Label-free and turn-on aptamer strategy for cancer cells detection based on a DNA-silver nanocluster fluorescence upon recognition-induced hybridization

Emerging Biohybrids of Aptamer-Based Nano-Biosensing Technologies for Effective Early Cancer Detection

Cancer is a leading global cause of mortality, which underscores the imperative of early detection for improved patient outcomes. Biorecognition molecules, especially aptamers, have emerged as highly effective tools for early and accurate cancer cell identification. Aptamers, with superior versatility in synthesis and modification, offer enhanced binding specificity and stability compared with conventional antibodies. Hence, this article reviews diagnostic strategies employing aptamer-based biohybrid nano-biosensing technologies, focusing on their utility in detecting cancer biomarkers and abnormal cells. Recent developments include the synthesis of nano-aptamers using diverse nanomaterials, such as metallic nanoparticles, metal oxide nanoparticles, carbon-derived substances, and biohybrid nanostructures. The integration of these nanomaterials with aptamers significantly enhances sensitivity and specificity, promising innovative and efficient approaches for cancer diagnosis. This convergence of nanotechnology with aptamer research holds the potential to revolutionize cancer treatment through rapid, accurate, and non-invasive diagnostic methods.

Fluorescent DNA-Silver nanoclusters in food safety detection: From synthesis to application

In recent years, the conventional preparation of silver nanoclusters (AgNCs) has attracted much attention due to their ultra-small size, tunable fluorescence, easy-to-engineer, as well as biocompatible material. Moreover, its great affinity towards cytosine bases on single-stranded DNA has led to the construction of biosensors, especially aptamers, for a broad variety of applications in food safety and environmental protection. In past years, numerous researchers paid attention to the construction of AgNCs aptasensor. Therefore, this review will be an effort to summarize the synthetic strategy along with the influences of factors on synthesis, categorize the sensing mechanism of aptamer-functionalized AgNCs biosensors, as well as their specific applications in food safety detection including heavy metal, toxin, and foodborne pathogenic bacteria. Furthermore, a brief conclusion and outlook regarding the prospects and challenges of their applications in food safety were drawn in line with the developments in DNA-AgNCs.

Targeted-Lymphoma Drug Delivery System Based on the Sgc8-c Aptamer

Aptamers are emerging as a promising new class of functional nucleic acids because they can specifically bind to any target with high affinity and be easily modified chemically with different pharmacophoric subunits for therapy. The truncated aptamer, Sgc8-c, binds to tyrosine-protein kinase-like 7 receptor, a promising cancer therapeutic target, allowing the recognition of haemato-oncological malignancies, among others. We have previously developed aptamer-drug conjugates by chemical synthesis, hybridizing Sgc8-c and dasatinib, a drug proposed for lymphoma chemotherapy. One of the best-characterised Sgc8-c-dasatinib hybrids, namely Sgc8-c-carb-da, was capable of releasing dasatinib at an endosomal-pH. Herein, we probed the therapeutic potential of this aptamer-drug conjugate. Sgc8-c-carb-da specifically inhibited murine A20 B lymphocyte growth and produced cell death, mainly by late apoptosis and necrosis. In addition, Sgc8-c-carb-da generated an arrest in cell proliferation, with a cell cycle arrest in the Sub-G1-peak. The mitochondrial potential was altered accordingly to these pathways. Moreover, using an in vitro cell-targeting assay that mimics in vivo conditions, we showed that Sgc8-c-carb-da displayed higher (2.5-fold) cytotoxic effects than dasatinib. These findings provide proof-of-concept of the therapeutic value of Sgc8-c-carb-da for lymphoma, creating new opportunities for the chemical synthesis of targeted biotherapeutics.

Synthesis, characterization and potential sensing application of carbon dots synthesized via the hydrothermal treatment of cow milk

Carbon quantum dots (CQDs) were synthesized in this study by hydrothermally treating cow milk. The procedure is simple, non-hazardous to the environment, and does not necessitate the use of any special instruments or chemicals. CQDs were practically almost circular when they were manufactured and had an average size of 7 nm. Carbon (67.36%), oxygen (22.73%), and nitrogen (9.91%) comprised the majority of their composition. They feature broad excitation-emission spectra, excitation-dependent emission, and temperature-dependent photoluminescence. They remained quite stable in the presence of a lot of salt, UV radiation, and storage time. Because luminescence quenching mechanisms are sensitive to and selective for Sn²⁺, they can be employed to create a nanosensor for detecting Sn²⁺.

Massively Parallel Selection of NanoCluster Beacons

NanoCluster Beacons (NCBs) are multicolor silver nanocluster probes whose fluorescence can be activated or tuned by a proximal DNA strand called the activator. While a single-nucleotide difference in a pair of activators can lead to drastically different activation outcomes, termed polar opposite twins (POTs), it is difficult to discover new POT-NCBs using the conventional low-throughput characterization approaches. Here, a high-throughput selection method is reported that takes advantage of repurposed next-generation-sequencing chips to screen the activation fluorescence of ≈40 000 activator sequences. It is found that the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs and positions 4-6 and 2-4 are hotspots to generate yellow-orange and red POTs, respectively. Based on these findings, a "zipper-bag" model is proposed that can explain how these hotspots facilitate the formation of distinct silver cluster chromophores and alter their chemical yields. Combining high-throughput screening with machine-learning algorithms, a pipeline is established to design bright and multicolor NCBs in silico.

DNA Templated Silver Nanoclusters for Bioanalytical Applications: A Review

Due to their unique programmability, biocompatibility, photostability and high fluorescent quantum yield, DNA templated silver nanoclusters (DNA Ag NCs) have attracted increasing attention for bioanalytical application. This review summarizes the recent developments in fluorescence properties of DNA templated Ag NCs, as well as their applications in bioanalysis. Finally, we herein discuss some current challenges in bioanalytical applications, to promote developments of DNA Ag NCs in biochemical analysis.

Exploring the fluorescence enhancement of the split G-quadruplex towards DNA-templated AgNCs and their application in omethoate detection

Based on the enhancement of split G-quadruplex on the fluorescence of DNA-templated AgNCs, a facile label-free and enzyme-free omethoate detection platform has been successfully constructed through the interaction between split G4 with DNA-AgNCs.

Cell imaging with multi-color DNA framework probes

Utilizing the programmability of the fractal DNA frameworks, multi-color probes were constructed by arranging fluorescent molecules and nucleic acid aptamers on the structure. Multiplexed cell imaging and classification was realized through pattern recognition.

Controllable synthesis of fluorescent silver nanoparticles with different length oligonucleotides

Silver nanomaterials have become important research topics in recent years. As a new type of fluorescent material, silver nanomaterials have been applied to fluorescent sensors, bioimaging and materials targeting cancer cells. Here, an approach to the oligonucleotide‐templated controllable formation of fluorescent Ag nanomaterials is reported. In this experiment, silver nanoparticles (NPs) were synthesised from oligonucleotides chains, sodium borohydride (NaBH₄) and silver nitrate (AgNO₃) by changing the molar ratio of DNA to sodium borohydride (NaBH₄) and silver nitrate (AgNO₃). Fluorescent assay and transmission electron microscopy were used to characterise the silver NPs. The optimal selection of DNA chains with different lengths as templates for the synthesis of silver NPs was found. This work successfully develops the capping oligonucleotides scaffolds of silver nanoclusters.

Metastatic and non-metastatic melanoma imaging using Sgc8-c aptamer PTK7-recognizer

Melanoma is one of the most aggressive and deadly skin cancers, and although histopathological criteria are used for its prognosis, biomarkers are necessary to identify the different evolution stages. The applications of molecular imaging include the in vivo diagnosis of cancer with probes that recognize the tumor-biomarkers specific expression allowing external image acquisitions and evaluation of the biological process in quali-quantitative ways. Aptamers are oligonucleotides that recognize targets with high affinity and specificity presenting advantages that make them interesting molecular imaging probes. Sgc8-c (DNA-aptamer) selectively recognizes PTK7-receptor overexpressed in various types of tumors. Herein, Sgc8-c was evaluated, for the first time, in a metastatic melanoma model as molecular imaging probe for in vivo diagnostic, as well as in a non-metastatic melanoma model. Firstly, two probes, radio- and fluorescent-probe, were in vitro evaluated verifying the high specific PTK7 recognition and its internalization in tumor cells by the endosomal route. Secondly, in vivo proof of concept was performed in animal tumor models. In addition, they have rapid clearance from blood exhibiting excellent target (tumor)/non-target organ ratios. Furthermore, optimal biodistribution was observed 24 h after probes injections accumulating almost exclusively in the tumor tissue. Sgc8-c is a potential tool for their specific use in the early detection of melanoma.

Wide-field determination of aqueous mercury(II) based on tail-extensible DNA fluorescent probe with tunable dynamic range

Mercury (Hg) is one of the most hazardous pollutants, widely distributed in water, atmosphere, and soil, while the Hg contents from different sources are greatly different. Until now, numerous reported methods are only suitable for a kind of sample because they cannot reconcile sensitivity and linear range. In this work, a tail-extensible DNA fluorescent probe for "turn on" detection of Hg²⁺ with tunable dynamic range and high sensitivity was developed, which was based on segmental hybridization between silver nanoclusters (AgNCs)-covered DNA and different guanine-rich DNAs. By adding adenine-guanine-cytosine (AGC) base repeats as a tail of the guanine-rich DNA, the formation constant of T-Hg²⁺-T complex was effectively modulated within two orders of magnitude. Based on it, a tunable dynamic range from 0.035 to 0.2 pM to 8.0-120.0 pM was achieved by combining four fluorescent probes with different tail lengths. The Hg²⁺contents from different sources were successfully measured. This evidenced the proposed sensor's application toward wide-field detection, which is useful for the direct and objective comparison of results from different sources, and therefore providing a way for solving the shortcomings of reported methods for Hg²⁺ detection. Additionally,this present method is simple, cost-effective and time-saving, ultrasensitive and highly selective, which is favorable for expanding its applications and subsequent mercury pollution control.

Autoregressive parametric modeling combined ANOVA approach for label-free-based cancerous and normal cells discrimination

Label free based methods received huge interest in the field of bio cell characterizations because they do not cause any cell damage nor contribute any change in its compositions. This work takes a close outlook of cancerous cells discrimination from normal cells utilizing parametric modeling approach. Autoregressive (AR) modeling technique is used to fit the measured optical transmittance profiles of both cancer and normal cells. The transmitted light intensity, when passes through the cells, gets affected by their intercellular compositions and membrane properties. In this study, four types of cells: lung-cancerous and normal, liver-cancerous and normal, were suspended in their corresponding medium and their transmission characteristics were collected and processed. The AR coefficients of each type of the cell were analyzed with the statistical technique called Analysis of variance (ANOVA), which provided the significant coefficients. The poles extracted from the significant coefficients resulted in an improved demarcation for normal and cancer cells. These outcomes can be further utilized for cell classification using statistical tools.

Structure and luminescence of DNA-templated silver clusters

DNA serves as a versatile template for few-atom silver clusters and their organized self-assembly. These clusters possess unique structural and photophysical properties that are programmed into the DNA template sequence, resulting in a rich palette of fluorophores which hold promise as chemical and biomolecular sensors, biolabels, and nanophotonic elements. Here, we review recent advances in the fundamental understanding of DNA-templated silver clusters (Ag N -DNAs), including the role played by the silver-mediated DNA complexes which are synthetic precursors to Ag N -DNAs, structure-property relations of Ag N -DNAs, and the excited state dynamics leading to fluorescence in these clusters. We also summarize the current understanding of how DNA sequence selects the properties of Ag N -DNAs and how sequence can be harnessed for informed design and for ordered multi-cluster assembly. To catalyze future research, we end with a discussion of several opportunities and challenges, both fundamental and applied, for the Ag N -DNA research community. A comprehensive fundamental understanding of this class of metal cluster fluorophores can provide the basis for rational design and for advancement of their applications in fluorescence-based sensing, biosciences, nanophotonics, and catalysis.

Earlier diagnoses of acute leukemia by a sandwich type of electrochemical aptasensor based on copper sulfide-graphene composite

Due to high affinity and specificity of aptamers, they are widely considered for construction of aptasensor to specific recognizing of analytes in biological complex matrix. So, in this work we design a high selective and sensitive aptasensor for leukemia cancer cells (CCRF-CEM) via superior catalytic effect of copper sulfide-graphene (CuS-GR) nanocomposite as label and Au-GR nanocomposite as sensing platform. The CuS-GR nano-composite (label component) is CuS nanoparticles that wrapping on graphene sheets. Its catalytic activity (CuS-GR) increases the current of sensor in parallel with adding of CCRF-CEM and provide sensitive detection of analytes. The detailed of signal amplification and effect on the aptasensor performance completely discussed. This sensor has a linear range of 50-1 × 10⁶ cell mL^-1, with a limit of detection of 18 cell mL^-1. Also, the developed aptasensor has a significance specificity, high sensitivity and accuracy. It was used for the identification of CCRF-CEM cells in blood samples.

A sensitive spectrophotometric ellipsometry based Aptasensor for the vascular endothelial growth factor detection

A sensitive and selective, aptamer and spectroscopic ellipsometry based sensor is reported here for the early diagnosis of breast cancer, which is a common type of cancer following lung cancer. It was aimed to develop a single-step and label-free assay for the sensitive and selective detection of VEGF₁₆₅. To this end, two different aptamers and spectroscopic ellipsometry were used. In the presented study, by determining the appropriate aptamer immobilization conditions, the spectroscopic ellipsometry technique was successfully applied for the detection of VEGF₁₆₅ at the range of 1 pM-1000 pM in the buffer. Aptasensors have a detection limit of 5.81 pM and 4.29 pM, respectively.

Sensor and Bioimaging Studies Based on Carbon Quantum Dots: The Green Chemistry Approach

Since carbon quantum dots have high photoluminescent efficiency, it has been a desired material in sensor and bioimaging applications. In recent years, the green chemistry approach has been preferred and the production of quantum dots has been reported in many studies using different precursors from natural, abundant, or waste sources. Hydrothermal, chemical oxidation, microwave supported, ultrasonic, solvothermal, pyrolysis, laser etching, solid-state, plasma, and electrochemical methods have been reported in the literature. In this review article, green chemistry strategies for carbon quantum dot synthesis is summarized and compared with conventional methods using methodologic and statistical data. Furthermore, a detailed discussion on sensor and bioimaging applications of carbon quantum dots produced with green synthesis approaches are presented with a special focus on the last decade.

Critical role of biosensing on the efficient monitoring of cancer proteins/biomarkers using label-free aptamer based bioassay

Cancer is the second most extended disease during the world with an improved death rate over the past several time. Due to the restrictions of cancer analysis methods, the patient's real survival rate is unknown. Therefore early stage diagnosis of cancer is crucial for its strong detection. Bio-analysis based on biomarkers may help to overcome this problem. Aptamers can be employed as high-affinity tools for cancer detection. The utilization of aptamer-based strategy in cancer investigation and strategy shows new opportunities in biotechnology. The label-free system is an important method to study biomolecules in different sizes, such as biomarkers in real-time because of their greatest sensitivity, selectivity, and multi examination. In this review (with 75 references), excellent features of the label-free aptasensors on the sensitive and accurate monitoring of cancer biomarkers were discussed. Also, the role of advanced of nanomaterials on the construction of label-free aptasensors were investigated. In addition, application of different detection methods such as electrochemical, optical, electronic, and photoelectrochemical (PEC), electrochemiluminescence (ECL) were surveyed. Finally, advantages and limitation of different strategies on the early stage diagnosis of cancer biomarkers were discussed. This article has been updated until July 2020.

A novel fluorescent nanoprobe that based on poly(thymine) single strand DNA-templated copper nanocluster for the detection of hydrogen peroxide

In this paper, a label-free fluorescence nanoprobe is constructed based on poly(thymine) single strand DNA-templated Copper nanocluster (denote as: T-CuNCs) for the detection of hydrogen peroxide. In the assay, the fluorescent T-CuNCs will generate though the reaction of Cu²⁺, poly(thymine) and sodium ascorbate. However, the hydroxyl radical (^.OH) will generated in the presence of H₂O₂, which is able to induced the oxidative lesions of poly(thymine) single chain DNA and lead to the poly(thymine) being splitted into shorter or single oligonucleotide fragments and lose the ability to template the fluorescent T-CuNCs again. Therefore, H₂O₂ can be detected by monitoring the fluorescence strength change of T-CuNCs. The experimental results show that the fluorescence intensity change of T-CuNCs has fantastic linearity versus H₂O₂ concentration in the range of 1-30 μM (R² = 0.9947) and 30-80 μM (R² = 0.9972) with the limit of detection (LOD) as low as 0.5 μM (S/N = 3). More important, the fluorescent nanoprobe was also successfully utilized on the detection of H₂O₂ in serum samples. Therefore, a label-free, costless and effective fluorescence method has been established for the detection of H₂O₂, the intrinsic properties of the nanoprobe endow its more potential applications in chemical and biological study.

A Concise Review on Multidimensional Silver Nanoparticle Health Aids and Threats

Benefits and Risk:

AgNps have beneficial approaches for cancer treatment and angiogenesisrelated diseases like rheumatoid arthritis, atherosclerosis, diabetic psoriasis, retinopathy, endometriosis, and adiposity.

Result:

The advancing nanotechnology-based therapy needs to be devised better, and it should offload the hitches of prevailing treatment approaches. Essential studies are required to explain the synergistic effect of two different cytotoxic agents.

Highly sensitive detection of cancer cells via split aptamer mediated proximity-induced hybridization chain reaction

Highly sensitive detection of cancer cells is of great importance for evaluating cancer development and improving survival rates. Here, we developed a split aptamer mediated proximity-induced hybridization chain reaction (HCR) strategy to meet this purpose. In this strategy, two split aptamer initiator probes, Sp-a and Sp-b, and two HCR hairpin probes, H1 and H2 were designed. The split aptamer initiator probes contained two components, split aptamer domains being responsible for target recognition, and the split initiator parts serving as the HCR promoter. In the presence of target cells, Sp-a and Sp-b would self-assemble on the cell surfaces, allowing the formation of an intact nicked initiator to activate the HCR reaction. Benefit from low background split aptamers and HCR amplification, this strategy presented high sensitivity in quantitative detection with a detection limit of 18 cells in 150 μL of binding buffer. Moreover, the approach exhibited excellent specificity to target cells in 10% fetal bovine serum and mixed cell samples, which was favorable for clinical diagnosis in complex biological environment. In addition, by changing the split aptamers attached to the split initiator, the proposed strategy can be expanded to detect various kinds of target cells. It may provide a novel and useful applicable platform for the sensitive detection of cancer cells in biomedicine and tumor-related studies.

Design of a ratiometric fluorescence sensor based on metal organic frameworks and Ru(bpy)32+-doped silica composites for 17β-Estradiol detection

17β-Estradiol (E2), an important endocrine disrupting compound, could be quantitatively detected by fluorescence resonance energy transfer (FRET) aptasensor, designed in this paper. Metal organic frameworks have large specific surface area and easily modifiable groups, which are helpful for the construction of aptasensor. Specifically, streptavidin was immobilized on the synthesized MIL-53-NH₂ by covalent bonding, and further linked with the biotin modified E2 aptamer (apt) through specific bonding between avidin and biotin to obtain the FRET donor probe (MIL-53-apt). Meanwhile, complementary DNA (cDNA) modified Ru(bpy)₃²⁺-doped silica nanoparticles (RuSiO₂-cDNA) were prepared through covalent bonding. They acted as the FRET acceptor probe, since its absorption spectrum showed large overlap with the emission spectrum of MIL-53-apt. In the presence of E2, aptamer modified donor probes tended to bind with E2, owing to their higher selectivity and affinity. Therefore, the optimal distance between FRET pairs was broken, resulting in the fluorescence emission recovery of donor and the fluorescence emission of acceptor decreased. Under optimal conditions, this proposed aptasensor displayed sensitive detection of E2 ranging from 0.5 to 1000 nM with a detection limit of 0.2 nM. Furthermore, the sensor provides a promising method for rapid and sensitive detection of other small biological molecules.

Aptamer based recognition of cancer cells: Recent progress and challenges in bioanalysis

Rapid and accurate monitoring of cancer cells with high sensitivity is essential for a successful cancer treatment. As high-affinity nucleic acid ligands, aptamers can improve the properties of detection methods by conjugating with intracellular or extracellular cancer biomarkers. Despite the advances in the early detection and treatment of cancer cells, lacking effective early detection tools is one of the causes of a high mortality rate. Aptasensors, which are based on the specificity of aptamer-target recognition, with transduction for analytical purposes have received particular attention due to their high sensitivity and selectivity, simple instrumentation, as well as low production cost. In this review, some selective and sensitive methods were summarized based on advanced nanomaterials towards aptasensing of cancer cells, such as blood, breast, cervical, colon, gastric, liver, and lung cancer cells. This review summarizes advances from 2010 to June 2020 in the development of aptasensors for cancer cell detection. Various aptasensing strategies are assessed according to their potential for reaching relevant limits of sensitivity, specificity, and degrees of multiplexing. Furthermore, we address the remaining challenges and opportunities to integrate aptasensing platforms into point-of-care solutions. Finally, the advantages and limitations of aptamer-based aptasensing strategies were reviewed.

Recent advances in optical aptasensor technology for amplification strategies in cancer diagnostics

Aptamers are chemically synthetic single-stranded DNA or RNA molecules selected by molecular evolution. They have been widely used as attractive tools in biosensing and bioimaging because they can bind to a large variety of targets with high sensitivity and high affinity and specificity. As recognition elements, aptamers contribute in particular to cancer diagnostics by recognizing different cancer biomarkers, while they can also facilitate ultrasensitive detection by further employing signal amplification elements. Optical techniques have been widely used for direct and real-time monitoring of cancer-related biomolecules and bioprocesses due to the high sensitivity, quick response, and simple operation, which has greatly benefited cancer diagnostics. In this review, we highlight recent advances in optical platform-based sensing strategies for cancer diagnostics aided by aptamers. Limitations and current challenges are also discussed.

Functionalized reduced graphene oxide with aptamer macroarray for cancer cell capture and fluorescence detection

An integrated aptamer macroarray functionalized with reduced graphene oxide (rGO) to specifically capture and sensitively detect cancer cells is reported. The capture for cancer cells is based on effective recognition of the modified rGO surface through the aptamer against epithelial cell adhesion molecule (EpCAM). The rough structure of rGO enhances morphologic interactions between rGO film interface and the cancer cells, while super-hydrophilicity of modified rGO hinders nonspecific cell capture. The synergistic interactions offer the aptamer macroarray high efficiency of cancer cell capture. By means of a turn-on fluorescence strategy based on the conformation change of the aptamer induced by the target recognition, the enriched cancer cells can be directly read out at excitation/emission wavelengths of 550/680 nm without washing, separation, and dying steps. The working range is 1 × 10² to 2 × 10⁴ cells per mL with a detection limit of 22 cells per mL. The results indicate that the aptamer macroarray has a considerable foreground for early diagnosis, therapy, and monitoring of cancer. Graphical abstract.

Classifying Cell Types with DNA-Encoded Ligand-Receptor Interactions on the Cell Membrane

Clustering, endocytosis, and intracellular transport of molecules on the cell membrane are critically dependent on the type of cells. However, the membrane-associated redistribution of molecules has not been exploited to realize cell classification for diagnostic purposes. Here, we develop a set of DNA-encoded artificial receptors and ligands to monitor the cell membrane redistribution. In this system, a cholesterol-modified single-stranded DNA strand serves as the receptor localized on the membrane, and a tetrahedral DNA framework (TDF) nanostructure with a complementary overhang serves as the ligand. The DNA-encoded receptor-ligand interaction is highly orthogonal, mimicking the dynamics of natural receptors and ligands on cells. We demonstrate that the dynamics of membrane redistribution can be resolved by the dual-color fluorescent patterns of the receptor-ligand interactions in a single image, which can be exploited to classify cell lines with high fidelity. This DNA-encoded method thus holds great promise for cell typing and diagnosis.

Aptamers and Antisense Oligonucleotides for Diagnosis and Treatment of Hematological Diseases

Aptamers or chemical antibodies are single-stranded DNA or RNA oligonucleotides that bind proteins and small molecules with high affinity and specificity by recognizing tertiary or quaternary structures as antibodies. Aptamers can be easily produced in vitro through a process known as systemic evolution of ligands by exponential enrichment (SELEX) or a cell-based SELEX procedure. Aptamers and modified aptamers, such as slow, off-rate, modified aptamers (SOMAmers), can bind to target molecules with less polar and more hydrophobic interactions showing slower dissociation rates, higher stability, and resistance to nuclease degradation. Aptamers and SOMAmers are largely employed for multiplex high-throughput proteomics analysis with high reproducibility and reliability, for tumor cell detection by flow cytometry or microscopy for research and clinical purposes. In addition, aptamers are increasingly used for novel drug delivery systems specifically targeting tumor cells, and as new anticancer molecules. In this review, we summarize current preclinical and clinical applications of aptamers in malignant and non-malignant hematological diseases.

DNA bioassays based on the fluorescence 'turn off' of silver nanocluster beacon

Recognition and quantification of oligonucleotide sequences play important roles in medical diagnosis. In this study, a new fluorescent oligonucleotide-stabilized silver nanocluster beacon (NCB) probe was designed for sensitive detection of oligonucleotide sequence targets. This probe contained two tailored DNA strands. One strand was a signal probe strand containing a cytosine-rich strand template for fluorescent silver nanocluster (Ag NC) synthesis and a detection sections at each end. The other strand was a fluorescence enhancing strand containing a guanine-rich section for signal enhancement at one end and a linker section complementary to one end of the signal probe strand. After synthesis of the Ag NCs and hybridization of the two strands, the fluorescence intensity of the as-prepared silver NCB was enhanced 200-fold compared with the Ag NCs. Two NCBs were designed to detect two disease-related oligonucleotide sequences, and results indicated that the two target oligonucleotide sequences in the range 50.0-600.0 and 50.0-200.0 nM could be linearly detected with detection limits of 20 and 25 nM, respectively. The developed fluorescence method using NCBs for oligonucleotide sequence detection was sensitive, facile and had potential for use in bioanalysis and diagnosis.

Homogenous Electrochemical Method for Ultrasensitive Detection of Tumor Cells Designed by Introduction of Poly(A) Tails onto Cell Membranes

Rapid and efficient detection of tumor cells is one of the central challenges for modern analytical technology. In this paper, we report a polyadenine (poly(A)) tail-based strategy for ultrasensitive detection of tumor cells in aqueous solution with an electrochemical technique. Specifically, tumor cell-specific EpCAM aptamers without any modification can tightly bind on cell membranes and facilitate the subsequent introduction of multiple poly(A) tails via programmable terminal deoxynucleotidyl transferase (TdT)-mediated elongation. Meanwhile, since tumor cells bearing poly(A) tails can be easily adsorbed onto the surface of gold electrodes through a strong interaction between adenosines and gold, a highly amplified electrochemical signal can be obtained. Thus, by virtue of poly(A) tails, the proposed method allows the detection of as low as 3 cells mL^-1. Compared with the previously reported methods for tumor cells detection, this poly(A)-based homogeneous electrochemical method needs just one enzyme and one aptamer without any modification and avoids the complex and time-consuming modification process of the working electrode, which holds great potential application in the future.

Structure-switching aptamer triggering hybridization displacement reaction for label-free detection of exosomes

Exosomes play important roles in intercellular communications, tumor migration and invasion. However, the specific detection of cancer exosomes remains as a big challenge due to its low concentration in biofluids. Therefore, the sensitive and selective detection of cancer cells-derived exosomes has attracted growing attention owing to their potential in diagnostic and prognostic applications. Activatable strategies have received great attention for the detection of low abundant analytes due to their high sensitivity. Herein, based on molecular recognition between DNA aptamer and exosome surface biomarker (protein tyrosine kinase-7), a novel activatable and label-free strategy was designed for highly sensitive and specific sensing of exosomes. In this work, the target exosomes trigger strand replacement reaction to form G-quadruplex, which result in an obvious fluorescence enhancement of N-methylmesoporphyrin IX due to the bonding between G-quadruplex and N-methylmesoporphyrin IX. Under the optimum experimental conditions, the linear range for exosomes was measured to be 5.0 × 10⁵-5.0 × 10⁷ particles/μL and the detection limit (LOD) was calculated to be 3.4 × 10⁵ particles/μL (3σ). This assay possesses high specificity to distinguish exosomes derived from different cell lines, and has successfully been validated in patient and healthy plasma samples. Furthermore, the probe can effectively detect the exosomes in 30% fetal bovine serum, indicating that the biological matrix has a negligible effect on this method. This developed label-free, convenient and highly sensitive biosensor will offer a great opportunity for exosomes quantification in biological study and clinical application.

In situ Analysis of Cancer Cells Based on DNA Signal Amplification and DNA Nanodevices

Cancer is a global disease which has been disturbing researchers in medicine and seriously threatens patients' health and lifetime around the world in the past several decades. Due to the characteristics of cancer cells, such as uncontrollable cell proliferation, cell invasion and metastasis to surrounding tissues, lower grade of differentiation, higher telomerase activity and others, it has been one of the most usual lethal factors, next to heart disease in incidence. Cancer mortality can be decreased by early diagnosis, and the people who with treatment at an early stage have an obvious improved survival rate. Consequently, early detection is significant for better understanding the pathogenesis of cancer and improving the prognosis of patients. In situ detection technique is a vital tool for imaging and cellular pathology research, which can provide effective information about tumor markers in the early cancer detection. In view of low expression of most tumor markers in the early stage of cancers, detection techniques based on DNA signal amplification and DNA nanodevices can provide a strong support for the diagnosis and detection of cancers. In this review, we summarize the research progress of different analytical techniques for detecting various tumor markers that have been reported in recent years. We compare different DNA amplification and nanodevices, then provide guidance and suggestions for better understanding in situ analysis of cancer cells.

Aptamer-tagged silver nanoclusters for cell image and Mucin1 detection in vitro

Development of specific cell imaging technology for accurate tumor early diagnosis and evaluation of drug therapeutic efficiency is in great demand. In this study, a simple and sensitive fluorescence method for Mucin1 (MUC1) image in situ and quantitative assay in vitro has been established using APT-tagged silver nanoclusters (APT-Agnes) containing a recognition unit of MUC1 aptamer as the label-free fluorescence probe. The principle of the method is that specific recognition and binding of MUC1 with aptamer can result in the fluorescence quenching of APT-Agnes. The method for MUC1 assay showed a linear range from 0.1 to 100 NM with a limit of detection of 0.05 nM. Furthermore, the fluorescent probe of APT-AgNCs was successfully used for detection of MUC1 in serum and MCF-7 cell imaging. In our point, the above results demonstrated that the new simple method provided an alternative for direct quantitative assay of MUC1 in homogeneous solution and cell imaging, which is helpful for biomedical study and clinical diagnosis related with MUC1.

A Simple, pH-Activatable Fluorescent Aptamer Probe with Ultralow Background for Bispecific Tumor Imaging

Activatable aptamer probes (AAPs) are promising in molecular imaging of tumors, but the reported shape-switching-dependent AAPs are still challenged by unsatisfied noise suppression, poor stability, and sophisticated sequence design. To address the problem, we constructed a pH-activatable aptamer probe (pH-AAP) by utilizing an acid-labile acetal linker as the responsive element to be fused with a tumor-targeted aptamer. Specifically, a Cy5-labeled aptamer was connected with the quencher BHQ2 through the acetal group, thus generating pH-AAP with quenched fluorescence. Due to the stable proximity of Cy5 to BHQ2, pH-AAP was found to have ultralow background with a quenching efficiency as high as 98%. In comparison with shape-switching-dependent AAPs, the noise suppression of pH-AAP was well maintained for a much longer time in both serum and mouse body, thus showing a robust fluorescence stability. By a combination of the fluorescence recovery induced by acid hydrolysis of acetal linkers and the tumor-targeted recognition of aptamers, pH-AAP could either specifically anchor the extracellular pH-activated signals on the target cell surface in an acidic tumor microenvironment or be activated by acidic lysosomes after it was internalized into target cells. As proof of concept, in vitro evaluation and in vivo imaging of A549 lung cancer cells were performed by using S6 aptamer as a demonstration. It was indicated that pH-AAP realized washing-free, bispecific, and contrast-enhanced tumor imaging. The strategy is simple and free of sequence modification, which promises to provide a universal platform for sensitive and precise tumor diagnosis.

A novel label-free terbium(iii)-aptamer based aptasensor for ultrasensitive and highly specific detection of acute lymphoma leukemia cells

Acute leukemia is a malignant clonal disease of hematopoietic stem cells with a high prevalence and mortality rate. However, there are no efficient tools to facilitate early diagnosis and treatment of leukemia. Therefore, development of new methods for the early diagnosis and prevention of leukemia, especially non-invasive diagnosis at the cellular level, is imperative. Here, a label-free signal-on fluorescence aptasensor based on terbium(iii)-aptamer (Tb³⁺-apt) was applied for the detection of leukemia. The aptamer sensitizes the fluorescence of Tb³⁺ and forms the strong fluorescent Tb³⁺-apt probe. The target cells, the T-cell acute lymphoblastic leukemia cell line (CCRF-CEM) combined with the Tb³⁺-apt probe to form the Tb³⁺-apt-CEM complex, were removed by centrifugation, and the supernatant containing a small amount of the Tb³⁺-apt probe was detected using a fluorescence spectrophotometer. The logarithm of cell concentration showed a good linear relationship (R² = 0.9881) with the fluorescence signal. The linear range for CCRF-CEM detection was 5-5 × 10⁶ cells per ml, while the detection limit was 5 cells per ml of the binding buffer. Clinical samples were collected from 100 cases, and the specificity and positive rates detected by this method were up to 94% and 90%, respectively. Therefore, a single-stranded DNA-sensitized terbium(iii) luminescence method diagnostic was developed which is rapid, sensitive, and economical and can be used for diagnosis of various types of leukemia at the early stage.

DNA three-way junction-actuated strand displacement for miRNA detection using a fluorescence light-up Ag nanocluster probe

A rapid and label-free fluorescence biosensing strategy for highly sensitive detection of microRNA-122 (miR-122) has been developed by the combination of DNA three-way junction (TWJ)-actuated strand displacement and a fluorescence light-up Ag nanocluster (AgNC) probe. In the presence of target miR-122, the attachment of miR-122 to its complementary DNA results in the unblocking of the toehold and branch migration domains in the TWJ, activating the strand displacement reaction (SDR) accompanied by the proximity between the G-rich DNA probe and DNA-AgNC probe; thus a remarkably enhanced fluorescence signal of AgNCs can be obtained owing to the G-rich fluorescence enhancement mechanism. The results reveal that this biosensor exhibits superb specificity and high sensitivity toward miR-122 with a detection limit of 0.030 nM. In addition, the practicality of the biosensor is demonstrated by analyzing miR-122 in three cell lines with satisfactory results. Furthermore, by the utilization of the toehold-mediated SDR and DNA-AgNC conjugates, this proposed strategy offers the advantages of rapidness, convenience, low cost, and simplified operation without the need for biological labeling and the addition of enzymes. Thus, the constructed biosensor might provide a valuable and practical tool for detecting miRNA and the related clinical diagnosis and fundamental biomedicine research.

Highly sensitive aflatoxin B1 sensor based on DNA-guided assembly of fluorescent probe and TdT-assisted DNA polymerization

A novel aptasensor, based on a perylene probe (PAPDI; N,N'-bis(propylenetrimethylammonium)-3,4,9,10-perylenediimide), was developed for the detection of aflatoxin B1 (AFB1) in maize samples. AuNPs/DNA composites were synthesized and integrated with aptamers-modified magnetic nanoparticles (MNPs) via DNA hybridization. For AFB1 determination, AuNPs/DNA composites were released from MNPs through specific binding of AFB1 with the aptamer and used for assembly of the PAPDI probe. To enhance the method sensitivity, terminal deoxynucleotidyl transferase (TdT)-catalyzed DNA polymerization was performed to elongate DNA on AuNPs/DNA composites. As a result, more PAPDI probes were assembled on the AuNPs/DNA composites. Through a multiple signal amplification strategy, the proposed method exhibited high sensitivity towards AFB1, with a detection limit of 0.01 nM (3.1 pg/mL). In summary, the proposed method has great potential to be a universal strategy for monitoring AFB1 in food samples.

DNA-Templated Silver Nanocluster/Porphyrin/MnO2 Platform for Label-Free Intracellular Zn2+ Imaging and Fluorescence-/Magnetic Resonance Imaging-Guided Photodynamic Therapy

Developing a theranostic platform that integrates diagnosis and treatment in one single nanostructure is necessary for efficient tumor treatment. Here, we presented a novel theranostic nanoprobe for nonlabeled fluorescence imaging of Zn²⁺ and 635 nm red light-triggered photodynamic therapy (PDT) by a multifunctional DNA-templated silver nanocluster/porphyrin/MnO₂ nanoplatform. MnO₂ nanosheets adsorbed hairpin DNA-silver nanoclusters (AgNCs) and porphyrin (P) by facile physisorption, which accelerate the transfection of nanoprobes and P into tumor cells. After entering the cells, the biodegradation of MnO₂ nanosheets by glutathione and acidic hydrogen peroxide released AgNCs for label-free Zn²⁺ fluorescence imaging by the hairpin DNA-fueled dynamic self-assembly of three-way DNA junction architectures, and the released Mn²⁺ could act as an effective magnetic resonance imaging (MRI) contrast agent. In addition, MnO₂ was decomposed in the acidic H₂O₂-ample environment and produced O₂ to overbear hypoxia-related PDT resistance, highly efficient PDT was obtained by excess singlet oxygen (¹O₂) release of P-AgNCs-MnO₂ nanoprobes under light irradiation compared with free P. In vitro and in vivo studies confirmed that P-AgNCs-MnO₂ exhibited high fluorescence specificity, excellent PDT effect, and good biocompatibility and could be used as a contrast agent for MRI. This theranostic platform provided a new avenue for the fluorescence and MRI diagnosis of tumors and efficient tumor treatment.

Duplexed aptamers: history, design, theory, and application to biosensing

Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.

Molecular Engineering of Functional Nucleic Acid Nanomaterials toward In Vivo Applications

Recent advances in nanotechnology and engineering have generated many nanomaterials with unique physical and chemical properties. Over the past decade, numerous nanomaterials are introduced into many research areas, such as sensors for environmental monitoring, food safety, point-of-care diagnostics, and as transducers for solar energy transfer. Meanwhile, functional nucleic acids (FNAs), including nucleic acid enzymes, aptamers, and aptazymes, have attracted major attention from the biomedical community due to their unique target recognition and catalytic properties. Benefiting from the recent progress of molecular engineering strategies, the physicochemical properties of nanomaterials are endowed by the target recognition and catalytic activity of FNAs in the presence of a target analyte, resulting in numerous smart nanoprobes for diverse applications including intracellular imaging, drug delivery, in vivo imaging, and tumor therapy. This progress report focuses on the recent advances in designing and engineering FNA-based nanomaterials, highlighting the functional outcomes toward in vivo applications. The challenges and opportunities for the future translation of FNA-based nanomaterials into clinical applications are also discussed.

A fluorescent aptasensor for the femtomolar detection of epidermal growth factor receptor-2 based on the proximity of G-rich sequences to Ag nanoclusters

Human epidermal growth factor receptor-2 (HER2) has been recognized as an important biomarker for the early diagnosis and management of breast cancer. However, there is still challenge in the clinical detection of HER2. In this work, a simple strategy for "turn on" fluorescent detection of HER2 with ultra-sensitivity and high specificity was developed. Herein, HER2-binding aptamer (HApt) and DNA2 containing G-rich sequences, templated sequences for Ag nanoclusters (AgNCs), and complementary bases at both ends were involved to achieve the double stranded DNA templated AgNCs (dsDNA-AgNCs) as a fluorescence probe for HER2 detection. In the presence of HER2, the highly specific binding of HER2 to HApt caused HApt separating from dsDNA-AgNCs, resulting in the folding of DNA2-AgNCs because of the complementary bases at both ends, which led to AgNCs' proximity to G-rich sequences, and therefore the enhanced fluorescence intensity. By monitoring the change in fluorescence signal (ΔF), HER2 was measured, and a linear range from 8.5 fM to 225 fM with a limit of detection (LOD) 0.0904 fM was obtained. More significantly, the detection of HER2 in serum samples was achieved with high accuracy, and the breast cancer patients were successfully discriminated from healthy persons. In summary, this strategy is simple, time-saving, cost-effective, ultrasensitive, specific, universal and more applicable for the detection of HER2. Therefore, we expect this present aptasensor can be used in the clinical detection of biomakers, which lays a potential foundation for the early diagnosis of cancer.

Improving NanoCluster Beacon performance by blocking the unlabeled NC probes

While NanoCluster Beacon (NCB) is a versatile molecular probe, it suffers from a low target-specific signal issue due to impurities. Here we show that adding a "blocker" strand to the reaction can effectively block the nonfunctional probes and enhance the target-specific signal by 14 fold at a 0.1 target/probe ratio.

The presence of a single-nucleotide mismatch in linker increases the fluorescence of guanine-enhanced DNA-templated Ag nanoclusters and their application for highly sensitive detection of cyanide

Fluorescence of DNA-templated silver nanoclusters can be enhanced by more than 100-fold by placing the nanoclusters in proximity to guanine-rich DNA sequences after hybridization. We found that the fluorescence of the guanine-enhanced silver nanoclusters is not increased with the guanine-rich DNA sequence closer to the silver nanoclusters. By studying the different numbers of mismatches in the linker sequences, we found that the presence of a single-nucleotide mismatch in the linker increases fluorescence more than the complementary nucleotide. Further study indicated the mismatch position of the linker sequence also affects the fluorescence of the hybridized DNA-Ag NCs. The evidence reported here indicated that the mismatch of the linker sequence affects the fluorescence enhancement of guanine-enhanced silver nanoclusters. We also found that DNA-Ag NCs is an excellent fluorescence sensor for cyanide, as cyanide effectively quenches the fluorescence of NCs at a very low concentration with high selectivity. Cyanide in the range from 0.10 μM to 0.35 μM could be linearly detected, with a detection limit of 25.6 nM.