Competition-Mediated FRET-Switching DNA Tetrahedron Molecular Beacon for Intracellular Molecular Detection

Targeted DNA Nanomachine Enables Specific miRNA-Responsive Singlet Oxygen Amplification for Precise Cutaneous Squamous Cancer Therapy

Photodynamic therapy (PDT) is a promising strategy for the treatment of skin-related tumors including cutaneous squamous cells carcinoma (cSCC). However, it is hard to balance the dosage off-target phototoxicity while maintaining satisfactory therapeutic effect. In addition, oxygen-dependent photosensitizers (PSs) are affected by tumor hypoxic environment, which further causes inefficient photocatalysis and reduces therapeutic effect. Herein, an intelligent DNA nanomachine based on tetrahedral DNA framework is proposed, incorporated with tumor-targeted aptamer and specific miRNA-responsive hairpin DNA catalytic assembly (HCA), for precise and high-efficient therapy of cSCC. After aptamer-mediated targeted delivery, a cSCC-specific miRNA selected by tissue sequencing analysis is used to activateHCA, for amplifying PSs and controllably releasing chemotherapeutic drugs. Sequential recognition can greatly improve tumor-specific accumulation and high-dose activation. Moreover, hemin is incorporated into DNA to catalytically produce oxygen. In vitro and in vivo experiments demonstrated that this DNA nanomachine greatly improved anti-tumor effect and realized effective ablation of cSCC in mice, with barely systemic toxicity and inflammation. It is anticipated that this strategy will promote biomedical applications of tumor-specific miRNA and provide a promising option for the non-invasive treatment of skin-associated tumors.

A dual-mode biosensor for microRNA detection based on DNA tetrahedron-gated nanochannels

A biosensor based on solid-state nanochannels of anodic aluminum oxide (AAO) membrane for both electrochemical and naked-eye detection of microRNA-31 (MiR-31) is proposed. For this purpose, MoS2 nanosheets, which possess different adsorption capabilities to single-stranded and double-stranded nucleic acids, are deposited onto the top surface of the AAO membrane. Moreover, multi-functional DNA nanostructure have been designed by linking a G-rich sequence for folding to a G-quadruplex at three vertices and a complementary sequence of MiR-31 at the other one vertex of a DNA tetrahedron. In the absence of MiR-31, the tetrahedron DNAzyme probe formed after the addition of hemin can mediate the deposition of insoluble on MoS2/AAO, which not only enables the color change of the membrane but also gates the transport of K3[Fe(CN)6] across the nanochannels. Therefore, the detection of MiR-31 is realized by both visual observation of the brown color and measuring the electrochemical redox current of [Fe(CN)6]3-. Using this biosensor, a detection limit as low as 0.06 fM is achieved. The dual-mode detection method also exhibits good specificity, reproducibility, and stability, demonstrating potential application in the diagnosis of oral squamous cell carcinoma and other related biological purposes.

Spatially Controlled DNA Frameworks for Sensitive Detection and Specific Isolation of Tumor Cells

High-affinity, specific, and sensitive probes are crucial for the specific recognition and identification of tumor cells from complex matrices. Multivalent binding is a powerful strategy, but the irrational spatial distribution of the functional moieties may reduce the probe performance. Here, we constructed a Janus DNA triangular prism nanostructure (3Zy1-JTP-3) for sensitive detection and specific isolation of tumor cells. Benefiting from spatial features of the triangular prism, the fluorescence intensity induced by 3Zy1-JTP-3 was almost 4 times that of the monovalent structure. Moreover, the DNA triangular prisms were connected to form hand-in-hand multivalent DNA triangular prism structures (Zy1-MTP), in which the fluorescence intensity and affinity were increased to 9-fold and 10-fold of 3Zy1-JTP-3, respectively. Furthermore, 3Zy1-JTP-3 and Zy1-MTP were combined with magnetic beads, and the latter showed higher capture efficiency (>90 %) in whole blood. This work provides a new strategy for the efficient capture of rare cells in complex biological samples.

MicroRNA Triggered Dimerization of DNA Tetrahedron for Enhanced Biosensing Performance of Solid-State Nanochannels Functionalized with MoS2 Nanosheets

Solid-state nanochannels (SSN) have great development potential as a biosensing interface. The integration of two-dimensional nanomaterials with nanochannels endows SSN with diverse properties, including distinguishing DNA nanostructures. In this study, by modifying MoS2 nanosheets, the outer surface of SSN could be endowed with robust adsorption properties for single-stranded DNA. Therefore, DNA tetrahedrons connected with single-stranded DNA could remain on the SSN surface, whereas DNA tetrahedron dimers with full double-stranded structures formed by the presence of target microRNA cannot be retained on the surface of nanochannels. The change in the DNA nanostructure generated by the target recognition process could cause variations of steric hindrance and electrostatic repulsion on the surface of the SSN. The variations were reflected by the free diffusion flux of [Fe(CN)6]3-. Then, the sensitive electrochemical detection method for microRNA was established, and the detection limit of the method for microRNA-31 was as low as 0.5 fM. The study provided a promising approach for the ultrasensitive detection of biomarkers, thereby offering potential means for early diagnosis of the related diseases.

Functionalizing tetrahedral framework nucleic acids-based nanostructures for tumor in situ imaging and treatment

Timely in situ imaging and effective treatment are efficient strategies in improving the therapeutic effect and survival rate of tumor patients. In recent years, there has been rapid progress in the development of DNA nanomaterials for tumor in situ imaging and treatment, due to their unsurpassed structural stability, excellent material editability, excellent biocompatibility and individual endocytic pathway. Tetrahedral framework nucleic acids (tFNAs), are a typical example of DNA nanostructures demonstrating superior stability, biocompatibility, cell-entry performance, and flexible drug-loading ability. tFNAs have been shown to be effective in achieving timely tumor in situ imaging and precise treatment. Therefore, the progress in the fabrication, characterization, modification and cellular internalization pathway of tFNAs-based functional systems and their potential in tumor in situ imaging and treatment applications were systematically reviewed in this article. In addition, challenges and future prospects of tFNAs in tumor in situ imaging and treatment as well as potential clinical applications were discussed.

Tuning quantum dots emission on DNA tetrahedron/silica nanosphere/graphene oxide nanointerface for ratiometric fluorescence assay of Pb2+ in multiplex samples

BACKGROUND

Assembling framework nucleic acid (FNA) nanoarchitectures and tuning luminescent quantum dots (QDs) for fluorescence assays represent a versatile strategy in analytical territory. Rationally, FNA constructs could offer a preferential orientation to efficiently recognize the target and improve detection sensitivity, meanwhile, regulating size-dependent multicolor emissions of QDs in one analytical setting for ratiometric fluorescence assay would greatly simplify operation procedures. Nonetheless, such FNA/QDs-based ratiometric fluorescence nanoprobes remain rarely explored.

RESULTS

We designed a sensitive and signal amplification-free fluorescence aptasensor for lead ions (Pb2+) that potentially cause extensive contamination to environment, cosmetic, food and pharmaceuticals. Red and green emission CdTe quantum dots (rQDs and gQDs) were facilely prepared. Moreover, silica nanosphere encapsulating rQDs served as quantitative internal reference and scaffold to anchor a predesigned FNA and DNA sandwich containing Pb2+ binding aptamer and gQD modified DNA signal reporter. On binding of Pb2+, the gQD-DNA signal reporter was set free, resulting in fluorescence quenching at graphene oxide (GO) interface. Owing to the rigid structure of FNA, the fluorescence signal reporter orderly arranged at the silica nanosphere could sensitively respond to Pb2+ stimulation. The dose-dependent fluorescence signal-off mode enabled ratiometric analysis of Pb2+ without cumbersome signal amplification. Linear relationship was established between fluorescence intensity ratio (I555/I720) and Pb2+ concentration from 10 nM to 2 μM, with detection limit of 1.7 nM (0.43 ppb), well addressing the need for Pb2+ routine monitoring. The designed nanoprobe was applied to detection of Pb2+ in soil, cosmetic, milk, drug, and serum samples, with the sensitivity comparable to conventional ICP-MS technique.

SIGNIFICANCE

Given the programmable design of FNA and efficient recognition of target, flexible tuning of QDs emission, and signal amplification-free strategy, the present fluorescence nanoprobe could be a technical criterion for other heavy metal ions detection in a straightforward manner.

Nanomaterials Connected to Bioreceptors to Introduce Efficient Biosensing Strategy for Diagnosis of the TORCH Infections: A Critical Review

TORCH infection is a significant risk factor for severe fetal damage, especially congenital malformations. Screening pregnant women for TORCH pathogens could reduce the incidence of adverse pregnancy outcomes and prevent birth defects. Hence, timely identification and inhibition of TORCH infections are effective ways to successfully prevent them in pregnant women. Recently, the superiority of biosensors in TORCH pathogen sensing has been emphasized due to their intrinsic benefits, such as rapid response time, portability, cost-effectiveness, much friendlier preparation and determination steps. With the introduction of advanced nanomaterials into biosensing, the diagnostic properties of biosensors have significantly improved. This study core presents and debates the current progress in biosensing systems for TORCH pathogens using various artificial and natural receptors. The incorporation of nanomaterials into various transduction systems can enhance diagnostic performance. The key performance characteristics of optical and electrochemical biosensors, such as response time, limit of detection (LOD), and linear detection range, are systematically discussed, along with the current TORCH pathogens used for constructing biosensors. Finally, the major problems that exist for converting scientific investigation into product development are also outlined.

Colorimetric Sensors for Chemical and Biological Sensing Applications

Colorimetric sensors have been widely used to detect numerous analytes due to their cost-effectiveness, high sensitivity and specificity, and clear visibility, even with the naked eye. In recent years, the emergence of advanced nanomaterials has greatly improved the development of colorimetric sensors. This review focuses on the recent (from the years 2015 to 2022) advances in the design, fabrication, and applications of colorimetric sensors. First, the classification and sensing mechanisms of colorimetric sensors are briefly described, and the design of colorimetric sensors based on several typical nanomaterials, including graphene and its derivatives, metal and metal oxide nanoparticles, DNA nanomaterials, quantum dots, and some other materials are discussed. Then the applications, especially for the detection of metallic and non-metallic ions, proteins, small molecules, gas, virus and bacteria, and DNA/RNA are summarized. Finally, the remaining challenges and future trends in the development of colorimetric sensors are also discussed.

Nucleic acid aptamers as aptasensors for plant biology

Our knowledge of cell- and tissue-specific quantification of phytohormones is heavily reliant on laborious mass spectrometry techniques. Genetically encoded biosensors have allowed spatial and some temporal quantification of phytohormones intracellularly, but there is still limited information on their intercellular distributions. Here, we review nucleic acid aptamers as an emerging biosensing platform for the detection and quantification of analytes with high affinity and specificity. Options for DNA aptamer technology are explained through selection, sequencing analysis and techniques for evaluating affinity and specificity, and we focus on previously developed DNA aptamers against various plant analytes. We suggest how these tools might be applied in planta for quantification of molecules of interest both intracellularly and intercellularly.

Colorimetric aptasensor for fumonisin B1 detection based on the DNA tetrahedra-functionalized magnetic beads and DNA hydrogel-coated bimetallic MOFzyme

The toxicity and incidence of fumonisin B₁ (FB₁) pose a major challenge to public health and the environment, prompting the development of alternative quantitative strategies for FB₁. Herein, a colorimetric aptasensor was constructed based on DNA tetrahedra-functionalized magnetic beads (MBs) and DNA hydrogel-coated Mn-Zr bimetallic metal-organic frameworks-based nanozyme (MOFzyme). Initially, MBs functionalized by DNA tetrahedra demonstrated excellent capturing capability for FB₁. Along with the capture of FB₁, catalyst DNA (C) was released into the supernatant. Aided by fuel DNA (F), C can trigger continuous cleavage of the main chains and cross-linking points of the DNA hydrogel through an entropy-driven DNA circuit integrated into the hydrogel coating. Subsequently, the bimetallic MOFzyme encapsulated inside the DNA hydrogel was exposed and exerted its superb peroxidase-like activity, producing a colorimetric signal whose intensity was positively dependent on the amount of FB₁. The developed aptasensor exhibited good linearity in the range of 5 × 10^-4 to 50 ng mL^-1 with a limit of detection (LOD) of 0.38 pg mL^-1, and reasonable specificity in different matrices. Furthermore, the aptasensor was successfully applied to quantify FB₁ in actual samples with recoveries fell within 92.25 %- 108.00 %, showing its great potential in environmental monitoring and food safety.

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.

Design and application of DNA nanostructures for organelle-targeted delivery of anticancer drugs

INTRODUCTION

DNA nanostructures targeting organelles are of great significance for the early diagnosis and precise therapy of human cancers. This review is expected to promote the development of DNA nanostructure-based cancer treatment with organelle-level precision in the future.

AREAS COVERED

In this review, we introduce the different principles for targeting organelles, summarize the progresses in the development of organelle-targeting DNA nanostructures, highlight their advantages and applications in disease treatment, and discuss current challenges and future prospects.

EXPERT OPINION

Accurate targeting is a basic problem for effective cancer treatment. However, current DNA nanostructures cannot meet the actual needs. Targeting specific organelles is expected to further improve the therapeutic effect and overcome tumor cell resistance, thereby holding great practical significance for tumor treatment in the clinic. With the deepening of the research on the molecular mechanism of disease development, especially on tumorigenesis and tumor progression, and increasing understanding of the behavior of biological materials in living cells, more versatile DNA nanostructures will be constructed to target subcellular organelles for drug delivery, essentially promoting the early diagnosis of cancers, classification, precise therapy and the estimation of prognosis in the future.

Aptamer based probes for living cell intracellular molecules detection

Biosensors have been employed for monitoring and imaging biological events and molecules. Sensitive detection of different biomolecules in vivo can reflect the changes of physiological conditions in real-time, which is of great significance for the diagnosis and treatment of diseases. The detection of intracellular molecules concentration change can indicate the occurrence and development of disease. But the analysis process of the existing detection methods, such as Western blot detection of intracellular protein, polymerase chain reaction (PCR) technique quantitative analysis of intracellular RNA and DNA, usually need to extract the cell lysis which is complex and time-consuming. Fluorescence bioimaging enables in situ monitoring of intracellular molecules in living cells. By combining the specificity of aptamer for intracellular molecules binding, and biocompatibility of fluorescent materials and nanomaterials, biosensors with different nanostructures have been developed to enter into living cells for analysis. This review summarizes the fluorescence detection methods based on aptamer for intracellular molecules detection. The principles, limit of detection, advantages, and disadvantages of different platforms for intracellular molecular fluorescent response are summarized and reviewed. Finally, the current challenges and future developments were discussed and proposed.

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.

An artificial enzyme cascade amplification strategy for highly sensitive and specific detection of breast cancer-derived exosomes

Tumor-related exosomes, which are heterogeneous membrane-enclosed nanovesicles shed from cancer cells, have been widely recognized as potential noninvasive biomarkers for early cancer diagnosis. Herein, an artificial enzyme cascade amplification strategy based on a switchable DNA tetrahedral (SDT) scaffold was proposed for quantification of breast cancer-derived exosomes. The SDT scaffold is composed of G-quadruplex mimicking DNAzyme sequences on its two single-stranded edges and glucose oxidase (GOx) on the four termini of the complementary strands. In the initial state, the SDT scaffold is blocked by the switch strand which consists of partial complementary domains with the DNA tetrahedron and a MUC1 aptamer. MCF-7 exosomes could release the quadruplex-forming sequences through the recognition of the MUC1 aptamer. The newly formed DNAzyme brings GOx into spatial proximity and induces high-efficiency enzyme cascade catalytic reactions on the SDT. Consequently, high sensitivity toward MCF-7 exosome analysis was obtained with a wide linear range of 3.8 × 10⁶ to 1.2 × 10⁸ particles per mL and a limit of detection of 1.51 × 10⁵ particles per mL. In addition, such a DNAzyme reconfiguration strategy was able to distinguish MCF-7 exosomes from other breast cancer cell derived exosomes, indicating its excellent method specificity. The proposed enzyme cascade strategy not only provides a novel signal transformation and amplification nanoplatform for quantifying the specific populations of exosomes, but also can be further expanded to the analysis of multiple cancer biomarkers.

A self-assembled DNA nanostructure as a FRET nanoflare for intracellular ATP imaging

Due to the incorporation of gold nanoparticles (AuNPs), previously reported AuNP-based FRET nanoflares still have some problems, such as non-negligible cytotoxicity and a time-consuming preparation procedure. In this communication, a novel AuNP-free FRET nanoflare for intracellular ATP imaging is developed based on a DNA nanostructure, which is self-assembled through cyclic U-type hybridization only involving a certain number of DNA strands.

Fluorescence coupled capillary electrophoresis as a strategy for tetrahedron DNA analysis

A strategy based on fluorescence coupled capillary electrophoresis (CE-FL) was developed for analyzing tetrahedron DNA (TD) and TD-doxorubicin (DOX) conjugate. Capillary gel electrophoresis exhibited desirable performance for separating TD and DNA strands. Under the optimized conditions, satisfactory repeatability concerning run-to-run and interday repeatability was obtained, and relative standard deviation value of resolution (n = 6) was 0.64%. Furthermore, the combination of CE and fluorescence detection provided a sensitive platform for quantifying TD concentration and calculating the damage degree of TD. The electrophoretograms indicated that CE-FL was a suitable TD assay method with high specificity and sensitivity. In addition, the application of CE-FL for TD fluorescence resonance energy transfer (FRET) research was also explored. Two types of DNA strands were utilized to interfere the formation of TD. The impact of partially complementary chain and completely complementary chain on FRET signal was explored, and the influence mechanism was discussed. After applying CE-FL for characterizing TD, we also combine CE and FRET to analyze TD-DOX conjugate. CE presented a favourable technique to monitor DOX loading and releasing processes. These noteworthy results offered a stepping stone for DNA nanomaterials assay by using CE-FL.

Nuclease-resistant signaling nanostructures made entirely of DNA oligonucleotides

Nucleic acid probes have the advantages of excellent biocompatibility, biodegradability, versatile functionalities and remarkable programmability. However, the low biostability of nucleic acid probes under complex physiological conditions limits their in vivo application. Despite impressive progress in the development of inorganic material-mediated biostable nucleic acid nanostructures, uncertain systemic toxicity of composite nanocarriers has hindered their application in living organisms. In the field of biomedicine, as a promising alternative capable of avoiding potential cytotoxicity, biologically stable nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in recent years, offering an exciting in vivo tool for cancer diagnosis and clinical treatment. In this review, we summarize the recent advances in the development of nuclease-resistant DNA nanostructures with different geometrical shapes, such as tetrahedron, octahedron, DNA triangular prism (DTP), DNA nanotubes and DNA origami, introduce innovative assembly strategies, and discuss unique structural advantages and especially biological applications in cellular imaging and targeted drug delivery in an organism. Finally, we conclude with the challenges in the clinical development of DNA nanostructures and present an outlook of the future of this rapidly expanding field.

Dual-MicroRNA-regulation of singlet oxygen generation by a DNA-tetrahedron-based molecular logic device

Endogenous miRNA expression patterns are extremely cell-type-specific, thereby offering high prediction accuracy for different cell identities. Here, a DNA-tetrahedron-based "AND" logic gate is utilized as a molecular device that recognizes dual-miRNA inputs through strand hybridization to activate a computation cascade that produces controlled singlet oxygen in live cells, resulting in the death of the target cell.

Tetrahedral DNA nanostructures as drug delivery and bioimaging platforms in cancer therapy

Structural DNA nanotechnology enables DNA to be used as nanomaterials for novel nanostructure construction with unprecedented functionalities. Artificial DNA nanostructures can be designed and generated with precisely controlled features, resulting in its utility in bionanotechnological and biomedical applications. A tetrahedral DNA nanostructure (TDN), the most popular DNA nanostructure, with high stability and simple synthesis procedure, is a promising candidate as nanocarriers in drug delivery and bioimaging platforms, particularly in precision medicine as well as diagnosis for cancer therapy. Recent evidence collectively indicated that TDN successfully enhanced cancer therapeutic efficiency both in vitro and in vivo. Here, we summarize the development of TDN and highlight various aspects of TDN applications in cancer therapy based on previous reports, including anticancer drug loading, photodynamic therapy, therapeutic oligonucleotides, bioimaging platforms, and other molecules and discuss a perspective in opportunities and challenges for future TDN‐based nanomedicine.

A DNA tetrahedron-based molecular computation device for the logic sensing of dual microRNAs in living cells

Endogenous miRNA expression patterns are specific to cell type and thus offer high prediction accuracy with regard to different cell identities compared to single miRNA analysis.

A versatile luminescent resonance energy transfer (LRET)-based ratiometric upconversion nanoprobe for intracellular miRNA biosensing

A versatile LRET-based ratiometric (LBRU) nanoprobe of NaYF₄:Yb,Er@NaYF₄@NH₂–mSiO₂/rhodamine B/C-DNA sandwich-structured nanocomposites has been developed for intracellular miRNA biosensing.

Aptamer-Functionalized Activatable DNA Tetrahedron Nanoprobe for PIWI-Interacting RNA Imaging and Regulating in Cancer Cells

It has been reported that PIWI-interacting RNAs (piRNAs) play critical roles in activating invasion and metastasis, evading growth suppressors, and sustaining proliferative signaling of cancer and can be regarded as a novel biomarker candidate. Thus, it is necessary to develop an effective method for imaging and regulating cancer-related piRNAs to diagnose and treat cancers. Herein, we designed aptamer-functionalized activatable DNA tetrahedron nanoprobes (apt-ADTNs) to image and regulate endogenous piRNAs in cancer cells. As proof of concept, overexpressed piRNA-36026 in MCF-7 cells was used for this study. In brief, aptamer AS1411 and piRNA-36026 antisequence with Cy5 fluorescent dye are appended from the DNA tetrahedron; then, a short oligonucleotide with black hole quencher 2 (Q-oligo) is complementary with piRNA-36026 antisequence to quench the fluorescence of Cy5. The apt-ADTNs can recognize the MCF-7 cells through aptamer AS1411, and then enter the cells. Q-oligo is detached from the apt-ADTNs because of the binding between apt-ADTNs and piRNA-36026, leading to the recovery of the Cy5 fluorescence signal. Meanwhile, the hybridization of apt-ADTNs and piRNA-36026 results in down-regulating of dissociative piRNA-36026 in cytoplasm and the subsequent apoptosis of MCF-7 cells. As the achievement of synchronously imaging and regulating piRNA-36026 in MCF-7 cells, we believe that this design holds great promise in application of diagnosis and therapy for cancer.

Accurate cancer cell identification and microRNA silencing induced therapy using tailored DNA tetrahedron nanostructures

Accurate cancer cell identification and efficient therapy are extremely desirable and challenging in clinics. Here, we reported the first example of DNA tetrahedron nanostructures (DTNSs) to real-time monitor and image three intracellular miRNAs based on the fluorescence "OFF" to "ON" mode, as well as to realize cancer therapy induced by miRNA silencing. DTNSs were self-assembled by seven customized single-stranded nucleic acid chains containing three recognition sequences for target miRNAs. In the three vertexes of DTNSs, fluorophores and quenchers were brought into close proximity, inducing fluorescence quenching. In the presence of target miRNAs, fluorophores and quenchers would be separated, resulting in fluorescence recovery. Owing to the unique tetrahedron-like spatial structure, DTNSs displayed improved resistance to enzymatic digestion and high cellular uptake efficiency, and exhibited the ability to simultaneously monitor three intracellular miRNAs. DTNSs not only effectively distinguished tumor cells from normal cells, but also identified cancer cell subtypes, which avoided false-positive signals and significantly improved the accuracy of cancer diagnosis. Moreover, the DTNSs could also act as an anti-cancer drug; antagomir-21 (one recognition sequence) was detached from DTNSs to silence endogenous miRNA-21 inside cells, which would suppress cancer cell migration and invasion, and finally induce cancer cell apoptosis; the result was demonstrated by experiments in vitro and in vivo. It is anticipated that the development of smart nanoplatforms will open a door for cancer diagnosis and treatment in clinical systems.

Functional DNA hexahedron for real-time detection of multiple microRNAs in living cells

Intracellular microRNA (miRNA) analysis in single cell is highly informative and offers valuable insights to its physiological and pathological state, but it must confront the pivotal challenge of gene probe delivery and conditional release. Herein, we report an assembled DNA mini-hexahedron (DMH) that can selectively package and protect miRNA probe, target-cell-specific delivery and release it based on the target sequence recognition for intracellular miRNA detection. In brief, the DMH is self-assembled from six single-stranded oligonucleotide strands through rational design, one of which containing AS1411 sequence for specific uptake. Two fluorescent dye labeled recognition strands are inserted into two DMH edges with quencher groups through partially complementary hybridization. We find that this DMH possesses great biocompatibility, good trans-membrane ability and are able to protect the gene cargo against enzymatic degradation and protein binding. Fluorescence restoration caused by the target-mediated competitive chain replacement reaction allows to simultaneous detection of two cancer-related intracellular miRNAs with little false-positive signal, providing a powerful tool to discriminate healthy normal cell and cancerous cell. Thus, the construct opens a new avenue to circumvent the challenges in gene delivery, specific delivery and intrinsic interferences resistance.

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.

Aptamer Conformation Switching-Induced Two-Stage Amplification for Fluorescent Detection of Proteins

Basing on the conformation change of aptamer caused by proteins, a simple and sensitive protein fluorescent assay strategy is proposed, which is assisted by the isothermal amplification reaction of polymerase and nicking endonuclease. In the presence of platelet-derived growth factor (PDGF-BB), the natural conformation of a DNA aptamer would change into a Y-shaped complex, which could hybridize with a molecular beacon (MB) and form a DNA duplex, leading to the open state of the MB and generating a fluorescence signal. Subsequently, with further assistance of isothermal recycling amplification strategies, the designed aptamer sensing platform showed an increment of fluorescence. As a benefit of this amplified strategy, the limit of detection (LOD) was lowered to 0.74 ng/mL, which is much lower than previous reports. This strategy not only offers a new simple, specific, and efficient platform to quantify the target protein in low concentrations, but also shows a powerful approach without multiple washing steps, as well as a precious implementation that has the potential to be integrated into portable, low-cost, and simplified devices for diagnostic applications.

Functional Imaging with Nucleic-Acid-Based Sensors: Technology, Application and Future Healthcare Prospects

Timely monitoring and assessment of human health plays a crucial role in maintaining the wellbeing of our advancing society. In addition to medical tools and devices, suitable probe agents are crucial to assist such monitoring, either in passive or active ways (i.e., sensors) through inducible signals. In this review we highlight recent developments in activatable optical sensors based on nucleic acids. Sensing mechanisms and bio-applications of these nucleic acid sensors in ex vivo assays, intracellular or in vivo settings are described. In addition, we discuss the limitations of these sensors and how nanotechnology can complement/enhance sensor properties to promote translation into clinical applications.

A DNA nanowire based localized catalytic hairpin assembly reaction for microRNA imaging in live cells

Here, we have developed a localized catalytic hairpin assembly (LCHA) strategy for intracellular miR-21 imaging by using DNA nanowires confining both hairpin probes in a compact space. The LCHA is constructed by interval hybridization of DNA hairpin probe pairs to a DNA nanowire with multiplex footholds generated by alternating chain hybridization. Compared to the conventional catalytic hairpin assembly (CHA) strategy, the LCHA significantly shortens the reaction time and enhances the sensitivity. Moreover, the proposed LCHA can serve as a carrier for delivery of probes into live cells as well as protect the probes from nuclease degradation and enhances the stability. We anticipate that this design can be widely applied in facilitating basic biomedical research and disease diagnosis.

Low Background Cascade Signal Amplification Electrochemical Sensing Platform for Tumor-Related mRNA Quantification by Target-Activated Hybridization Chain Reaction and Electroactive Cargo Release

Herein a low background cascade signal amplification electrochemical sensing platform has been proposed for the ultrasensitive detection of mRNA (mRNA) by coupling the target-activated hybridization chain reaction and electroactive cargo release from mesoporous silica nanocontainers (MSNs). In this sensing platform, the 5'-phosphate-terminated DNA (5'-PO₄ cDNA) complement to target mRNA is hybridized with the trigger DNA and anchor DNA on the surface of the MSNs, aiming at forming a double-stranded DNA gate molecule and sealing the methylene blue (MB) in the inner pores of the MSNs. In the presence of target mRNA, the 5'-PO₄ cDNA is displaced from the MSNs and competitively hybridizes with mRNA, which led to the liberation of the trigger DNA and the opening of the MSNs pore. The liberated trigger DNA can be then immobilized onto the electrode surface through hybridization with the capture DNA, triggering HCR on the electrode surface. At the same time, the MB released from the MSNs will selectively intercalate into the HCR long dsDNA polymers, giving rise to significant electrochemical response. In addition, due to the λ-exonuclease (λ-Exo) cleavage reaction-assisted target recycling, more amounts of trigger DNA will be liberated and trigger HCR, and numerous MB are uncapped and intercalate into the HCR products. As proof of concept, thymidine kinase 1 (TK1) mRNA was used as a model target. Featured with amplification efficiency, label-free capability, and low background signal, the strategy could quantitatively detect TK1 mRNA down to 2.0 aM with a linear calibration range from 0.1 fM to 1 pM. We have also demonstrated the practical application of our proposed sensing platform for detecting TK1 mRNA in real samples, opening up new avenues for highly sensitive quantification of biomarkers in bioanalysis and clinical diagnosis.

Framework-Nucleic-Acid-Enabled Biosensor Development

Nucleic acids have been actively exploited to develop various exquisite nanostructures due to their unparalleled programmability. Especially, framework nucleic acids (FNAs) with tailorable functionality and precise addressability hold great promise for biomedical applications. In this review, we summarize recent progress of FNA-enabled biosensing in homogeneous solutions, on heterogeneous surfaces, and inside cells. We describe the strategies to translate the structural order and rigidity of FNAs to interfacial engineering with high controllability, and approaches to realize multiplexing for highly parallel in vitro detection. We also envision the marriage of the currently available FNA tool sets with other emerging technologies to develop a new generation of biosensors for precision diagnosis and bioimaging.

Poly-adenine-mediated fluorescent spherical nucleic acid probes for live-cell imaging of endogenous tumor-related mRNA

Identification of tumor-related mRNA in living cells hold great promise for early cancer diagnosis and pathological research. Herein, we present poly-adenine (polyA)-mediated fluorescent spherical nucleic acid (FSNA) probes for intracellular mRNA detection with regulable sensitivities by programmably adjusting the loading density of DNA on gold nano-interface. Gold nanoparticles (AuNPs) functionalized with polyA-tailed recognition sequences were hybridized to fluorescent "reporter" strands to fabricate fluorescence-quenched FSNA probes. While exposed to target gene, the "reporter" strands were released from FSNA through strand displacement and fluorescence was recovered. With polyA20 tail as the attaching block, the detection limit of FSNA probes was calculated to be 0.31 nM, which is ~55 fold lower than that of thiolated probes without surface density regulation. Quantitative intracellular mRNA detection and imaging could be achieved with polyA-mediated FSNA probes within 2 hours, indicating their application potential in rapid and sensitive intracellular target imaging.

Ratiometric optical nanoprobes enable accurate molecular detection and imaging

Exploring and understanding biological and pathological changes are of great significance for early diagnosis and therapy of diseases. Optical sensing and imaging approaches have experienced major progress in this field. Particularly, an emergence of various functional optical nanoprobes has provided enhanced sensitivity, specificity, targeting ability, as well as multiplexing and multimodal capabilities due to improvements in their intrinsic physicochemical and optical properties. However, one of the biggest challenges of conventional optical nanoprobes is their absolute intensity-dependent signal readout, which causes inaccurate sensing and imaging results due to the presence of various analyte-independent factors that can cause fluctuations in their absolute signal intensity. Ratiometric measurements provide built-in self-calibration for signal correction, enabling more sensitive and reliable detection. Optimizing nanoprobe designs with ratiometric strategies can surmount many of the limitations encountered by traditional optical nanoprobes. This review first elaborates upon existing optical nanoprobes that exploit ratiometric measurements for improved sensing and imaging, including fluorescence, surface enhanced Raman scattering (SERS), and photoacoustic nanoprobes. Next, a thorough discussion is provided on design strategies for these nanoprobes, and their potential biomedical applications for targeting specific biomolecule populations (e.g. cancer biomarkers and small molecules with physiological relevance), for imaging the tumor microenvironment (e.g. pH, reactive oxygen species, hypoxia, enzyme and metal ions), as well as for intraoperative image guidance of tumor-resection procedures.

Spiny Nanorod and Upconversion Nanoparticle Satellite Assemblies for Ultrasensitive Detection of Messenger RNA in Living Cells

Quantitation and in situ monitoring of target mRNA (mRNA) in living cells remains a significant challenge for the chemical and biomedical communities. To quantitatively detect mRNA expression levels in living cells, we have developed DNA-driven gold nanorod coated platinum-upconversion nanoparticle satellite assemblies (termed Au NR@Pt-UCNP satellites) for intracellular thymidine kinase 1 (TK1) mRNA analysis. The nanostructures were capable of recognizing target mRNA in a sequence-specific manner as luminescence of UCNPs was effectively quenched by Au NR@Pt within the assemblies. Following recognition, UCNPs detached from Au NR@Pt, resulting in luminescence restoration to achieve effective in situ imaging and quantifiable detection of target mRNA. The upconversional luminescence intensity of confocal images showed a good linear relationship with intracellular TK1 mRNA ranging from 1.17 to 65.21 fmol/10 μg RNA and a limit of detection (LOD) of 0.67 fmol/10 μg RNA. We believe that our present assay can be broadly applied for detection of endogenous biomolecules at the cellular and tissue levels and restoration of tissue homeostasis in vivo.

A Smart DNA Tweezer for Detection of Human Telomerase Activity

Reliable and accurate detection of telomerase activity is crucial to better understand its role in cancer cells and to further explore its function in cancer diagnosis and treatment. Here, we construct a smart DNA tweezer (DT) for detection of telomerase activity. The DT is assembled by three specially designed single-stranded oligonucleotides: a central strand dually labeled with donor/acceptor fluorophores and two arm strands containing overhangs complementary to telomerase reaction products (TRPs). It can get closed through hybridization with TRPs and get reopen through strand displacement reaction by TRPs' complementary sequences. First, under the action of telomerase, telomerase binding substrates (TS) are elongated to generate TRPs ended with telomeric repeats (TTAGGG) _n. TRPs hybridize with the two arm overhangs cooperatively and strain DT to closed state, inducing an increased fluorescence resonance energy transfer (FRET) efficiency, which is utilized for telomerase activity detection. Second, upon introduction of a removal strand (RS) complementary to TRPs, the closed DT is relaxed to open state via the toehold-mediated strand displacement, inducing a decreased FRET efficiency, which is utilized for determination of TRP length distribution. The detection limit of telomerase activity is equivalent to 141 cells/μL for HeLa cells, and telomerase-active cellular extracts can be differentiated from telomerase-inactive cellular extracts. Furthermore, TRPs owning 1, 2, 3, 4, and ≥5 telomeric repeats are identified to account for 25.6%, 20.5%, 15.7%, 12.5%, and 25.7%, respectively. The proposed strategy will offer a new approach for reliable, accurate detection of telomerase activity and product length distribution for deeper studying its role and function in cancer.

DNA Nanotechnology-Enabled Drug Delivery Systems

Over the past decade, we have seen rapid advances in applying nanotechnology in biomedical areas including bioimaging, biodetection, and drug delivery. As an emerging field, DNA nanotechnology offers simple yet powerful design techniques for self-assembly of nanostructures with unique advantages and high potential in enhancing drug targeting and reducing drug toxicity. Various sequence programming and optimization approaches have been developed to design DNA nanostructures with precisely engineered, controllable size, shape, surface chemistry, and function. Potent anticancer drug molecules, including Doxorubicin and CpG oligonucleotides, have been successfully loaded on DNA nanostructures to increase their cell uptake efficiency. These advances have implicated the bright future of DNA nanotechnology-enabled nanomedicine. In this review, we begin with the origin of DNA nanotechnology, followed by summarizing state-of-the-art strategies for the construction of DNA nanostructures and drug payloads delivered by DNA nanovehicles. Further, we discuss the cellular fates of DNA nanostructures as well as challenges and opportunities for DNA nanostructure-based drug delivery.

Fluorescence and photoacoustic dual-mode imaging of tumor-related mRNA with a covalent linkage-based DNA nanoprobe

A fluorescence and photoacoustic dual-mode DNA nanoprobe based on covalent linkage was developed for detecting tumor-associated mRNA.

Direct Detection of Nucleic Acid with Minimizing Background and Improving Sensitivity Based on a Conformation-Discriminating Indicator

As is well-known, the nucleic acid indicator-based strategy is one of the major approaches to monitor the nucleic acid hybridization-mediated recognition events in biochemical analysis, displaying obvious advantages including simplicity, low cost, convenience, and generality. However, conventional indicators either hold strong self-fluorescence or can be lighted by both ssDNA and dsDNA, lacking absolute selectivity for a certain conformation, always with high background interference and low sensitivity in sensing; and additional processing (e.g., nanomaterial-mediated background suppression, and enzyme-catalyzed signal amplification) is generally required to improve the detection performance. In this work, a carbazole derivative, EBCB, has been synthesized and screened as a dsDNA-specific fluorescent indicator. Compared with conventional indicators under the same conditions, EBCB displayed a much higher selective coefficient for dsDNA, with little self-fluorescence and negligible effect from ssDNA. Based on its superior capability in DNA conformation-discrimination, high sensitivity with minimizing background interference was demonstrated for direct detection of nucleic acid, and monitoring nucleic acid-based circuitry with good reversibity, resulting in low detection limit and high capability for discriminating base-mismatching. Thus, we expect that this highly specific DNA conformation-discriminating indicator will hold good potential for application in biochemical sensing and molecular logic switching.