Development of Dual-Aptamers for Constructing Sandwich-Type Pancreatic Polypeptide Assay

Process, advances, and perspectives of graphene oxide-SELEX for the development of aptamer molecular probes: A comprehensive review

BACKGROUND

Aptamers are screened via the systematic evolution of ligands by exponential enrichment (SELEX) and are widely used in molecular diagnostics and targeted therapies. The development of efficient and convenient SELEX technology has facilitated rapid access to high-performance aptamers, thereby advancing the aptamer industry. Graphene oxide (GO) serves as an immobilization matrix for libraries in GO-SELEX, making it suitable for screening aptamers against diverse targets.

RESULTS

This review summarizes the detailed steps involved in GO-SELEX, including monitoring methods, various sublibrary acquisition methods, and practical applications from its inception to the present day. In addition, the potential of GO-SELEX in the development of broad-spectrum aptamers is explored, and its current limitations for future development are emphasized. This review effectively promotes the application of the GO-SELEX technique by providing valuable insights and assisting researchers interested in conducting related studies.

SIGNIFICANCE AND NOVELTY

To date, no review on the topic of GO-SELEX has been published, making it challenging for researchers to initiate studies in this area. We believe that this review will broaden the SELEX options available to researchers, ensuring that they can meet the growing demand for molecular probes in the scientific domain.

Tuning quantum dots emission on DNA tetrahedron/silica nanosphere/graphene oxide nanointerface for ratiometric fluorescence assay of Pb2+ in multiplex samples

BACKGROUND

Assembling framework nucleic acid (FNA) nanoarchitectures and tuning luminescent quantum dots (QDs) for fluorescence assays represent a versatile strategy in analytical territory. Rationally, FNA constructs could offer a preferential orientation to efficiently recognize the target and improve detection sensitivity, meanwhile, regulating size-dependent multicolor emissions of QDs in one analytical setting for ratiometric fluorescence assay would greatly simplify operation procedures. Nonetheless, such FNA/QDs-based ratiometric fluorescence nanoprobes remain rarely explored.

RESULTS

We designed a sensitive and signal amplification-free fluorescence aptasensor for lead ions (Pb2+) that potentially cause extensive contamination to environment, cosmetic, food and pharmaceuticals. Red and green emission CdTe quantum dots (rQDs and gQDs) were facilely prepared. Moreover, silica nanosphere encapsulating rQDs served as quantitative internal reference and scaffold to anchor a predesigned FNA and DNA sandwich containing Pb2+ binding aptamer and gQD modified DNA signal reporter. On binding of Pb2+, the gQD-DNA signal reporter was set free, resulting in fluorescence quenching at graphene oxide (GO) interface. Owing to the rigid structure of FNA, the fluorescence signal reporter orderly arranged at the silica nanosphere could sensitively respond to Pb2+ stimulation. The dose-dependent fluorescence signal-off mode enabled ratiometric analysis of Pb2+ without cumbersome signal amplification. Linear relationship was established between fluorescence intensity ratio (I555/I720) and Pb2+ concentration from 10 nM to 2 μM, with detection limit of 1.7 nM (0.43 ppb), well addressing the need for Pb2+ routine monitoring. The designed nanoprobe was applied to detection of Pb2+ in soil, cosmetic, milk, drug, and serum samples, with the sensitivity comparable to conventional ICP-MS technique.

SIGNIFICANCE

Given the programmable design of FNA and efficient recognition of target, flexible tuning of QDs emission, and signal amplification-free strategy, the present fluorescence nanoprobe could be a technical criterion for other heavy metal ions detection in a straightforward manner.

Molecularly imprinted polymers outperform lectin counterparts and enable more precise cancer diagnosis

Accurately analysing the particular glycosylation status of protein biomarkers is of significant importance in the precise, early diagnosis of cancer. Existing methods mainly rely on the use of antibodies and lectins. However, due to the macroscopic and microscopic heterogeneity of glycans, precise analysis of glycosylation status still remains a challenge. Molecularly imprinted polymers (MIPs), as a synthetic alternative to antibodies or lectins, may provide new solutions but have not yet been explored. Herein, we report an appealing strategy called triple MIP-based plasmonic immunosandwich assay (triMIP-PISA) for precise cancer diagnosis in terms of the relative glycosylation expression of glycoprotein biomarkers. As proof of the principle, alpha fetoprotein (AFP), which has been used as a clinical biomarker for early detection of hepatocellular carcinoma (HCC), as well as its Lens culinaris agglutinin (LCA)-reactive fraction (AFP-L3), which is mainly composed of core-fucosylated glycans, were used as two target proteoforms to test in this study. Using two MIPs that can specifically recognize the peptide sequence of AFP as well as a fucose-imprinted MIP that can specifically recognize the AFP-L3 fraction, facile simultaneous plasmon-enhanced Raman detection of AFP and AFP-L3 in serum was achieved, which allowed HCC patients to be distinguished from healthy individuals. Due to the excellent recognition properties of the MIPs that are comparable to those of antibodies and superior to those of lectins, our triMIP-PISA method exhibited improved precision as compared with an antibody plus lectin-based immunofluorescence assay. Thus, this strategy opened a new avenue towards the precise diagnosis of cancer.

Generation of Thermally Stable Affinity Pairs for Sensitive, Specific Immunoassays

Many point-of-care diagnostic tests rely on a pair of monoclonal antibodies that bind to two distinct epitopes of a molecule of interest. This protocol describes the identification and generation of such affinity pairs based on an easily produced small protein scaffold rcSso7d which can substitute monoclonal antibodies. These strong binding variants are identified from a large yeast display library. The approach described can be significantly faster than antibody generation and epitope binning, yielding affinity pairs synthesized in common bacterial protein synthesis strains, enabling the rapid generation of novel diagnostic tools.

DNA aptamer against EV-A71 VP1 protein: selection and application

BACKGROUND

Enterovirus 71 (EV-A71) is a highly infectious pathogen associated with hand, foot and mouth disease, herpangina, and various neurological complications, so it is important for the early detection and treatment of EV-A71. An aptamer is a nucleotide sequence that screened in vitro by the technology named systematic evolution of ligands by exponential enrichment technology (SELEX). Similar to antibodies, aptamers can bind to the targets with high specificity and affinity. Besides, emerging aptamers have many advantages comparing with antibodies, such as ease of synthesis and modification, having a wide variety of target materials, low manufacturing cost and easy flexibility in amending. Therefore, aptamers are promising in virus detection and anti-virus therapy.

METHODS

Aptamers were selected by SELEX. Specificity, affinity and second structure were used to characterize the selected aptamers. Chemiluminescence was adopted to build an aptamer-based detection method for EV-A71. Cytopathogenic effects trial, the level of intracellular EV-A71 RNA and protein expression were used to evaluate the antiviral effect of the selected aptamers.

RESULTS

Three DNA aptamers with high specificity and affinity for EV-A71structual protein VP1 were screened out. A rapid chemiluminutesescence aptamer biosensor for EV-A71 detection was designed out. The selected aptamers could inhibit the RNA replication and protein expression of EV-A71 in RD cells and ameliorate the cytopathogenic effects.

CONCLUSIONS

The aptamers against EV-A71 have the potentiality to be applied as attractive candidates used for EV-A71 detection and treatment in the future.

The discovery of lactoferrin dual aptamers through surface plasmon resonance imaging combined with a bioinformation analysis

An analytical method for screening aptamers for different recognition sites in lactoferrin (Lac) molecules has been developed based on Surface Plasmon Resonance imaging (SPRi), combined with the cluster classification calculation of a quasi-aptamer library strategy and molecular docking simulation analysis. Using the software simulation, a homology analysis was performed on the selected quasi-aptamer sequences, which could be divided into 8 different families. Based on the principle of biomolecular recognition, a label-free, high-throughput dual immune site screening method was established, in which the nucleic acid aptamers of recognizing ability for lactoferrin molecules were fixed onto the surface of the SPRi sensor chip and could bind to the lactoferrin molecules. Then, the aptamer candidates to be paired were introduced, and the recognition event of the second immune site was judged by observing the binding signal of SPRi. The paired SPRi signal was generated only when the site identified by the second nucleic acid molecule was different from the first immune site. Based on this principle, a pair of Lac nucleic acid aptamers (Lac-8 and Lac-25) was finally screened and confirmed using computerized simulation, and has been employed to assay Lac in milk by ELONA (Enzyme-Linked Oligonucleotide Assay).

Ratiometric Fluorescent DNA Nanostructure for Mitochondrial ATP Imaging in Living Cells Based on Hybridization Chain Reaction

For intracellular molecular detection, the appropriate probes should include the abilities to enter target cells noninvasively, target specific sites, and then respond to the analytes reliably. Herein, a ratiometric fluorescent DNA nanostructure (RFDN) was designed for mitochondrial adenosine triphosphate (ATP) imaging in living cells. The DNA nanostructure was constructed by continuous hybridization of two hairpin DNA strands (HS1-Cy3 and HS2-Cy5) under the initiation of the trigger. HS1-Cy3 and HS2-Cy5 contained split aptamer fragments of ATP and are labeled with a fluorescent donor (Cy3) and acceptor (Cy5), respectively. The RFDN integrated multiple split aptamer fragments and increased the local concentration of sensing probes. The binding of ATP to aptamer fragments on the RFDN shortened the distance between Cy3 and Cy5, resulting in obvious ratiometric signals (fluorescence resonance energy transfer). The RFDN showed good biocompatibility and can be internalized into cells in a caveolin-dependent endocytosis pathway. The co-localization imaging results indicated that the DNA nanostructure could target the mitochondria via Cy3 and Cy5. Moreover, the confocal imaging results showed that the intracellular ATP changes stimulated by drugs in living cells could be indicated by the RFDN. In this way, the RFDN is expected to be a simple, flexible, and general platform for chemo/biosensing in living cells.

Engineering and Application of a Myoglobin Binding Split Aptamer

Given that a split aptamer provides a chance for the development of a sandwich assay for targets with only one aptamer, it has received extensive attention in biosensing. However, due to the lack of binding mechanisms and reliable methods, there were still a few split aptamers that bind to proteins. In this work, cardiac biomarker myoglobin (Myo) was selected as a model, a new strategy of engineering split aptamers was explored with atomic force spectroscopy (AFM), and split aptamers against target protein could be achieved by choosing the optimal binding probability between split aptamers and target. Then, the obtained split aptamers were designed for Myo detection based on dynamic light scattering (DLS). The results demonstrated that the obtained split aptamers could be used to detect targets in human serum. The strategy of engineering split aptamers has the advantages of being intuitive and reliable and could be a general strategy for obtaining split aptamers.

Convenient Construction of Orthogonal Dual Aptamer-Based Plasmonic Immunosandwich Assay for Probing Protein Disease Markers in Complex Samples and Living Animals

Aptamers, because of their outstanding merits including simple synthesis and easy modification, have been widely used as antibody alternatives to construct novel immunosandwich assays. Dual aptamer-based sandwich assays exhibit multiple advantages over conventional immunosandwich assays and single aptamer-based sandwich assays. However, their construction is hampered by the limited knowledge of binding orthogonality of aptamers reported in the literature. Herein, we present a new strategy for conveniently constructing an orthogonal dual aptamer-based plasmonic immunosandwich assay (odA-PISA) for probing proteins in complex samples and living animals. An orthogonal aptamer pair was first efficiently selected from the aptamers reported in the literature by affinity capillary electrophoresis. Then, a target protein-capturing gold thin-layer-coated probe and silver nanoparticle-based Raman labeling nanotags were conveniently prepared with the selected aptamers and used to construct the assay. The double aptamers used ensured the specificity, whereas the plasmonic coupling effect between the target-capturing probe and the generated Raman nanotags significantly enhanced the Raman signal intensity, providing high sensitivity. As a proof of principle, alkaline phosphatase (ALP) was used as the target. The constructed odA-PISA exhibited high specificity and high sensitivity toward ALP, giving cross-reactivity ≤ 4.2% and the limit of detection of 3.8 pM (S/N = 4). The quantitative determination of ALP in human serum and probing ALP in tumor-bearing mice were achieved, showing the great application potential of the method. This strategy is widely applicable to other protein disease markers. Therefore, it opened a new access to the construction of sensitive dual aptamer-based sandwich assays for real-world applications, particularly disease diagnosis.

Exploring Interactions of Aptamers with Aβ40 Amyloid Aggregates and Its Application: Detection of Amyloid Aggregates

The exhaustive investigating interactions between recognition probes and amyloid aggregates, especially simultaneous recognition events, are challenging and crucial for the design of biosensing probes and further diagnosis of amyloid diseases. In the present work, the interactions of aptamers (Apts) with β-amyloid (Aβ) aggregates were explored thoroughly by single-molecule force spectroscopy (SMFS). Indeed, it was found that the interaction of aptamer1 (Apt1)-amyloid aggregates was different from that of aptamer2 (Apt2)-Aβ₄₀ aggregates at the single-molecule level. Especially, the interaction force of Apt1-Aβ₄₀ fibril showed a double distinguishing Gaussian fitting. The only unimodal distribution of the force histogram was displayed for the interactions of Apt2-Aβ₄₀ oligomer, Apt2-Aβ₄₀ fibril, and Apt1-Aβ₄₀ oligomer. More intriguingly, two Apts could bind to amyloid aggregates simultaneously. With the assistance of two Apts recognition, a novel sensitive dual Apt-based surface plasmon resonance (SPR) sensor using Au nanoparticles (AuNPs) was developed for quantifying Aβ₄₀ aggregates. The dual Apt-based SPR sensor not only avoided the limitation of steric hindrance and epitope but also employed simple operation as well as inexpensive recognition probes. A detection limit as low as 0.2 pM for Aβ₄₀ oligomer and 0.05 pM for Aβ₄₀ fibril could be achieved. Moreover, the established sensor could be successfully applied to detect Aβ₄₀ aggregates in artificial cerebrospinal fluid (CSF) and undiluted real CSF. This work could provide a strategy to monitor a simultaneous recognition event using SMFS and broaden the application of Apts in the diagnosis of neurodegenerative diseases.

Beyond Epitope Binning: Directed in Vitro Selection of Complementary Pairs of Binding Proteins

Many biotechnological applications require the simultaneous binding of affinity reagents to nonoverlapping target epitopes, the most prominent example being sandwich immunoassays. Typically, affinity pairs are identified via post facto functional analysis of clones that were not selected for complementarity. Here, we developed the Rapid Affinity Pair Identification via Directed Selection (RAPIDS) process, which enables the efficient identification of affinity reagents that function together as complementary pairs, from in vitro libraries of ∼10⁹ variants. We used RAPIDS to develop highly specific affinity pairs against biomarkers of tuberculosis, Zika virus, and sepsis. Without additional trial-and-error screening, these affinity pairs exhibited utility in multiple assay formats. The RAPIDS process applies selective pressure to hundreds of thousands of potential affinity pairs to efficiently identify complementary pairs that bind to separate epitopes without binding to one another or nontargets, yielding diagnostic assays that are sensitive and specific by design.

Investigation of the interaction between split aptamer and vascular endothelial growth factor 165 using single molecule force spectroscopy

Understanding the binding of split aptamer/its target could become a breakthrough in the application of split aptamer. Herein, vascular endothelial growth factor (VEGF), a major biomarker of human diseases, was used as a model, and its interaction with split aptamer was explored with single molecule force spectroscopy (SMFS). SMFS demonstrated that the interaction force of split aptamer/VEGF₁₆₅ was 169.44 ± 6.59 pN at the loading rate of 35.2 nN/s, and the binding probability of split aptamer/VEGF₁₆₅ was dependent on the concentration of VEGF₁₆₅ . On the basis of dynamic force spectroscopy results, one activation barrier in the dissociation process of split aptamer/VEGF₁₆₅ complexes was revealed, which was similar to that of the intact aptamer/VEGF₁₆₅ . Besides, the dissociation rate constant (k_off ) of split aptamer/VEGF₁₆₅ was close to that of intact aptamer/VEGF₁₆₅ , and the interaction force of split aptamer/VEGF₁₆₅ was higher than the force of intact aptamer/VEGF₁₆₅ . It indicated that split aptamer also possessed high affinity with VEGF₁₆₅ . The work can provide a new method for exploring the interaction of split aptamer/its targets at single-molecule level.

Construction of Bio/Nanointerfaces: Stable Gold Nanoparticle Bioconjugates in Complex Systems

The real application of DNA-functionalized gold nanoparticles (DNA-Au NPs) was limited by decreased stability and irreversible aggregation in high-ionic strength solutions and complex systems. Therefore, exploring a kind of DNA-Au NPs with excellent stability in high-ionic strength solutions and complex systems is challenging and significant. Herein, a novel universal bioconjugate strategy for constructing ultrastable DNA-Au NPs was designed based on the combination of polydopamine (PDA) shell and DNA linker. The obtained DNA-linked Au@polydopamine nanoparticles (DNA-Au@PDA NPs) showed colloidal stability in high-ionic strength solution and complex systems (such as human serum and cell culture supernatant). Moreover, the nanoparticles still maintained good dispersion after multiple freeze-thaw cycles. The high stability of DNA-Au@PDA NPs may be attributed to increasing the electrostatic and steric repulsions among nanoparticles through the effect of both PDA shell and DNA linker on Au@PDA NPs. For investigating the application of such nanoparticles, a highly sensitive assay for miRNA 141 detection was developed using DNA-Au@PDA NPs coupled with dynamic light scattering (DLS). Comparing with the regular DNA-Au NPs, DNA-Au@PDA NPs could detect as low as 50 pM miRNA 141 even in human whole serum. Taken together, the features of Bio/Nanointerface make the nanoparticle suitable for various applications in harsh biological and environmental conditions due to the stability. This work may provide a universal modification method for obtaining stable nanoparticles.

Orthogonal dual molecularly imprinted polymer-based plasmonic immunosandwich assay: A double characteristic recognition strategy for specific detection of glycoproteins

Sensitive and specific detection methods are critical to the detection of glycoproteins. Immunoassay has been a powerful tool for this purpose, in which antibodies or their mimics particularly molecularly imprinted polymers (MIPs) are used for specific recognition. Epitope and glycan are two structure features of a glycoprotein. However, immunoassays based on simultaneous recognition towards the two characteristics have been scarcely explored so far. Herein we present a new strategy called orthogonal dual molecularly imprinted polymer-based plasmonic immunosandwich assay (odMIP-PISA). It relies on double recognition towards a target glycoprotein by two different types of MIPs, using epitope-imprinted gold nanoparticles (AuNPs)-coated slide as capturing substrate to recognize the peptide epitope and glycans-imprinted Raman-active silver nanoparticles as labeling nanotags to recognize the glycans. Carcinoembryonic antigen (CEA), a routinely used marker for colon cancer, was used as a test glycoprotein. The orthogonal double recognition apparently improved the specificity, reducing the maximum cross-reactivity from 14.4% for epitope recognition and 15.2% for glycan recognition to 8.2% for double recognition. Meanwhile, the plasmonic nanostructure-based Raman detection provided ultrahigh sensitivity, yielding a limit of detection of 5.56 × 10^-14 M (S/N = 10). Through measuring the CEA level in human serum, this method permitted differentiation of colon cancer patient from healthy individual. Compared with the traditional immunoassay, odMIP-PISA exhibited multiple advantages, including simplified procedure (6 steps), speed (30 min), reduced cost, and so on. Therefore, this new approach holds great promise in many applications particularly clinical diagnosis.

Magnetic Separation-Based Multiple SELEX for Effectively Selecting Aptamers against Saxitoxin, Domoic Acid, and Tetrodotoxin

In this study, a novel magnetic separation-based multiple systematic evolution of ligands by exponential enrichment (SELEX) was applied to select aptamers simultaneously against three kinds of marine biotoxins, including domoic acid (DA), saxitoxin (STX), and tetrodotoxin (TTX). Magnetic reduced graphene oxide (MRGO) was prepared to adsorb unbound ssDNAs and simplify the separation step. In the multiple SELEX, after the initial twelve rounds of selection against mixed targets and the subsequent four respective rounds of selection against each single target, the three resulting ssDNA pools were cloned, sequenced, and analyzed. Several aptamer candidates were selected and subjected to the binding affinity and specificity test. Finally, DA-06 ( K_d = 62.07 ± 19.97 nM), TTX-07 ( K_d = 44.12 ± 15.38 nM), and STX-41 ( K_d = 61.44 ± 23.18 nM) showed high affinity and good specificity for DA, TTX, and STX, respectively. They were also applied to detect and quantify DA, TTX, and STX successfully. The other two multitarget aptamers, DA-01 and TTX-27, were also obtained, which can bind with either DA or TTX. These aptamers provide alternative recognition molecules to antibodies for biosensor applications.