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DNA Nanotechnology: From Structure To Functionality
W. Wong, J. Chen, Jinglin Fu, Xiaoyi Fu, G. Ke, Megan E. Kizer, Yuhan Kong, H. Kuang, Feng Li, X. H. Liang, H. Liu, Yizhen Liu, Hongmin Meng, Brian Minevich, Sung Won Oh, Lixia Shi, Yun Tan, Leilei Tian, Fuan Wang, Guan A. Wang, Lihua Wang, Maggie Wang, Zhicheng Wang, Zixiang Wei, Xuemei Xu, C. Fan, Yonggang Ke, Ying Zhu, Jiliang Liu
Published 2020 ·
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Time to take this seriously.
Self-assembly, which is ubiquitous in living systems, also stimulates countless synthetic molecular self-assembling systems. Most synthetic self-assemblies are realized by passive processes, going from high-energy states to thermodynamic equilibrium. Conversely, living systems work out of equilibrium, meaning they are energy-consuming, dissipative and active. In recently years, chemists have made extensive efforts to design artificial active self-assembly systems, which will be pivotal to emulating and understanding life. Among various strategies, emerging approaches based on DNA nanotechnology have attracted a lot of attention. Structuralas well as dynamic-DNA-nanotechnology offer diverse tools with which to design building blocks and to shape their assembly behaviors. To achieve active self-assembly, a synergy of diverse DNA techniques is essential, including structural design, controllable assembly–disassembly, autonomous assembly, molecular circuits, biochemical oscillators, and so on. In this review, we introduce progress towards, or related to, active assembly via DNA nanotechnology. Dynamic DNA assembly systems ranging from passive assembly–disassembly systems, to autonomous assembly systems to sophisticated artificial metabolism and time-clocking oscillation systems will be discussed. We catalogue these systems from the perspective of free energy change with the reaction process. We end the review with a brief outlook and discussion.
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Dynamically Programmed Switchable DNA Hydrogels Based on a DNA Circuit Mechanism.
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Electrostatic nucleic acid nanoassembly enables hybridization chain reaction in living cells for ultrasensitive mRNA imaging.
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SERS-active Au@Ag nanorod dimers for ultrasensitive dopamine detection.
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Advances in Industrial Biotechnology Using CRISPR-Cas Systems.
P. D. Donohoue (2018)
Polyhedra Self-Assembled from DNA Tripods and Characterized with 3D DNA-PAINT
Ryosuke Iinuma (2014)
Transition from isolated to collective modes in plasmonic oligomers.
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Sensitive Zn(2+) sensor based on biofunctionalized nanopores via combination of DNAzyme and DNA supersandwich structures.
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Nonlinear Regulation of Enzyme-free DNA Circuitry with Ultrasensitive Switches.
Wei Lai (2019)
Controlled aggregation of DNA functionalized poly(phenylene-vinylene).
Daniel Gudnason (2018)
An aptamer-tethered, DNAzyme-embedded molecular beacon for simultaneous detection and regulation of tumor-related genes in living cells.
Shengfeng Wang (2019)
Low-Fouling Surface Plasmon Resonance Sensor for Highly Sensitive Detection of MicroRNA in a Complex Matrix Based on the DNA Tetrahedron.
Wenyan Nie (2018)
A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms.
Qingsheng Guo (2016)
Plasmonic Au-Ag Janus Nanoparticle Engineered Ratiometric Surface-Enhanced Raman Scattering Aptasensor for Ochratoxin A Detection.
Fangjie Zheng (2019)
Simultaneous Drug Targeting of the Promoter MYC G-Quadruplex and BCL2 i-Motif in Diffuse Large B-Cell Lymphoma Delays Tumor Growth.
Samantha Kendrick (2017)
Single-stranded DNA and RNA origami
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Engineering target-responsive hydrogels based on aptamer-target interactions.
Huanghao Yang (2008)
Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation
Antonia A Dominguez (2016)
A Responsive "Nano String Light" for Highly Efficient mRNA Imaging in Living Cells via Accelerated DNA Cascade Reaction.
Kewei Ren (2018)
Target-responsive DNA hydrogel mediated "stop-flow" microfluidic paper-based analytic device for rapid, portable and visual detection of multiple targets.
Xiaofeng Wei (2015)
Site-specific covalent labeling of His-tag fused proteins with a reactive Ni(II)-NTA probe.
Sho-hei Uchinomiya (2009)
Multifluorophore DNA Origami Beacon as a Biosensing Platform.
Denis Selnihhin (2018)
Programmed Switching of Single Polymer Conformation on DNA Origami.
Abhichart Krissanaprasit (2016)
RNAi therapeutic and its innovative biotechnological evolution.
Yuhua Weng (2019)
Electrochemical detection of nucleic acids, proteins, small molecules and cells using a DNA-nanostructure-based universal biosensing platform
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On the biophysics and kinetics of toehold-mediated DNA strand displacement
Niranjan Srinivas (2013)
Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences
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Phase behavior of nanoparticles assembled by DNA linkers.
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Label-free and enzyme-free colorimetric detection of microRNA by catalyzed hairpin assembly coupled with hybridization chain reaction.
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A highly sensitive immuno-PCR assay for detection of H5N1 avian influenza virus
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Streptavidin-triggered signal amplified fluorescence polarization for analysis of DNA-protein interactions.
Jae-Won Choi (2016)
Real-time quantitative PCR.
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How to Construct DNA Hydrogels for Environmental Applications: Advanced Water Treatment and Environmental Analysis.
Yingrong Wang (2018)
Effective expression of small interfering RNA in human cells
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Stabilization of VEGF G-quadruplex and inhibition of angiogenesis by quindoline derivatives.
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Multilayer DNA origami packed on a square lattice.
Yonggang Ke (2009)
Amplified electrochemiluminescence detection of nucleic acids by hairpin probe-based isothermal amplification.
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Aptazyme-Gold Nanoparticle Sensor for Amplified Molecular Probing in Living Cells.
Y. Yang (2016)
In vitro selection of RNA molecules that bind specific ligands
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Toehold-Mediated Displacement of an Adenosine-Binding Aptamer from a DNA Duplex by its Ligand.
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Design and self-assembly of two-dimensional DNA crystals
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Conditionally fluorescent molecular probes for detecting single base changes in double-stranded DNA.
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Environmentally responsive plasmonic nanoassemblies for biosensing.
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Recent progresses in DNA nanostructure-based biosensors for detection of tumor markers.
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Yingwei Zhang (2019)
A switchable DNA origami nanochannel for regulating molecular transport at the nanometer scale.
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Fast and quantitative differentiation of single-base mismatched DNA by initial reaction rate of catalytic hairpin assembly.
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Sequence-regulated copolymers via tandem catalysis of living radical polymerization and in situ transesterification.
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Photon-upconverting nanoparticles for optical encoding and multiplexing of cells, biomolecules, and microspheres.
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Step-Growth Polymerization of Inorganic Nanoparticles
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A Pharmacological Chaperone Molecule Induces Cancer Cell Death by Restoring Tertiary DNA Structures in Mutant hTERT Promoters.
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Noncovalent Binding to DNA: Still a Target in Developing Anticancer Agents.
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Molecular dynamics study of thrombin capture by aptamers TBA26 and TBA29 coupled to a DNA origami
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DNA Nanotechnology-Enabled Drug Delivery Systems.
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Visual detection of gene mutations based on isothermal strand-displacement polymerase reaction and lateral flow strip.
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Triple Raman Label-Encoded Gold Nanoparticle Trimers for Simultaneous Heavy Metal Ion Detection.
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Colorimetric biosensing using smart materials.
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Highly sensitive ligand-binding assays in pre-clinical and clinical applications: immuno-PCR and other emerging techniques.
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Genetical Implications of the Structure of Deoxyribonucleic Acid
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Sensitive detection of intracellular RNA of human telomerase by using graphene oxide as a carrier to deliver the assembly element of hybridization chain reaction.
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Design of a novel electrochemical biosensor based on intramolecular G-quadruplex DNA for selective determination of lead(II) ions
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Simultaneous Measurement of the Dissolution Kinetics of Responsive DNA Hydrogels at Multiple Length Scales.
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Hybridization chain reaction-based fluorescence immunoassay using DNA intercalating dye for signal readout.
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Complex shapes self-assembled from single-stranded DNA tiles
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Label-free electrochemical detection of HepG2 tumor cells with a self-assembled DNA nanostructure-based aptasensor
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Control of DNA strand displacement kinetics using toehold exchange.
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Enzyme-free quantification of exosomal microRNA by the target-triggered assembly of the polymer DNAzyme nanostructure.
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Ribozyme catalysis: not different, just worse
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A Chiral-Nanoassemblies-Enabled Strategy for Simultaneously Profiling Surface Glycoprotein and MicroRNA in Living Cells.
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Self-assembly of DNA Nanohydrogels with Controllable Size and Stimuli-Responsive Property for Targeted Gene Regulation Therapy
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DNA-Nanotechnology-Enabled Chiral Plasmonics: From Static to Dynamic.
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Aptasensor for environmental monitoring
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A Graphene-Silver Nanoparticle-Silicon Sandwich SERS Chip for Quantitative Detection of Molecules and Capture, Discrimination, and Inactivation of Bacteria.
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Binary self-assembly of highly symmetric DNA nanocages via sticky-end engineering
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Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage
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Biological Molecules-Governed Plasmonic Nanoparticle Dimers with Tailored Optical Behaviors.
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DNA cage delivery to mammalian cells.
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Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc02761g
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Quadruplex DNA: sequence, topology and structure
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Three-arm nucleic acid junctions are flexible.
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Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9
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Ultrasensitive SERS detection of VEGF based on a self-assembled Ag ornamented-AU pyramid superstructure.
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Monolithic 3D Cross-Linked Polymeric Graphene Materials and the Likes: Preparation and Their Redox Catalytic Applications.
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The current state and future directions of RNAi-based therapeutics
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Long Non-Coding RNAs in the Regulation of Gene Expression: Physiology and Disease
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Lifetime-engineered NIR-II nanoparticles unlock multiplexed in vivo imaging
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Knocking down disease: a progress report on siRNA therapeutics
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Beyond the Fold: Emerging Biological Applications of DNA Origami
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DNA-guided crystallization of colloidal nanoparticles
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Precisely Controlled 2D Free-Floating Nanosheets of Amphiphilic Molecules through Frame-Guided Assembly.
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Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA
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"Sense-and-Treat" DNA Nanodevice for Synergetic Destruction of Circulating Tumor Cells.
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Ultrasensitive Detection of Prostate-Specific Antigen and Thrombin Based on Gold-Upconversion Nanoparticle Assembled Pyramids.
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A mechanism for gene conversion in fungi.
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Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications.
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"DNA Origami Traffic Lights" with a Split Aptamer Sensor for a Bicolor Fluorescence Readout.
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Site-specific DNA-antibody conjugates for specific and sensitive immuno-PCR
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KRAS oncogene repression in colon cancer cell lines by G-quadruplex binding indolo[3,2-c]quinolines
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Electrochemical Biosensors for Cancer Biomarkers Detection: Recent Advances and Challenges
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Dual-Mode Ultrasensitive Quantification of MicroRNA in Living Cells by Chiroplasmonic Nanopyramids Self-Assembled from Gold and Upconversion Nanoparticles.
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Aluminum Nanocrystals: A Sustainable Substrate for Quantitative SERS-Based DNA Detection.
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Circulating mutant DNA to assess tumor dynamics
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Magnetic Bead-Based Multiplex DNA Sequence Detection of Genetically Modified Organisms Using Quantum Dot-Encoded Silicon Dioxide Nanoparticles
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I-motif DNA structures are formed in the nuclei of human cells
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Nucleic acid dendrimers: novel biopolymer structures
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Cuboid Vesicles Formed by Frame-Guided Assembly on DNA Origami Scaffolds.
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Interparticle coupling effect on the surface plasmon resonance of gold nanoparticles: from theory to applications.
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Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes.
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An immobile nucleic acid junction constructed from oligonucleotides
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Aptasensor with Expanded Nucleotide Using DNA Nanotetrahedra for Electrochemical Detection of Cancerous Exosomes.
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Structural studies of LNA:RNA duplexes by NMR: conformations and implications for RNase H activity.
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Voltammetric determination of DNA based on regulation of DNA strand displacement using an allosteric DNA toehold
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Three-Dimensional DNA Origami as Programmable Anchoring Points for Bioreceptors in Fiber Optic Surface Plasmon Resonance Biosensing.
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Reversible Self-Assembly of Nanoprobes in Live Cells for Dynamic Intracellular pH Imaging.
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Modular DNA strand-displacement controllers for directing material expansion
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Toehold-mediated DNA logic gates based on host-guest DNA-GNPs.
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A System for Stable Expression of Short Interfering RNAs in Mammalian Cells
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Programming molecular topologies from single-stranded nucleic acids
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A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles.
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DNA block copolymers: functional materials for nanoscience and biomedicine.
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Combining cooperativity with sequestration: a novel strategy for discrimination of single nucleotide variants.
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Stabilization and induction of oligonucleotide i-motif structure via graphene quantum dots.
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A pH-responsive DNA nanomachine-controlled catalytic assembly of gold nanoparticles.
Dongbao Yao (2016)
Designer DNA architecture offers precise and multivalent spatial pattern-recognition for viral sensing and inhibition
Paul S Kwon (2019)
MRI detection of thrombin with aptamer functionalized superparamagnetic iron oxide nanoparticles.
M. V. Yigit (2008)
DNA Polymer Nanoparticles Programmed via Supersandwich Hybridization for Imaging and Therapy of Cancer Cells.
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A single-stranded architecture for cotranscriptional folding of RNA nanostructures
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Enzyme Immobilization: The Quest for Optimum Performance
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Quadruplex priming amplification combined with nicking enzyme for diagnostics.
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Metabolic compartmentation: symbiotic, organellar, multienzymic, and microenvironmental.
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Advancement of the Emerging Field of RNA Nanotechnology
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Versatile Electrochemiluminescence and Electrochemical "On-Off" Assays of Methyltransferases and Aflatoxin B1 Based on a Novel Multifunctional DNA Nanotube.
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An in situ assembly of a DNA-streptavidin dendrimer nanostructure: a new amplified quartz crystal microbalance platform for nucleic acid sensing.
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A simple and rapid method for the preparation of plant genomic DNA for PCR analysis.
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Immunomagnetic antibody plus aptamer pseudo-DNA nanocatenane followed by rolling circle amplication for highly-sensitive CTC detection.
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A Ratiometric Fluorescent Bioprobe Based on Carbon Dots and Acridone Derivate for Signal Amplification Detection Exosomal microRNA.
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RNA mimics of green fluorescent protein
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mRNA-Initiated, Three-Dimensional DNA Amplifier Able to Function inside Living Cells.
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Enzyme-Free Nucleic Acid Logic Circuits
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Aptamer/Protein Proximity Binding-Triggered Molecular Machine for Amplified Electrochemical Sensing of Thrombin.
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Biomedical Applications of DNA-Based Hydrogels
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Immuno-PCR: a promising ultrasensitive diagnostic method to detect antigens and antibodies.
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A DNA Origami-Based Chiral Plasmonic Sensing Device.
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Dynamic Chiral Nanoparticle Assemblies and Specific Chiroplasmonic Analysis of Cancer Cells.
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A DNA-Based Nanocarrier for Efficient Gene Delivery and Combined Cancer Therapy.
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Addressable activated cascade DNA sequential logic circuit model for processing identical input molecules.
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Perspectives on chemistry and therapeutic applications of Locked Nucleic Acid (LNA).
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A naphthalene diimide G-quadruplex ligand inhibits cell growth and down-regulates BCL-2 expression in an imatinib-resistant gastrointestinal cancer cell line.
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Chirality-based Au@Ag Nanorod Dimers Sensor for Ultrasensitive PSA Detection.
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DNA origami/gold nanorod hybrid nanostructures for the circumvention of drug resistance.
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Protein detection using proximity-dependent DNA ligation assays
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Molecular engineering of chiral colloidal liquid crystals using DNA origami.
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Smart nanocontainers and nanoreactors.
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Electrochemical Biosensor for MicroRNA Detection Based on Cascade Hybridization Chain Reaction
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An autonomous molecular computer for logical control of gene expression
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Coupling hybridization chain reaction with catalytic hairpin assembly enables non-enzymatic and sensitive fluorescent detection of microRNA cancer biomarkers.
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Chiral Inorganic Nanostructures.
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Dual Quantification of MicroRNAs and Telomerase in Living Cells.
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Site-selective photoinduced cleavage and profiling of DNA by chiral semiconductor nanoparticles
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Lighting Up MicroRNA in Living Cells by the Disassembly of Lock-Like DNA-Programmed UCNPs-AuNPs through the Target Cycling Amplification Strategy.
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Aptamers as targeted therapeutics: current potential and challenges
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A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
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A Facile Method for Reversibly Linking a Recombinant Protein to DNA
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DNA Origami with Complex Curvatures in Three-Dimensional Space
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The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes.
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Role of Dicer in posttranscriptional RNA silencing.
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Bioinspired fluorescent dipeptide nanoparticles for targeted cancer cell imaging and real-time monitoring of drug release.
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Targeting the BCL2 Gene Promoter G‐Quadruplex with a New Class of Furopyridazinone‐Based Molecules
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Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues
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Detecting antigens by quantitative immuno-PCR
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Cell penetrating thiazole peptides inhibit c-MYC expression via site-specific targeting of c-MYC G-quadruplex
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Alternating Plasmonic Nanoparticle Heterochains Made by Polymerase Chain Reaction and Their Optical Properties.
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Detection of single-nucleotide polymorphisms using an ON-OFF switching of regenerated biosensor based on a locked nucleic acid-integrated and toehold-mediated strand displacement reaction.
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DETECTION OF CIRCULATING TUMOR DNA IN EARLY AND LATE STAGE HUMAN MALIGNANCIES
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Aptamers as therapeutic and diagnostic agents.
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DNAzyme-based biosensor for detection of lead ion: A review
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An autonomous nonenzymatic concatenated DNA circuit for amplified imaging of intracellular ATP.
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Highly selective detection of single-nucleotide polymorphisms using a quartz crystal microbalance biosensor based on the toehold-mediated strand displacement reaction.
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Serial processing of biological reactions using flow-through microfluidic devices: coupled PCR/LDR for the detection of low-abundant DNA point mutations.
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An aptamer-enabled DNA nanobox for protein sensing.
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Highly sensitive and selective label-free optical detection of mercuric ions using photon upconverting nanoparticles.
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Rational design of "turn-on" allosteric DNAzyme catalytic beacons for aqueous mercury ions with ultrahigh sensitivity and selectivity.
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From binary to quaternary: high-tolerance of multi-acceptors enables development of efficient polymer solar cells
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Intelligent DNA machine for the ultrasensitive colorimetric detection of nucleic acids.
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Solution-based circuits enable rapid and multiplexed pathogen detection.
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Two-dimensional nanoparticle arrays show the organizational power of robust DNA motifs.
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Rapid prototyping of 3D DNA-origami shapes with caDNAno
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A DNA tetrahedron-based molecular beacon for tumor-related mRNA detection in living cells.
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DNA assembly of carbon dots and 5-fluorouracil used for room-temperature phosphorescence turn-on sensing of AFP and AFP-triggered simultaneous release of dual-drug
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Assembled plasmonic asymmetric heterodimers with tailorable chiroptical response.
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Simple and Efficient Method to Purify DNA–Protein Conjugates and Its Sensing Applications
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Construction of a Multiple-aptamer-based DNA Logic Device on Live Cell Membranes via Associative Toehold Activation for Accurate Cancer Cell Identification.
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DNA meets synthetic polymers--highly versatile hybrid materials.
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The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides.
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Genome sequencing identifies major causes of severe intellectual disability
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Amplified MicroRNA Detection and Intracellular Imaging Based on an Autonomous and Catalytic Assembly of DNAzyme.
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Engineering of switchable aptamer micelle flares for molecular imaging in living cells.
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Immuno-PCR: high sensitivity detection of proteins by nucleic acid amplification.
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A Singlet Oxygen Generating Agent by Chirality-dependent Plasmonic Shell-Satellite Nanoassembly.
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Versatile Catalytic Deoxyribozyme Vehicles for Multimodal Imaging-Guided Efficient Gene Regulation and Photothermal Therapy.
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DNA nanotechnology for nucleic acid analysis: multifunctional molecular DNA machine for RNA detection.
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Coupling a universal DNA circuit with graphene sheets/polyaniline/AuNPs nanocomposites for the detection of BCR/ABL fusion gene.
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Diagnostic Applications of Nucleic Acid Circuits
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Metal Sensing by DNA.
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Spatial Organization of Enzyme Cascade on a DNA Origami Nanostructure.
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A universal probe design for colorimetric detection of single-nucleotide variation with visible readout and high specificity
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Propeller-Like Nanorod-Upconversion Nanoparticle Assemblies with Intense Chiroptical Activity and Luminescence Enhancement in Aqueous Phase.
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Portable and sensitive quantitative detection of DNA based on personal glucose meters and isothermal circular strand-displacement polymerization reaction.
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Photoactive Hybrid AuNR-Pt@Ag2S Core–Satellite Nanostructures for Near-Infrared Quantitive Cell Imaging
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Recent Progress of Targeted G-Quadruplex-Preferred Ligands Toward Cancer Therapy
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A hemin/G-quadruplex acts as an NADH oxidase and NADH peroxidase mimicking DNAzyme.
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Frequent Homologous Recombination Events between Molecules of One RNA Component in a Multipartite RNA Virus
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Chiral Upconversion Heterodimers for Quantitative Analysis and Bioimaging of Antibiotic-Resistant Bacteria In Vivo.
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Fluorescence Resonance Energy Transfer-Based DNA Nanoprism with a Split Aptamer for Adenosine Triphosphate Sensing in Living Cells.
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Au nanorod helical superstructures with designed chirality.
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Multilayer DNA origami packed on hexagonal and hybrid lattices.
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Efficient colorimetric fluoride anion chemosensors based-on simple naphthodipyrrolidone dyes
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MicroRNA signatures in human cancers
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DNA aptamer-based carrier for loading proteins and enhancing the enzymatic activity
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The importance of loop length on the stability of i-motif structures
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Self-assembly of chiral nanoparticle pyramids with strong R/S optical activity.
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Reversible plasmonic probe sensitive for pH in micro/nanospaces based on i-motif-modulated morpholino-gold nanoparticle assembly.
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Nucleus-targeted DNA tetrahedron as a nanocarrier of metal complexes for enhanced glioma therapy.
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Higher order DNA structure in macronuclear chromatin of the hypotrichous ciliate Oxytricha nova.
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In-situ immuno-PCR to detect antigens
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Demonstration that Drug-targeted Down-regulation of MYC in Non-Hodgkins Lymphoma Is Directly Mediated through the Promoter G-quadruplex*
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Preparation, Single-Molecule Manipulation, and Energy Transfer Investigation of a Polyfluorene-graft-DNA polymer.
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Nucleic acid hybridization on an electrically reconfigurable network of gold-coated magnetic nanoparticles enables microRNA detection in blood
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Structures of helical junctions in nucleic acids
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DNA biomolecular-electronic encoder and decoder devices constructed by multiplex biosensors
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Programming chain-growth copolymerization of DNA hairpin tiles for in-vitro hierarchical supramolecular organization
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Superlattices assembled through shape-induced directional binding
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Ultraselective electrochemiluminescence biosensor based on locked nucleic acid modified toehold-mediated strand displacement reaction and junction-probe.
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