Engineering a Facile Aptamer "Molecule-Doctor" with Hairpin-Contained I-Motif Enables Accurate Imaging and Killing of Cancer Cells

Functional nucleic acid-based fluorescence imaging for tumor microenvironment monitoring: A review

BACKGROUND

The tumor microenvironment (TME) refers to the complex ecological system surrounding tumor cells, which is intimately associated with regulating tumor cell growth, invasive behavior, and metastatic capacity. Hence, in situ imaging of related bioactivity with resolution in the TME is critical for early cancer detection and accurate diagnosis. In recent years, fluorescence imaging technology has become a widely used tool in TME research due to its non-invasive nature, high spatiotemporal resolution, and capability for real-time monitoring. Among these advancements, signal probes designed based on functional nucleic acids (FNAs) provide a promising and innovative toolkit for targeted imaging analysis of the TME.

RESULTS

This review provides a comprehensive discussion on the construction of FNA-based biosensors and their advancements in TME monitoring. In this review, we initially provide a systematic summary of the current targeting strategies of FNA-based biosensors for visual monitoring of the TME, focusing on targeting cell surface and extracellular matrix components. Subsequently, we further explore the application of FNA-based biosensors in monitoring the TME. These biosensors have successfully achieved the monitoring of key parameters, bioactive molecules and other tumor markers in the tumor microenvironment due to their excellent molecular recognition ability and high sensitivity. Finally, we discuss some of the challenges currently faced in the field. In response to these challenges, we propose potential research directions and look forward to the future development prospects of this field.

SIGNIFICANCE

Unlike previous reviews of biosensors based on FNAs for imaging tumor markers in the TME, this work is the first to review how such biosensors can be anchored in the TME. With continued efforts and advancements, we believe an increasing number of FNA-based fluorescence imaging probes will be utilized for TME imaging. This progress will significantly enhance our understanding of disease pathogenesis and progression, thereby offering substantial potential in biosensing and imaging analysis.

A controllable DNA: structural features and advanced applications of i-motif

The i-motif consists of two parallel-stranded duplexes, stabilized by intercalated semi-protonated cytosine-cytosine (C·C+) pairing. Initially, the i-motif was thought to be unstable under physiological pH, which limited its biological interest. However, recent studies have demonstrated the presence of i-motifs in regulatory regions of the human genome at neutral pH, making their study biologically relevant. In addition, in the field of nanotechnology, the reversible pH-responsive properties of i-motif structures have been utilized to construct functional nanostructures for biomedical diagnostics and therapeutics. In this review, we present an overview of the structural features of i-motifs, the factors affecting their stability, and detection methods. Furthermore, we focus on summarizing recent advances in the application of i-motif-based functional nanostructures at the cellular level. The challenges and future prospects of i-motifs in nanomedicine are also discussed at the end of this paper.

DNA Logic Gate-Triggered Membrane Fusion for Accurately Detecting and Killing Cancer Cells

Accurately and sensitively identifying and killing cancer cells, especially those in deep tissues, is of paramount importance but presents significant challenges. Herein, a membrane protein and adenosine triphosphate (ATP)-driven DNA logic gate-modified liposome is designed to coat zinc peroxide (ZP) nanoparticles integrated with nanozymes (ZP/RuTe@L/DNA) to accurately identify and induce cell apoptosis in cancer cells through a reactive oxygen species (ROS)-mediated mechanism under acid conditions in cancer cells. In this system, DNA logic gate-functionalized liposomes are loaded with ZP and nanozymes, while HeLa cancer cells are functionalized with a DNA segment that is complementary to a segment of the DNA logic gate. For the DNA logic gate, a DNA aptamer was employed for membrane protein recognition, and another aptamer was used for the response of extracellular ATP. Activation of the DNA logic gate occurs only when both biomarkers are simultaneously present. Once activated, the DNA logic gate-modified liposome could hybridize with DNA segment-modified HeLa cells, leading to liposome-HeLa cell fusion and the release of ZP/RuTe into HeLa cells. Under acid conditions, ZP could decompose to release H2O2 and Zn2+, which could promote the production of •O2- and H2O2 by inhibiting the electron transport chain. Concurrently, the released RuTe exhibits glutathione (GSH) depletion and peroxidase (POD) and nicotinamide adenine dinucleotide (NADH) peroxidase-like activities, generating highly toxic hydroxyl radical (•OH), disrupting the cellular redox homeostasis, and inducing cell apoptosis. The ZP/RuTe@L/DNA system could not only accurately detect cancer cells in complex cell mixtures but also present a novel method for liposome-membrane fusion processes in drug delivery. This study presents significant potential for application in precise cancer diagnosis and therapy.

Unveiling the unusual i-motif-derived architecture of a DNA aptamer exhibiting high affinity for influenza A virus

Non-canonical nucleic acid structures play significant roles in cellular processes through selective interactions with proteins. While both natural and artificial G-quadruplexes have been extensively studied, the functions of i-motifs remain less understood. This study investigates the artificial aptamer BV42, which binds strongly to influenza A virus hemagglutinin and unexpectedly retains its i-motif structure even at neutral pH. However, BV42 conformational heterogeneity hinders detailed structural analysis. Molecular dynamics simulations and chemical modifications of BV42 helped us to identify a potential binding site, allowing for aptamer redesign to eliminate the conformational diversity while retaining binding affinity. Nuclear magnetic resonance spectroscopy confirmed the i-motif/duplex junction with the three-cytosine loop nearby. This study highlights the unique structural features of the functional i-motif and its role in molecular recognition of the target.

Functionalities of pH-responsive DNA nanostructures in tumor-targeted strategies

Nanostructures integrating pH-sensitive DNA motifs have emerged as versatile platforms for active tumor targeting, owing to their ability to undergo conformation changes in response to the common acidic environment of the tumor extracellular matrix and endocytosis pathway. This review summarizes the latest advances in the design and application of various pH-responsive DNA nanostructures for tumor-targeted strategies, including tumor recognition, cell imaging, dynamic nanocarrier construction, and controlled drug release. A comprehensive framework for pH-controlled multi-stage tumor targeting is introduced, addressing the divergences in targeting strategies for extracellular and intracellular environments. The unique attributes, practical performance and application challenges of pH-responsive DNA nanostructures are also critically discussed to provide guidance for future development in this field.

Aptamer-controlled stimuli-responsive drug release

Aptamers have been widely researched and applied in nanomedicine due to their programmable, activatable, and switchable properties. However, there are few reviews on aptamer-controlled stimuli-responsive drug delivery. This article highlights the mechanisms and advantages of aptamers in the construction of stimuli-responsive drug delivery systems. We summarize the assembly/reconfiguration mechanisms of aptamers in controlled release systems. The assembly and drug release strategies of drug delivery systems are illustrated. Specifically, we focus on the binding mechanisms to the target and the factors that induce/inhibit the binding to the stimuli, such as strand, pH, light, and temperature. The applications of aptamer-based stimuli-responsive drug release are elaborated. The challenges are discussed, and the future directions are proposed.

Design of a Membrane-Anchored DNAzyme-Based Molecular Machine for Enhanced Cancer Therapy by Customized Cascade Regulation

Synthetic DNAzyme-based structures enable dynamic cell regulation. However, engineering an effective and targeted DNAzyme-based structure to perform customizable multistep regulation remains largely unexplored. Herein, we designed a membrane-anchored DNAzyme-based molecular machine to implement dynamic inter- and intracellular cascade regulation, which realizes efficient T-cell/cancer cell interactions and subsequent receptor mediated cancer cell uptake. Using CD8+ T-cells and HeLa cancer cells as a proof of concept, we demonstrate that the designed DNAzyme-based molecular machine enables customized cascade regulation including (1) specific recognition between T-cells and cancer cells, (2) specific response and fluorescence sensing upon extracellular stimuli, and (3) cascade regulation including intercellular distance shortening, cell-cell communication, and intracellular delivery of anticancer drugs. Together, this work provides a promising pathway for customized cascade cell regulation based on a DNAzyme-based molecular machine, which enables enhanced cancer therapy by combining T-cell immunotherapy and chemotherapy.

Development of Bivalent Aptamer-DNA Carrier-Doxorubicin Conjugates for Targeted Killing of Esophageal Squamous Cell Carcinoma Cells

Esophageal cancer ranks the seventh in cancer incidence and the sixth in cancer death. Esophageal squamous cell carcinoma (ESCC) accounts for approximately 90% of the total cases of esophageal cancer. Chemotherapy is the most effective drug-based method for treatment of esophageal cancer. However, severe side effects of traditional chemotherapy limit its treatment efficacy. Targeted chemotherapy can deliver chemotherapeutic drugs to cancer cells and specifically kill these cells with reduced side effects. In the work, the bivalent aptamer-DNA carrier (BAD) was designed by using an ESCC cell-specific aptamer as the recognition molecule and a GC base-rich DNA sequence as the drug carrier. With doxorubicin (Dox) as chemotherapeutic drugs, the bivalent aptamer-DNA-Dox conjugate (BADD) was constructed for targeted killing of ESCC cells. Firstly, the truncated A2(35) aptamer with a retained binding ability was obtained through optimization of an intact A2(80) aptamer and was used to fuse with DNA carrier sequences for constructing the BAD through simple DNA hybridization. The results of gel electrophoresis and flow cytometry analysis showed that the BAD was successfully constructed and had a stronger binding affinity than monovalent A2(35). Then, the BAD was loaded with Dox drugs to construct the BADD through noncovalent intercalation. The results of fluorescence spectra and flow cytometry assays showed that the BADD was successfully constructed and can bind to target cells strongly. Confocal imaging further displayed that the BADD can be specifically internalized into target cells and release Dox. The results of CCK-8 assays, Calcein AM/PI staining, and wound healing assays demonstrated that the BADD can specifically kill target cells, but not control cells. Our results demonstrate that the developed BADD can specifically deliver doxorubicin to target ESCC cells and selectively kill these cells, offering a potentially effective strategy for targeted chemotherapy of ESCC.

NETosis-Inspired Cell Surface-Constrained Framework Nucleic Acids Traps (FNATs) for Cascaded Extracellular Recognition and Cellular Behavior Modulation

Upon pathogenic stimulation, activated neutrophils release nuclear DNA into the extracellular environment, forming web-like DNA structures known as neutrophil extracellular traps (NETs), which capture and kill bacteria, fungi, and cancer cells. This phenomenon is commonly referred to as NETosis. Inspired by this, we introduce a cell surface-constrained web-like framework nucleic acids traps (FNATs) with programmable extracellular recognition capability and cellular behavior modulation. This approach facilitates dynamic key chemical signaling molecule recognition such as adenosine triphosphate (ATP), which is elevated in the extracellular microenvironment, and triggers FNA self-assembly. This, in turn, leads to in situ tightly interwoven FNAs formation on the cell surface, thereby inhibiting target cell migration. Furthermore, it activates a photosensitizer-capturing switch, chlorin e6 (Ce6), and induces cell self-destruction. This cascade platform provides new potential tools for visualizing dynamic extracellular activities and manipulating cellular behaviors using programmable in situ self-assembling DNA molecular devices.

DNA-Based Fluorescent Nanoprobe for Cancer Cell Membrane Imaging

As an important barrier between the cytoplasm and the microenvironment of the cell, the cell membrane is essential for the maintenance of normal cellular physiological activities. An abnormal cell membrane is a crucial symbol of body dysfunction and the occurrence of variant diseases; therefore, the visualization and monitoring of biomolecules associated with cell membranes and disease markers are of utmost importance in revealing the biological functions of cell membranes. Due to their biocompatibility, programmability, and modifiability, DNA nanomaterials have become increasingly popular in cell fluorescence imaging in recent years. In addition, DNA nanomaterials can be combined with the cell membrane in a specific manner to enable the real-time imaging of signal molecules on the cell membrane, allowing for the real-time monitoring of disease occurrence and progression. This article examines the recent application of DNA nanomaterials for fluorescence imaging on cell membranes. First, we present the conditions for imaging DNA nanomaterials in the cell membrane microenvironment, such as the ATP, pH, etc. Second, we summarize the imaging applications of cell membrane receptors and other molecules. Finally, some difficulties and challenges associated with DNA nanomaterials in the imaging of cell membranes are presented.

Engineered aptamers for molecular imaging

Molecular imaging, including quantification and molecular interaction studies, plays a crucial role in visualizing and analysing molecular events occurring within cells or organisms, thus facilitating the understanding of biological processes. Moreover, molecular imaging offers promising applications for early disease diagnosis and therapeutic evaluation. Aptamers are oligonucleotides that can recognize targets with a high affinity and specificity by folding themselves into various three-dimensional structures, thus serving as ideal molecular recognition elements in molecular imaging. This review summarizes the commonly employed aptamers in molecular imaging and outlines the prevalent design approaches for their applications. Furthermore, it highlights the successful application of aptamers to a wide range of targets and imaging modalities. Finally, the review concludes with a forward-looking perspective on future advancements in aptamer-based molecular imaging.

Framework Nucleic Acid-Based Multifunctional Tumor Theranostic Nanosystem for miRNA Fluorescence Imaging and Chemo/Gene Therapy

Intelligent stimulus-responsive theranostic systems capable of specifically sensing low-abundance tumor-related biomarkers and efficiently killing tumors remain a pressing endeavor. Here, we report a multifunctional framework nucleic acid (FNA) nanosystem for simultaneous imaging of microRNA-21 (miR-21) and combined chemo/gene therapy. To achieve this, two FNA nanoarchitectures labeled with Cy5/BHQ2 signal tags were designed, each of which contained an AS1411 aptamer, two pairs of DNA/RNA hybrids, a pH-sensitive DNA catcher, and doxorubicin (DOX) intercalating between cytosine and guanine in the tetrahedral DNA nanostructure (TDN). In the acidic tumor microenvironment, the DNA catchers spontaneously triggered to form an i-motif and create an FNA dimer (dFNA) while releasing DOX molecules to exert a cytotoxic effect. In addition, the overexpressed miR-21 in tumor cells dismantled the DNA/RNA hybrids to produce vascular endothelial growth factor-associated siRNA via a toehold-mediated strand displacement reaction, thus enabling a potent RNA interfering. Also importantly, the liberated miR-21 could initiate cascade-reaction amplification to efficiently activate the Cy5 signal reporters, thereby realizing on-site fluorescence imaging of miR-21 in living cells. The exquisitely designed FNA-based nanosystem showed favorable biocompatibility and stability as well as acid-driven DOX release characteristics. Owing to the aptamer-guided targeting delivery, specific uptake of the FNA-based theranostic nanosystem by HepG2 cells was verified with confocal laser scanning microscopy and flow cytometry analyses, which therefore resulted in apoptosis of HepG2 cells while doing minimal damage to normal H9c2 and HL-7702 cells. Strikingly, both in vitro and in vivo experiments demonstrated the achievements of the FNA-enabled miR-21 imaging and synergistically enhanced chemo/gene therapy. This work thus represents a noteworthy advance on the FNA-based theranostic strategy that can effectively avoid the undesirable premature leakage of anticarcinogen and off-target of siRNA, and achieve on-demand reagents release for tumor diagnostics and treatment.

A cell-surface-anchored DNA probe coupled with hybridization chain reaction enzyme-free dual signal amplification for sensitive electrochemical detection of the cellular microenvironment

The cellular microenvironment plays key roles in regulating physiological processes. However, it is still a challenge to detect it with quantification. Here, a simple, biocompatible, and universal strategy based on cell surface-anchored specific DNAzymes and hybridization chain reaction enzyme-free signal amplification for cellular microenvironment electrochemical detection is presented. In this strategy, the cell could be captured on the surface of the electrode via aptamer-target recognition. On the other hand, the DNAzyme hybridized with the substrate strand as a metal ion probe was anchored on the surface of the cell. In the presence of metal ions, the substrate strand could be cleaved into two fragments by the DNAzyme and released from the cell surface. Then, the DNA modified gold nanoparticles (AuNPs) could be captured on the electrode. Subsequently, an alternative hybridization reaction of two hairpin probes was triggered by the carried initiators forming nicked double helices. For signal readout, hemin could be inserted into the double-helix DNA long chain via electrostatic interaction, which could electro-reduce hydrogen peroxide to generate an electrochemical signal. Based on the intrinsic advantages of DNAzymes, including rapid kinetics, high sensitivity, and high selectivity, and the signal amplification strategy, this method should be able to monitor and semi-quantify target metal ions in the cellular microenvironment. Furthermore, this method shows potential for various targets by employing different DNA probes in the cellular microenvironment, providing a platform for bioanalysis.

Multivalent aptamer nanoscaffold cytosensor for glioma circulating tumor cells during Epithelial-Mesenchymal transition

The key factor that causes glioma invasion and metastasis is circulating tumor cells (CTCs) undergoing epithelial-mesenchymal transition (EMT). Effective analysis of EMT-CTCs can provide an important foundation for early detection and prognosis monitoring of glioma, but the changes in the biomarkers of CTCs in different states of EMT make detection difficult. In this study, we developed a multivalent aptamer nanoscaffold-based electrochemical cytosensor (MAS-cytosensor) to efficiently detect EMT-CTCs. The two chains forming the MAS are composed of a specific aptamer detector, a binding region for DNA self-assembly, and a foothold for interface anchoring. When target CTCs exist, the bisaptamer detector on MAS can sensitively identify CTCs and pull them to the electrode surface, generating electrochemical signals. It has been demonstrated that the MAS-cytosensor can not only detect EMT-CTCs sensitively (detection limit of 6 cells/mL in buffer), but also allows for further downstream analysis after release with high viability. Overall, this cytosensor provides a reliable detection solution for CTCs regardless of their EMT status, and provides an efficient method for in-depth study role of the post-EMT CTCs in clinical application and metastasis mechanisms.

Self-assembly of DNA nanostructure containing cell-specific aptamer as a precise drug delivery system for cancer therapy in non-small cell lung cancer

Background

As the most common subtype in lung cancer, the precise and efficient treatment for non-small cell lung cancer (NSCLC) remains an outstanding challenge owing to early metastasis and poor prognosis. Chemotherapy, the most commonly used treatment modality, is a difficult choice for many cancer patients due to insufficient drug accumulation in tumor sites and severe systemic side-effects. In this study, we constructed a cell-specific aptamer-modified DNA nanostructure (Apt-NS) as a targeting drug delivery system achieving the precision therapy for lung cancer.

Methods

The synthesis of DNA nanostructure and its stability were evaluated using gel electrophoresis. The targeting properties and internalization mechanism were investigated via flow cytometry and confocal analyses. Drug loading, release, and targeted drug delivery were determined by fluorescence detection, Zeta potentials assay, and confocal imaging. CCK8 assays, colony formation, cell apoptosis, metastasis analyses and in vivo experiments were conducted to assess the biological functions of DNA nanostructure.

Results

Self-assembled DNA nanoparticles (Apt-NS) had excellent stability to serum and DNase I and the ability to specifically recognize A549 cells. Upon specific binding, the drug-loaded nanoparticles (Apt-NS-DOX) were internalized into target cells by clathrin-mediated endocytosis. Subsequently, DOX could be released from Apt-NS-DOX based on the degradation of the lysosome. Apt-NS-DOX exerted significant suppression of cell proliferation, invasion and migration, and also enhanced cell apoptosis due to the excellent performance of drug delivery and intracellular release, while maintaining a superior biosafety. In addition, the antitumor effects of Apt-NS-DOX were further confirmed using in vivo models.

Conclusions

Our study provided cell-specific aptamer-modified DNA nanostructures as a drug-delivery system targeting A549 cells, which could precisely and efficiently transport chemotherapeutic drug into tumor cells, exerting enhanced antineoplastic efficacy. These findings highlight that DNA nanostructure serving as an ideal drug delivery system in cancer treatment appears great promise in biomedical applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-022-01701-5.

Activatable Dual Cancer-Related RNA Imaging and Combined Gene-Chemotherapy through the Target-Induced Intracellular Disassembly of Functionalized DNA Tetrahedron

The desire for a cancer theranostic system with simultaneously accurate diagnosis and efficient therapy is undeniably interminable. Heretofore, theranostic systems with simple components were designed for cancer theranostics but with confined accuracy of diagnosis and side effects of administered drugs. Here, we report an activatable theranostic system for simultaneously imaging dual cancer-related RNAs, mRNA Bcl-2 and piRNA-36026, and combined gene-chemotherapy through the target-induced intracellular disassembly of DNA tetrahedron. Briefly, five customized oligonucleotides are used to assemble the functionalized DNA tetrahedron. The relevant functional nucleic acids, including the antisequence of mRNA Bcl-2, the antisequence of piRNA-36026, and aptamer AS1411, are designed in the customized oligonucleotides with the signal reporters Cy3 and Cy5. Doxorubicin (DOX) is loaded in the functionalized DNA tetrahedron by inlaying between cytosine and guanine to form the activatable cancer theranostic system. The activatable cancer theranostic system is able to recognize MCF-7 cells by aptamer AS1411 and then enter the cells. In the presence of targets, the antisequences in the activatable cancer theranostic system hybridize with intracellular mRNA Bcl-2 and piRNA-36026, leading to the fluorescence signal recovery of Cy3 and Cy5 and the downregulation of two targets in the cytoplasm as well as the consequent apoptosis of MCF-7 cells in the form of gene therapy. Interestingly, as the antisequences are designed in the assembly strands, the hybridization between targets and the antisequences results in the disassembly of the activatable cancer theranostic system and the release of DOX as well as sequential chemotherapy. Advantageously, the activatable cancer theranostic system can achieve imaging of dual cancer-related RNAs with an imaging time window as long as 15 h and exhibit an obvious therapeutic effect in vivo. Therefore, this work is in furtherance of exploration for activatable cancer theranostic systems with high accuracy and efficiency and sheds new light on the development of precision medicine.