their stability and cell uptake efficiency both increase, making aptamer-AuNPs suitable for biomedical applications. Additionally, drugs can be efficiently conjugated with DNA aptamer-AuNPs to further enhance their therapeutic efficiency. This review focuses on the applications of DNA aptamer-based AuNPs in several biomedical areas, including anticoagulation, anticancer, antibacterial, and antiviral applications.

Molecularly Imprinted Polymers with DNA Aptamer Fragments as Macromonomers

Molecularly imprinted polymers (MIPs) are produced in the presence of a template molecule. After removing the template, the cavity can selectively rebind the template. MIPs are attractive functional materials with a low cost and high stability, but traditional MIPs often suffer from low binding affinity. This study employs DNA aptamer fragments as macromonomers to improve MIPs. The DNA aptamer for adenosine was first split into two halves, fluorescently labeled, and copolymerized into MIPs. With a fluorescence quenching assay, the importance of imprinting was confirmed. Further studies were carried out using isothermal titration calorimetry (ITC). Compared to the mixture of the free aptamer fragments, their MIPs doubled the binding affinity. Each free aptamer fragment alone cannot bind adenosine, whereas MIPs containing each fragment are effective binders. We further shortened one of the aptamer fragments, and the DNA length was pushed to as short as six nucleotides, yielding MIPs with a dissociation constant of 27 μM adenosine. This study provides a new method for preparing functional MIP materials by combining high-affinity biopolymer fragments with low-cost synthetic monomers, allowing higher binding affinity and providing a method for signaling binding based on DNA chemistry.

Split aptamer mediated endonuclease amplification for small-molecule detection

A novel, highly sensitive split aptamer mediated endonuclease amplification strategy for the construction of aptameric sensors is reported.

Trapping RNase A on MCM41 pores: effects on structure stability, product inhibition and overall enzymatic activity

Catalytic activity of enzymes can be drastically modified by immobilization on surfaces of different materials. It is particularly effective when the dimensions of the biomolecules and adsorption sites on the material surfaces are commensurate. This can be utilized to hinder the biological activity of degradation enzymes and switch off undesired biological processes. Ribonucleases are particularly attractive targets for complete sequestration being efficient at disintegrating viable RNA molecules. Here we show that efficient quenching of ribonuclease A activity can be achieved by immobilization on the surface of MCM41 porous silica. Electron microscopy, isothermal titration calorimetry, differential scanning calorimetry and adsorption isotherm measurements of ribonuclease A on the MCM41 surface are used to demonstrate that the enzyme adsorbs on the external surface of the porous silica through electrostatic interactions that overcome the unfavorable entropy change as the protein gets trapped on the surface, and that immobilization shifts up its denaturation temperature by 20-25 °C. Real-time kinetic measurements, using single injection titration calorimetry, demonstrate that enzymatic activity towards hydrolysis of cyclic nucleotides is lowered by nearly two orders of magnitude on MCM41 and that active inhibition by the formed product is much less effective on the surface than in solution.

Antithrombotic functions of small molecule-capped gold nanoparticles

Here we report the antithrombotic functions of pyrimidinethiol-capped gold nanoparticles (Au_DAPT NPs). They can prolong coagulation parameters when injected intravenously in normal mice. Applied in two typical thrombosis models, mice tail thrombosis and pulmonary thromboembolism, gold NPs can inhibit both thrombosis and improve the survival rates of mice tremendously, without increasing the bleeding risk. The anticoagulant mechanisms include inhibiting the platelet aggregation as well as interfering with thrombin and fibrin generation.

Hyperbranched rolling circle amplification based electrochemiluminescence aptasensor for ultrasensitive detection of thrombin

An ultrasensitive electrochemiluminescence (ECL) aptamer sensor for protein (thrombin as an example) detection based on hyperbranched rolling circle amplification (HRCA) had been developed. A complementary single-strand DNA (CDNA) of the thrombin aptamer had been modified on the gold electrode firstly, and then hybridized with thrombin aptamer to make the aptamer immobilized on the electrode surface, in the presence of thrombin, aptamer-thrombin bioaffinity complexes formed and made thrombin aptamer leave the electrode surface. Thus, the linear padlock probe hybridized with the free CDNA on the electrode surface and circularized by Escherichia coli DNA ligase. Subsequently, the linear padlock probe was served as a template for the initiation of HRCA reaction, and a lot of dsDNA modified on the electrode surface. Then Ru(phen)₃²⁺ (acted as the ECL indicator) intercalates specifically into double-stranded DNA (dsDNA) grooves to generate ECL signal. The ECL intensity of the system has a linear relationship with thrombin concentration in the range of 3.0-300 aM with a detection limit of 1.2 aM (S/N=3). The proposed method combines the high sensitivity of ECL, exponential amplification of HRCA for signal enhancement and high selectivity of aptamer.

A convenient sandwich assay of thrombin in biological media using nanoparticle-enhanced fluorescence polarization

A new aptamer biosensor was presented for the detection of thrombin in this work, which was based on fluorescence polarization (FP) using silica nanoparticles as enhancement probe. The silica nanoparticles covered by streptavidin were tagged with a thrombin aptamer (5'-biotin-GGTTGGTGTGGTTGG-3'), which was bound to the surface of silica nanoparticle through the specific interaction between streptavidin and biotin. In the presence of thrombin, it induced the aptamer to form quadruplex structure. When the other thrombin aptamer labeled with fluorescein (5'-FAM-AGTCCGTGGTAGGGCAGGTTGGGGTGACT-3') was added to the above system, a sandwich structure can form at the surface of silica nanoparticles. The fluorescence polarization was therefore enhanced and quantification between fluorescence polarization signal and concentration of thrombin was built. The sensor provided a linear range from 0.6 to 100 nM for thrombin with a detection limit of 0.20 nM (3.29 SB/m, according to the recent recommendation of IUPAC) in a homogeneous media. The same linear range was obtained in spiked human serum samples with a slightly higher detection limit (0.26 nM), demonstrating high anti-interference of the sensor in a complex biological sample matrix. And the sensor can be used to monitor spiked concentration of thrombin level in real human plasma with satisfactory results obtained.

Scanning electrochemical microscopy for study of aptamer-thrombin interfacial interactions on gold disk microelectrodes

A feasibility for the determination of thrombin on gold disk microelectrodes (GDMs) using scanning electrochemical microscopy (SECM) is reported. The assembly process step-by-step of thrombin aptasensor on GDMs is monitored by SECM. SECM analysis reveals the immobilization of thrombin aptamers on GDMs. The interaction between thrombin aptamers and thrombin on GDMs is imaged by SECM with feedback mode using ferrocenemethanol as an electrochemical mediator. The formation of thrombin/thrombin aptamer complex on GDMs results in a decrease in the tip peak current on spatial SECM images. This method is able to linearly and selectively detect thrombin over a linear range from 10(-12) to 10(-5)M with a detection limit of 6.07 fM.

A selective artificial enzyme inhibitor based on nanoparticle-enzyme interactions and molecular imprinting

A novel and general strategy is developed to design selective artificial enzyme inhibitor based on nanoparticleenzyme inter actions and molecular imprinting. Due to the creation of specific binding cavities, the resulting artificial inhibitor has high inhibition efficiency for the target enzyme, and shows great target-selectivity over other enzymes of similar function and proteins of compaable mole cular weight.

Preparation of water-soluble hyperbranched polyester nanoparticles with sulfonic acid functional groups and their micelles behavior, anticoagulant effect and cytotoxicity

Biocompatibility of nanoparticles has been attracting great interest in the development of nanoscience and nanotechnology. Herein, the aliphatic water-soluble hyperbranched polyester nanoparticles with sulfonic acid functional groups (HBPE-SO3 NPs) were synthesized and characterized. They are amphiphilic polymeric nanoparticles with hydrophobic hyperbranched polyester (HBPE) core and hydrophilic sulfonic acid terminal groups. Based on our observations, we believe there are two forms of HBPE-SO3 NPs in water under different conditions: unimolecular micelles and large multimolecular micelles. The biocompatibility and anticoagulant effect of the HBPE-SO3 NPs were investigated using coagulation tests, hemolysis assay, morphological changes of red blood cells (RBCs), complement and platelet activation detection, and cytotoxicity (MTT). The results confirmed that the sulfonic acid terminal groups can substantially enhance the anticoagulant property of HBPE, and the HBPE-SO3 NPs have the potential to be used in nanomedicine due to their good bioproperties.

Hot Spot-Localized Artificial Antibodies for Label-Free Plasmonic Biosensing

The development of biomolecular imprinting over the last decade has raised promising perspectives in replacing natural antibodies with artificial antibodies. A significant number of reports have been dedicated to imprinting of organic and inorganic nanostructures, but very few were performed on nanomaterials with a transduction function. Herein we describe a relatively fast and efficient plasmonic hot spot-localized surface imprinting of gold nanorods using reversible template immobilization and siloxane co-polymerization. The technique enables a fine control of the imprinting process at the nanometer scale and provides a nanobiosensor with high selectivity and reusability. Proof of concept is established by the detection of neutrophil gelatinase-associated lipocalin (NGAL), a biomarker for acute kidney injury, using localized surface plasmon resonance spectroscopy. The work represents a valuable step towards plasmonic nanobiosensors with synthetic antibodies for label-free and cost-efficient diagnostic assays. We expect that this novel class of surface imprinted plasmonic nanomaterials will open up new possibilities in advancing biomedical applications of plasmonic nanostructures.

Enzyme-free colorimetric bioassay based on gold nanoparticle-catalyzed dye decolorization

A novel, enzyme-free and aptamer-based colorimetric platform for protein detection has been developed, which takes advantage of aptamer-functionalized magnetic beads (MBs) for target capture, concentration and separation, and aptamer-conjugated gold nanoparticle (AuNP)-catalyzed color bleaching reaction of methyl orange (MO) to generate the colorimetric signals. It was demonstrated that the proposed colorimetric sensing strategy enables simple, cost-effective, sensitive and specific thrombin detection without the use of any enhancing solutions and enzymes. Herein, by naked eye observation, we can detect the human thrombin with a detection limit of approximately 320 pM, which can be further decreased to 30 pM with the help of a UV-vis instrument. In addition, this method also works for targets with two or more binding sites.

Pulsed-laser desorption/ionization of clusters from biofunctional gold nanoparticles: implications for protein detections

In this paper, we describe a pulsed-laser desorption/ionization mass spectrometry (LDI-MS) approach for the detection of proteins with femtomolar sensitivity through the analysis of gold (Au) clusters desorbed from aptamer-modified gold nanoparticles (Apt-AuNPs) on a nitrocellulose membrane (NCM). After the target protein (thrombin) was selectively captured by the surface-bound 29-mer thrombin-binding aptamer (TBA(29)), the thrombin/TBA(29)-AuNP complexes were concentrated and deposited onto the NCM to form a highly efficient background-free surface-assisted LDI substrate. Under pulsed laser irradiation (355 nm), the binding of thrombin decreased the desorption and/or ionization efficiencies of the Au atoms from the AuNP surfaces. The resulting decreases in the intensities of the signals for Au clusters in the mass spectra provided a highly amplified target-labeling indicator for the targeted protein. Under optimized conditions, this probe was highly sensitive (limit of detection: ca. 50 fM) and selective (by at least 1000-fold over other proteins) toward thrombin; it also improved reproducibility (<5%) of ion production by presenting a more-homogeneous substrate surface, thereby enabling LDI-based measurements for the accurate and precise quantification of thrombin in human serum. This novel LDI-MS approach allows high-speed analyses of low-abundance thrombin with ultrahigh sensitivity; decorating the AuNP surfaces with other aptamers also allowed amplification of other biological signals.

Polyvalent nucleic acid aptamers and modulation of their activity: a focus on the thrombin binding aptamer

Nucleic acid-based aptamers can be selected from combinatorial libraries of synthetic oligonucleotides to bind, with affinity and specificity similar to antibodies, a wide range of biomedically relevant targets. Compared to protein therapeutics, aptamers exhibit significant advantages in terms of size, non-immunogenicity and wide synthetic accessibility. Various chemical modifications have been introduced in the natural oligonucleotide backbone of aptamers in order to increase their half-life, as well as their pharmacological properties. Very effective alternative approaches, devised in order to improve both the aptamer activity and stability, were based on the design of polyvalent aptamers, able to establish multivalent interactions with the target: thus, multiple copies of an aptamer can be assembled on the same molecular- or nanomaterial-based scaffold. In the present review, the thrombin binding aptamers (TBAs) are analyzed as a model system to study multiple-aptamer constructs aimed at improving their anticoagulation activity in terms of binding to the target and stability to enzymatic degradation. Indeed - even if the large number of chemically modified TBAs investigated in the last 20 years has led to encouraging results - a significant progress has been obtained only recently with bivalent or engineered dendritic TBA aptamers, or assemblies of TBAs on nanoparticles and DNA nanostructures. Furthermore, the modulation of the aptamers activity by means of tailored drug-active reversal agents, especially in the field of anticoagulant aptamers, as well as the reversibility of the TBA activity through the use of antidotes, such as porphyrins, complementary oligonucleotides or of external stimuli, are discussed.