Logic-Gated Cell-Derived Nanovesicles via DNA-Based Smart Recognition Module

Programmable PCR-like Nonenzymatic DNA Molecular Circuit for Split-Free Autocatalytic Amplification

Nonenzymatic autocatalytic DNA circuits, capable of exponential signal amplification, exhibit superior amplification efficiency compared to traditional single or cascade DNA amplification circuits, which offer only linear or quadratic signal amplification. However, autocatalytic DNA circuits are currently limited by complicated splitting designs, low autocatalytic efficiency, the need for additional probes, and a lack of universal design principles. Herein, we developed a PCR-like split-free autocatalytic amplification (SAA) DNA circuit with a simple design but extraordinary autocatalytic efficiency for effective biosensing. The SAA system could consecutively perform multiple cycles of a three-step process upon initiation, target recognition, replicating, and recycling, which is programmed to mimic the basic three reaction steps of PCR and constantly yield numerous new split-free target replicates to expedite the whole reaction, ultimately producing an exponentially amplified signal. The PCR-like sigmoidal kinetics, the ability to accurately execute the programmed instructions, and the high autocatalytic capability of the SAA system are demonstrated, which achieves the same target replication as the PCR but without the need for enzymes and precise control of temperature. The SAA circuit, characterized by exponential signal amplification, simple design, and minimal components, offers a promising approach for developing highly efficient universal DNA circuits. This enables the analysis of low-abundance biomarkers with minimal signal leakage, holding significant potential for biochemical research and clinical diagnosis.

Empowering DNA-Based Information Processing: Computation and Data Storage

Information processing is a critical topic in the digital age, as silicon-based circuits face unprecedented challenges such as data explosion, immense energy consumption, and approaching physical limits. Deoxyribonucleic acid (DNA), naturally selected as a carrier for storing and using genetic information, possesses unique advantages for information processing, which has given rise to the emerging fields of DNA computing and DNA data storage. To meet the growing practical demands, a wide variety of materials and interfaces have been introduced into DNA information processing technologies, leading to significant advancements. This review summarizes the advances in materials and interfaces that facilitate DNA computation and DNA data storage. We begin with a brief overview of the fundamental functions and principles of DNA computation and DNA data storage. Subsequently, we delve into DNA computing systems based on various materials and interfaces, including microbeads, nanomaterials, DNA nanostructures, hydrophilic-hydrophobic compartmentalization, hydrogels, metal-organic frameworks, and microfluidics. We also explore DNA data storage systems, encompassing encapsulation materials, microfluidics techniques, DNA nanostructures, and living cells. Finally, we discuss the current bottlenecks and obstacles in the fields and provide insights into potential future developments.

Advancements in Engineering Tetrahedral Framework Nucleic Acids for Biomedical Innovations

Tetrahedral framework nucleic acids (tFNAs) are renowned for their controllable self-assembly, exceptional programmability, and excellent biocompatibility, which have led to their widespread application in the biomedical field. Beyond these features, tFNAs demonstrate unique chemical and biological properties including high cellular uptake efficiency, structural bio-stability, and tissue permeability, which are derived from their distinctive 3D structure. To date, an extensive range of tFNA-based nanostructures are intelligently designed and developed for various biomedical applications such as drug delivery, gene therapy, biosensing, and tissue engineering, among other emerging fields. In addition to their role in drug delivery systems, tFNAs also possess intrinsic properties that render them highly effective as therapeutic agents in the treatment of complex diseases, including arthritis, neurodegenerative disorders, and cardiovascular diseases. This dual functionality significantly enhances the utility of tFNAs in biomedical research, presenting valuable opportunities for the development of next-generation medical technologies across diverse therapeutic and diagnostic platforms. Consequently, this review comprehensively introduces the latest advancements of tFNAs in the biomedical field, with a focus on their benefits and applications as drug delivery nanoplatforms, and their inherent capabilities as therapeutic agents. Furthermore, the current limitations, challenges, and future perspectives of tFNAs are explored.

DNA Nanomaterial-Empowered Surface Engineering of Extracellular Vesicles

Extracellular vesicles (EVs) are cell-secreted biological nanoparticles that are critical mediators of intercellular communication. They contain diverse bioactive components, which are promising diagnostic biomarkers and therapeutic agents. Their nanosized membrane-bound structures and innate ability to transport functional cargo across major biological barriers make them promising candidates as drug delivery vehicles. However, the complex biology and heterogeneity of EVs pose significant challenges for their controlled and actionable applications in diagnostics and therapeutics. Recently, DNA molecules with high biocompatibility emerge as excellent functional blocks for surface engineering of EVs. The robust Watson-Crick base pairing of DNA molecules and the resulting programmable DNA nanomaterials provide the EV surface with precise structural customization and adjustable physical and chemical properties, creating unprecedented opportunities for EV biomedical applications. This review focuses on the recent advances in the utilization of programmable DNA to engineer EV surfaces. The biology, function, and biomedical applications of EVs are summarized and the state-of-the-art achievements in EV isolation, analysis, and delivery based on DNA nanomaterials are introduced. Finally, the challenges and new frontiers in EV engineering are discussed.

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.

Ultrasensitive Photoelectrochemical Biosensor for Dual-miRNAs Detection Based on Molecular Logic Gates and Methylene Blue Sensitized ZnO@CdS@Au Nanorods

The occurrence of cancer is often closely related to multiple tumor markers, so it is important to develop multitarget detection methods. By the proper design of the input signals and logical operations of DNA logic gates, detection and diagnosis of cancer at different stages can be achieved. For example, in the early stages, specific input signals can be designed to correspond to early specific tumor markers, thereby achieving early cancer detection. In the late stage, logic gates for multitarget detection can be designed to simultaneously detect multiple biomarkers to improve diagnostic accuracy and comprehensiveness. In this work, we constructed a dual-target-triggered DNA logic gate for anchoring DNA tetrahedra, where methylene blue was embedded in the DNA tetrahedra to sensitize ZnO@CdS@Au, achieving ultrasensitive detection of the target substance. We tested the response of AND and OR logic gates to the platform. For AND logic gates, the sensing platform only responds when both miRNAs are present. In the concentration range of 10 aM to 10 nM, the photoelectric signal gradually increases with an increase of the target concentration. Subsequently, we used OR logic gates for miRNA detection. Even if only one target exists, the sensing platform exhibits excellent performance. Similarly, within the concentration range of 10 aM to 10 nM, the photoelectric signal gradually increases with an increase of the target concentration. The minimum detection limit is 1.10 aM. Whether it is the need to detect multiple targets simultaneously or only one of them, we can achieve it by selecting the appropriate logic gate. This strategy holds promising application prospects in fields such as biosensing, medical diagnosis, and environmental monitoring.

Emerging trends in CDs@hydrogels composites: from materials to applications

Carbon dots (CDs) are nanoscale carbon materials with unique optical properties and biocompatibility. Their applications are limited by their tendency to aggregate or oxidize in aqueous environments. Turning weakness to strengths, CDs can be incorporated with hydrogels, which are three-dimensional networks of crosslinked polymers that can retain large amounts of water. Hydrogels can provide a stable and tunable matrix for CDs, enhancing their fluorescence, stability, and functionality. CDs@hydrogels, known for their ease of synthesis, strong binding capabilities, and rich surface functional groups, have emerged as promising composite materials. In this review, recent advances in the synthesis and characterization of CDs@hydrogels, composite materials composed of CDs and various types of natural or synthetic hydrogels, are summarized. The potential applications of CDs@hydrogels in fluorescence sensing, adsorption, drug delivery, antibacterial activity, flexible electronics, and energy storage are also highlighted. The current challenges and future prospects of CDs@hydrogels systems for the novel functional materials are discussed.

Sea Anemone-like Nanomachine Based on DNA Strand Displacement Composed of Three Boolean Logic Gates: Diversified Input for Intracellular Multitarget Detection

Efficient and accurate acquisition of cellular biomolecular information is crucial for exploring cell fate, achieving early diagnosis, and the effective treatment of various diseases. However, current DNA biosensors are mostly limited to single-target detection, with few complex logic circuits for comprehensive analysis of three or more targets. Herein, we designed a sea anemone-like DNA nanomachine based on DNA strand displacement composed of three logic gates (YES-AND-YES) and delivered into the cells using gold nano bipyramid carriers. The AND gate activation depends on the trigger chain released by upstream DNA strand displacement reactions, while the output signal relies on the downstream DNAzyme structure. Under the influence of diverse inputs (including enzymes, miRNA, and metal ions), the interconnected logic gates simultaneously perform logical analysis on multiple targets, generating a unique output signal in the YES/NO format. This sensor can successfully distinguish healthy cells from tumor cells and can be further used for the diagnosis of different tumor cells, providing a promising platform for accurate cell-type identification.

Tumor diagnosis using carbon-based quantum dots: Detection based on the hallmarks of cancer

Carbon-based quantum dots (CQDs) have been shown to have promising application value in tumor diagnosis. Their use, however, is severely hindered by the complicated nature of the nanostructures in the CQDs. Furthermore, it seems impossible to formulate the mechanisms involved using the inadequate theoretical frameworks that are currently available for CQDs. In this review, we re-consider the structure-property relationships of CQDs and summarize the current state of development of CQDs-based tumor diagnosis based on biological theories that are fully developed. The advantages and deficiencies of recent research on CQDs-based tumor diagnosis are thus explained in terms of the manifestation of nine essential changes in cell physiology. This review makes significant progress in addressing related problems encountered with other nanomaterials.

DNA Logical Device Combining an Entropy-Driven Catalytic Amplification Strategy for the Simultaneous Detection of Exosomal Multiplex miRNAs In Situ

Exosomal miRNAs are considered promising biomarkers for cancer diagnosis, but their accuracy is severely compromised by the low content of miRNAs and the large amount of exosomal miRNAs released from normal cells. Here, we presented a dual-specific miRNA's logical recognition triggered by an entropy-driven catalysis (EDC)-enhanced system in exosomes for accurate detection of liver cancer-cell-derived exosomal miR-21 and miR-122. Taking advantage of the accurate analytical performance of the logic device, the excellent membrane penetration of gold nanoparticles, and the outstanding amplification ability of the EDC reaction, this method exhibits high sensitivity and selectivity for the detection of tumor-derived exosomal miRNAs in situ. Moreover, due to its excellent performance, this logic device can effectively distinguish liver cancer patients from healthy donors by determining the amount of cancer-cell-derived exosomal miRNAs. Overall, this strategy has great potential for analyzing various types of exosomes and provides a viable tool to improve the accuracy of cancer diagnosis.

Recent Advances in Design and Application of Nanomaterials-Based Colorimetric Biosensors for Agri-food Safety Analysis

A colorimetric sensor detects an analyte by utilizing the optical properties of the sensor unit, such as absorption or reflection, to generate a structural color that serves as the output signal to detect an analyte. Detecting the refractive index of an analyte by recording the color change of the sensor structure on its surface has several advantages, including simple operation, low cost, suitability for onsite analysis, and real-time detection. Colorimetric sensors have drawn much attention owing to their rapidity, simplicity, high sensitivity and selectivity. This Review discusses the use of colorimetric sensors in the food industry, including their applications for detecting food contaminants. The Review also provides insight into the scope of future research in this area.

Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications

This review article introduces mechanistic aspects and applications of photochemically deprotected ortho-nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell-cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.

Construction of DNA-based molecular circuits using normally open and normally closed switches driven by lambda exonuclease

Building synthetic molecular circuits is an important way to realize ion detection, information processing, and molecular computing. However, it is still challenging to implement the NOT logic controlled by a single molecule input in synthetic molecular circuits wherein the presence or absence of the molecule represents the ON or OFF state of the input. Here, based on lambda exonuclease (λ exo), for the first time, we propose the normally open (NO) and normally closed (NC) switching strategy with a unified signal transmission mechanism to build molecular circuits. Specifically, the opposite logic can be output with or without a single signal, and the state of the switch can be adjusted by the addition order and time interval of the upstream signal and switch signal, which endows the switch with time-responsive characteristics. In addition, a time-delay relay with the function of delayed disconnection is developed to realize quantitative control of outputs, which has the potential to meet the automation control need of the system. Finally, digital square and square root circuits are constructed by cascading the NO and NC switches, which demonstrates the versatility of switches. Our design can be extended to time logic and complex digital computing circuits for use in information processing and nanomachines.

Biomimetic retractable DNA nanocarrier with sensitive responsivity for efficient drug delivery and enhanced photothermal therapy

BACKGROUND

The coalition of DNA nanotechnology with diversiform inorganic nanoparticles offers powerful tools for the design and construction of stimuli-responsive drug delivery systems with spatiotemporal controllability, but it remains challenging to achieve high-density oligonucleotides modification close to inorganic nanocores for their sensitive responsivity to optical or thermal signals.

RESULTS

Inspired by Actinia with retractable tentacles, here we design an artificial nano-Actinia consisted of collapsible DNA architectures attached on gold nanoparticle (AuNP) for efficient drug delivery and enhanced photothermal therapy. The collapsible spheroidal architectures are formed by the hybridization of long DNA strand produced in situ through rolling circle amplification with bundling DNA strands, and contain numerous double-helical segments for the intercalative binding of quercetin as the anti-cancer drug. Under 800-nm light irradiation, the photothermal conversion of AuNPs induces intensive localized heating, which unwinds the double helixes and leads to the disassembly of DNA nanospheres on the surface of AuNPs. The consequently released quercetin can inhibit the expression of heat shock protein 27 and decrease the thermal resistance of tumor cells, thus enhancing photothermal therapy efficacy.

CONCLUSIONS

By combining the deformable DNA nanostructures with gold nanocores, this Actinia-mimetic nanocarrier presents a promising tool for the development of DNA-AuNPs complex and opens a new horizon for the stimuli-responsive drug delivery.

Reconfigurable DNA triplex structure for pH responsive logic gates†

The DNA triplex is a special DNA structure often used as a logic gate substrate due to its high stability, programmability, and pH responsiveness. However, multiple triplex structures with different C−G−C⁺ proportions must be introduced into existing triplex logic gates due to the numerous logic calculations involved. This requirement complicates circuit design and results in many reaction by-products, greatly restricting the construction of large-scale logic circuits. Thus, we designed a new reconfigurable DNA triplex structure (RDTS) and constructed the pH-responsive logic gates through its conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. The use of these logic calculations necessitates fewer substrates, further enhancing the extensibility of the logic circuit. This result is expected to promote the development of the triplex in molecular computing and facilitate the completion of large-scale computing networks.

We constructed pH-responsive logic gates through substrate conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. Our logic gates necessitate fewer substrates when two types of logic calculations are needed.

Digging into the biophysical features of cell membranes with lipid-DNA conjugates

Lipid-DNA conjugates have emerged as highly useful tools to modify the cell membranes. These conjugates generally consist of a lipid anchor for membrane modification and a functional DNA nanostructure for membrane analysis or regulation. There are several unique properties of these lipid-DNA conjugates, especially including their programmability, fast and efficient membrane insertion, and precise sequence-specific assembly. These unique properties have enabled a broad range of biophysical applications on live cell membranes. In this review, we will mainly focus on recent tremendous progress, especially during the past three years, in regulating the biophysical features of these lipid-DNA conjugates and their key applications in studying cell membrane biophysics. Some insights into the current challenges and future directions of this interdisciplinary field have also been provided.

Exploring the Structural Diversity of DNA Bottlebrush Polymers Using an Oligonucleotide Macromonomer Approach

Herein, we demonstrate that macromonomers consisting of organics-soluble, chemically protected oligonucleotides (protDNA) and poly(ethylene glycol) (PEG) chains can be converted into bottlebrush polymers of distinct architectures via ring-opening metathesis polymerization (ROMP). Using a custom norbornene-containing phosphoramidite, two types of macromonomers were obtained: a linear norbornene-protDNA-PEG structure and a Y-shaped structure where the polymerizable norbornene group is situated at the junction where protDNA and PEG meet. With this strategy, the PEG chains can be placed either near the backbone of the bottlebrush or on its periphery, and in principle anywhere between these two extremes by adjusting the norbornene location, which makes this strategy attractive for constructing architecturally sophisticated oligonucleotide-containing copolymers.

Engineering a dual-responsive, exosome-surface anchored DNA nanosensor for microenvironment monitoring in vivo

We propose an azoreductase and pH dual-responsive amphiphilic pyramidal tetrahedral DNA probe to construct a circulating exosome-surface anchored nanosensor for microenvironment monitoring in vivo. Based on the shuttle behavior, biocompatibility of the exosomes, and easy synthesis and modification of nucleic acids, both in vitro and in vivo results demonstrate that this nanosensor has excellent performance for activatable O₂ and pH imaging, and thus can distinguish disease areas from normal tissue areas. We expect it to be a useful tool for obtaining early abnormal fluctuations in the microenvironment, which is of great significance for the early detection of diseases.

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.