I-Motif-Based in Situ Bipedal Hybridization Chain Reaction for Specific Activatable Imaging and Enhanced Delivery of Antisense Oligonucleotides

Acidic Extracellular pH-Activated Allosteric DNA Nanodevice for Fluorescence Imaging of APE1 Activity in Tumor Cells

Allostery is a phenomenon where the binding of a ligand at one allosteric site influences the affinity for another ligand at an active site. Different from orthosteric regulation, it allows for more precise control of biomolecular activity and enhances the stability of the molecules. Inspired by allosteric regulation of natural molecules, we present a Y-shaped allosteric DNA nanodevice, termed YssAP, that was pH-responsive and functionalized with the AS1411 aptamer for accurate fluorescence imaging of human apurinic/apyrimidinic endonuclease (APE1) activity in tumor cells. With rational design, YssAP could not be cut by APE1, and Cy5 was in the proximity of BHQ2, leading to suppressed signal emission. In contrast, since acidic pH acted as an allosteric effector, YssAP underwent a conformational change into an activated DNA probe (YdsAP) at acidic extracellular pH. After entering the tumor cell via the specific recognition of AS1411 aptamer, the overexpressed APE1 in the tumor cell cut the AP site on YdsAP. Cy5 moved far away from BHQ2, resulting in a strong signal output. Compared with the direct construction of the APE1 substrate, allosteric DNA nanodevices have more accurate imaging effects, which can be precisely adjusted by changing the switching state. We anticipate that this strategy will be applied in the screening of APE1 inhibitors and precise tumor diagnosis.

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.

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.

Telomerase-activated Au@DNA nanomachine for targeted chemo-photodynamic synergistic therapy

We successfully designed a smart activatable nanomachine for cancer synergistic therapy. Photodynamic therapy (PDT) and chemotherapy can be activated by intracellular telomerase while anti-cancer drugs can be effectively transported into tumour cells. An Sgc8 aptamer was designed, which can specifically distinguish tumour cells from normal cells and perform targeted therapy. The nanomachine entered the tumour cells by recognising PTK7, which is overexpressed on the surface of cancer cells. Then, the "switch" of the system was opened by TP sequence extension under telomerase stimulus. So, the chemotherapeutic drug DOX was released to achieve the chemotherapy, and the Ce6 labelled Sgc8-apt was released to activate the PDT. It was found that if no telomerase existed, the Ce6 would always be in an "off" state and could not activate the PDT. Telomerase is the key to controlling the activation of the PDT, which effectively reduces the damage photosensitisers cause to normal cells. Using in vitro and in vivo experiments, the nanomachine shows an excellent performance in targeted synergistic therapy, which is expected to be utilised in the future.

Application of intelligent responsive DNA self-assembling nanomaterials in drug delivery

Smart nanomaterials are nano-scaled materials that respond in a controllable and reversible way to external physical or chemical stimuli. DNA self-assembly is an effective way to construct smart nanomaterials with precise structure, diverse functions and wide applications. Among them, static structures such as DNA polyhedron, DNA nanocages and DNA hydrogels, as well as dynamic reactions such as catalytic hairpin reaction, hybridization chain reaction and rolling circle amplification, can serve as the basis for building smart nanomaterials. Due to the advantages of DNA, such as good biocompatibility, simple synthesis, rational design, and good stability, these materials have attracted increasing attention in the fields of pharmaceuticals and biology. Based on their specific response design, DNA self-assembled smart nanomaterials can deliver a variety of drugs, including small molecules, nucleic acids, proteins and other drugs; and they play important roles in enhancing cellular uptake, resisting enzymatic degradation, controlling drug release, and so on. This review focuses on different assembly methods of DNA self-assembled smart nanomaterials, therapeutic strategies based on various intelligent responses, and their applications in drug delivery. Finally, the opportunities and challenges of smart nanomaterials based on DNA self-assembly are summarized.

A pH-responsive magnetic resonance tuning probe for precise imaging of bacterial infection in vivo

Accurate and sensitive detection of bacteria is essential for treating bacterial infections. Herein, a pH-responsive magnetic resonance tuning (MRET) probe, whose T₁-weighted signal is activated in the bacteria-infected acid microenvironment, is developed for in situ accurately magnetic resonance imaging (MRI) of bacterial infection in vivo. The MRET probe (MDVG-1) is an assembly of paramagnetic enhancer (gadolinium-modified i-motif DNA₃, abbreviated as Gd-DNA₃-Gd) and the precursor of superparamagnetic quencher (DNA and vancomycin-modified magnetic nanoparticle, abbreviated as MDV). The T₁-weighted signal of Gd-DNA₃-Gd is quenched once the formation of MDVG-1 (MRET ON). Interestingly, the MDVG-1 probe was disassembled into the monomers of Gd-DNA₃-Gd and MDV under the bacteria-infected acid microenvironment, resulting significantly enhanced T₁-weighted signal at the infected site (MRET OFF). The pH-responsive MRET probe-based enhanced MRI signal and bacteria targeting significantly improve the distinction between bacterial infectious tissues and sterile inflamed tissues, which provides a promising approach for accurately detecting bacterial infection in vivo. STATEMENT OF SIGNIFICANCE: : Detecting pathogenic bacteria in vivo based on magnetic resonance imaging (MRI) strategy has been exploring recently. Although various bacterial-targeted MRI probes have been developed to image bacteria in vivo, the MRI signal of these MRI probes is always "on", which inevitably generates nonspecific background MRI signals, affecting the accuracy of MRI to a certain extent. In the current study, based on the magnetic resonance tuning (MRET) phenomenon, we present a pH-responsive MRET probe (MDVG-1) with T₂-weighted imaging to T₁-weighted imaging switchable properties to achieve in situ precise imaging of bacterial infection in vivo.

Polydopamine-coated i-motif DNA/Gold nanoplatforms for synergistic photothermal-chemotherapy

The combination of photothermal therapy with chemotherapy has gradually developed into promising cancer therapy. Here, a synergistic photothermal-chemotherapy nanoplatform based on polydopamine (PDA)-coated gold nanoparticles (AuNPs) were facilely achieved via the in situ polymerization of dopamine (DA) on the surface of AuNPs. This nanoplatform exhibited augmented photothermal conversion efficiency and enhanced colloidal stability in comparison with uncoated PDA shell AuNPs. The i-motif DNA nanostructure was assembled on PDA-coated AuNPs, which could be transformed into a C-quadruplex structure under an acidic environment, showing a characteristic pH response. The PDA shell served as a linker between the AuNPs and the i-motif DNA nanostructure. To enhance the specific cellular uptake, the AS1411 aptamer was introduced to the DNA nanostructure employed as a targeting ligand. In addition, Dox-loaded NPs (DAu@PDA-AS141) showed the pH/photothermal-responsive release of Dox. The photothermal effect of DAu@PDA-AS141 elicited excellent photothermal performance and efficient cancer cell inhibition under 808 nm near-infrared (NIR) irradiation. Overall, these results demonstrate that the DAu@PDA-AS141 nanoplatform shows great potential in synergistic photothermal-chemotherapy.

Recent progress in the development of DNA-based biosensors integrated with hybridization chain reaction or catalytic hairpin assembly

As isothermal, enzyme-free signal amplification strategies, hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) possess the advantages such as high amplification efficiency, excellent biocompatibility, mild reactions, and easy operation. Therefore, they have been widely applied in DNA-based biosensors for detecting small molecules, nucleic acids, and proteins. In this review, we summarize the recent progress of DNA-based sensors employing typical and advanced HCR and CHA strategies, including branched HCR or CHA, localized HCR or CHA, and cascaded reactions. In addition, the bottlenecks of implementing HCR and CHA in biosensing applications are discussed, such as high background signals, lower amplification efficiency than enzyme-assisted techniques, slow kinetics, poor stability, and internalization of DNA probes in cellular applications.

A sequentially triggered DNA nanocapsule for targeted drug delivery based on pH-responsive i-motif and tumor cell-specific aptamer

Targeted drug delivery with minor off-target effects is urgently needed for precise cancer treatments. Here, a sequentially triggered strategy based on double targeting elements is designed to meet this purpose. By using an acidic pH-responsive i-motif DNA and a tumor cell-specific aptamer as targeting elements, a smart dual-targeted DNA nanocapsule (ZBI5-DOX) was constructed. ZBI5-DOX can be firstly triggered by acidic pH, and then bind to target cells via aptamer recognition and thus targeted release of the carried DOX chemotherapeutics. With this smart DNA nanocapsule, the carried DOX could be precisely delivered to target SMMC-7721 tumor cells in acidic conditions. After drug treatments, selective cytotoxicity of the DNA nanocapsule was successfully achieved. Meanwhile, the DNA nanocapsule had a specific inhibition effect on target cell migration and invasion. Therefore, this sequentially triggered strategy may provide deep insight into the next generation of targeted drug delivery.

Prospects and challenges of dynamic DNA nanostructures in biomedical applications

The physicochemical nature of DNA allows the assembly of highly predictable structures via several fabrication strategies, which have been applied to make breakthroughs in various fields. Moreover, DNA nanostructures are regarded as materials with excellent editability and biocompatibility for biomedical applications. The ongoing maintenance and release of new DNA structure design tools ease the work and make large and arbitrary DNA structures feasible for different applications. However, the nature of DNA nanostructures endows them with several stimulus-responsive mechanisms capable of responding to biomolecules, such as nucleic acids and proteins, as well as biophysical environmental parameters, such as temperature and pH. Via these mechanisms, stimulus-responsive dynamic DNA nanostructures have been applied in several biomedical settings, including basic research, active drug delivery, biosensor development, and tissue engineering. These applications have shown the versatility of dynamic DNA nanostructures, with unignorable merits that exceed those of their traditional counterparts, such as polymers and metal particles. However, there are stability, yield, exogenous DNA, and ethical considerations regarding their clinical translation. In this review, we first introduce the recent efforts and discoveries in DNA nanotechnology, highlighting the uses of dynamic DNA nanostructures in biomedical applications. Then, several dynamic DNA nanostructures are presented, and their typical biomedical applications, including their use as DNA aptamers, ion concentration/pH-sensitive DNA molecules, DNA nanostructures capable of strand displacement reactions, and protein-based dynamic DNA nanostructures, are discussed. Finally, the challenges regarding the biomedical applications of dynamic DNA nanostructures are discussed.

Functionalizing Framework Nucleic-Acid-Based Nanostructures for Biomedical Application

Strategies for functionalizing diverse tetrahedral framework nucleic acids (tFNAs) have been extensively explored since the first successful fabrication of tFNA by Turberfield. One-pot annealing of at least four DNA single strands is the most common method to prepare tFNA, as it optimizes the cost, yield, and speed of assembly. Herein, the focus is on four key merits of tFNAs and their potential for biomedical applications. The natural ability of tFNA to scavenge reactive oxygen species, along with remarkable enhancement in cellular endocytosis and tissue permeability based on its appropriate size and geometry, promotes cell-material interactions to direct or probe cell behavior, especially to treat inflammatory and degenerative diseases. Moreover, the structural programmability of tFNA enables the development of static tFNA-based nanomaterials via engineering of functional oligonucleotides or therapeutic molecules, and dynamic tFNAs via attachment of stimuli-responsive DNA apparatuses, leading to potential applications in targeted therapies, tissue regeneration, antitumor strategies, and antibacterial treatment. Although there are impressive performance and significant progress, the challenges and prospects of functionalizing tFNA-based nanostructures are still indicated in this review.

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

Herein, we subtly engineered a pH and membrane receptor dual-activatable aptamer therapeutic for bispecific tumor cell imaging and in situ drug release by utilizing a hairpin-contained i-motif as the acid-responsive element to be complementary with a tumor-targeted aptamer, named as an aptamer "molecule-doctor" (pH-Apt-MD). Specifically, the pH-Apt-MD consisted of two DNA strands, where the Apt-sgc8c was labeled with AF488 and Cy3 at its 5'- and 3'-end, respectively. The I-strand, a hairpin-contained i-motif, was complementary to the Apt-sgc8c strand partially, labeled with a BHQ2 in the middle, thus generating Cy3 with quenched fluorescence and only AF488-emitted fluorescence. The double-helix region of pH-Apt-MD was designed rich in GC bases, providing sites for doxorubicin (Dox) intercalation. Once target cells were encountered, the pH-Apt-MD disassembled due to the specific recognition of the aptamer and conformation change of the i-motif, with activated fluorescence resonance energy transfer (FRET) signals between AF488 and Cy3, accompanied by Dox release in situ. Benefiting from the design of the hairpin-contained i-motif, the pH-Apt-MD presented a narrow pH response range (pH 6.0-6.8) with a transition midpoint (pH^T) of 6.50 ± 0.04. Furthermore, living cell studies revealed that the stimuli-responsive FRET signal activation of pH-Apt-MD was successfully achieved on the HCT116 cell surface with ultralow background and enhanced imaging contrast. Then, the cytotoxicity experiments proved that accurate drug release and cell killing were realized to target cells in an acidic microenvironment. As a facile double stimuli-responsive strategy, the pH-Apt-MD may hold great promise for application in precise diagnosis and therapy of cancer cells.

Endogenous miRNA-Activated DNA Nanomachine for Intracellular miRNA Imaging and Gene Silencing

The development of multifunctional nanoplatforms that integrate both diagnostic and therapeutic functions has always been extremely desirable and challenging in the cancer combat. Here, we report an endogenous miRNA-activated DNA nanomachine (EMDN) in living cells for concurrent sensitive miRNA imaging and activatable gene silencing. EMDN is constructed by interval hybridization of two functional DNA monomers (R/HP and F) to a DNA nanowire generated by hybridization chain reaction. After the target cell-specific transportation of EMDN, intracellular let-7a miRNA initiates the DNA nanomachine by DNA strand displacement cascades, resulting in an amplified fluorescence resonance energy-transfer signal and the release of many free HP sequences. The restoration of HP hairpin structures further activates the split-DNAzyme to identify and cleave the EGR-1 mRNA to realize gene silencing therapy. The proposed EMDN shows efficient cell internalization, good biological stability, rapid reaction kinetics, and the ability to avoid false-positive signals, thus ensuring reliable miRNA imaging in living cells. Meanwhile, the controlled activation of the split-DNAzyme activity regulated by the intracellular specific miRNA may be promising in the precise treatment of cancer. Collectively, this strategy provides a valuable nanoplatform for early clinical diagnosis and activatable gene therapy of tumors.

In Situ Hand-in-Hand DNA Tile Assembly: A pH-Driven and Aptamer-Targeted DNA Nanostructure for TK1 mRNA Visualization and Synergetic Killing of Cancer Cells

In situ stimuli-responsive molecular devices have gained much attention in biomedical areas due to their characteristics of increased image contrast and drug accumulation. Herein, we present a hand-in-hand in situ tile assembly for improved visualization of TK1 mRNA and killing of cancer cells. A pH-responsive and aptamer-functionalized tile motif (pH-Apt-TM) was first formed by four single-strand DNA, possessing pH-responsiveness and intracellular TK1 mRNA recognition capacity. When encountering target cells, the pH-Apt-TM could recognize target receptors on the cell surface through the aptamer domain. Meanwhile, the extracellular acidic pH gathered the pH-Apt-TM into a multifunctional hand-in-hand DNA tile assembly (HDTA) on the cells' surface. Compared to the pH-Apt-TM, studies revealed that the HDTA exhibited enhanced recognition, efficient cellular uptake, and improved visualization of TK1 mRNA, accompanied by gene silencing. Moreover, using Dox as a chemotherapeutic model, specific drug delivery and enhanced cell killing were achieved with target cells.

A smart multiantenna gene theranostic system based on the programmed assembly of hypoxia-related siRNAs

The systemic therapeutic utilisation of RNA interference (RNAi) is limited by the non-specific off-target effects, which can have severe adverse impacts in clinical applications. The accurate use of RNAi requires tumour-specific on-demand conditional activation to eliminate the off-target effects of RNAi, for which conventional RNAi systems cannot be used. Herein, a tumourous biomarker-activated RNAi platform is achieved through the careful design of RNAi prodrugs in extracellular vesicles (EVs) with cancer-specific recognition/activation features. These RNAi prodrugs are assembled by splitting and reconstituting the principal siRNAs into a hybridisation chain reaction (HCR) amplification machine. EVs facilitate the specific and efficient internalisation of RNAi prodrugs into target tumour cells, where endogenous microRNAs (miRNAs) promote immediate and autonomous HCR-amplified RNAi activation to simultaneously silence multiantenna hypoxia-related genes. With multiple guaranteed cancer recognition and synergistic therapy features, the miRNA-initiated HCR-promoted RNAi cascade holds great promise for personalised theranostics that enable reliable diagnosis and programmable on-demand therapy.

A functional DNA-modified dual-response gold nanoprobe for simultaneously imaging the acidic microenvironment and membrane proteins of tumor cells

Tumor progression is a complicated process influenced by multiple factors, in which the acidic tumor microenvironment (TME) and altered tumor-associated membrane proteins (TA-MPs) are closely involved. Monitoring the status of these factors is of significance for tumor progression research. Here, we develop a novel probe for simultaneously imaging the acidic TME and TA-MPs in situ. In this probe, i-motif-forming sequences (strand I) are conjugated to a gold nanoparticle (AuNP) via gold-sulfur bonds for acid-response. Extended aptamers (strand A) for protein recognition are labeled with Cy3 and Cy5 respectively at two ends. The extended part of strand A hybridizes with strand I to quench Cy3 by the proximal AuNP, and the protein recognition part hybridizes with a strand labeled with BHQ2 (strand Q) to quench Cy5. When the integrated probe encounters an acidic TME, the strand I fold into i-motif quadruplexes and release the AQ duplexes from the AuNP, enabling Cy3 to be lit to indicate the acidic TME. The aptamers in AQ duplexes bind to target proteins, removing the hybridization between strand A and Q thus leading to the fluorescence recovery of Cy5 for in-situ imaging of the proteins. Fluorescence measurement and confocal microscopy imaging showed that the probe could sensitively respond to the alteration in acidity from pH 7.4 into pH 6.5, which is coincide with the acidity gap of extracellular microenvironment between normal and tumor cells. Besides, it enabled the in-situ imaging of MUC1 proteins on living cell surface, revealing their expression level and distribution. This probe demonstrates a new approach for simultaneously imaging the acidic TME and TA-MPs, providing a useful tool for multifactor research of tumor progression.

Hybridizing clinical translatability with enzyme-free DNA signal amplifiers: recent advances in nucleic acid detection and imaging

Nucleic acids have become viable prognostic and diagnostic biomarkers for a diverse class of diseases, particularly cancer. However, the low femtomolar to attomolar concentration of nucleic acids in human samples require sensors with excellent detection capabilities; many past and current platforms fall short or are economically difficult. Strand-mediated signal amplifiers such as hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) are superior methods for detecting trace amounts of biomolecules because one target molecule triggers the continuous production of synthetic double-helical DNA. This cascade event is highly discriminatory to the target via sequence specificity, and it can be coupled with fluorescence, electrochemistry, magnetic moment, and electrochemiluminescence for signal reporting. Here, we review recent advances in enhancing the sensing abilities in HCR and CHA for improved live-cell imaging efficiency, lowered limit of detection, and optimized multiplexity. We further outline the potential for clinical translatability of HCR and CHA by summarizing progress in employing these two tools for in vivo imaging, human sample testing, and sensing-treating dualities. We finally discuss their future prospects and suggest clinically-relevant experiments to supplement further related research.

The Recent Development of Hybridization Chain Reaction Strategies in Biosensors

With the continuous development of biosensors, researchers have focused increasing attention on various signal amplification strategies to pursue superior performance for more applications. In comparison with other signal amplification strategies, hybridization chain reaction (HCR) as a powerful signal amplification technique shows its certain charm owing to nonenzymatic and isothermal features. Recently, on the basis of conventional HCR, this technique has been developed and improved rapidly, and a variety of HCR-based biosensors with excellent performance have been reported. Herein, we present a systematic and critical review on the research progress of HCR in biosensors in the last five years, including the newly developed HCR strategies such as multibranched HCR, migration HCR, localized HCR, in situ HCR, netlike HCR, and so on, as well as the combination strategies of HCR with isothermal signal amplification techniques, nanomaterials, and functional DNA molecules. By illustrating some representative works, we also summarize the advantage and challenge of HCR in biosensors, and offer a deep discussion of the latest progress and future development trends of HCR in biosensors.

Aptamer-tethered self-assembled FRET-flares for microRNA imaging in living cancer cells

We report an aptamer-tethered, self-assembled DNA nanowire as a multivalent vehicle for the intracellular delivery of FRET flares. The FRET flares are bound to the nanowire and fluorescently labeled donors and acceptors at two ends, respectively. In the absence of targets, the flares are captured by binding with the nanowires, separating the donor and acceptor (low FRET). However, in the presence of target miRNAs, the flares are displaced from the nanowire, subsequently forming hairpin structures that bring the donor and acceptor into close proximity (high FRET).