DNA-Templated Anchoring of Proteins for Programmable Cell Functionalization and Immunological Response.

Membrane protein engineering exhibits great potential for cell functionalization. Although genetic strategies are sophisticated for membrane protein engineering, there still exist some issues, including transgene insertional mutagenesis, laborious, complicated procedures, and low tunability. Herein, we report a DNA-templated anchoring of exogenous proteins on living cell membranes to realize programmable functionalization of living cells. Using DNA as a scaffold, the model cell membranes are readily modified with proteins, on which the density and ratio of proteins as well as their interactions can be precisely controlled through predictable DNA hybridization. Then, the natural killer (NK) cells were engineered to gain the ability to eliminate the immune checkpoint signaling at the NK-tumor synapse, which remarkably promoted NK cell activation in immunotherapy. Given the versatile functions of exogenous proteins and flexible designs of programmable DNA, this method has the potential to facilitate membrane-protein-based cell engineering and therapy.

A Semisynthetic Bioluminescence Sensor for Ratiometric Imaging of Metal Ions In Vivo Using DNAzymes Conjugated to An Engineered Nano-Luciferase.

DNA-based probes have gained significant attention as versatile tools for biochemical analysis, benefiting from their programmability and biocompatibility. However, most existing DNA-based probes rely on fluorescence as the signal output, which can be problematic due to issues like autofluorescence and scattering when applied in complex biological materials such as living cells or tissues. Herein, we report the development of bioluminescent nucleic acid (bioLUNA) sensors that offer laser excitation-independent and ratiometric imaging of the target in vivo. The system is based on computational modelling and mutagenesis investigations of a genetic fusion between circular permutated Nano-luciferase (NLuc) and HaloTag, enabling the conjugation of the protein with a DNAzyme. In the presence of Zn2+ , the DNAzyme sensor releases the fluorophore-labelled strand, leading to a reduction in bioluminescent resonance energy transfer (BRET) between the luciferase and fluorophore. Consequently, this process induces ratiometric changes in the bioluminescent signal. We demonstrated that this bioLUNA sensor enabled imaging of both exogenous Zn2+ in vivo and endogenous Zn2+ efflux in normal epithelial prostate and prostate tumors. This work expands the DNAzyme sensors to using bioluminescence and thus has enriched the toolbox of nucleic acid sensors for a broad range of biomedical applications.

DNA origami-based protein networks: from basic construction to emerging applications.

Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.

Valency-Controlled Molecular Spherical Nucleic Acids with Tunable Biosensing Performances.

Spherical nucleic acids (SNAs) play critical roles in many fields, such as molecular diagnostics, disease therapeutics, and materials application. Due to the important role of DNA density on the properties of SNAs, the controlled synthesis of monodisperse SNAs with precise DNA density is an important approach for the structure-function relationship study and finite functions regulation of SNAs. In particular, the construction of monodisperse SNAs in a valency-tunable and site-specific manner is highly important; however, it is still challenging. Herein, on the basis of the high controllability, nanometer precision, and addressable modification ability of framework nucleic acid (FNA), we develop the concept of valency-controlled framework nucleic acid core-based molecular spherical nucleic acids (FNA-mSNAs) with tunable biosensing performances. The FNA-mSNAs consist of a valency-tunable FNA-based DNA nanocube as the core and a controlled, precise number of DNA strands per core. By simply alternating the binding site number for shell DNA strands on the DNA nanocube, homogeneous FNA-mSNAs with different valencies were easily designed, which enabled the molecular level study of the effect of valency on their properties, such as nuclease stability and cellular uptake. Furthermore, taking advantage of the addressable modification ability of FNA, the first heterogeneous molecular SNAs with tunable valency were demonstrated. Importantly, the valency of heterogeneous FNA-mSNAs was able to tune their biosensing performance, such as response dynamics, detection sensitivity, and response range. With these remarkable features, FNA-mSNAs provide new research methods for the development of functional SNAs at the molecular level for a wide range of biological applications.

DNAzyme-gold nanoparticle-based probes for biosensing and bioimaging.

The deoxyribozyme (DNAzyme) is a specific nucleic acid with high catalytic activity in the presence of coenzyme factors. Because of its good programmability, high stability and excellent activity, DNAzyme is considered to be a promising material in many fields, such as environmental monitoring, food regulation, biosensing and gene therapy. Gold nanoparticles exhibit excellent photoelectric properties, and can also provide DNAzyme with enhanced cell transfection and excellent resistance to nuclease degradation. Therefore, DNAzyme-gold nanoparticle complexes have attracted much attention in many areas, particularly in biosensing and bioimaging. In this review, we first provide a brief introduction of the structure and catalytic activity of DNAzymes, as well as several methods for preparing DNAzyme-gold nanoparticles. Then, the discussion focuses on applications of DNAzyme-gold nanoparticle-based probes in biosensing and bioimaging in recent years (especially in the past five years). Based on their output signals, these sensors are divided into fluorescence sensors, colorimetric sensors, electrochemical sensors, photoelectrochemical sensors and other sensors. Finally, we discuss several challenges and opportunities in this emerging field.

Size-selective molecular recognition based on a confined DNA molecular sieve using cavity-tunable framework nucleic acids.

Size selectivity is an important mechanism for molecular recognition based on the size difference between targets and non-targets. However, rational design of an artificial size-selective molecular recognition system for biological targets in living cells remains challenging. Herein, we construct a DNA molecular sieve for size-selective molecular recognition to improve the biosensing selectivity in living cells. The system consists of functional nucleic acid probes (e.g., DNAzymes, aptamers and molecular beacons) encapsulated into the inner cavity of framework nucleic acid. Thus, small target molecules are able to enter the cavity for efficient molecular recognition, while large molecules are prohibited. The system not only effectively protect probes from nuclease degradation and nonspecific proteins binding, but also successfully realize size-selective discrimination between mature microRNA and precursor microRNA in living cells. Therefore, the DNA molecular sieve provides a simple, general, efficient and controllable approach for size-selective molecular recognition in biomedical studies and clinical diagnoses.

"Apollo Program" in Nanoscale: Landing and Exploring Cell-Surface with DNA Nanotechnology.

Plasma membranes are the fundamental mediators through which cells communicate with their surrounding environment. The techniques to monitor or synthetically manipulate the cell membranes are attractive tools to engineer the functions of cells as well as their local microenvironment. Current advances of biomolecular science enable the insertion of functional compounds onto cell-surface via external integration or genetic engineering to manipulate cell membrane function. Recently, the DNA nanotechnology made it possible to use synthetic DNA as an emerging and promising molecular toolkit for anchoring and exploring cell-surface. In this review, the latest advances of DNA nanotechnology on cell-surface are summarized. We first give an overview of commonly used strategies for installing DNA nanodevices onto cell-surface including amphiphilic interaction, covalent modification, and affinity labeling. Then the biological applications of DNA nanodevices on cell membranes are reviewed. By integrating functional nucleic acids as recognition elements, DNA sensors are fabricated to monitor the cellular microenvironment and membrane activities. In addition, the programmable behaviors of DNA on cell-surface are also discussed, which include biomimicry and the regulation of membrane functions. Finally, we analyze the current challenges in the development of DNA nanotechnology on cell-surface as well as their prospects in bioimaging and cancer therapy.

Aptamer-Functionalized DNA Nanostructures for Biological Applications.

DNA nanostructures hold great promise for various applications due to their remarkable properties, including programmable assembly, nanometric positional precision, and dynamic structural control. The past few decades have seen the development of various kinds of DNA nanostructures that can be employed as useful tools in fields such as chemistry, materials, biology, and medicine. Aptamers are short single-stranded nucleic acids that bind to specific targets with excellent selectivity and high affinity and play critical roles in molecular recognition. Recently, many attempts have been made to integrate aptamers with DNA nanostructures for a range of biological applications. This review starts with an introduction to the features of aptamer-functionalized DNA nanostructures. The discussion then focuses on recent progress (particularly during the last five years) in the applications of these nanostructures in areas such as biosensing, bioimaging, cancer therapy, and biophysics. Finally, challenges involved in the practical application of aptamer-functionalized DNA nanostructures are discussed, and perspectives on future directions for research into and applications of aptamer-functionalized DNA nanostructures are provided.

Hybridization chain reaction-based nanoprobe for cancer cell recognition and amplified photodynamic therapy.

Precision diagnosis and effective treatment are the cores of early cancer therapy. Here, for the first time, we report a hybridization chain reaction-based nanoprobe for selective and sensitive cancer cell recognition and amplified photodynamic therapy.

Aptamer-functionalized nanoscale metal-organic frameworks for targeted photodynamic therapy.

Photodynamic therapy (PDT) has been applied in clinical cancer treatment. Here we report an aptamer-functionalized nanoscale metal-organic framework for targeted PDT. Our nanosystem can be easily prepared and successfully used for targeted PDT with a significantly enhanced therapeutic efficacy in vitro and in vivo. Methods: By combining the strong binding ability between phosphate-terminated aptamers and Zr-based nanoscale metal-organic frameworks (Zr-NMOFs) and the intercalation of photosensitizer TMPyP4 within the G-quadruplex DNA structure, TMPyP4-G4-aptamer-NMOFs were prepared. The characteristics and photodynamic performance of TMPyP4-G4-aptamer-NMOFs were examined after preparation. Then, we studied their stability, specific recognition ability, and phototoxicity in vitro. For in vivo experiments, the nanosystem was intratumorally injected into a HeLa subcutaneous xenograft tumor mouse model. After irradiation on day 0, mice were further injected with the nanosystem on day 5 and were again subjected to laser irradiation for 30 min. Tumor volumes and body weights of all mice were measured by caliper every 2 days after the treatment. Results: The nanosystem induced 90% cell death of targeted cells. In contrast, the control cells maintained about 40% cell viability at the same concentration of nanosystem. For the in vivo experiments, the nanosystem-treated group maintained more than 76% inhibition within the entire experimental period. Conclusion: We have demonstrated that our smart TMPyP4-G4-sgc8-NMOFs nanosystem can be used for targeted cancer therapy with high efficiency.

Sub-5 nm nanobowl gaps electrochemically templated by SiO2-coated Au nanoparticles as surface-enhanced Raman scattering hot spots.

Large-area submonolayer and monolayer Au nanoparticle (NP) arrays with sub-5 nm nanobowl gaps for giant electromagnetic enhancement were created by partially embedding SiO2-coated Au NP arrays in an electrochemically deposited Au film, followed by the removal of the SiO2 shells.