DNA Nanotags for Multiplexed Single-Particle Electron Microscopy and In Situ Electron Cryotomography

DNA nanostructures present new opportunities as Nanotags for electron microscopy (EM) imaging, leveraging their high programmability, unique shapes, biomolecule conjugation capability, and stability compatible with standard cryogenic sample preparation protocols. This perspective highlights the potential of DNA Nanotags to enable high-throughput multiplexed EM analysis and facilitate in situ particle identification for cryogenic electron tomography (cryo-ET). Meanwhile, applying Nanotags in live-cell environments requires the efficient cellular uptake of intact structures and successful cytosolic migration. Promising strategies such as employing direct cytosolic delivery platforms and expressing RNA-based Nanotags in situ are discussed, while more systematic studies are needed to fully understand the intracellular trafficking and achieve precise localization of DNA Nanotags.

• Publication year

  2024

• Venue

  JACS Au

• Publication date

  2024-12-27

• Fields of study

  Biology, Medicine, Materials Science, Engineering

• Identifiers
  DOI 10.1021/jacsau.4c00986PMID 39886579PMCID 11775714
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Cryo-electron tomography pipeline for plasma membranes

  2025cited by this paper
• DeepETPicker: Fast and accurate 3D particle picking for cryo-electron tomography using weakly supervised deep learning

  2024cited by this paper
• Cell–Surface Binding of DNA Nanostructures for Enhanced Intracellular and Intranuclear Delivery

  2024cited by this paper
• Programmable in vitro and in vivo folding of single-stranded nucleic-acid wireframe origami

  2024cited by this paper
• Genetically Encoded FerriTag as a Specific Label for Cryo-Electron Tomography

  2024cited by this paper
• High-resolution in situ structures of mammalian respiratory supercomplexes

  2024cited by this paper
• Accurate size-based protein localization from cryo-ET tomograms

  2024cited by this paper
• Cryo-electron tomography pipeline for plasma membranes

  2024cited by this paper
• A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns

  2024cited by this paper
• A modular DNA origami nanocompartment for engineering a cell-free, protein unfolding and degradation pathway

  2024cited by this paper
• Safe and effective in vivo delivery of DNA and RNA using proteolipid vehicles.

  2024cited by this paper
• Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds

  2024cited by this paper
• Coating tetrahedral DNA framework with endosomolytic peptides for improved stability and cytosolic delivery

  2024cited by this paper
• CytoDirect: A Nucleic Acid Nanodevice for Specific and Efficient Delivery of Functional Payloads to the Cytoplasm.

  2023cited by this paper
• Genetically encoded multimeric tags for subcellular protein localization in cryo-EM

  2023cited by this paper
• Reversible Protection and Targeted Delivery of DNA Origami with a Disulfide-Containing Cationic Polymer.

  2023cited by this paper
• A DNA Origami-Based Gene Editing System for Efficient Gene Therapy in Vivo.

  2023influential reference
• The substrate and inhibitor binding mechanism of polyspecific transporter OAT1 revealed by high-resolution cryo-EM

  2023cited by this paper
• A facile method to prepare non-cationic mRNA lipid-nanoparticles based on frame guided assembly strategy

  2023cited by this paper
• Programmable multispecific DNA-origami-based T-cell engagers

  2023cited by this paper
• Particle picking in tomograms

  2023cited by this paper
• A novel His-tag-binding aptamer for recombinant protein detection and T cell-based immunotherapy.

  2023cited by this paper
• Genetically Encoded DNA Origami for Gene Therapy In Vivo.

  2023cited by this paper
• Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges

  2023cited by this paper
• Synthetic Cell Armor Made of DNA Origami

  2023cited by this paper
• Endosomal escape for cell-targeted proteins. Going out after going in.

  2023influential reference
• Virus Mimetic Framework DNA as a Non-LNP Gene Carrier for Modulated Cell Endocytosis and Apoptosis.

  2023cited by this paper
• High-Resolution Structural Analysis of Dyneins by Cryo-electron Microscopy.

  2023cited by this paper
• Enhanced Functional Properties of Three DNA Origami Nanostructures as Doxorubicin Carriers to Breast Cancer Cells.

  2022cited by this paper
• OUP accepted manuscript

  2022cited by this paper
• Multi-curve fitting and tubulin-lattice signal removal for structure determination of large microtubule-based motors

  2022cited by this paper
• Automated design of 3D DNA origami with non-rasterized 2D curvature

  2022cited by this paper
• Cationic lipid modification of DNA tetrahedral nanocages enhances their cellular uptake.

  2022cited by this paper
• "Shutter" Effects Enhance Protein Diffusion in Dynamic and Rigid Molecular Networks.

  2022cited by this paper
• A step-by-step protocol for capturing conformational snapshots of ligand gated ion channels by single-particle cryo-EM

  2022cited by this paper
• An ER-targeting DNA Nanodevice for Autophagy-dependent Degradation of Proteins in Membrane-bound Organelles.

  2022cited by this paper
• Nanoscale organization of two-dimensional multimeric pMHC reagents with DNA origami for CD8+ T cell detection

  2022cited by this paper
• Progressive assembly of multi-domain protein structures from cryo-EM density maps

  2022cited by this paper
• Identifying proteins in the cell by tagging techniques for cryo-electron microscopy.

  2022cited by this paper
• The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer

  2022cited by this paper
• Modular Imaging Scaffold for Single-Particle Electron Microscopy.

  2021cited by this paper
• Protein Corona Inhibits Endosomal Escape of Functionalized DNA Nanostructures in Living Cells.

  2021cited by this paper
• Machine learning-based real-time object locator/evaluator for cryo-EM data collection

  2021cited by this paper
• Shaping nanoparticle diffusion through biological barriers to drug delivery

  2021cited by this paper
• Determinants of Ligand-Functionalized DNA Nanostructure–Cell Interactions

  2021cited by this paper
• DNA Origami Penetration in Cell Spheroid Tissue Models is Enhanced by Wireframe Design

  2021cited by this paper
• Particle-by-particle in situ characterization of the protein corona via real-time 3D single-particle tracking spectroscopy.

  2021cited by this paper
• RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds

  2021cited by this paper
• Evolving cryo-EM structural approaches for GPCR drug discovery

  2021cited by this paper
• Identifying heterogeneous diffusion states in the cytoplasm by a hidden Markov model

  2021cited by this paper
• The effects of overhang placement and multivalency on cell labeling by DNA origami.

  2021cited by this paper
• DNA origami signposts for identifying proteins on cell membranes by electron cryotomography

  2021influential reference
• Size-Dependent Electroporation of Dye-Loaded Polymer Nanoparticles for Efficient and Safe Intracellular Delivery.

  2020cited by this paper
• DNA Origami-Enabled Engineering of Ligand-Drug Conjugates for Targeted Drug Delivery.

  2020cited by this paper
• Enhanced Transport of Shape and Rigidity-tuned α-lactalbumin Nanotubes across Intestinal Mucus and Cellular Barriers.

  2020cited by this paper
• Single-particle cryo-EM at atomic resolution

  2020cited by this paper
• DNA density-dependent uptake of DNA origami-based two-or three-dimensional nanostructures by immune cells.

  2020cited by this paper
• Endocytosis: The Nanoparticle and Submicron Nanocompounds Gateway into the Cell

  2020cited by this paper
• Genetically encoded tags for direct synthesis of EM-visible gold nanoparticles in cells

  2020cited by this paper
• Molecular goniometers for single-particle cryo-electron microscopy of DNA-binding proteins

  2020cited by this paper
• Disulfide-Containing Molecular Sticker Assists Cellular Delivery of DNA Nanoassemblies by Bypassing Endocytosis

  2020cited by this paper
• Time-resolved cryoEM using Spotiton

  2020cited by this paper
• Engineering Aptamer Switches for Multifunctional Stimulus‐Responsive Nanosystems

  2020cited by this paper
• tagPAINT: covalent labelling of genetically encoded protein tags for DNA-PAINT imaging

  2019cited by this paper
• Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges.

  2019cited by this paper
• Cationic Albumin Encapsulated DNA Origami for Enhanced Cellular Transfection and Stability

  2019cited by this paper
• A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo

  2018cited by this paper
• Visualization of the Cellular Uptake and Trafficking of DNA Origami Nanostructures in Cancer Cells.

  2018cited by this paper
• DNA Nanotechnology-Enabled Drug Delivery Systems.

  2018cited by this paper
• Modulation of the Cellular Uptake of DNA Origami through Control over Mass and Shape.

  2018cited by this paper
• On the Stability of DNA Origami Nanostructures in Low-Magnesium Buffers.

  2018cited by this paper
• Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins.

  2018cited by this paper
• In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs

  2018cited by this paper
• Cryo-EM in drug discovery: achievements, limitations and prospects

  2018cited by this paper
• Redox Engineering of Cytochrome c using DNA Nanostructure-Based Charged Encapsulation and Spatial Control.

  2018cited by this paper
• FerriTag is a new genetically-encoded inducible tag for correlative light-electron microscopy

  2018cited by this paper
• Non-specific interactions govern cytosolic diffusion of nanosized objects in mammalian cells

  2018cited by this paper
• Control of Membrane Binding and Diffusion of Cholesteryl-Modified DNA Origami Nanostructures by DNA Spacers.

  2018cited by this paper
• Structural stability of DNA origami nanostructures under application-specific conditions

  2018cited by this paper
• DNA Nanostructure-Programmed Like-Charge Attraction at the Cell-Membrane Interface

  2018cited by this paper
• DNA Aptamers for the Functionalisation of DNA Origami Nanostructures

  2018cited by this paper
• "DNA Origami Traffic Lights" with a Split Aptamer Sensor for a Bicolor Fluorescence Readout.

  2017cited by this paper
• Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation

  2017cited by this paper
• How Ligands Illuminate GPCR Molecular Pharmacology.

  2017cited by this paper
• Spatial Organization of Enzyme Cascade on a DNA Origami Nanostructure.

  2017cited by this paper
• Single-stranded DNA and RNA origami

  2017cited by this paper
• Single Particle Tracking: From Theory to Biophysical Applications.

  2017cited by this paper
• Spotiton: New Features and Applications

  2017cited by this paper
• Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes

  2017cited by this paper
• A new method for vitrifying samples for cryoEM.

  2016cited by this paper
• Aptamers as targeted therapeutics: current potential and challenges

  2016cited by this paper
• Design of a molecular support for cryo-EM structure determination

  2016cited by this paper
• Designer nanoscale DNA assemblies programmed from the top down

  2016cited by this paper
• Electrotransfection of Polyamine Folded DNA Origami Structures.

  2016cited by this paper
• Tumor-Penetrating Peptide-Modified DNA Tetrahedron for Targeting Drug Delivery.

  2016cited by this paper
• Assembly of multienzyme complexes on DNA nanostructures

  2016cited by this paper
• Intracellular Delivery of a Planar DNA Origami Structure by the Transferrin-Receptor Internalization Pathway.

  2016cited by this paper
• Multiplexed TEM Specimen Preparation and Analysis of Plasmonic Nanoparticles

  2015cited by this paper
• Self-assembled DNA nanoclews for the efficient delivery of CRISPR-Cas9 for genome editing.

  2015cited by this paper
• Mapping protein binding sites on the biomolecular corona of nanoparticles.

  2015cited by this paper

• Recent Advances in Targeting Regions of Interest for In Situ Cryo-Electron Tomography of Cellular Architecture.

  2026cites this paper
• Analyzing DNA Origami Nanostructure Assembly by Dynamic Light Scattering and Nanoparticle Tracking Analysis

  2025cites this paper