Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology

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.

Selection and identification of a prohibitin 2-binding DNA aptamer for tumor tissue imaging and targeted chemotherapy

Tumor cell-targeting molecules play a vital role in cancer diagnosis, targeted therapy, and biomarker discovery. Aptamers are emerging as novel targeting molecules with unique advantages in cancer research. In this work, we have developed several DNA aptamers through cell-based systematic evolution of ligands by exponential enrichment (Cell-SELEX). The selected SYL-6 aptamer can bind to a variety of cancer cells with high signal. Tumor tissue imaging demonstrated that SYL-6-Cy5 fluorescent probe was able to recognize multiple clinical tumor tissues but not the normal tissues, which indicates great potential of SYL-6 for clinical tumor diagnosis. Meanwhile, we identified prohibitin 2 (PHB2) as the molecular target of SYL-6 using mass spectrometry, pull-down and RNA interference assays. Moreover, SYL-6 can be used as a delivery vehicle to carry with doxorubicin (Dox) chemotherapeutic agents for antitumor targeted chemotherapy. The constructed SYL-6-Dox can not only selectively kill tumor cells in vitro, but also inhibit tumor growth with reduced side effects in vivo. This work may provide a general tumor cell-targeting molecule and a potential biomarker for cancer diagnosis and targeted therapy.

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

Precise Control of Trypsin Immobilization by a Programmable DNA Tetrahedron Designed for Ultrafast Proteome Digestion and Accurate Protein Quantification

In proteomics research, with advantages including short digestion times and reusable applications, immobilized enzyme reactors (IMERs) have been paid increasing attention. However, traditional IMERs ignore the reasonable spatial arrangement of trypsin on the supporting matrixes, resulting in the partial overlapping of the active domain on trypsin and reducing digesting efficiency. In this work, a DNA tetrahedron (DNA TET)-based IMER Fe3O4-GO-AuNPs-DNA TET-Trypsin was designed and prepared. The distance between vertices of DNA TETs effectively controls the distribution of trypsin on the nanomaterials; thus, highly efficient protein digestion and accurate quantitative results can be achieved. Compared to the in-solution digestion (12-16 h), the sequence coverage of bovine serum albumin was up to 91% after a 2-min digestion by the new IMER. In addition, 3328 proteins and 18,488 peptides can be identified from HeLa cell protein extract after a 20-min digestion. For the first time, human growth hormone reference material was rapidly and accurately quantified after a 4-h digestion by IMER. Therefore, this new IMER has great application potential in proteomics research and SI traceable quantification.

Electrical Characterization and Analysis of Single Cells and Related Applications

Biological parameters extracted from electrical signals from various body parts have been used for many years to analyze the human body and its behavior. In addition, electrical signals from cancer cell lines, normal cells, and viruses, among others, have been widely used for the detection of various diseases. Single-cell parameters such as cell and cytoplasmic conductivity, relaxation frequency, and membrane capacitance are important. There are many techniques available to characterize biomaterials, such as nanotechnology, microstrip cavity resonance measurement, etc. This article reviews single-cell isolation and sorting techniques, such as the micropipette separation method, separation and sorting system (dual electrophoretic array system), DEPArray sorting system (dielectrophoretic array system), cell selector sorting system, and microfluidic and valve devices, and discusses their respective advantages and disadvantages. Furthermore, it summarizes common single-cell electrical manipulations, such as single-cell amperometry (SCA), electrical impedance sensing (EIS), impedance flow cytometry (IFC), cell-based electrical impedance (CEI), microelectromechanical systems (MEMS), and integrated microelectrode array (IMA). The article also enumerates the application and significance of single-cell electrochemical analysis from the perspectives of CTC liquid biopsy, recombinant adenovirus, tumor cells like lung cancer DTCs (LC-DTCs), and single-cell metabolomics analysis. The paper concludes with a discussion of the current limitations faced by single-cell analysis techniques along with future directions and potential application scenarios.

Research Progress in Surface-Enhanced Infrared Absorption Spectroscopy: From Performance Optimization, Sensing Applications, to System Integration

Infrared absorption spectroscopy is an effective tool for the detection and identification of molecules. However, its application is limited by the low infrared absorption cross-section of the molecule, resulting in low sensitivity and a poor signal-to-noise ratio. Surface-Enhanced Infrared Absorption (SEIRA) spectroscopy is a breakthrough technique that exploits the field-enhancing properties of periodic nanostructures to amplify the vibrational signals of trace molecules. The fascinating properties of SEIRA technology have aroused great interest, driving diverse sensing applications. In this review, we first discuss three ways for SEIRA performance optimization, including material selection, sensitivity enhancement, and bandwidth improvement. Subsequently, we discuss the potential applications of SEIRA technology in fields such as biomedicine and environmental monitoring. In recent years, we have ushered in a new era characterized by the Internet of Things, sensor networks, and wearable devices. These new demands spurred the pursuit of miniaturized and consolidated infrared spectroscopy systems and chips. In addition, the rise of machine learning has injected new vitality into SEIRA, bringing smart device design and data analysis to the foreground. The final section of this review explores the anticipated trajectory that SEIRA technology might take, highlighting future trends and possibilities.

Advances of medical nanorobots for future cancer treatments

Early detection and diagnosis of many cancers is very challenging. Late stage detection of a cancer always leads to high mortality rates. It is imperative to develop novel and more sensitive and effective diagnosis and therapeutic methods for cancer treatments. The development of new cancer treatments has become a crucial aspect of medical advancements. Nanobots, as one of the most promising applications of nanomedicines, are at the forefront of multidisciplinary research. With the progress of nanotechnology, nanobots enable the assembly and deployment of functional molecular/nanosized machines and are increasingly being utilized in cancer diagnosis and therapeutic treatment. In recent years, various practical applications of nanobots for cancer treatments have transitioned from theory to practice, from in vitro experiments to in vivo applications. In this paper, we review and analyze the recent advancements of nanobots in cancer treatments, with a particular emphasis on their key fundamental features and their applications in drug delivery, tumor sensing and diagnosis, targeted therapy, minimally invasive surgery, and other comprehensive treatments. At the same time, we discuss the challenges and the potential research opportunities for nanobots in revolutionizing cancer treatments. In the future, medical nanobots are expected to become more sophisticated and capable of performing multiple medical functions and tasks, ultimately becoming true nanosubmarines in the bloodstream.

Nanoproteomics deciphers the prognostic value of EGFR family proteins-based liquid biopsy

Monitoring tumor-associated protein status in serum can effectively track tumors and avoid time-consuming, costly, and invasive tissue biopsy. Epidermal growth factor receptor (EGFR) family proteins are often recommended in the clinical management of multiple solid tumors. However, the low-abundance of serum EGFR (sEGFR) family proteins hinders the depth-understanding of their function and tumor management. Herein, a nanoproteomics approach coupling with aptamer-modified MOFs (NMOFs-Apt) with mass spectrometry was developed for the enrichment and quantitative analysis of sEGFR family proteins. This nanoproteomics approach exhibited high sensitivity and specificity for sEGFR family protein quantification, with the limit of quantification as low as 1.00 nM. After detecting 626 patients' sEGFR family proteins with various malignant tumors, we concluded that the levels of serum proteins had a moderate concordance with tissue counterparts. Metastatic breast cancer patients with a high level of serum human epidermal growth factor receptor 2 (sHER2) and a low level of sEGFR had a poor prognosis, and patients with a sHER2 decrease of more than 20% had longer disease-free time after receiving chemotherapy. This nanoproteomics method provided a simple and effective approach for low-abundant serum protein detection and our results clarified the potential of sHER2 and sEGFR as cancer markers.

Luminescent Guests Encapsulated in Metal-Organic Frameworks for Portable Fluorescence Sensor and Visual Detection Applications: A Review

Metal-organic frameworks (MOFs) have excellent applicability in several fields and have significant structural advantages, due to their open pore structure, high porosity, large specific surface area, and easily modifiable and functionalized porous surface. In addition, a variety of luminescent guest (LG) species can be encapsulated in the pores of MOFs, giving MOFs a broader luminescent capability. The applications of a variety of LG@MOF sensors, constructed by doping MOFs with LGs such as lanthanide ions, carbon quantum dots, luminescent complexes, organic dyes, and metal nanoclusters, for fluorescence detection of various target analyses such as ions, biomarkers, pesticides, and preservatives are systematically introduced in this review. The development of these sensors for portable visual fluorescence sensing applications is then covered. Finally, the challenges that these sectors currently face, as well as the potential for future growth, are briefly discussed.

Molecular elements: novel approaches for molecular building

Classically, a molecular element (ME) is a pure substance composed of two or more atoms of the same element. However, MEs, in the context of this review, can be any molecules as elements bonded together into the backbone of synthetic oligonucleotides (ONs) with designed sequences and functions, including natural A, T, C, G, U, and unnatural bases. The use of MEs can facilitate the synthesis of designer molecules and smart materials. In particular, we discuss the landmarks associated with DNA structure and related technologies, as well as the extensive application of ONs, the ideal type of molecules for intervention therapy aimed at correcting disease-causing genetic errors (indels). It is herein concluded that the discovery of ON therapeutics and the fabrication of designer molecules or nanostructures depend on the ME concept that we previously published. Accordingly, ME will be our focal point as we discuss related research directions and perspectives in making molecules and materials. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.

Generation of an Aptamer Targeting Receptor-Type Tyrosine-Protein Phosphatase F

Cell-SELEX is a powerful tool to generate aptamers that specifically bind the native molecules on living cells. Here, we report an aptamer ZAJ4a generated by cell-SELEX. The molecular target of ZAJ4a was pulled down by the enriched cell-SELEX pool and identified to be the receptor-type tyrosine-protein phosphatase F (PTPRF) through a stable isotope labeling using amino acids in cell culture (SILAC)-based quantitative proteomic method. ZAJ4a showed high binding affinity with nanomolar range to cancer cells expressing PTPRF. Meanwhile, PTPRF was proven to highly express on several cancer cell lines using ZAJ4a as a molecular probe and to highly express in many kinds of cancer samples using gene expression profiling interactive analysis (GEPIA2) from the TCGA and GTEx databases. These results indicate that the aptamer generated by cell-SELEX showed good specificity at the molecular level. This cell-SELEX and target identification strategies show great potential for identifying biomarkers on the cell surface.

A biocatalytic peptidobiosensing molecular bridge for detecting osteosarcoma marker protein

A biosensing scheme requiring only one-step sample incubation before signal collection, and using a compact "three-in-one" probe of target-binding, signal conversion, and amplification, may greatly simplify the design of biosensors. Therefore, sparing the multi-step addition of enzymes, protein, and nanomaterial, as well as the associated complexity and non-specific interactions. In this work, a peptide probe aimed at such compact features has been designed, based on protein-triggered, conformation-driven, and Cu (II) facilitated side-chain di-tyrosine cyclization. This design can use target-probe recognition to induce discriminated cross-linking and self-cleavage of the probe, resulting in retention or dissociation of a signal amplification motif from the search and consequently quantitative detection performance. The method has also been tested preliminarily in fractioned osteosarcoma clinical samples, showing an acceptable coherence between signal readout and clinical diagnosis. On the basis of these early findings, it is reasonable to assume that the proposed probe will be beneficial for the next development of tumor screening and prognosis sensors.

Application of aptamer functionalized nanomaterials in targeting therapeutics of typical tumors

Cancer is a major cause of human death all over the world. Traditional cancer treatments include surgery, radiotherapy, chemotherapy, immunotherapy, and hormone therapy. Although these conventional treatment methods improve the overall survival rate, there are some problems, such as easy recurrence, poor treatment, and great side effects. Targeted therapy of tumors is a hot research topic at present. Nanomaterials are essential carriers of targeted drug delivery, and nucleic acid aptamers have become one of the most important targets for targeted tumor therapy because of their high stability, high affinity, and high selectivity. At present, aptamer-functionalized nanomaterials (AFNs), which combine the unique selective recognition characteristics of aptamers with the high-loading performance of nanomaterials, have been widely studied in the field of targeted tumor therapy. Based on the reported application of AFNs in the biomedical field, we introduce the characteristics of aptamer and nanomaterials, and the advantages of AFNs first. Then introduce the conventional treatment methods for glioma, oral cancer, lung cancer, breast cancer, liver cancer, colon cancer, pancreatic cancer, ovarian cancer, and prostate cancer, and the application of AFNs in targeted therapy of these tumors. Finally, we discuss the progress and challenges of AFNs in this field.

ZIF-8 base-aptamer "gate-lock" probes enable the visualization of a cascade response between deoxynivalenol and cytochrome c inside living cells

Zeolitic imidazolate framework (ZIF-8) base-aptamer "gate-lock" biomaterial probes have been synthesized for monitoring intracellular deoxynivalenol (DON) and cytochrome c (cyt c) levels. The aptamer and organic fluorescent dye were regarded as a recognition element and a sensing element, respectively. In the presence of DON, the aptamers of DON and cyt c were specifically bound with the DON and induced cyt c, leading to the dissociation of aptamers from the porous surface of the probes. The gate was subsequently opened to release methylene blue (MB) and Rhodamine 6G (Rh6G), and their fluorescence (emission of MB at 700 nm and Rh6G at 550 nm) significantly recovered within 6 h. Cell imaging successfully monitored the exposure of DON and the biological process of cyt c discharge triggered by the activation of the DON-induced apoptosis pathway. In addition, the response between DON and cyt c was observed during the apoptosis process, which is of high significance for the comprehensive and systematic development of mycotoxins cytotoxicity.

DNA Aptamer Selected against Esophageal Squamous Cell Carcinoma for Tissue Imaging and Targeted Therapy with Integrin β1 as a Molecular Target

Esophageal cancer, especially esophageal squamous cell carcinoma (ESCC), poses a serious threat to human health. It is urgently needed to develop recognition tools and discover molecular targets for early diagnosis and targeted therapy of esophageal cancer. Here, we developed several DNA aptamers that can bind to ESCC KYSE410 cells with a nanomolar range of dissociation constants by using cell-based systematic evolution of ligands by exponential enrichment (cell-SELEX). The selected A2 aptamer is found to strongly bind with multiple cancer cells, including several ESCC cell lines. Tissue imaging displayed that the A2 aptamer can specifically recognize clinical ESCC tissues but not the adjacent tissues. Moreover, we identified integrin β1 as the binding target of A2 through pull-down and RNA interference assays. Meanwhile, molecular docking and mutation assays suggested that A2 probably binds to integrin β1 through the nucleotides of DA16-DG21, and competitive binding and structural alignment assays indicated that A2 shares the overlapped binding sites with laminin and arginine-glycine-aspartate ligands. Furthermore, we engineered A2-induced targeted therapy for ESCC. By constructing A2-tethered DNA nanoassemblies carrying multiple doxorubicin (Dox) molecules as antitumor agents, inhibition of tumor cell growth in vitro and in vivo was achieved. This work provides a useful targeting tool and a potential molecular target for cancer diagnosis and targeted therapy and is helpful for understanding the integrin mechanism and developing integrin inhibitors.

Identification of PHB2 as a Potential Biomarker of Luminal A Breast Cancer Cells Using a Cell-Specific Aptamer

Precise diagnosis of breast cancer molecular subtypes remains a great challenge in clinics. The present molecular biomarkers are not specific enough to classify breast cancer subtypes precisely, which requests for more accurate and specific molecular biomarkers to be discovered. Aptamers evolved by the cell-systematic evolution of ligands by exponential enrichment (SELEX) method show great potential in the discovery and identification of cell membrane targets via aptamer-based cell membrane protein pull-down, which has been regarded as a novel and powerful weapon for the discovery and identification of new molecular biomarkers. Herein, a cell membrane protein PHB2 was identified as a potential molecular biomarker specifically expressed in the cell membranes of MCF-7 breast cancer cells using a DNA aptamer MF3Ec. Further experiments demonstrated that the PHB2 protein is differentially expressed in the cell membranes of MCF-7, SK-BR-3, and MDA-MB-231 breast cancer cells and MCF-10A cells, and the binding molecular domains of aptamer MF3Ec and anti-PHB2 antibodies to the PHB2 protein are different due to there being no obvious competitions between aptamer MF3Ec and anti-PHB2 antibodies in the binding to the cell membranes of target MCF-7 cells. Due to those four cells belonging to luminal A, HER2-positive, and triple-negative breast cancer cell subtypes and human normal mammary epithelial cells, respectively, the PHB2 protein in the cell membrane may be a potential biomarker for precise diagnosis of the luminal A breast cancer cell subtype, which is endowed with the ability to differentiate the luminal A breast cancer cell subtype from HER2-positive and triple-negative breast cancer cell subtypes and human normal mammary epithelial cells, providing a new molecular biomarker and therapeutic target for the accurate and precise classification and diagnostics and personalized therapy of breast cancer.

An Optically Controlled Virtual Microsensor for Biomarker Detection In Vivo

Current technologies for the real-time analysis of biomarkers in vivo, such as needle-type microelectrodes and molecular imaging methods based on exogenous contrast agents, are still facing great challenges in either invasive detection or lack of active control of the imaging probes. In this study, by combining the design concepts of needle-type microelectrodes and the fluorescence imaging method, a new technique is developed for detecting biomarkers in vivo, named as "optically controlled virtual microsensor" (OCViM). OCViM is established by the organic integration of a specially shaped laser beam and fluorescent nanoprobe, which serve as the virtual handle and sensor tip, respectively. The laser beam can trap and manipulate the nanoprobe in a programmable manner, and meanwhile excite it to generate fluorescence emission for biosensing. On this basis, fully active control of the nanoprobe is achieved noninvasively in vivo, and multipoint detection can be realized at sub-micrometer resolution by shifting a nanoprobe among multiple positions. By using OCViM, the overexpression and heterogenous distribution of biomarkers in the thrombus is studied in living zebrafish, which is further utilized for the evaluation of antithrombotic drugs. OCViM may provide a powerful tool for the mechanism study of thrombus progression and the evaluation of antithrombotic drugs.

Aptamer-Based Triple Serum Fluorescence Intensity Assay: A Novel and Feasible Method for the Clinical Diagnosis of Primary Hepatic Carcinoma

Background and Aims

Aptamers are artificial ligands that bind to biological targets with high specificity and affinity. We previously selected a group of aptamers against the serum of primary hepatic carcinoma (PHC) via systematic evolution of ligands by exponential and enrichment (SELEX) method, and some of the aptamers were valuable for PHC diagnosis in polyacrylamide gel electrophoresis (PAGE) analysis. Here, we used aptamers to develop a novel method suitable for the clinical diagnosis of PHC.

Methods

The intensities of serum autofluorescence, cell-free DNA (cfDNA)-related fluorescence and aptamer-related fluorescence, named the aptamer-based triple serum fluorescence intensity (ATSFI), were sequentially measured at 8 °C and 37 °C in one tube by using a real-time polymerase chain reaction (PCR) system as a fluorimeter in patients with PHC (n=346) or liver cirrhosis (n=321). The diagnostic performances of ATSFI indicators alone and in combination were evaluated by area under the receiver operator characteristic curve (AUROC), and the underlying clinical mechanisms were analyzed by bivariate correlation.

Results

The measurement of ATSFI was high throughput, rapid, convenient, and low cost. The aptamer-related fluorescence indicator SEA-SE37 was the most valuable for PHC diagnosis among all fluorescence indicators and superior to alpha-fetoprotein (AFP) (AUROC 0.879 vs. 0.836). The logistic model of ATSFI indicators exhibited excellent diagnostic performance for PHC, including AFP-negative, early and small PHCs, with AUROCs of 0.935-0.950 and accuracies of 86.8-88.3%. The diagnostic performance was further improved when ATSFI indicators were combined with AFP, with AUROCs of approximately 0.95 and accuracies of approximately 90%, suggesting ATSFI was independent of but complementary to AFP in PHC diagnosis. ATSFI models were highly valuable in clinical decision-making. The aptamer-related fluorescence intensity was generally independent of the clinicopathological characteristics of PHC but correlated with laboratory characteristics of PHC serum.

Conclusions

The ATSFI assay is a novel, robust and feasible method for the clinical diagnosis of PHC.

Electrochemical Aptamer Biosensor Based on ATP-Induced 2D DNA Structure Switching for Rapid and Ultrasensitive Detection of ATP

Herein, a two-dimensional (2D) DNA structure with multiple ATP aptamers was elegantly designed to establish an electrochemical biosensor for rapid and sensitive detection of ATP based on ATP-induced structure switching. Concretely, the prepared 2D DNA structure containing numerous ATP aptamers as ATP-specific toehold switches could not only immobilize a large number of methylene blue (MB) for generating a remarkable electrochemical signal, but also greatly increase the local concentration of ATP aptamers to obviously enhance the capture efficiency of ATP. Once the target ATP interacted with the toehold switches, the 2D DNA structure could be sharply collapsed to trigger the burst release of MB from the electrode surface, ultimately resulting in a significantly decreased electrochemical signal for ultrasensitive detection of target ATP over a short period of time. Impressively, by dexterously adjusting the length of the ATP-specific toehold switches to 15-base, optimization of the binding affinity between ATP and the toehold switches was achieved for cutting down the detection time to 30 min and achieving a low detection limit of 0.3 pM, which addressed the shortcoming of time-consuming and poor sensitivity in the previous sensors with a small quantity of ATP aptamers and deficient binding affinity to ATP. Consequently, this strategy opened a promising avenue for ultrasensitive and rapid detection of various biomolecules in biomedical application and disease diagnosis.

Engineered Aptamer-Organic Amphiphile Self-Assemblies for Biomedical Applications: Progress and Challenges

Currently, nucleic acid aptamers are exploited as robust targeting ligands in the biomedical field, due to their specific molecular recognition, little immunogenicity, low cost, ect. Thanks to the facile chemical modification and high hydrophilicity, aptamers can be site-specifically linked with hydrophobic moieties to prepare aptamer-organic amphiphiles (AOAs), which spontaneously assemble into aptamer-organic amphiphile self-assemblies (AOASs). These polyvalent self-assemblies feature with enhanced target-binding ability, increased resistance to nuclease, and efficient cargo-loading, making them powerful platforms for bioapplications, including targeted drug delivery, cell-based cancer therapy, biosensing, and bioimaging. Besides, the morphology of AOASs can be elaborately manipulated for smarter biomedical functions, by regulating the hydrophilicity/hydrophobicity ratio of AOAs. Benefiting from the boom in DNA synthesis technology and nanotechnology, various types of AOASs, including aptamer-polymer amphiphile self-assemblies, aptamer-lipid amphiphile self-assemblies, aptamer-cell self-assemblies, ect, have been constructed with great biomedical potential. Particularly, stimuli-responsive AOASs with transformable structure can realize site-specific drug release, enhanced tumor penetration, and specific target molecule detection. Herein, the general synthesis methods of oligonucleotide-organic amphiphiles are firstly summarized. Then recent progress in different types of AOASs for bioapplications and strategies for morphology control are systematically reviewed. The present challenges and future perspectives of this field are also discussed.

Profiling Cancer Cells by Cell-SELEX: Use of Aptamers for Discovery of Actionable Biomarkers and Therapeutic Applications Thereof

The identification of tumor cell-specific surface markers is a key step towards personalized cancer medicine, allowing early assessment and accurate diagnosis, and development of efficacious targeted therapies. Despite significant efforts, currently the spectrum of cell membrane targets associated with approved treatments is still limited, causing an inability to treat a large number of cancers. What mainly limits the number of ideal clinical biomarkers is the high complexity and heterogeneity of several human cancers and still-limited methods for molecular profiling of specific cancer types. Thanks to the simplicity, versatility and effectiveness of its application, cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technology is a valid complement to the present strategies for biomarkers' discovery. We and other researchers worldwide are attempting to apply cell-SELEX to the generation of oligonucleotide aptamers as tools for both identifying new cancer biomarkers and targeting them by innovative therapeutic strategies. In this review, we discuss the potential of cell-SELEX for increasing the currently limited repertoire of actionable cancer cell-surface biomarkers and focus on the use of the selected aptamers as components of innovative conjugates and nano-formulations for cancer therapy.

Effectively Selecting Aptamers for Targeting Aromatic Biogenic Amines and Their Application in Aptasensing Establishment

It is necessary to detect the biogenic amine (BA) content in food due to their toxicological effects and their role as an index of freshness for protein-rich foods. Aptamer-based techniques have the potential to provide alternative methods for sensitive and efficient monitoring of BAs. Herein, we described the selection and characterization of DNA aptamers for tyramine (TYR) and β-phenethylamine (PHE) using a one-pot coupled with separate selection strategy. During the selection process, melting curve analysis was developed to monitor the enrichment of the aptamer species, and a saturation of the selection was found at the 14th round. Based on the fluorescence assay, aptamers TYR-2 and PHE-2 showed high affinity to TYR and PHE with the dissociation constant values of 64.28 ± 10.4 and 71.64 ± 11.47 nM, respectively. The circular dichromatic and molecular docking technologies were employed for the preliminary binding mechanism analysis. The obtained aptamers TYR-2 and PHE-2 were used in a fluorescence method for the TYR and PHE determination with limits of detection of 0.34 and 0.39 ng/mL, respectively. In addition, the developed aptasensor was further applied to the TYR and PHE detection in pork and beer samples, and the recovery rate was between 95.6 and 104.2%. It was demonstrated that the selected aptamers had enormous potential as a molecular probe for the identification and determination of BAs.

Evolution of DNA aptamers against esophageal squamous cell carcinoma using cell-SELEX

Esophageal cancer is the ninth most common cancer and the sixth most common cause of cancer-related death worldwide, and the esophageal squamous cell carcinoma (ESCC) subtype accounts for about 90% of all cases of esophageal cancer globally. Currently, ESCC is usually diagnosed in late stages, and targeted therapy is lacking. Therefore, the development of ESCC-specific recognition molecules for an early detection and targeted treatment of ESCC is urgently needed. Aptamers are an excellent molecular recognition tool with unique advantages. In this manuscript, three aptamers (S2, S3, and S8) specific to ESCC cells were successfully screened via cell-SELEX. The experimental results displayed the high affinities of the three aptamers for target KYSE150 cells with dissociation constants in the nanomolar range. The specificity evaluation showed that S2 only bound target KYSE150 cells, but S3 and S8 were capable of targeting a series of ESCC cells. Moreover, several truncated aptamers were generated through sequence optimization. In particular, an ultrashort aptamer S3-2-3 with only 18 bases was successfully obtained; after labeling with Cy5 dyes, it was feasible for the specific imaging of ESCC tissues. Furthermore, the target types of the selected aptamers were preliminarily identified as membrane proteins, and target proteins could be captured by S3-2-3, which may be useful for biomarker discovery. Therefore, the selected aptamers hold great potential for clinical diagnosis, biomarker discovery, and the targeted therapy of ESCC.

The synchronization of multiple signal amplifications for label-free and sensitive aptamer-based sensing of a protein biomarker

The abnormal variation of the mucin 1 (MUC1) protein level is associated with the development of multiple cancers, and the monitoring of trace MUC1 can be useful for early disease diagnosis. Here, on the basis of the synchronization of DNA-fueled sequence recycling and dual rolling circle amplification (RCA), the establishment of a non-label and highly sensitive fluorescent aptamer-based detection strategy for the MUC1 protein biomarker is described. The target MUC1 binds the aptamer hairpin probe and causes its structure switching to release an ssDNA tail to trigger the recycling of the complex via two toehold-mediated strand displacement reactions under assistance of a fuel DNA. Such a recycling amplification leads to the formation of a partial dsDNA duplex with two primers at both ends, which cooperatively bind the circular DNA ring template to start the dual RCA to produce many G-quadruplex sequences. The protoporphyrin IX dye further associates with the G-quadruplex structures to show a dramatically elevated fluorescent signal for sensitively detecting MUC1 with a low detection limit of 0.5 pM. The established aptamer-based detecting strategy is also highly selective and can realize assay of MUC1 in diluted human serums, highlighting its potential for the detection of different protein biomarkers at low contents.

Electrochemiluminescence aptasensor for Siglec-5 detection based on MoS2@Au nanocomposites emitter and exonuclease III-powered DNA walker

Lectins are highly specific binding proteins for glycoproteins which widely exist in living organisms, playing a vital role in exploring the biological evolution process, such as cellular proliferation, differentiation, carcinogenesis and apoptosis. Therefore, the content monitoring of lectin becomes particularly significant and urgent in the bioanalytical application. In this work, we fabricated an aptasensor, majorly capitalizing the eminent affinity between sialic acid-binding immunoglobulin (Ig)-like lectin 5 (Siglec-5) and nucleic acids aptamer (K19), with nontoxic MoS₂@Au nanocomposites as electrochemiluminescence (ECL) emitters based on exonuclease III (Exo III)-powered DNA walker for the bioassays of Siglec-5. The DNA track was constructed on the emitters' surface, providing a reliable platform for the DNA walker's autonomous move. In the assay, the primer DNA in the DNA duplex was replaced by Siglec-5 due to the aptamer interactions and repeatedly released to participate in the movement of the DNA walker, further triggering cascade signal amplification. Finally, our aptasensor indicates significant potential for assays of Siglec-5 with a detection limit of 8.9 pM.

Graphene-nucleic acid biointerface-engineered biosensors with tunable dynamic range

Programmed biosensors with tunable quantification range and sensitivity would greatly broaden their application in medical diagnosis, food safety and environmental analysis. Herein, we proposed a graphene-nucleic acid biointerface-engineered biosensor, allowing target molecules to be detected with adjustable dynamic ranges and sensitivities. The biosensors were programmed by simply tuning the poly A tail of aptamer probes. The tuning of the poly A tail would allow the interaction between aptamer probes and graphene oxide (GO) to be modulated, in turn programing the competitive binding processes of aptamer probes to target molecules and GO. The biosensors, termed affinity-tunable aptasensors (atAptasensors) could be easily tuned with different dynamic ranges by using aptamer probes with different tail lengths, and the dynamic range could be extended to be over 3 orders by a combined use of multiple aptamer probes. Remarkably, the specificity of aptamer probes could be increased by increasing the interaction between aptamer probes and GO. Reliability of atAptasensor for ATP detection was tested in serum and milk samples, and we also applied atAptasensor for culture-independent analysis of microorganism pollution.

Aptamer-Based Detection of Circulating Targets for Precision Medicine

The past decade has witnessed ongoing progress in precision medicine to improve human health. As an emerging diagnostic technique, liquid biopsy can provide real-time, comprehensive, dynamic physiological and pathological information in a noninvasive manner, opening a new window for precision medicine. Liquid biopsy depends on the sensitive and reliable detection of circulating targets (e.g., cells, extracellular vesicles, proteins, microRNAs) from body fluids, the performance of which is largely governed by recognition ligands. Aptamers are single-stranded functional oligonucleotides, capable of folding into unique tertiary structures to bind to their targets with superior specificity and affinity. Their mature evolution procedure, facile modification, and affinity regulation, as well as versatile structural design and engineering, make aptamers ideal recognition ligands for liquid biopsy. In this review, we present a broad overview of aptamer-based liquid biopsy techniques for precision medicine. We begin with recent advances in aptamer selection, followed by a summary of state-of-the-art strategies for multivalent aptamer assembly and aptamer interface modification. We will further describe aptamer-based micro-/nanoisolation platforms, aptamer-enabled release methods, and aptamer-assisted signal amplification and detection strategies. Finally, we present our perspectives regarding the opportunities and challenges of aptamer-based liquid biopsy for precision medicine.

Aptamer Generated by Cell-SELEX for Specific Targeting of Human Glioma Cells

The most prevalent primary brain tumors are gliomas, which start in the glial cells. Although there have been significant technological advances in surgery and radio-chemotherapy, the prognosis and survival of patients with malignant gliomas remain poor. For routine diagnosis of glioma, computed tomography and magnetic resonance imaging primarily depend on anatomical changes and fail to detect the cellular changes that occur early in the development of malignant gliomas. Therefore, it is urgent to find effective molecular diagnostic tools to detect early stages of malignant gliomas. Currently, cell-based Systematic Evolution of Ligands by EXponential enrichment (cell-SELEX) technology is one effective tool to obtain DNA or RNA aptamers capable of differentiating the molecular signatures among different types of cell lines. Using cell-SELEX, we generated and characterized an aptamer, termed S6-1b, that can distinguish the molecular differences between glioma cell line SHG44 and human astrocytes. Under the conditions of 4 and 37 °C, respectively, the dissociation constants of aptamer-cell interaction were both measured in the low nanomolar range. The aptamer S6-1b also exhibited excellent selectivity, making it suitable for use in a complex biological environment. Furthermore, the aptamer can effectively target glioma cells for in vivo fluorescence imaging of tumors. The target type of aptamer S6-1b was identified as a cell membrane protein. Our work indicates that aptamer S6-1b has diagnostic and therapeutic potential to specifically deliver imaging or therapeutic agents to malignant gliomas.

Tetraphenylpyrazine-Based Luminescent Metal-Organic Framework for Chemical Sensing of Carcinoids Biomarkers

A new non-interpenetrated three-dimensional (3D) pillared-layered TPP-based LMOF [Zn₃(TPyTPP)_0.5(BDC)₃]·8DMF (denoted as Zn-MOF 1) was successfully prepared (TPyTPP = tetrakis(4-(pyridin-4-yl)phenyl)pyrazine and H₂BDC = 1,4-benzenedicarboxylic acid). Zn-MOF 1 was characterized by single-crystal X-ray diffraction, PXRD, IR, N₂ adsorption, thermogravimetric analysis, and luminescent spectrum. Impressively, luminescent sensing studies reveal that activated Zn-MOF 1 not only displays excellent luminescence-quenching efficiency with the values of high K_sv and low LODs toward 5-hydroxytryptamine (5-HT) and 5-hydroxyindole-3-acetic acid (5-HIAA), respectively, but also possesses outstanding sensing characteristics in terms of fast response, high sensitivity, and specific selectivity. Zn-MOF 1 performs as efficient sensing of carcinoid biomarkers to provide a fresh detection platform for the diagnosis of carcinoids. In addition, the sensing mechanism was also explored on the basis of ultraviolet-visible (UV-vis) absorption, DFT calculations, and structural analysis.

Electrical properties characterization of single yeast cells by dielectrophoretic motion and electro-rotation

The electrical parameters of single cells are label-free and intrinsic properties that can reflect the physiological characteristics. In recent years, many measurement methods based on impedance spectroscopy and rotation spectrum analysis have been developed. However, most of these works need to measure the response at whole frequency range to obtain DEP spectra and estimate the electrical parameters by fitting method, which are time-consuming and limit the measurement throughput. Therefore, improving the measurement throughput for single cells is an essential problem to be solved addressed. In this paper we present a microfluidic chip that combines dielectrophoretic motion and electro-rotation technology for single-cell electrical properties characterization. Since the movement and rotation speed of single cell in mediums are related to the electrical parameters of itself, electric signals and medium, the electrical properties can be obtained by measuring and analyzing the movement trajectory and rotation speed of the cell. Numerical simulations were performed to analyze the electric field distribution of the chip under different signal configurations, which predict the movement trajectory and rotation state, and determine the values of electric field on the cells. Based on the simulation results, cell focusing, dielectrophoretic motion and electro-rotation were successfully realized. By analyzing the movement trajectory and rotation speed, the conductivity of wall and the permittivity of membrane of yeast cells were characterized. The measurement method avoids the time-consuming of the traditional rotational spectra method, and can realize rapid and efficiency and single-cell electrical characterization.

A novel method combining aptamer-Ag10NPs based microfluidic biochip with bright field imaging for detection of KPC-2-expressing bacteria

The β-lactam drugs resistance poses a serious threat to human health throughout the world. Klebsiella pneumoniae carbapenemase 2 (KPC-2) is a carbapenemase that produced in bacteria can hydrolyze carbapenems, which typically considered as the antibiotics of last resort. Therefore, there is an urgent need to quickly and accurately detect whether bacteria express KPC-2. In this paper, a PDMS/glass microfluidic biochip integrated with aptamer-modified Ag₁₀NPs nano-biosensors was developed for rapid, simple and specific pathogenic bacteria detection, more importantly, the biochip was combined with bright field imaging, then the captured bacteria could be observed and counted directly without using extra chemical labeling. KPC-2-expressing Escherichia coli (KPC-2 E.coli) was used as the target bacterium with a detected limit of 10² CFU and capture efficiency exceeded 90%. This method is remarkably specific towards KPC-2 E.coli over other non-resistant bacteria, and pathogen assay only takes ∼1 h to complete in a ready-to-use microfluidic biochip. Furthermore, the effective capture and fast counting of microfluidic biochip system demonstrates its potential for the rapid detection of antibiotic-resistant bacteria.

Dual Triple Helix-Aptamer Probes for Mix-and-Read Detecting Antibiotics in Fish and Milk

Antibiotic abuse in agricultural products leads to serious food safety issues. To this end, we proposed a mix-and-read and enzyme-free amplified assay for antibiotics based on a dual triple helix-aptamer probe, potentially applicable for on-site monitoring of antibiotic residues. A dual triple helix-aptamer probe can leverage the response toward target molecules without enzyme-based amplification, rendering it sensitive and robust for profiling target molecules. The proposed assay allowed mix-and-read detection of chloramphenicol with a detection limit of 0.18 nM. Besides, it accommodated for specifically resolving chloramphenicol among other antibiotics. Chloramphenicol residual in aquatic products in fish and milk can be precisely determined. Thus, the aptamer probe deems to enrich the toolbox for managing antibiotic use.

Nucleic Acid Aptamers for Molecular Diagnostics and Therapeutics: Advances and Perspectives

The advent of SELEX (systematic evolution of ligands by exponential enrichment) technology has shown the ability to evolve artificial ligands with affinity and specificity able to meet growing clinical demand for probes that can, for example, distinguish between the target leukemia cells and other cancer cells within the matrix of heterogeneity, which characterizes cancer cells. Though antibodies are the conventional and ideal choice as a molecular recognition tool for many applications, aptamers complement the use of antibodies due to many unique advantages, such as small size, low cost, and facile chemical modification. This Minireview will focus on the novel applications of aptamers and SELEX, as well as opportunities to develop molecular tools able to meet future clinical needs in biomedicine.

Recognition-Driven Remodeling of Dual-Split Aptamer Triggering In Situ Hybridization Chain Reaction for Activatable and Autonomous Identification of Cancer Cells

Proximity-dependent hybridization chain reaction (HCR) has shown great potential in sensing biomolecules on the cell surface. However, the requirement of two adjacent bioevents occurring simultaneously limits its application. To solve the problem, split aptamers with target binding ability were introduced to combine with split triggers for initiating HCR, thus producing a novel dual-split aptamer probe (DSAP). By employing cancer-related receptors as models, in situ HCR on a cancer cell surface induced by recognition-driven remodeling of the DSAP was demonstrated. The DSAP consisted of two sequences. Each contained two segments; one derived from split aptamers and the other originated in split triggers. In the presence of target cells, split aptamers reassembled on the cell surface under the "induced-fit effect", thus forcing two split triggers close to each other. The remodeled DSAP worked as an intact trigger, which opened the H1 hairpin probe and then hybridized with the H2 hairpin probe, thus initiating HCR to produce an activated fluorescence signal. As a proof of concept, human liver cancer SMMC-7721 cells and their split ZY11 aptamer were used to construct the DSAP. Results indicated that the DSAP realized sensitive analysis of target cells, permitting the actual detection of 20 cells in the buffer. Moreover, the specific identification of target cells in mixed cell samples and the quantitative analysis of target cells in serum were also achieved. The DSAP strategy is facile and universal, which not only would expand the application range of HCR but also might be developed as a multitarget detection technique for bioanalysis.

High-efficiency enrichment enables identification of aptamers to circulating Plasmodium falciparum-infected erythrocytes

Plasmodium falciparum is the causative agent of the deadliest human malaria. New molecules are needed that can specifically bind to erythrocytes that are infected with P. falciparum for diagnostic purposes, to disrupt host-parasite interactions, or to deliver chemotherapeutics. Aptamer technology has the potential to revolutionize biological diagnostics and therapeutics; however, broad adoption is hindered by the high failure rate of the systematic evolution of ligands by exponential enrichment (SELEX). Here we performed parallel SELEX experiments to compare the impact of two different methods for single-strand recovery on the efficiency of aptamer enrichment. Our experimental results and analysis of SELEX publications spanning 13 years implicate the alkaline denaturation step as a significant cause for inefficient aptamer selection. Thus, we applied an exonuclease single-strand recovery step in our SELEX to direct aptamers to the surface of erythrocytes infected with P. falciparum. The selected aptamers bind with high affinity (low nanomolar K_d values) and selectivity to exposed surface proteins of both laboratory parasite strains as well isolates from patients in Asia and Africa with clinical malaria. The results obtained in this study potentially open new approaches to malaria diagnosis and surveillance.

Prion Protein Targeted by a Prostate Cancer Cell Binding Aptamer, a Potential Tumor Marker?

Cell-SELEX is an effective strategy to discover aptamers that can distinguish the molecular signatures of target cells from control cells. The molecular targets of such aptamers have the potential to be biomarkers. Here, we report target identification of aptamer wy-5a generated by cell-SELEX against a prostate cancer cell line, PC-3. This aptamer specifically binds PC-3 cells and a doxorubicin-resistant breast cell line, MCF-7R, as well as tissue sections of prostate cancer with high risk of metastasis. Prion protein was identified to be the molecular target of wy-5a by stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomic method. The octapeptide repeat region of prion protein was demonstrated to be the binding site of aptamer wy-5a. The expression levels of prion protein in cancer tissues were further tested by immunohistochemical staining of tissue sections from 48 prostate cancer patients and 98 breast cancer patients. The results suggest that prion protein has the potential to be one of the referenced markers of prostate and breast cancers.

Engineering Multivalence Aptamer Probes for Amplified and Label-Free Detection of Antibiotics in Aquatic Products

Excessive use of antibiotics in aquatic products is a serious problem for food safety and human health, and on-site detection of antibiotics is highly demanded. Herein, we proposed multivalence aptamer probes, allowing sensitive, label-free, and homogeneous detection of antibiotics in different aquatic products. Compared to commonly used aptamers, multivalence aptamer probes can provide multiple binding sites and a higher affinity for target molecules, and the iterative binding on different binding sites contributes to an amplified recognition effect, sharply increasing the response and sensitivity of aptamer probes. The 2-valence aptamer probes conferred a limit of detection of 0.097 nM for kanamycin detection, where it is estimated that their sensitivity is enhanced 12 times compared to 1-valence aptamer probes. Meanwhile, multivalence aptamer probes allowed us to specifically identify kanamycin among other antibiotics. It could detect kanamycin residual in aquatic products including river eel and puffer fish, as well as tap water with high precision. A multivalence design strategy of aptamer probes would significantly improve the detection performance of aptamers, facilitating the translation of aptamer for food safety control.