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Functionalizing DNA origami to investigate and interact with biological systems

NATURE REVIEWS MATERIALS (2023)

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Review Pharmacology & Pharmacy

Critical review of nucleic acid nanotechnology to identify gaps and inform a strategy for accelerated clinical translation

Kirill A. Afonin et al.

Summary: The field of therapeutic nucleic acid nanotechnology has made significant advances, with the emergence of nucleic acid nanoparticles (NANPs) offering unique properties for applications in cancer diagnosis and therapy, regulation of blood coagulation disorders, and the development of novel vaccines, immunotherapies, and gene therapies.

ADVANCED DRUG DELIVERY REVIEWS (2022)

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Article Multidisciplinary Sciences

Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility

Jeroen F. van Dyck et al.

Summary: Recent interest in oligonucleotide nanostructures has led to the use of mass spectrometry and ion mobility to study their assembly. In this study, the authors use these techniques to characterize the structure of a hexameric DNA barrel and its intermediates and byproducts. They demonstrate the ability of these methods to determine the mass, charge state, and size of noncovalent DNA assemblies and reveal the role of ionic strength in their assembly. They also identify previously undetected higher-order assemblies and assign them to larger geometric structures.

NATURE COMMUNICATIONS (2022)

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Article Chemistry, Multidisciplinary

DNA-Origami-Templated Growth of Multilamellar Lipid Assemblies

Sofia Julin et al.

Summary: Lipids play a crucial role in cellular compartments, and co-assembly of DNA origami with cationic lipids enhances the order and stability of lipid structures. This complexation strategy effectively protects DNA origami against nuclease digestion, opening up new possibilities for the construction of cell-membrane-associated components.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

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Article Chemistry, Multidisciplinary

A Tubular DNA Nanodevice as a siRNA/Chemo-Drug Co-delivery Vehicle for Combined Cancer Therapy

Zhaoran Wang et al.

Summary: By utilizing the DNA origami technique, a DNA nanodevice was constructed with siRNA and doxorubicin incorporated, enabling the release of siRNA in response to intracellular glutathione in tumors. This innovative strategy combining RNA interference and chemotherapy showed potent antitumor activity and marked biocompatibility, representing a promising approach for precise drug design in cancer therapy.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

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Article Biotechnology & Applied Microbiology

Molecular goniometers for single-particle cryo-electron microscopy of DNA-binding proteins

Tural Aksel et al.

Summary: The researchers used DNA origami technology to create molecular goniometers to assist in accurately positioning small DNA-binding proteins in cryo-electron microscopy for visualization and structural analysis. This approach is particularly effective for DNA-binding proteins with helical pseudosymmetry.

NATURE BIOTECHNOLOGY (2021)

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Article Chemistry, Physical

A DNA nanodevice-based vaccine for cancer immunotherapy

Shaoli Liu et al.

Summary: A DNA nanodevice vaccine has been developed to stimulate a tumor-specific cytotoxic T lymphocyte response, leading to inhibition of tumor growth and prevention of metastasis. The vaccine utilizes molecular adjuvants and antigen peptides within a tubular DNA nanostructure to trigger T-cell activation and cancer cytotoxicity, showing promising results in mouse cancer models. The vaccination generates long-term T-cell responses which effectively protect against tumor rechallenge.

NATURE MATERIALS (2021)

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Article Nanoscience & Nanotechnology

Protein Corona Inhibits Endosomal Escape of Functionalized DNA Nanostructures in Living Cells

Barbora Smolkova et al.

Summary: DNA nanostructures can be controlled and programmed in a EE-DN manner, and are increasingly used in various biomedical applications such as therapeutic agent delivery. Most nanomaterials become covered by a protein corona when exposed to biological liquids, affecting their cellular uptake and biological response. Studies have shown that cellular uptake of functionalized DNs is linearly dependent on cell size, and the protein corona plays a role in determining the endolysosomal vesicle escape efficiency of DNs coated with an endosome escape peptide.

ACS APPLIED MATERIALS & INTERFACES (2021)

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Article Chemistry, Multidisciplinary

Quantification of Strand Accessibility in Biostable DNA Origami with Single-Staple Resolution

Alexandra S. Eklund et al.

Summary: DNA-based nanostructures have gained interest for biomedical applications due to recent developments in protective coating strategies. Functionalized with DNA base pairing, these nanostructures' accessibility for targeting or imaging labels remains a focus of study. Evaluating this accessibility on a single handle strand level using DNA-PAINT shows that hybridization kinetics are maintained, even after applying a protective coating, enabling bioassays requiring functionality and stability.

ACS NANO (2021)

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Article Biochemical Research Methods

Chemo-Mechanical Modulation of Cell Motions Using DNA Nanosprings

Deepak Karna et al.

Summary: By utilizing DNA origami nanosprings, the clustering of integrin molecules can be controlled under different pH conditions to modulate cell motions. The nanospring coils and inhibits cell movement under acidic conditions, while it uncoils and allows cells to move under neutral conditions.

BIOCONJUGATE CHEMISTRY (2021)

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Article Biochemical Research Methods

One-Pot Synthesis of Defined-Length ssDNA for Multiscaffold DNA Origami

Willem E. M. Noteborn et al.

Summary: This study describes a simple and effective method using PCR and T7 exonuclease to produce single-stranded DNA scaffolds of defined lengths.

BIOCONJUGATE CHEMISTRY (2021)

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Article Chemistry, Physical

DNA-Origami-Based Assembly of Au@Ag Nanostar Dimer Nanoantennas for Label-Free Sensing of Pyocyanin

Vishaldeep Kaur et al.

Summary: This study designs bimetallic Ag coated Au nanostar dimers with controlled nanogap using rectangular DNA origami, showing utility as efficient SERS substrate for ultrasensitive and label-free detection of the biomarker pyocyanin. Detection limit of pyocyanin with nanoantenna biosensor was 335 pM, paving a facile route for early warning of severe bacterial infections at ultralow concentrations in infected human bodies.

CHEMPHYSCHEM (2021)

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Article Chemistry, Multidisciplinary

Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation

Zhengxiao Zhang et al.

Summary: By designing new substrates, sequence-selective rapid crosslinking reactions of protein modular adaptors (MAs) with SNAP-tag can be achieved, improving the selectivity and efficiency of the reaction.

CHEMISTRY-A EUROPEAN JOURNAL (2021)

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Article Biochemistry & Molecular Biology

Dynamic multimerization of Dab2-Myosin VI complexes regulates cargo processivity while minimizing cortical actin reorganization

Ashim Rai et al.

Summary: This study demonstrates that dynamic multimerization of myosin VI-Dab2 complexes enables cargo processivity without significant reorganization of cortical actin networks.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

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Article Multidisciplinary Sciences

DNA origami demonstrate the unique stimulatory power of single pMHCs as T cell antigens

Joschka Hellmeier et al.

Summary: By engineering a biomimetic interface, the study found that pairs of antibody-bound TCR5 serve as minimal receptor entities for effective TCR triggering, while transiently engaging antigenic pMHCs can also stimulate T cells effectively as isolated entities.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Multidisciplinary Sciences

A DNA origami-based aptamer nanoarray for potent and reversible anticoagulation in hemodialysis

Shuai Zhao et al.

Summary: This study presents a promising nanoagent based on DNA origami technology that can effectively prevent thrombosis and exhibit enhanced anticoagulant effects in animal models.

NATURE COMMUNICATIONS (2021)

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Article Chemistry, Multidisciplinary

Spatial Regulation of T-Cell Signaling by Programmed Death-Ligand 1 on Wireframe DNA Origami Flat Sheets

Trixy Fang et al.

Summary: The spatial organization of PD-L1 plays a crucial role in regulating T-cell signaling, with PD-L1 ligands at 200 nm distance being more effective in inhibiting T-cell activation and reducing IL-2 expression compared to closer distances. These findings may guide the development of nanomedicine-based immunomodulatory therapies in the future.

ACS NANO (2021)

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Article Biochemistry & Molecular Biology

DNA origami signposts for identifying proteins on cell membranes by electron cryotomography

Emma Silvester et al.

Summary: Electron cryotomography (cryoET) has revolutionized our understanding of biological function by revealing molecular details of membranes, viruses, and cells. A new tagging strategy using DNA origami allows for precise identification of individual protein complexes in tomograms without relying on metal clusters, making it suitable for a wide range of biological surfaces in cryoET studies.

CELL (2021)

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Article Multidisciplinary Sciences

DNA origami patterning of synthetic T cell receptors reveals spatial control of the sensitivity and kinetics of activation

Rui Dong et al.

Summary: The spatial arrangement of receptors determines the ligand density threshold for triggering and encodes the temporal kinetics of signaling activities in triggering cellular activation. Cells measure spatial arrangements of ligands, translate that information into distinct signaling dynamics, providing insights into engineering immunotherapies.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Biochemistry & Molecular Biology

Unraveling the interaction between doxorubicin and DNA origami nanostructures for customizable chemotherapeutic drug release

Heini Ijas et al.

Summary: The study characterized and optimized the loading of doxorubicin (DOX) into different 2D and 3D scaffolded DNA origami nanostructures (DONs) through in-depth spectroscopic analysis. The research found that under experimental conditions, all DONs exhibited similar DOX binding capacities. The study also investigated drug release profiles and mechanisms of DOX aggregation, identifying factors such as pH, magnesium, and DOX concentration that have been overlooked in previous experiments.

NUCLEIC ACIDS RESEARCH (2021)

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Article Chemistry, Multidisciplinary

Amphiphilic and Biocompatible DNA Origami-Based Emulsion Formation and Nanopore Release for Anti-Melanogenesis Therapy

Hao Huang et al.

Summary: Programmable engineered DNA origami offers endless possibilities for customizing nanostructures. In this study, an amphiphilic triangular DNA origami with a central nanopore was fabricated, serving as a stabilizer for W/O/W emulsion, achieving constant release, and demonstrating advantages in anti-melanogenesis therapy.

SMALL (2021)

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Article Chemistry, Multidisciplinary

DNA Origami Frameworks Enabled Self-Protective siRNA Delivery for Dual Enhancement of Chemo-Photothermal Combination Therapy

Tingting Xu et al.

Summary: The study utilized octahedral DNA origami frameworks (OctDOFs) as a nanovehicle for precise organization and orchestrated delivery of siRNAs, chemodrugs, and photothermal agents in cancer treatment, demonstrating superior cytotoxicity and tumor inhibition efficacy in vitro and in vivo. This nanovehicle creates a promising siRNA delivery platform for precise medication and combination therapy.

SMALL (2021)

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Article Chemistry, Multidisciplinary

An Orthogonal Covalent Connector System for the Efficient Assembly of Enzyme Cascades on DNA Nanostructures

Sandra Kroell et al.

Summary: This study reports a rational re-engineering of the genetically fusible SNAP-tag linker, resulting in increased coupling efficiency with benzylguanine-modified oligonucleotides and DNA origami nanostructures. The novel linker, combined with another efficient oligonucleotide binding tag, allowed orthogonal assembly of an enzyme cascade on DON, showing higher activity than free solubilized enzymes. This connector system and the validation methods used represent important tools for further developing multienzyme systems based on DNA origami nanostructures.

SMALL (2021)

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Article Chemistry, Multidisciplinary

Cryo-Electron Microscopy and Mass Analysis of Oligolysine-Coated DNA Nanostructures

Eva Bertosin et al.

Summary: Cationic coatings can enhance the stability of synthetic DNA objects in low ionic strength environments, but may also induce deformations such as twisting and bending. Higher-density coatings can lead to internal structural deformations in DNA origami objects. The coatings effectively prevent strand dissociation, but may cause certain structural alterations.

ACS NANO (2021)

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Article Chemistry, Physical

Integrated computer-aided engineering and design for DNA assemblies

Chao-Min Huang et al.

Summary: Recent studies have shown that integrating molecular dynamics-based computer-aided engineering with computer-aided design allows for the rapid construction of large three-dimensional DNA assemblies with control over their geometry, mechanics, and dynamics, expanding the scope of structural complexity and design capabilities for DNA assemblies.

NATURE MATERIALS (2021)

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Article Multidisciplinary Sciences

HBD1 protein with a tandem repeat of two HMG-box domains is a DNA clip to organize chloroplast nucleoids in Chlamydomonas reinhardtii

Mari Takusagawa et al.

Summary: The study identified a protein named HBD1, structurally similar to key mitochondrial nucleoid proteins, critical for the maintenance and stability of chloroplast nucleoids. The presence of HBD1 helps compact DNA and influence the distribution of nucleoids. The research also revealed the functional similarity between HBD1 and mitochondrial nucleoids.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Nanoscience & Nanotechnology

Aptamer-Integrated Scaffolds for Biologically Functional DNA Origami Structures

Xiaoxing Chen et al.

Summary: The study introduced a strategy to produce customized scaffolds with integrated aptamer sequences for the direct construction of functional DNA origami structures. Results showed efficient and stable integration of various aptamers in the scaffolds, leading to increased binding efficiency and stronger resistance to degradation. This scalable method provides a new way to construct more stable and functionally robust DNA origami structures for broader applications.

ACS APPLIED MATERIALS & INTERFACES (2021)

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Article Chemistry, Multidisciplinary

Strategies for the Site-Specific Decoration of DNA Origami Nanostructures with Functionally Intact Proteins

Joschka Hellmeier et al.

Summary: DNA origami structures provide flexible scaffolds for organizing biomolecules with nanometer precision, but functionalizing them with proteins while maintaining stoichiometry and protein functionality remains challenging. This study systematically evaluated different strategies for site-specific decoration of DNA origami structures, with a focus on efficiency, stoichiometry, and protein functionality. The study found that using charge-neutral peptide nucleic acid emerged as the best strategy for achieving high yield and preserving protein functionality.

ACS NANO (2021)

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Article Chemistry, Multidisciplinary

Reconstitution of Ultrawide DNA Origami Pores in Liposomes for Transmembrane Transport of Macromolecules

Alessio Fragasso et al.

Summary: Researchers have successfully constructed DNA origami nanopores with an inner diameter of 30 nm, which can be inserted into the lipid membrane of GUVs to facilitate transmembrane molecular transport, demonstrating the ability to form large membrane-spanning open pores. This technique holds great potential for applications in fields such as biomimetics, synthetic biology, and drug delivery.

ACS NANO (2021)

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Article Chemistry, Multidisciplinary

In Situ Covalent Functionalization of DNA Origami Virus-like Particles

Grant A. Knappe et al.

Summary: Researchers have developed a versatile DNA origami functionalization and characterization platform for biomedical applications. By utilizing click chemistry, they achieved quantitative in situ conversion of various moieties. This platform allows for broader access to covalently functionalized DNA origami.

ACS NANO (2021)

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Article Chemistry, Multidisciplinary

Clustering of Death Receptor for Apoptosis Using Nanoscale Patterns of Peptides

Yang Wang et al.

Summary: The nanoscale spatial organization of TNF receptors on cell surfaces plays a crucial role in regulating cellular fate. The use of DNA origami nanostructures to pattern TNF-related apoptosis-inducing ligand-mimicking peptides has shown potential in inducing death receptor clustering and apoptosis in human breast cancer cells, offering a new strategy to improve TNF superfamily activation methods.

ACS NANO (2021)

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Article Chemistry, Multidisciplinary

DNA Origami Penetration in Cell Spheroid Tissue Models is Enhanced by Wireframe Design

Yang Wang et al.

Summary: This study investigates the uptake and penetration of DNA origami structures in cell and cell spheroid tissue models to evaluate the efficacy of DNA origami-based delivery. The results show that wireframe rods can penetrate deeper and exhibit higher cytotoxicity in CSTMs compared to lattice-based rods. The choice of structural design method is suggested to be a crucial parameter for the application of DNA origami in drug delivery based on differences in structural mechanics and interaction with cell receptors.

ADVANCED MATERIALS (2021)

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Article Chemistry, Analytical

Profiling and Regulating Proteins That Adsorb to DNA Materials in Human Serum

Fan Xu et al.

Summary: This study conducted proteomic analysis to profile proteins that bind to DNA materials in human serum, revealing distinctive protein profiles for each DNA material and significant differences in profiles when serum originates from healthy donors vs prostate cancer patients. Furthermore, tethering single-stranded DNA onto DNA material can regulate protein profiles and improve biological performance.

ANALYTICAL CHEMISTRY (2021)

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Article Chemistry, Multidisciplinary

DNA-Origami NanoTrap for Studying the Selective Barriers Formed by Phenylalanine-Glycine-Rich Nucleoporins

Qi Shen et al.

Summary: Researchers have developed a biomimetic construct called NanoTrap using DNA nanotechnology to better understand how nucleoporins in the nuclear pore complex establish a selective barrier. The type of FG motif, grafting density, and spatial arrangement were found to be critical determinants of an effective diffusion barrier, with diffusion barriers formed with cohesive FG interactions dominating in mixed-FG-nup scenarios.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Chemistry, Multidisciplinary

Determinants of Ligand-Functionalized DNA Nanostructure-Cell Interactions

Glenn A. O. Cremers et al.

Summary: The study investigated the tunable design parameters of antibody-functionalized DNA nanostructures binding to therapeutically relevant receptors, revealing key insights into receptor binding efficiency governed mainly by nanostructure size and DNA handle location.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

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Article Chemistry, Multidisciplinary

Accessing and Assessing the Cell-Surface Glycocalyx Using DNA Origami

Piyumi Wijesekara et al.

Summary: This study demonstrated that DNA nanotiles can effectively predict cell-to-cell accessibility by anchoring on the glycocalyx, providing a functional measure of glycocalyx barrier integrity. Compared to PLB anchoring, the glycocalyx-anchoring mechanism enhanced cell-surface stability and cellular uptake of nanotiles.

NANO LETTERS (2021)

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Article Chemistry, Physical

Programmable icosahedral shell system for virus trapping

Christian Sigl et al.

Summary: This study introduces a programmable icosahedral canvas for the self-assembly of icosahedral shells with viral trapping and antiviral properties. It demonstrates the potential of a new broad-spectrum antiviral platform that could alleviate many threats to global public health.

NATURE MATERIALS (2021)

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Article Biochemistry & Molecular Biology

Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

Hyungmin Jun et al.

Summary: ATHENA is an open-source software that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami, expanding the possibilities of designing 3D DNA-based assemblies. The software also allows external editing of sequences and provides atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

NUCLEIC ACIDS RESEARCH (2021)

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Article Biochemistry & Molecular Biology

A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules

Yuchen Wang et al.

Summary: Single molecule force spectroscopy is a powerful method for studying the structure, conformational changes, and kinetic properties of biological and synthetic macromolecules. Researchers have developed a nanoscale DNA force spectrometer that can apply both tensile and compressive forces with tunable mechanical properties, providing a versatile tool for designing nanoscale mechanical devices.

NUCLEIC ACIDS RESEARCH (2021)

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Article Chemistry, Multidisciplinary

Nanoscale FasL Organization on DNA Origami to Decipher Apoptosis Signal Activation in Cells

Ricarda M. L. Berger et al.

Summary: Cell signaling is initiated by specific protein patterns on the plasma membrane. DNA origami-based nanoagents with precise arrangements of death receptor ligand FasL were introduced to cells, leading to faster and more efficient signaling compared to naturally occurring soluble FasL. This discovery provides unprecedented control over molecular signaling and a new strategy for driving specific cell responses.

SMALL (2021)

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Article Multidisciplinary Sciences

Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells

Kevin Jahnke et al.

Summary: By combining genetically engineered E. coli and DNA origami structures, researchers have successfully demonstrated the use of light and proton gradients to drive synthetic cellular systems. This strategic merger of bottom-up and top-down approaches in synthetic biology offers an efficient pathway for engineering synthetic cells.

NATURE COMMUNICATIONS (2021)

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Article Biology

Tight nanoscale clustering of Fcγ receptors using DNA origami promotes phagocytosis

Nadja Kern et al.

Summary: The study reveals that macrophages use information about local ligand densities to control engulfment decisions, enhancing engulfment efficiency by increasing receptor clustering.

ELIFE (2021)

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Article Chemistry, Multidisciplinary

Reconstructing Soma-Soma Synapse-like Vesicular Exocytosis with DNA Origami

Jiangbo Liu et al.

Summary: Researches developed a method based on DNA origami nanostructures to reconstruct soma-soma synapse-like junctions, demonstrating the maintenance of intercellular communication. This strategy provides a versatile platform for studying synaptic communications.

ACS CENTRAL SCIENCE (2021)

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Article Chemistry, Multidisciplinary

Folate-Functionalized DNA Origami for Targeted Delivery of Doxorubicin to Triple-Negative Breast Cancer

Suchetan Pal et al.

Summary: Researchers have developed folate-functionalized DNA origami structures that can effectively target and kill cells overexpressing FOLR1, with better efficacy than non-targeted structures. This study is expected to enable target-specific delivery of anticancer drug combinations to drug-resistant cancer cells using versatile DNA origami nanostructures.

FRONTIERS IN CHEMISTRY (2021)

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Article Chemistry, Multidisciplinary

Dynamic Shape Transformation of a DNA Scaffold Applied for an Enzyme Nanocarrier

Peng Lin et al.

Summary: A three-dimensional DNA scaffold was designed with the ability to undergo shape transition, allowing enzymes to be assembled in an open state and subsequently transformed and enclosed using short DNA closing keys while maintaining their catalytic activity. The nanocarrier with efficient encapsulation ability is potentially applicable for drug delivery, biosensing, biocatalytic, and diagnostic tools.

FRONTIERS IN CHEMISTRY (2021)

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Article Chemistry, Multidisciplinary

A tetrahedral DNA nanorobot with conformational change in response to molecular trigger

Fengyu Liu et al.

Summary: The article discusses a stable tetrahedral DNA nanorobot that can undergo controlled conformational changes in response to the stimulation of a specific molecular biomarker, EpCAM. The nanorobot shows low cytotoxicity and target specificity, making it a promising tool for precise monitoring of EpCAM-positive cells.

NANOSCALE (2021)

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Article Chemistry, Multidisciplinary

An RNA/DNA hybrid origami-based nanoplatform for efficient gene therapy

Xiaohui Wu et al.

Summary: A novel RNA/DNA hybrid origami was developed for efficient gene therapy, showing high delivery efficacy of homologous gene therapy drugs and controllable release of antisenses in response to intracellular digestion. The tailored origami demonstrated noticeable inhibition of cell proliferation by silencing the tumor-associated gene PLK1, providing a promising strategy for gene therapy development.

NANOSCALE (2021)

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Article Chemistry, Multidisciplinary

Construction of an optically controllable CRISPR-Cas9 system using a DNA origami nanostructure

Katsuhiko Abe et al.

Summary: The study demonstrates photo-controlled sequence-selective dsDNA cleavage using a DNA origami structure with Cas9 nuclease. The activity of Cas9 was suppressed inside the ring-shaped DNA origami and restored after photoirradiation.

CHEMICAL COMMUNICATIONS (2021)

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Article Chemistry, Multidisciplinary

The effects of overhang placement and multivalency on cell labeling by DNA origami†

Ying Liu et al.

Summary: Structural DNA nanotechnology can guide and affix biomolecules to cell surfaces through targeted binding, with the efficiency highly dependent on the shape of DNA origami and the location of binding overhangs. Edge-decorated nanotiles showed successful labeling of cells, and modulating the labeling efficiency can be achieved by adjusting the proximity of binding overhangs towards the edges and vertices. The findings provide guidelines for rational design of future functional DNA nanostructures.

NANOSCALE (2021)

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Article Chemistry, Multidisciplinary

A large, square-shaped, DNA origami nanopore with sealing function on a giant vesicle membrane

Shoji Iwabuchi et al.

Summary: By designing a membrane nanopore using DNA origami technology, the permeation of large molecules from the external environment was achieved, and selective transport of molecules was enabled by adding DNA strands. This design helps facilitate communication between artificial cells and their external environment.

CHEMICAL COMMUNICATIONS (2021)

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Article Chemistry, Multidisciplinary

DNA modification and visualization on an origami-based enzyme nano-factory

Elmar Weinhold et al.

Summary: The recent focus of DNA nanotechnology has been on functionalizing DNA origami for multiple applications. A novel DNA enzyme nano-factory has been constructed which significantly enhances local concentration and can potentially be expanded to a multi-enzyme system controlled by simple to complex molecules made of DNA, RNA or proteins.

NANOSCALE (2021)

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Article Multidisciplinary Sciences

Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice

Alexander A. Cohen et al.

Summary: The study developed nanoparticles displaying the receptor binding domain (RBD) of SARS-CoV-2 and other animal coronaviruses, which induced cross-reactive antibody responses in mice. Immunization with mosaic RBD nanoparticles resulted in superior neutralization of heterologous viruses, providing a potential strategy for simultaneous protection against multiple coronaviruses.

SCIENCE (2021)

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Article Multidisciplinary Sciences

DNA origami

Swarup Dey et al.

Summary: DNA origami technology, a bottom-up method for constructing nanostructures, offers high precision and controllability. It finds wide applications in nanofabrication, nanophotonics, nanoelectronics, catalysis, computation, bioimaging, and more. However, challenges such as size limits, stability issues, and scale of production need to be addressed for further advancement in the field.

NATURE REVIEWS METHODS PRIMERS (2021)

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Article Chemistry, Physical

Reversible membrane deformations by straight DNA origami filaments

Henri G. Franquelim et al.

Summary: The study demonstrates the formation and effects of membrane-bound filaments using DNA origami to mimic cytoskeletal elements. By manipulating the MgCl2 concentration, control over the polymerization and depolymerization of DNA origami is achieved, leading to the formation of helical structures bound to the membrane. This approach provides a new insight into shaping membranes by straight cytoskeletal-like objects.

SOFT MATTER (2021)

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Article Chemistry, Multidisciplinary

Enhancing Biocompatible Stability of DNA Nanostructures Using Dendritic Oligonucleotides and Brick Motifs

Youngeun Kim et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

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Article Nanoscience & Nanotechnology

Aptamer-Functionalized DNA Origami for Targeted Codelivery of Antisense Oligonucleotides and Doxorubicin to Enhance Therapy in Drug-Resistant Cancer Cells

Qingshan Pan et al.

ACS APPLIED MATERIALS & INTERFACES (2020)

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Article Chemistry, Multidisciplinary

Extrusion of RNA from a DNA-Origami-Based Nanofactory

Jaeseung Hahn et al.

ACS NANO (2020)

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Article Chemistry, Multidisciplinary

Hierarchical Assembly of Nucleic Acid/Coiled-Coil Peptide Nanostructures

Alex Buchberger et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

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Article Chemistry, Multidisciplinary

Glutaraldehyde Cross-Linking of Oligolysines Coating DNA Origami Greatly Reduces Susceptibility to Nuclease Degradation

Frances M. Anastassacos et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

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Article Nanoscience & Nanotechnology

Biophysical characterisation of DNA origami nanostructures reveals inaccessibility to intercalation binding sites

Helen L. Miller et al.

NANOTECHNOLOGY (2020)

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Article Chemistry, Physical

Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome

Bas J. H. M. Rosier et al.

NATURE CATALYSIS (2020)

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Article Multidisciplinary Sciences

DNA origami protection and molecular interfacing through engineered sequence-defined peptoids

Shih-Ting Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Chemistry, Multidisciplinary

DNA Origami-Enabled Engineering of Ligand-Drug Conjugates for Targeted Drug Delivery

Zhilei Ge et al.

SMALL (2020)

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Article Chemistry, Multidisciplinary

Programming Dynamic Assembly of Viral Proteins with DNA Origami

Kun Zhou et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

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Article Biochemical Research Methods

Cotranscriptional Folding of a Bio-orthogonal Fluorescent Scaffolded RNA Origami

Emanuela Torelli et al.

ACS SYNTHETIC BIOLOGY (2020)

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Article Chemistry, Multidisciplinary

Programmable Assembly of Iron Oxide Nanoparticles Using DNA Origami

Travis A. Meyer et al.

NANO LETTERS (2020)

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Article Chemistry, Multidisciplinary

Opportunities, Barriers, and a Strategy for Overcoming Translational Challenges to Therapeutic Nucleic Acid Nanotechnology

Kirill A. Afonin et al.

ACS NANO (2020)

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Article Chemistry, Multidisciplinary

Postsynthetic Functionalization of DNA-Nanocomposites with Proteins Yields Bioinstructive Matrices for Cell Culture Applications

Yong Hu et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

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Article Chemistry, Multidisciplinary

An Intelligent DNA Nanorobot for Autonomous Anticoagulation

Linlin Yang et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

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Role of nanoscale antigen organization on B-cell activation probed using DNA origami

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NATURE NANOTECHNOLOGY (2020)

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Direct Observation of Dynamic Interactions between Orientation-Controlled Nucleosomes in a DNA Origami Frame

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Capturing transient antibody conformations with DNA origami epitopes

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DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability

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Meta-DNA structures

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DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells

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Regulation of cell binding and entry by DNA origami mediated spatial distribution of aptamers

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Single-molecule DNA origami aptasensors for real-time biomarker detection

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Mosaic nanoparticle display of diverse influenza virus hemagglutinins elicits broad B cell responses

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DNA nanostructures coordinate gene silencing in mature plants

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Proof-of-Concept Multistage Biomimetic Liposomal DNA Origami Nanosystem for the Remote Loading of Doxorubicin

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Rotation tracking of genome-processing enzymes using DNA origami rotors

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Probing the nanoscale organisation and multivalency of cell surface receptors: DNA origami nanoarrays for cellular studies with single-molecule control

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DNA Origami Scaffolds as Templates for Functional Tetrameric Kir3 K+ Channels

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Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation

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Block Copolymer Micellization as a Protection Strategy for DNA Origami

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Analyzing DNA Nanotechnology: A Call to Arms For The Analytical Chemistry Community

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Aptamer-tagged DNA origami for spatially addressable detection of aflatoxin B1

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Placing molecules with Bohr radius resolution using DNA origami

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Daunorubicin-Loaded DNA Origami Nanostructures Circumvent Drug-Resistance Mechanisms in a Leukemia Model

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Large-Conductance Transmembrane Porin Made from DNA Origami

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Orthogonal Protein Assembly on DNA Nanostructures Using Relaxases

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Directional Regulation of Enzyme Pathways through the Control of Substrate Channeling on a DNA Origami Scaffold

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Sequence-Dependent Fluorescence of Cy3-and Cy5-Labeled Double-Stranded DNA

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BIOCONJUGATE CHEMISTRY (2016)

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Article Biochemistry & Molecular Biology

A Rationally Designed Connector for Assembly of Protein-Functionalized DNA Nanostructures

Katja J. Kossmann et al.

CHEMBIOCHEM (2016)

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Article Chemistry, Multidisciplinary

Observation of intracellular interactions between DNA origami and lysosomes by the fluorescence localization method

Meifang Fu et al.

CHEMICAL COMMUNICATIONS (2016)

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Article Chemistry, Multidisciplinary

Cellular delivery of enzyme-loaded DNA origami

Ari Ora et al.

CHEMICAL COMMUNICATIONS (2016)

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Article Cell Biology

Cargo Rigidity Affects the Sensitivity of Dynein Ensembles to Individual Motor Pausing

Amalia R. Driller-Colangelo et al.

CYTOSKELETON (2016)

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Article Chemistry, Multidisciplinary

A Programmable DNA Origami Platform to Organize SNAREs for Membrane Fusion

Weiming Xu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)

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Article Chemistry, Multidisciplinary

Light-Triggered Release of Bioactive Molecules from DNA Nanostructures

Richie E. Kohman et al.

NANO LETTERS (2016)

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Article Chemistry, Multidisciplinary

Electrotransfection of Polyamine Folded DNA Origami Structures

Aradhana Chopra et al.

NANO LETTERS (2016)

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Article Chemistry, Multidisciplinary

Exploring Nucleosome Unwrapping Using DNA Origami

Jonas J. Funke et al.

NANO LETTERS (2016)

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Article Chemistry, Multidisciplinary

A switchable DNA origami nanochannel for regulating molecular transport at the nanometer scale

Dianming Wang et al.

NANOSCALE (2016)

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Article Chemistry, Multidisciplinary

Cationic polymers for DNA origami coating - examining their binding efficiency and tuning the enzymatic reaction rates

Jenny K. Kiviaho et al.

NANOSCALE (2016)

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Article Chemistry, Multidisciplinary

Self-assembly of size-controlled liposomes on DNA nanotemplates

Yang Yang et al.

NATURE CHEMISTRY (2016)

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Article Nanoscience & Nanotechnology

Optical imaging of individual biomolecules in densely packed clusters

Mingjie Dai et al.

NATURE NANOTECHNOLOGY (2016)

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Article Nanoscience & Nanotechnology

Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores

Nicholas A. W. Bell et al.

NATURE NANOTECHNOLOGY (2016)

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Article Biochemical Research Methods

Assembly of multienzyme complexes on DNA nanostructures

Jinglin Fu et al.

NATURE PROTOCOLS (2016)

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Article Multidisciplinary Sciences

Thought-Controlled Nanoscale Robots in a Living Host

Shachar Arnon et al.

PLOS ONE (2016)

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Article Biochemistry & Molecular Biology

Patterning protein complexes on DNA nanostructures using a GFP nanobody

R. F. Sommese et al.

PROTEIN SCIENCE (2016)

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Article Multidisciplinary Sciences

DNA NANOTECHNOLOGY Designer nanoscale DNA assemblies programmed from the top down

Remi Veneziano et al.

SCIENCE (2016)

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Article Chemistry, Multidisciplinary

Intracellular Delivery of a Planar DNA Origami Structure by the Transferrin-Receptor Internalization Pathway

David H. Schaffert et al.

SMALL (2016)

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Article Multidisciplinary Sciences

Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion

Zhao Zhao et al.

NATURE COMMUNICATIONS (2016)

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Article Multidisciplinary Sciences

A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads

M. Iwaki et al.

NATURE COMMUNICATIONS (2016)

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Article Multidisciplinary Sciences

Regulation at a distance of biomolecular interactions using a DNA origami nanoactuator

Yonggang Ke et al.

NATURE COMMUNICATIONS (2016)

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Article Multidisciplinary Sciences

Programmable DNA Nanosystem for Molecular Interrogation

Divita Mathur et al.

SCIENTIFIC REPORTS (2016)

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Review Chemistry, Multidisciplinary

Strain-Promoted 1,3-Dipolar Cycloaddition of Cycloalkynes and Organic Azides

Jan Dommerholt et al.

TOPICS IN CURRENT CHEMISTRY (2016)

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Article Multidisciplinary Sciences

Uncovering the forces between nucleosomes using DNA origami

Jonas J. Funke et al.

SCIENCE ADVANCES (2016)

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Article Multidisciplinary Sciences

A Quick-responsive DNA Nanotechnology Device for Bio-molecular Homeostasis Regulation

Songlin Wu et al.

SCIENTIFIC REPORTS (2016)

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Article Chemistry, Multidisciplinary

Electron Microscopic Visualization of Protein Assemblies on Flattened DNA Origami

Leena Mallik et al.

ACS NANO (2015)

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Article Chemistry, Multidisciplinary

Purification of Functionalized DNA Origami Nanostructures

Alan Shaw et al.

ACS NANO (2015)

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Article Chemistry, Multidisciplinary

Assembly and Purification of Enzyme-Functionalized DNA Origami Structures

Christopher Timm et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2015)

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Article Chemistry, Multidisciplinary

Multiscale Origami Structures as Interface for Cells

Alessandro Angelin et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2015)

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Article Chemistry, Multidisciplinary

Amphipathic DNA Origami Nanoparticles to Scaffold and Deform Lipid Membrane Vesicles

Aleksander Czogalla et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2015)

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Article Chemistry, Multidisciplinary

A modular zinc finger adaptor accelerates the covalent linkage of proteins at specific locations on DNA nanoscaffolds

Eiji Nakata et al.

CHEMICAL COMMUNICATIONS (2015)

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Article Chemistry, Multidisciplinary

A modular DNA origami-based enzyme cascade nanoreactor

Veikko Linko et al.

CHEMICAL COMMUNICATIONS (2015)

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Article Chemistry, Multidisciplinary

Designed Intercalators for Modification of DNA Origami Surface Properties

Josipa Brglez et al.

CHEMISTRY-A EUROPEAN JOURNAL (2015)

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Article Chemistry, Multidisciplinary

Absolute Arrangement of Subunits in Cytoskeletal Septin Filaments in Cells Measured by Fluorescence Microscopy

Charlotte Kaplan et al.

NANO LETTERS (2015)

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Article Multidisciplinary Sciences

DNA rendering of polyhedral meshes at the nanoscale

Erik Benson et al.

NATURE (2015)

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Article Chemistry, Organic

Photocleavable ligands for protein decoration of DNA nanostructures

Josipa Brglez et al.

ORGANIC & BIOMOLECULAR CHEMISTRY (2015)

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Article Multidisciplinary Sciences

Using Protein Dimers to Maximize the Protein Hybridization Efficiency with Multisite DNA Origami Scaffolds

Vikash Verma et al.

PLOS ONE (2015)

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Article Chemistry, Multidisciplinary

Selective Binding of DNA Origami on Biomimetic Lipid Patches

Michael Hirtz et al.

SMALL (2015)

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Article Chemistry, Multidisciplinary

A Self-Assembled DNA Origami-Gold Nanorod Complex for Cancer Theranostics

Qiao Jiang et al.

SMALL (2015)

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Article Multidisciplinary Sciences

Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries

Thorsten L. Schmidt et al.

NATURE COMMUNICATIONS (2015)

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Article Multidisciplinary Sciences

Super-Resolution Imaging Conditions for enhanced Yellow Fluorescent Protein (eYFP) Demonstrated on DNA Origami Nanorulers

Ija Jusuk et al.

SCIENTIFIC REPORTS (2015)

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Article Chemistry, Multidisciplinary

DNA Origami Nanoneedles on Freestanding Lipid Membranes as a Tool To Observe Isotropic-Nematic Transition in Two Dimensions

Aleksander Czogalla et al.

NANO LETTERS (2015)

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Article Chemistry, Multidisciplinary

Cellular Uptake of Tile-Assembled DNA Nanotubes

Samet Kocabey et al.

NANOMATERIALS (2015)

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Article Nanoscience & Nanotechnology

Novel Rolling Circle Amplification and DNA Origami-Based DNA Belt-Involved Signal Amplification Assay for Highly Sensitive Detection of Prostate-Specific Antigen (PSA)

Juan Yan et al.

ACS APPLIED MATERIALS & INTERFACES (2014)

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Article Chemistry, Multidisciplinary

DNA Origami as an In Vivo Drug Delivery Vehicle for Cancer Therapy

Qian Zhang et al.

ACS NANO (2014)

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Article Chemistry, Multidisciplinary

DNA-Cholesterol Barges as Programmable Membrane-Exploring Agents

Alexander Johnson-Buck et al.

ACS NANO (2014)

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Article Chemistry, Multidisciplinary

Facile and Scalable Preparation of Pure and Dense DNA Origami Solutions

Evi Stahl et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)

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Article Chemistry, Multidisciplinary

Hydrophobic Actuation of a DNA Origami Bilayer Structure

Jonathan List et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)

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Review Biochemistry & Molecular Biology

Click Chemistry in Complex Mixtures: Bioorthogonal Bioconjugation

Craig S. McKay et al.

CHEMISTRY & BIOLOGY (2014)

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Article Chemistry, Multidisciplinary

Photoresponsive DNA Nanocapsule Having an Open/Close System for Capture and Release of Nanomaterials

Tomohiro Takenaka et al.

CHEMISTRY-A EUROPEAN JOURNAL (2014)

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Article Chemistry, Multidisciplinary

Virus-Encapsulated DNA Origami Nanostructures for Cellular Delivery

Joona Mikkila et al.

NANO LETTERS (2014)

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Article Biochemical Research Methods

Spatial control of membrane receptor function using ligand nanocalipers

Alan Shaw et al.

NATURE METHODS (2014)

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Article Nanoscience & Nanotechnology

Universal compting by DNA origami robots in a living animal

Yaniv Amir et al.

NATURE NANOTECHNOLOGY (2014)

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Article Nanoscience & Nanotechnology

Amyloid fibrils nucleated and organized by DNA origami constructions

Anuttara Udomprasert et al.

NATURE NANOTECHNOLOGY (2014)

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Article Biochemical Research Methods

Quantification of cellular uptake of DNA nanostructures by qPCR

Anders Hauge Okholm et al.

METHODS (2014)

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Article Chemistry, Multidisciplinary

Enzymatic Ligation of Large Biomolecules to DNA

Rasmus Scholer Sorensen et al.

ACS NANO (2013)

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Article Biochemistry & Molecular Biology

Sensitization of Transforming Growth Factor-β Signaling by Multiple Peptides Patterned on DNA Nanostructures

Ronnie O. Pedersen et al.

BIOMACROMOLECULES (2013)

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Article Chemistry, Multidisciplinary

Single-Step Rapid Assembly of DNA Origami Nanostructures for Addressable Nanoscale Bioreactors

Yanming Fu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

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Article Biochemical Research Methods

Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides

Cosimo Ducani et al.

NATURE METHODS (2013)

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Article Biochemistry & Molecular Biology

Purification of DNA-origami nanostructures by rate-zonal centrifugation

Chenxiang Lin et al.

NUCLEIC ACIDS RESEARCH (2013)

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Article Chemistry, Multidisciplinary

DNA Origami Delivery System for Cancer Therapy with Tunable Release Properties

Yong-Xing Zhao et al.

ACS NANO (2012)

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Review Chemistry, Multidisciplinary

DNA Origami: The Art of Folding DNA

Barbara Sacca et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2012)

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Article Chemistry, Multidisciplinary

Zinc-Finger Proteins for Site-Specific Protein Positioning on DNA-Origami Structures

Eiji Nakata et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2012)

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Article Chemistry, Multidisciplinary

Visualization of the intracellular location and stability of DNA origami with a label-free fluorescent probe

Xibo Shen et al.

CHEMICAL COMMUNICATIONS (2012)

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Article Chemistry, Multidisciplinary

DNA Origami as a Carrier for Circumvention of Drug Resistance

Qiao Jiang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

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Article Multidisciplinary Sciences

Three-Dimensional Structures Self-Assembled from DNA Bricks

Yonggang Ke et al.

SCIENCE (2012)

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Article Multidisciplinary Sciences

A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads

Shawn M. Douglas et al.

SCIENCE (2012)

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Article Multidisciplinary Sciences

Tug-of-War in Motor Protein Ensembles Revealed with a Programmable DNA Origami Scaffold

N. D. Derr et al.

SCIENCE (2012)

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Review Biochemistry & Molecular Biology

Choosing an effective protein bioconjugation strategy

Nicholas Stephanopoulos et al.

NATURE CHEMICAL BIOLOGY (2011)

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Article Chemistry, Multidisciplinary

Orthogonal Protein Decoration of DNA Origami

Barbara Sacca et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2010)

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Article Chemistry, Multidisciplinary

Stepwise and reversible nanopatterning of proteins on a DNA origami scaffold

Kentaro Numajiri et al.

CHEMICAL COMMUNICATIONS (2010)

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Review Biochemistry & Molecular Biology

Advances in RNA structure analysis by chemical probing

Kevin M. Weeks

CURRENT OPINION IN STRUCTURAL BIOLOGY (2010)

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Article Chemistry, Multidisciplinary

Discrete and Active Enzyme Nanoarrays on DNA Origami Scaffolds Purified by Affinity Tag Separation

Kentaro Numajiri et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

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Article Chemistry, Multidisciplinary

Immobilization and One-Dimensional Arrangement of Virus Capsids with Nanoscale Precision Using DNA Origami

Nicholas Stephanopoulos et al.

NANO LETTERS (2010)

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Article Nanoscience & Nanotechnology

Single-molecule chemical reactions on DNA origami

Niels V. Voigt et al.

NATURE NANOTECHNOLOGY (2010)

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Article Biochemistry & Molecular Biology

Precisely Programmed and Robust 2D Streptavidin Nanoarrays by Using Periodical Nanometer-Scale Wells Embedded in DNA Origami Assembly

Akinori Kuzuya et al.

CHEMBIOCHEM (2009)

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Article Chemistry, Multidisciplinary

NTA Directed Protein Nanopatterning on DNA Origami Nanoconstructs

Wanqiu Shen et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)

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Article Nanoscience & Nanotechnology

DNA origami as a nanoscale template for protein assembly

Anton Kuzyk et al.

NANOTECHNOLOGY (2009)

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Article Multidisciplinary Sciences

Self-assembly of DNA into nanoscale three-dimensional shapes

Shawn M. Douglas et al.

NATURE (2009)

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Article Multidisciplinary Sciences

Folding DNA into Twisted and Curved Nanoscale Shapes

Hendrik Dietz et al.

SCIENCE (2009)

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Article Chemistry, Analytical

Monitoring of real-time streptavidin-biotin binding kinetics using droplet microfluidics

Monpichar Srisa-Art et al.

ANALYTICAL CHEMISTRY (2008)

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Article Biotechnology & Applied Microbiology

A combinatorial library of lipid-like materials for delivery of RNAi therapeutics

Akin Akinc et al.

NATURE BIOTECHNOLOGY (2008)

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Article Biochemical Research Methods

Footprinting protein-DNA complexes using the hydroxyl radical

Swapan S. Jain et al.

NATURE PROTOCOLS (2008)

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Article Multidisciplinary Sciences

Folding DNA to create nanoscale shapes and patterns

PWK Rothemund

NATURE (2006)

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Review Pharmacology & Pharmacy

Solid lipid nanoparticles -: Production, characterization and applications

W Mehnert et al.

ADVANCED DRUG DELIVERY REVIEWS (2001)

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Article Biochemistry & Molecular Biology

Reduced antibody response to streptavidin through site-directed mutagenesis

DL Meyer et al.

PROTEIN SCIENCE (2001)

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