Glycan-Imprinted Magnetic Nanoparticle-Based SELEX for Efficient Screening of Glycoprotein-Binding Aptamers

Design of pH-responsive molecularly imprinted polymer as a carrier for controlled and sustainable capecitabine release

A molecularly imprinting polymer (MIP) carrier with pH-responsivity was designed to construct a drug delivery system (DDS) focusing on controlled and sustainable capecitabine (CAPE) release. The pH-responsive characteristic was achieved by the functionalization of SiO2 substrate with 4-formylphenylboronic acid, accompanied by the introduction of fluorescein isothiocyanate for the visualization of the intracellular localization of the nanocarrier. Experimental results indicated that CAPE was adsorbed onto the drug carrier with satisfactory encapsulation efficiency. The controlled release of CAPE was realized based on the break of borate ester bonds between -B(OH)2 and cis-diols in the weakly acidic environment. Density functional theory computations were conducted to investigate the adsorption/release mechanism. Moreover, in vitro experiments confirmed the good biocompatibility and ideal inhibition efficiency of the developed DDS. The MIP can act as an eligible carrier and exhibits the great potential in practical applications for tumor treatment.

Aptamer-based assembly systems for SARS-CoV-2 detection and therapeutics

Nucleic acid aptamers are oligonucleotide chains with molecular recognition properties. Compared with antibodies, aptamers show advantages given that they are readily produced via chemical synthesis and elicit minimal immunogenicity in biomedicine applications. Notably, aptamer-encoded nucleic acid assemblies further improve the binding affinity of aptamers with the targets due to their multivalent synergistic interactions. Specially, aptamers can be engineered with special topological arrangements in nucleic acid assemblies, which demonstrate spatial and valence matching towards antigens on viruses, thus showing potential in the detection and therapeutic applications of viruses. This review presents the recent progress on the aptamers explored for SARS-CoV-2 detection and infection treatment, wherein applications of aptamer-based assembly systems are introduced in detail. Screening methods and chemical modification strategies for aptamers are comprehensively summarized, and the types of aptamers employed against different target domains of SARS-CoV-2 are illustrated. The evolution of aptamer-based assembly systems for the detection and neutralization of SARS-CoV-2, as well as the construction principle and characteristics of aptamer-based DNA assemblies are demonstrated. The typically representative works are presented to demonstrate how to assemble aptamers rationally and elaborately for specific applications in SARS-CoV-2 diagnosis and neutralization. Finally, we provide deep insights into the current challenges and future perspectives towards aptamer-based nucleic acid assemblies for virus detection and neutralization in nanomedicine.

Advances in aptamer-based biosensors for monitoring foodborne pathogens

Biosensors are analytical devices for detecting a wide range of targets, including cells, proteins, DNA, enzymes, and chemical and biological compounds. They mostly rely on using bioprobes with a high binding affinity to the target for specific detection. However, low specificity and effectiveness of the conventional biosensors has led to the search for novel materials, that can specifically detect biomolecules. Aptamers are a group of single-stranded DNA or RNA oligonucleotides, that can bind to their targets with high specificity and serve as effective bioprobes for developing aptamer-based biosensors. Aptamers have a shorter production time, high stability, compared to traditional bioprobes, and possess ability to develop them for specific target molecules for tailored applications. Thus, various aptasensing approaches, including electrochemical, optical, surface plasmon resonance and chip-dependent approaches, have been investigated in recent times for various biological targets, including foodborne pathogens. Hence, this article is an overview of various conventional foodborne pathogen detection methods, their limitations and the ability of aptamer-based biosensors to overcome those limitations and replace them. In addition, the current status and advances in aptamer-based biosensors for the detection of foodborne pathogens to ensure food safety were also discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05889-8.

Functional Interface for Glycoprotein Sensing: Focusing on Biosensors

Glycosylated proteins or glycoproteins make up a large family of glycoconjugates, and they participate in a variety of fundamental biological events. Glycoproteins have become important biomarkers in the diagnosis and treatment of a number of tumors. Biosensors are quite suitable for glycoprotein detection. The design and fabrication of a functional sensing interface play a crucial role in the biosensor construction to target glycoproteins. The functional interface, particularly receptors, typically determines the key characteristics of a biosensor, such as selectivity and sensitivity. Antibody, peptide, aptamer, boronic acid derivative, lectin, and molecularly imprinted polymer are all capable receptors for glycoprotein recognition, and each of these will be discussed. Most glycoproteins exist in low abundance, thus rendering signal amplification techniques indispensable. Nucleic acid-mediated and nanomaterial-mediated signal amplification for the detection of glycoproteins will be focused on herein. This review aims to highlight these different functional interfaces for glycoprotein sensing.

A review on magnetic beads-based SELEX technologies: Applications from small to large target molecules

This review summarizes the stepwise strategy and key points for magnetic beads (MBs)-based aptamer selection which is suitable for isolating aptamers against small and large molecules via systematic evolution of ligands by exponential enrichment (SELEX). Particularities, if any, are discussed according to the target size. Examples targeting small molecules (<1000 Da) such as xenobiotics, toxins, pesticides, herbicides, illegal additives, hormones, and large targets such as proteins (biomarkers, pathogens) are discussed and presented in tabular formats. Of special interest are the latest advances in more efficient alternatives, which are based on novel instrumentation, materials or microelectronics, such as fluorescence MBs-SELEX or microfluidic chip system-assisted MBs-SELEX. Limitations and perspectives of MBs-SELEX are also reviewed. Taken together, this review aims to provide practical insights into MBs-SELEX technologies and their ability to screen multiple potential aptamers against targets from small to large molecules.

Selection and application of highly specific Salmonella typhimurium aptamers against matrix interference

In practical applications, the structure and performance of aptamers can be influenced by the presence of sample matrices, which interferes with the specific binding between the aptamer and its target. In this work, to obtain aptamer chains resistant to matrix interference, four typical food matrices were introduced as negative selection targets and selection environments in the process of selecting aptamers for Salmonella typhimurium using the systematic evolution of ligands by exponential enrichment (SELEX) technology. As a result, some highly specific candidate aptamers for Salmonella typhimurium (BB-34, BB-37, ROU-8, ROU-9, ROU-14, ROU-24, DAN-3, NAI-12, and NAI-21) were successfully obtained. Based on the characterization results of secondary structure, affinity, and specificity of these candidate aptamers, ROU-24 selected in the pork matrix and BB-34 selected in the binding buffer were chosen to develop label-free fluorescence aptasensors for the sensitive and rapid detection of the Salmonella typhimurium and verify the performance against matrix interference. The ROU-24-based aptasensor demonstrated a larger linear range and better specificity compared to the BB-34-based aptasensor. Meanwhile, the recovery rate of the ROU-24-based aptasensor in real sample detection (ranging from 94.2% to 110.7%) was significantly higher than that of the BB-34-based aptasensor. These results illustrated that the negative selection of food matrices induced in SELEX could enhance specific binding between the aptamer and its target and the performance against matrix interference. Overall, the label-free fluorescence aptasensors were developed and successfully validated in different foodstuffs, demonstrating a theoretical and practical basis for the study of aptamers against matrix interference.

Recent progress of SELEX methods for screening nucleic acid aptamers

Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.

Molecular imprinted electrochemical sensor for ovalbumin detection based on boronate affinity and signal amplification approach

Ovalbumin (OVA), a class of glycoproteins, is the main allergen in hen egg white that often causes allergies in humans, especially in babies. Therefore, it is pivotal to be able to detect and separate OVA. This work presents an ingenious sandwich-structured magnetic molecular imprinted electrochemical sensor for OVA detection by utilizing boronate affinity and signal amplification strategy. With anti-OVA antibody-modified gold nanoparticles (AuNPs) as amplifiers, the imprinted cavities in the probe could capture protein to form a sandwich structure. Due to its specific recognition of antibody and molecular imprinted polymers and the signal amplification of AuNPs, the sensor had good selectivity and sensitivity toward OVA and a low detection limit of 3.0 fg/mL. The sensor also had excellent stability and could satisfactorily detect OVA in real red wine samples.

Targeted degradation of ABCG2 for reversing multidrug resistance by hypervalent bispecific gold nanoparticle-anchored aptamer chimeras

Hypervalent bispecific gold nanoparticle-anchored aptamer chimeras (AuNP-APTACs) were designed as a new tool of lysosome-targeting chimeras (LYTACs) for efficient degradation of the ATP-binding cassette, subfamily G, isoform 2 protein (ABCG2) to reverse multidrug resistance (MDR) of cancer cells. The AuNP-APTACs could effectively increase the accumulation of drugs in drug-resistant cancer cells and provide comparable efficacy to small-molecule inhibitors. Thus, this new strategy provides a new way to reverse MDR, holding great promise in cancer therapy.

A novel highly sensitive compilation-detachment fluorescence sensing strategy based on RNA-cleavage DNAzyme for MDA-MB-231 breast cancer biomarker determination

Herein, we designed a novel and highly sensitive fluorescence multicomponent detachable platform for MDA-MB-231 breast cancer cell detection as a model. The RNA cleavage DNAzyme was used as a central operator of the multicomponent probe through which compilation and induced detachment of probe was done. During the compilation step, the dsDNA-Sybr green 1 complexes on gold nanoparticles (GNP@dsDNA@SG1) were assembled. The intercalated Sybr green in the DNA structure has been used as an amplified signal generator on one site of DNAzyme and magnetic nanoparticles (MNP) act as a biological carrier and probe collector on the opposite side. The enzyme activator co-factor (MDA-MB-231 cell cytoplasmic protein) provokes the activation of the catalytic core of enzyme sequence in the DNAzyme molecule, followed by cleavage reaction in the substrate sequence and releasing GNP@ dsDNA@SG1 into the solution. The results indicate that the Sybr green emission fluorescence (520 nm) increases with the increment of MDA-MB-231 protein concentration in the linear dynamic range of 8.10 × 10^-2 to 1.95 ng ml^-1 (0.77 × 10^-3-0.019 cell ml^-1) with a detection limit (LOD) of 1/72 × 10^-2 pg ml^-1 under optimal conditions. The proposed immunosensor has great potential in developing ultrasensitive and rapid diagnostic platforms.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.

Surface acoustic wave-assisted microfluidic isolation of aptamers

Aptamers are synthetic single-stranded nucleic acid molecules that bind to biochemical targets with high affinity and specificity. The method of systematic evolution of ligands by exponential enrichment (SELEX) is widely used to isolate aptamers from randomized oligonucleotides. Recently, microfluidic technology has been applied to improve the efficiency and reduce the cost in SELEX processes. In this work, we present an approach that exploits surface acoustic waves to improve the affinity selection process in microfluidic SELEX. Acoustic streaming is used to enhance the interactions of the solution-based oligonucleotide molecules with microbead-immobilized target molecules, allowing the identification of high-affinity aptamer candidates in a more efficient manner. For demonstration, a DNA aptamer is isolated within three rounds of selection in 5 h to specifically bind to immunoglobulin E, a representative target protein, with an equilibrium dissociation constant of approximately 22.6 nM.

Rationally Screened and Designed ABCG2-Binding Aptamers for Targeting Cancer Stem Cells and Reversing Multidrug Resistance

The ATP-binding cassette, subfamily G, isoform 2 protein (ABCG2), as an important member of ABC transporters, plays a key role in multidrug resistance (MDR) in cancer and has been widely considered as a marker of cancer stem cells (CSC). Reagents capable of simultaneously targeting ABCG2 and reversing MDR have great clinical application values, but their development is highly challenging. Herein, ABCG2 glycosylated extracellular region-binding aptamers were efficiently screened by a cladded molecularly imprinted polymer (cMIP)-based in vitro screening method and further rationally engineered into cyclic bivalent aptamers. Experiments showed that both the monovalent and cyclic bivalent aptamers could specifically bind ABCG2 and thereby specially target CSC of human colorectal carcinomas (CoCSC), while the latter could effectively reverse MDR in drug-resistant liver cancer cells (HepG2/ADR). Different from currently predominant small molecule inhibitors, the reversal of MDR relied on a different mechanism; the cyclic bivalent aptamers bound the two monomers of ABCG2 dimers simultaneously and thereby blocked the ABCG2-mediated drug-pumping channel, resulting in increased intracellular accumulation of substrate drugs. This study opened a new access to the development of affinity reagents for targeting CSC and reversing MDR, holding great prospects in cancer diagnosis and treatment.

Enrichment of IgG and HRP glycoprotein by dipeptide-based polymeric material

Separation, purification, and identification of glycoproteins are essential for understanding their vital roles in biological and pathological processes. However, glycoproteins are difficult to be captured due to their low abundance, strong interference from non-glycosylated proteins. Here, we report a promising dipeptide-based saccharide recognition platform to selectively enrich two typical glycoproteins, named immunoglobin G (IgG) and horseradish peroxidase (HRP). Different from the conventional glycoprotein enrichment method based on boronic acid affinity or hydrophilic interaction with glycans, the present method was established based on affinity between Pro-Glu (PE) dipeptide and mannose, which is a key unit in the pentasaccharide core of the IgG and HRP glycans. The prepared PE homopolymer surface was proved to selectively bind IgG and HRP superior to that of bovine serum albumin (BSA). Benefiting from this feature, selective enrichment of IgG and HRP was achieved from a protein mixture containing 200-fold BSA interference by using polyPE@SiO₂ under a dispersive solid-phase extraction (dSPE) mode. High adsorption capacity, controllable and selective adsorption behaviors, as well as satisfactory recovery demonstrated the high potential of the dipeptide-based polymeric material in IgG and HRP enrichment. This study might provide a new insight to solve the challenging problem of glycoprotein separation.

A selectivity-enhanced ratiometric fluorescence imprinted sensor based on synergistic effect of covalent and non-covalent recognition units for ultrasensitive detection of ribavirin

Development of methods with high selectivity and sensitivity for detection of trace ribavirin (RBV) is of great importance for environmental protection and food safety. Herein, we proposed a simple yet valid strategy to construct the highly selective ratiometric fluorescence sensing platform (BA-LMOFs@MIP) for analysis of RBV based on boric acid-functionalized lanthanide metal-organic framework (BA-LMOFs) coupled with molecularly imprinted polymer (MIP). In this strategy, BA-LMOFs featured with dual-emission and pH-responsive behavior were first synthesized as supporter. Benefiting from boric acid group of BA-LMOFs, RBV was easily immobilized onto its surface, taking advantage of template immobilization-based surface imprinting means to fabricate BA-LMOFs@MIP with dual recognition sites for the first time. The synergistic effect of covalent boronate affinity-based recognition unit and non-covalent imprinting sites enabled BA-LMOFs@MIP to exhibit superior selectivity and binding efficiency to RBV. BA-LMOFs as signal tag endowed BA-LMOFs@MIP with desirable sensitivity, photostability and hydrophilicity. More importantly, BA-LMOFs@MIP-based sensor displayed a wide linear range for RBV from 25 to 1200 ng mL^-1 with a detection limit down to 7.62 ng mL^-1. The sensor was finally applied to RBV determination in real samples, and the obtained results revealed that BA-LMOFs@MIP would be a promising candidate for monitoring of RBV in complex systems.

Improved detection and recognition of glycoproteins using fluorescent polymers with a molecular imprint based on glycopeptides

Highly specific novel glycopeptide-based fluorescent molecularly imprinting polymers (g-FMIPs) were constructed to recognize and determine the target glycoprotein in complex biological samples. The glycopeptide of ovalbumin (OVA), with the unique structural characteristics of glycan and peptide, and potential application in improving the specificity recognition of g-FMIPs, was selected as the template molecule. The nitrogen-doped graphene quantum dots (N-GQDs) were introduced for fluorescence response. The obtained g-FMIPs possessed rapid binding kinetics and high adsorption capacity. Notably, the g-FMIPs exhibited remarkable selectivity and sensitivity with a high imprinting factor of 6.57, good linearity of 0.625 - 5.00 μM, and limit of detection of 0.208 μM. After treatment with g-FMIPs, the concentration of OVA in eluted solution was 1.07 μM. The obtained recoveries at 1.43 μM, 2.86 μM, and 4.29 μM spiked concentrations were 97.2%, 93.5%, and 101%, respectively, and the relative standard deviations were 2.6%, 4.2%, and 1.1%, respectively. In summary, the proposed strategy will expand the MIPs construction method and its application prospects in precision recognition and sensitive detection of trace glycoproteins from complex biosamples.

A heparan-sulfate-bearing syndecan-1 glycoform is a distinct surface marker for intra-tumoral myeloid-derived suppressor cells

Myeloid-derived suppressor cells (MDSCs) infiltrate cancer tissue, promote tumor growth, and are associated with resistance to cancer therapies. However, there is no practical approach available to distinguish MDSCs from mature counterparts inside tumors. Here, we show that a recently isolated thioaptamer probe (T1) binds to MDSC subsets in colorectal and pancreatic tumors with high specificity. Whole transcriptome and functional analysis revealed that T1-binding cells contain polymorphonuclear (PMN)-MDSCs characterized by several immunosuppression pathways, ROS production, and T cell suppression activity, whereas T1-non-binding PMNs were mature and nonsuppressive. We identified syndecan-1 as the T1-interacting protein on MDSCs and chronic myelogenous leukemia K562 cell line. Heparan sulfate chains were essential in T1-binding. Inside tumors PMN-MDSCs expressed heparan sulfate biogenesis enzymes at higher levels. Tumor-cell-derived soluble factor(s) enhanced MDSCs' affinity for T1. Overall, we uncovered heparan-sulfate-dependent MDSC modulation in the tumor microenvironment and identified T1 as tool preferentially targeting tumor-promoting myeloid cell subsets.

Identification of a novel DNA aptamer that selectively targets lung cancer serum

Lung cancer is the leading cause of cancer-related deaths worldwide. Early diagnosis and treatment is critical to improving the 5 year survival rate of lung cancer. The identification of new options for early-stage diagnosis and therapy of lung cancer still represents a crucial challenge. Therefore, a new diagnostic method is urgently needed. In this study, we used a new modified SELEX, called serum-SELEX, to isolate aptamers that can specifically bind lung cancer serum, without any prior knowledge of their target. Among the obtained candidate aptamer sequences, Ap-LC-19 was identified as the optimal aptamer probe with the lowest dissociation constant (K d) value of 15 ± 8.6 nM and higher affinity assessed by qPCR. Furthermore, this molecule could be a suitable aptamer for lung cancer serum and could be used as a recognition element in aptamer-based biosensors for efficient early diagnosis of lung cancer or as an innovative tool for targeted therapy. In addition, we performed MALDI-TOF MS followed by secondary peptide sequencing MS analysis for the identification of the aptamer targeted proteins. CLEC3B could be useful biomarkers for early detection of lung cancer and in monitoring its evolution.

Systematic Evolution of Ligands by Exponential Enrichment Technologies and Aptamer-Based Applications: Recent Progress and Challenges in Precision Medicine of Infectious Diseases

Infectious diseases are considered as a pressing challenge to global public health. Accurate and rapid diagnostics tools for early recognition of the pathogen, as well as individualized precision therapy are essential for controlling the spread of infectious diseases. Aptamers, which were screened by systematic evolution of ligands by exponential enrichment (SELEX), can bind to targets with high affinity and specificity so that have exciting potential in both diagnosis and treatment of infectious diseases. In this review, we provide a comprehensive overview of the latest development of SELEX technology and focus on the applications of aptamer-based technologies in infectious diseases, such as targeted drug-delivery, treatments and biosensors for diagnosing. The challenges and the future development in this field of clinical application will also be discussed.

Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies

Aptamers are artificial nucleic acid ligands that have been employed in various fundamental studies and applications, such as biological analyses, disease diagnostics, targeted therapeutics, and environmental pollutant detection. This review focuses on the recent advances in aptamer discovery strategies that have been used to detect various chemicals and biomolecules. Recent examples of the strategies discussed here are based on the classification of these micro/nanomaterial-mediated systematic evolution of ligands by exponential enrichment (SELEX) platforms into three categories: bead-mediated, carbon-based nanomaterial-mediated, and other nanoparticle-mediated strategies. In addition to describing the advantages and limitations of the aforementioned strategies, this review discusses potential strategies to develop high-performance aptamers.

β-Amyloid Peptide 1-42-Conjugated Magnetic Nanoparticles for the Isolation and Purification of Glycoproteins in Egg White

Aβ_1-42-conjugated magnetic nanoparticles, Aβ_1-42@MNP, were prepared by covalently coupling Aβ_1-42 to hyperbranched polyethyleneimine (PEI)-modified magnetic nanoparticles via N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC). Aβ_1-42's high binding capacity to glycosyl groups facilitates Aβ_1-42@MNP composite to be a promising selective adsorbent for glycoproteins in egg whites. In our study, under conditions of pH 4.0, the adsorption efficiency of Aβ_1-42@MNP composite for ovalbumin (100 μg mL^-1) was 98.4% and its maximum adsorption capacity was 344.8 mg g ^-1; under the condition of pH 4.0 and 200 mmol L^-1 NaCl, its adsorption efficiencies for ovalbumin and ovotransferrin were 96.9% and 60.0%, respectively. According to these primary data, in practice, ovalbumin was removed from egg white by Aβ_1-42@MNP composite at pH 4.0 (step I), and then after adding NaCl until the final salt concentration reached 200 mmol L^-1 (pretreated egg white), we utilized the same adsorbent to further isolate/purify glycoproteins (step II). SDS-PAGE results showed that Aβ_1-42@MNP composite could largely remove ovalbumin in step I and could isolate/purify the remaining ovalbumin and ovotransferrin in step II. LC-MS/MS analysis results showed that the removal of ovalbumin reduced its percentage in egg white samples from 32.93% to 11.05% in step I and the remaining ovalbumin and ovotransferrin were enriched in step II, where the final percentage reached 11.6% and 12.6%, respectively. In summary, 81 protein species were identified after two-step extraction with Aβ_1-42@MNP on egg white, while only 46 protein species were identified directly from raw egg white without any pretreatment. This work well illustrates the excellent adsorption performance of Aβ_1-42@MNP composite to glycoproteins and its potential in the application of proteomic studies on low-abundance proteins in egg white.

X-aptamers targeting Thy-1 membrane glycoprotein in pancreatic ductal adenocarcinoma

Modified DNA aptamers incorporated with amino-acid like side chains or drug-like ligands can offer unique advantages and enhance specificity as affinity ligands. Thy-1 membrane glycoprotein (THY1 or CD90) was previously identified as a biomarker candidate of neovasculature in pancreatic ductal adenocarcinoma (PDAC). The current study developed and evaluated modified DNA X-aptamers targeting THY1 in PDAC. The expression and glycosylation of THY1 in PDAC tumor tissues were assessed using immunohistochemistry and quantitative proteomics. Bead-based X-aptamer library that contains 108 different sequences was used to screen for high affinity THY1 X-aptamers. The sequences of the X-aptamers were analyzed with the next-generation sequencing. The affinities of the selected X-aptamers to THY1 were quantitatively evaluated with flow cytometry. Three high affinity THY1 X-aptamers, including XA-B217, XA-B216 and XA-A9, were selected after library screening and affinity binding evaluation. These three X-aptamers demonstrated a high binding affinity and specificity to THY1 protein and the THY1 expressing cell lines, using THY1 antibody as a comparison. The development of these X-aptamers provides highly specific and non-immunogenic affinity ligands for THY1 binding in the context of biomarker development and clinical applications. They could be further exploited to assist molecular imaging of PDAC targeting THY1.

PEI-assisted boronate affinity magnetic nanoparticle-based SELEX for efficient in vitro evolution of saponin-binding aptamers

Branched polyethyleneimine assisted boronate affinity magnetic nanoparticle-based aptamer evolution platform.

Efficient Screening of Glycan-Specific Aptamers Using a Glycosylated Peptide as a Scaffold

Abnormal glycan structures are valuable biomarkers for disease states; the development of glycan-specific binders is thereby significantly important. However, the structural homology and weak immunogenicity of glycans pose major hurdles in the evolution of antibodies, while the poor availability of complex glycans also has extremely hindered the selection of anti-glycan aptamers. Herein, we present a new approach to efficiently screen aptamers toward specific glycans with a complex structure, using a glycosylated peptide as a scaffold. In this method, using peptide-imprinted magnetic nanoparticles (MNPs) as a versatile platform, a glycopeptide tryptically digested from a native glycoprotein was selectively entrapped for positive selection, while a nonglycosylated analogue with an identical peptide sequence was synthesized for negative selection. Alternating positive and negative selection steps were carried out to guide the directed evolution of glycan-binding aptamers. As proof of the principle, the biantennary digalactosylated disialylated N-glycan A2G2S2, against which there have been no antibodies and lectins so far, was employed as the target. With the glycoprotein transferrin as a source of target glycan, two satisfied anti-A2G2S2 aptamers were selected within seven rounds. Since A2G2S2 is upregulated in cancerous liver cells, carboxyfluorescein (FAM)-labeled aptamers were prepared as fluorescent imaging reagents, and successful differentiation of cancerous liver cells over normal liver cells was achieved, which demonstrated the application feasibility of the selected aptamers. This approach obviated a tedious glycan preparation process and allowed favorable expose of the intrinsic flexible conformation of natural glycans. Therefore, it holds great promise for developing glycan-specific aptamers for challenging applications such as cancer targeting.

A rational route to hybrid aptamer-molecularly imprinted magnetic nanoprobe for recognition of protein biomarkers in human serum

Although antibody has played a great role in highly specific recognition of protein biomarkers, it faces poor stability, reproducibility, high-cost and time-consuming preparation, etc. Here, aptamer and molecularly imprinted polymers (MIPs), both as promising substitutes of antibody, were integrated onto magnetic nanoparticles by Au-S bonds and SiO₂ as imprinted layer for preparing a new nanoprobe. Highly specific and sensitive recognition of different protein biomarkers, such as insulin for diabetes and alpha-fetoprotein (AFP) for hepatic carcinoma, were achieved respectively by the system of combining hybrid aptamer-molecularly imprinted magnetic nanoprobe and mass spectrometry. With the double affinities offered by aptamer-MIPs, insulin can be detected at 0.5 ng mL^-1 in human serum dilution, the equlibrium dissociation constant between nanoprobe and insulin is measured as 23.61 ± 2.27 μM. Likewise, AFP can be sufficiently detected in human saliva dilution from 1000 ng mL^-1 to 20 ng mL^-1, and two patients with hepatic carcinoma are discriminated from healthy person due to the abnormally high expression of AFP in serum.

Epitope-Imprinted Magnetic Nanoparticles as a General Platform for Efficient In Vitro Evolution of Protein-Binding Aptamers

Aptamers are usually created by in vitro selection using a strategy termed systematic evolution of ligands by exponential enrichment (SELEX). Although numerous SELEX alternatives with improved selection efficiency have been developed, the overall success rate of SELEX at present is still not very ideal, which remains a great obstacle to aptamer-based research and application. In this study, an efficient and facile SELEX method was developed for in vitro screening of protein-binding aptamers, applying epitope-imprinted magnetic nanoparticles (MNPs) that exhibit highly favorable binding properties as a general affinity platform. As a proof of the principle, myoglobin (Mb) and β₂-microglobulin were employed as two target proteins. Two satisfied aptamers toward each target protein, with the dissociation constant at the 10^-8 M level and cross-reactivity less than 16.5%, were selected within three rounds, taking only 1 day. A dual aptamer-based fluorescence sandwich assay was constructed using a pair of the selected aptamers. The resulting assay allowed for quantitatively detecting Mb in human serum and distinguishing acute myocardial infarction patients from healthy individuals. The epitope-imprinted MNP-based SELEX is straightforward and generally applicable for a wide range of target proteins, providing a promising aptamer selection tool for aptamer-based research and real-world applications.

Aptamers targeting protein-specific glycosylation in tumor biomarkers: general selection, characterization and structural modeling

Detecting specific protein glycoforms is attracting particular attention due to its potential to improve the performance of current cancer biomarkers. Although natural receptors such as lectins and antibodies have served as powerful tools for the detection of protein-bound glycans, the development of effective receptors able to integrate in the recognition both the glycan and peptide moieties is still challenging. Here we report a method for selecting aptamers toward the glycosylation site of a protein. It allows identification of an aptamer that binds with nM affinity to prostate-specific antigen, discriminating it from proteins with a similar glycosylation pattern. We also computationally predict the structure of the selected aptamer and characterize its complex with the glycoprotein by docking and molecular dynamics calculations, further supporting the binary recognition event. This study opens a new route for the identification of aptamers for the binary recognition of glycoproteins, useful for diagnostic and therapeutic applications.

Binary recognition of the glycoprotein prostate specific antigen by aptamers: a tool for detecting aberrant glycosylation associated with cancer.

Glycan Nanobiosensors

This review paper comprehensively summarizes advances made in the design of glycan nanobiosensors using diverse forms of nanomaterials. In particular, the paper covers the application of gold nanoparticles, quantum dots, magnetic nanoparticles, carbon nanoparticles, hybrid types of nanoparticles, proteins as nanoscaffolds and various nanoscale-based approaches to designing such nanoscale probes. The article covers innovative immobilization strategies for the conjugation of glycans on nanoparticles. Summaries of the detection schemes applied, the analytes detected and the key operational characteristics of such nanobiosensors are provided in the form of tables for each particular type of nanomaterial.

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.

Novel methods in glycomics: a 2019 update

Introduction: Glycomics, which aims to define the glycome of a biological system to better assess the biological attributes of the glycans, has attracted increasing interest. However, the complexity and diversity of glycans present challenging barriers to glycome definition. Technological advances are major drivers in glycomics.Areas covered: This review summarizes the main methods and emphasizes the most recent advances in mass spectrometry-based methods regarding glycomics following the general workflow in glycomic analysis.Expert opinion: Recent mass spectrometry-based technological advances have significantly lowered the barriers in glycomics. The field of glycomics is moving toward both generic and precise analysis.

Decoding glycans: deciphering the sugary secrets to be coherent on the implication

Neoteric techniques, skills, and methodological advances in glycobiology and glycochemistry have been instrumental in pertinent discoveries to pave way for a new era in biomedical sciences. Glycans are sugar-based polymers that coat cells and decorate majority of proteins, forming glycoproteins. They are also found deposited in extracellular spaces between cells, attached to soluble signaling molecules, and are key players in several biological processes including regulation of immune responses and cell–cell interactions. Laboratory manipulations of protein, DNA and other macromolecules celebrate the accelerated research in respective fields, but the same seems unlikely for the complex sugar polymers. The structural complex polymers are neither synthesized using a known template nor are dynamically stable with respect to a cell's metabolic rate. What is more, sugar isomers—structurally distinct molecules with the same chemical formula—can be employed to construct varied glycans, but are almost impossible to tell apart based on molecular weight alone. The apparent lack of a glycan alphabet further reflects on an enduring question: how little do we know about the sugars? Evidently, glycan-based therapeutic potentials and glycomimetics are propitious advances for the future that have not been well exploited, and with a few conspicuous anomalies. Here, we contour the most notable contributions to enhance our ability to utilize the complex glycans as therapeutics. Diagnostic strategies concerning recurrent diseases and headways to address the challenges are also discussed.

A glycan toolbox for pathogenic and cancerous interventions. The review article sheds light on the sweet secrets of this complex structure.

Nano-crystalline cellulose-coated magnetic nanoparticles for affinity adsorption of glycoproteins

A new core–shell structured nanomaterial based on Fe₃O₄ nanoparticles and 2,3-dialdehyde nanocrystalline cellulose (DAC) coatings and its high efficiency in the preconcentration of glycoproteins were described in this work.

Signalling molecular recognition nanocavities with multiple functional groups prepared by molecular imprinting and sequential post-imprinting modifications for prostate cancer biomarker glycoprotein detection

Novel sequential post-imprinting modifications were demonstrated on the development of multi-functionalized molecularly imprinted polymers for a biomarker glycoprotein.

Adsorption of DNA Oligonucleotides by Boronic Acid-Functionalized Hydrogel Nanoparticles

Boronic acid-functionalized hydrogels were commonly used for covalent binding of cis-diol-contained molecules such as glucose, but noncovalent adsorption by boronic acids was less studied. DNA as an important polymer has been used to enhance the function of hydrogels including boronic acid-containing gels. In this work, noncovalent interactions between DNA oligonucleotides and boronic acid-containing hydrogel nanoparticles were studied in detail. The gels were composed of either poly(N-isopropylacrylamide) or with additional 5.6 mol % of 3-acrylamidophenylboronic acid (AAPBA). DNA adsorption on the AAPBA-containing gels was achieved with a high salt concentration, which can be explained by electrostatic repulsion between DNA and boronic acid. The critical role of boronic acid was confirmed by adding competing cis-diol-containing molecules such as glucose, fructose, and cytidine. Hydrogen bonding and hydrophobic interactions are important for DNA adsorption based on inhibited adsorption by urea and dimethyl sulfoxide. Polycytosine DNA showed a higher adsorption capacity compared to the other three types of DNA homopolymers. When T₁₅ and T₁₄-rU were compared, no covalent binding was detected for T₁₄-rU, suggesting that a single terminal diol was insufficient to support covalent binding at the low concentration of DNA used. Finally, the boronic acid-containing gels were able to adsorb an aptamer and inhibit its binding function. Binding was rescued by adding glucose to block the boronic acids. This study demonstrates noncovalent boronic acid interactions with DNA, and this information could be useful for designing and optimization of related biosensors and materials.

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.