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A novel photosensitive dual-sensor for simultaneous detection of nucleic acids and small chemical molecules
摘要： Sensors that can rapidly and specifically detect nucleic acids and chemical molecules can revolutionize the diagnosis and treatment of diseases by allowing molecular-level informations to be used during the routine medicines. In this study, we demonstrated a novel dual-sensor that can be used to simultaneously detect any nucleic acids and chemical molecules whose binding aptamers can be found or synthesized. In the developed dual-sensor, the specifically designed PTG (a photosensitive azobenzene derivative carrying one photo-isomerizable azobenzene moiety, one threoninol terminal and one guanidinium terminal) molecules are introduced into the unwinding region of two T7 promoters, and two DNA bubbles are introduced upstream of the two T7 promoters. Without the target, the indicating gene in the dual-tensor would not be expressed since the binding with RNAPs (RNA polymerases) cannot melt the T7 promoter for the indicating gene due to the integration of the DNA double strands via the PTG molecules, manifesting the absence of the target nucleic acid and chemical molecule. While with the presence of the target nucleic acid and/or chemical molecule, the indicating gene would be expressed as the T7 promoter contained in the enlarged DNA bubble can be melted and transcribed by the bound RNAPs as the enlarged DNA bubble can help the separation of the two DNA strands, demonstrating the existence of target nucleic acid and/or chemical molecule.
关键词： Nucleic acids,DNA melting,Gene expression,DNA nanotechnology,Dual-sensor
更新于2025-09-23 15:23:52
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Single Particle Tracking and Super-Resolution Imaging of Membrane-Assisted Stop-and-Go Diffusion and Lattice Assembly of DNA Origami
摘要： DNA nanostructures offer the possibility to mimic functional biological membrane components due to their nanometer-precise shape configurability and versatile biochemical functionality. Here we show that the diffusional behavior of DNA nanostructures and their assembly into higher order membrane-bound lattices can be controlled in a stop-and-go manner and that the process can be monitored with super-resolution imaging. The DNA structures are transiently immobilized on glass-supported lipid bilayers by changing the mono- and divalent cation concentrations of the surrounding buffer. Using DNA-PAINT super-resolution microscopy, we confirm the fixation of DNA origami structures with different shapes. On mica-supported lipid bilayers, in contrast, we observe residual movement. By increasing the concentration of NaCl and depleting MgCl2, a large fraction of DNA structures restarts to diffuse freely on both substrates. After addition of a set of oligonucleotides that enables three Y-shaped monomers to assemble into a three-legged shape (triskelion), the triskelia can be stopped and super-resolved. Exchanging buffer and adding another set of oligonucleotides triggers the triskelia to diffuse and assemble into hexagonal 2D lattices. This stop-and-go imaging technique provides a way to control and observe the diffusional behavior of DNA nanostructures on lipid membranes that could also lead to control of membrane-associated cargos.
关键词： single-particle tracking,DNA origami,diffusion,super-resolution microscopy,lipid membrane,DNA nanotechnology
更新于2025-09-23 15:23:52
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Fluorescence Resonance Energy Transfer-Based Photonic Circuits Using Single-Stranded Tile Self-Assembly and DNA Strand Displacement
摘要： Structural DNA nanotechnology has great potential in the fabrication of complicated nanostructures and devices capable of bio-sensing and logic function. A variety of nanostructures with desired shapes have been created in the past few decades. But the application of nanostructures remains to be fully studied. Here, we present a novel biological information processing system constructed on a self-assembled, spatially addressable single-stranded tile (SST) nanostructure as DNA nano-manipulation platform that created by SST self-assembly technology. Utilizing DNA strand displacement technology, the fluorescent dye that is pre-assembled in the nano-manipulation platform is transferred from the original position to the destination, which can achieve photonic logic circuits by FRET signal cascades, including logic AND, OR, and NOT gates. And this transfer process is successfully validated by visual DSD software. The transfer process proposed in this study may provide a novel method to design complicated biological information processing system constructed on a SST nanostructure, and can be further used to develop intelligent delivery of drug molecules in vivo.
关键词： Single-Stranded Tile,Intelligent Delivery,FRET,DNA Nanotechnology,Photonic Logic Circuits,DNA Strand Displacement
更新于2025-09-23 15:22:29
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A Review on Optical Imaging of DNA Nanostructures and Dynamic Processes
摘要： This article reviews recent advances in optical imaging methods for characterizing self-assembled DNA nanosystems, with particular emphasis on super-resolved fluorescence microscopy. Several advanced strategies are developed to obtain accurate and detailed images of intricate DNA nanogeometries and to perform precise tracking of molecular motions in dynamic processes. We present state-of-the-art instruments and imaging strategies including localization microscopy and spectral imaging. We discuss how they are used in biological studies and biomedical applications, and also provide current challenges and future outlook. Overall, this review serves as a practical guide in optical microscopy for the field of DNA nanotechnology.
关键词： super-resolution microscopy,fluorescence microscopy,optical imaging,DNA nanostructures,DNA nanotechnology
更新于2025-09-23 15:21:21
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Thermoplasmonica??Triggered Release of Loads from DNAa??Modified Hydrogel Microcapsules Functionalized with Au Nanoparticles or Au Nanorods
摘要： Microcapsules consisting of hydrogel shells cross-linked by glucosamine–boronate ester complexes and duplex nucleic acids, loaded with dyes or drugs and functionalized with Au nanoparticles (Au NPs) or Au nanorods (Au NRs), are developed. Irradiation of Au NPs or Au NRs results in the thermoplasmonic heating of the microcapsules, and the dissociation of the nucleic acid cross-linkers. The separation of duplex nucleic acid cross-linkers leads to low-stiffness hydrogel shells, allowing the release of loads. Switching off the light-induced plasmonic heating results in the regeneration of stiff hydrogel shells protecting the microcapsules, leading to the blockage of release processes. The thermoplasmonic release of tetramethylrhodamine-dextran, Texas Red-dextran, doxorubicin-dextran (DOX-D), or camptothecin-carboxymethylcellulose (CPT-CMC) from the microcapsules is introduced. By loading the microcapsules with two different drugs (DOX-D and CPT-CMC), the light-controlled dose release is demonstrated. Cellular experiments show efficient permeation of Au NPs/DOX-D or Au NRs/DOX-D microcapsules into MDA-MB-231 cancer cells and inefficient uptake by MCF-10A epithelial breast cells. Cytotoxicity experiments reveal selective thermoplasmon-induced cytotoxicity of the microcapsules toward MDA-MB-231 cancer cells as compared to MCF-10A cells. Also, selective cytotoxicity towards MDA-MB-231 cancer cells upon irradiation of the Au NPs- and Au NRs-functionalized microcapsules at λ = 532 or 910 nm is demonstrated.
关键词： doxorubicin,cytotoxicity,DNA nanotechnology,plasmon,switchable drug release
更新于2025-09-23 15:21:01
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Three dimension nanoparticle assemblies with tunable plasmonics via a layer-by-layer process
摘要： Recently, DNA has emerged as a designer material for the controlled assembly of nanoparticles. The unique programmability of Watson-crick base pairing offers limitless control over assembly via specific interactions. At the same time, reliance on non-specific interactions, such as layer-by-layer (LbL) assembly offers a simple assembly method, albeit with limited control. Here, by assembling DNA-capped gold nanoparticles in a LbL fashion we combine these two approaches and present a simple and robust method to construct large-scale three-dimensional nanoparticle assemblies with readily tunable plasmonics. Through variation of the DNA ligand and the nanoparticle core size the morphology of the three-dimensional nanoparticle assemblies was carefully adjustabed. These morphological changes, confirmed using grazing incidence x-ray scattering, enabled the tuning of the plasmonic behavior of the three-dimensional nanoparticle assemblies. The morphology could also be modified in real-time through water vapor induced swelling enabling dynamic tuning of the optical properties. The introduction of the DNA ligand to the LbL assembly method presented here imparted tunability to the process previously inaccessible with other nanoparticle ligands and presents a platform with which to create optically active materials of various compositions.
关键词： Layer-by-layer,Plasmonics,DNA nanotechnology,Nanoparticle assembly
更新于2025-09-12 10:27:22
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Polarized Single-Particle Quantum Dot Emitters through Programmable Cluster Assembly
摘要： Although fluorescence and lifetimes of nanoscale emitters can be manipulated by plasmonic materials, it is harder to control polarization due to strict requirements on emitter environments. An ability to engineer 3D nano-architectures with nanoscale precision is needed for controlled polarization of nanoscale emitters. Here, we show that prescribed 3D hetero-cluster architectures with polarized emission can be successfully assembled from nanoscale fluorescent emitters and metallic nanoparticles using DNA-based self-assembly methods. An octahedral DNA origami frame serves as a programmable scaffold for heterogeneous nanoparticle assembly into prescribed clusters. Internal space and external connections of the frames are programmed to coordinate spherical quantum dots (QDs) and gold nanoparticles (AuNPs) into hetero-cluster architectures through site-specific DNA encodings. We demonstrate and characterize assembly of these architectures using in-situ and ex-situ structural methods. These cluster nanodevices exhibit polarized light emission with a plasmon-induced dipole along the QD-AuNP nanocluster axis, as observed by single-cluster optical probing. Moreover, emittance properties can be tuned via cluster design. Through a systematic study, we analyzed and established the correlation between cluster architecture, cluster orientation and polarized emission at a single-emitter level. Excellent correspondence between the optical behavior of these clusters and theoretical predictions was observed. This approach provides the basis for rational creation of single-emitter 3D nanodevices with controllable polarization output using a highly customizable DNA assembly platform.
关键词： DNA nanotechnology,polarization,fluorescence,quantum dots,nanoparticles cluster,self-assembly
更新于2025-09-12 10:27:22
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A rotary plasmonic nanoclock
摘要： One of the fundamental challenges in nanophotonics is to gain full control over nanoscale optical elements. The precise spatiotemporal arrangement determines their interactions and collective behavior. To this end, DNA nanotechnology is employed as an unprecedented tool to create nanophotonic devices with excellent spatial addressability and temporal programmability. However, most of the current DNA-assembled nanophotonic devices can only reconfigure among random or very few defined states. Here, we demonstrate a DNA-assembled rotary plasmonic nanoclock. In this system, a rotor gold nanorod can carry out directional and reversible 360° rotation with respect to a stator gold nanorod, transitioning among 16 well-defined configurations powered by DNA fuels. The full-turn rotation process is monitored by optical spectroscopy in real time. We further demonstrate autonomous rotation of the plasmonic nanoclock powered by DNAzyme-RNA interactions. Such assembly approaches pave a viable route towards advanced nanophotonic systems entirely from the bottom-up.
关键词： DNA nanotechnology,nanophotonics,DNAzyme-RNA interactions,plasmonic nanoclock,gold nanorod
更新于2025-09-11 14:15:04