DNA nanotechnology articles within Nature Communications

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  • Article
    | Open Access

    The p53 tumor suppressor gene is frequently mutated in liver cancer. Here the authors show that restoration of p53 expression with a mRNA nanoparticle platform elicits anti-tumor immune responses and promotes response to immune checkpoint blockade in preclinical models of p53-null hepatocellular carcinoma.

    • Yuling Xiao
    • , Jiang Chen
    •  & Jinjun Shi

  • Article
    | Open Access

    Biological molecular motors convert chemical energy into mechanical motion by coupling catalytic reactions to large-scale structural transitions. Here, the authors report the design of a rotating DNA nanomechanism that comprises a camshaft whose rotary motion can be transformed into reciprocating large-scale transitions in the structure of the surrounding stator.

    • Eva Bertosin
    • , Christopher M. Maffeo
    •  & Hendrik Dietz

  • Article
    | Open Access

    The self-assembly of colloidal particles can be applied to create new structures and materials in the framework of systems chemistry. The authors demonstrate the realization of autonomous oscillating structure formation on the meso-scale, relevant for systems relying on DNA interactions.

    • H. Dehne
    • , A. Reitenbach
    •  & A. R. Bausch

  • Article
    | Open Access

    DNA supercoiling can result in underwinding with negative supercoiling or overwinding with positive supercoiling of the DNA double helix. Here the authors reveal insights into the dynamic relationship between DNA supercoiling-induced sequence-dependent disruptions to base pairing, DNA looping, and the shape of the DNA molecule.

    • Jonathan M. Fogg
    • , Allison K. Judge
    •  & Lynn Zechiedrich

  • Article
    | Open Access

    The concentration of a biomarker in solution can be determined by counting single molecules. Here the authors report a digital immunoassay scheme with solid-state nanopore readout to quantify a target protein and use this to measure thyroid-stimulating hormone from human serum.

    • Liqun He
    • , Daniel R. Tessier
    •  & Vincent Tabard-Cossa

  • Article
    | Open Access

    Controlling the threshold response in synthetic molecular structures is challenging. Here, the authors report on the buckling of ring-shaped DNA origami structures into twisted architectures via mechanical instability, induced by DNA intercalators.

    • Young-Joo Kim
    • , Junho Park
    •  & Do-Nyun Kim

  • Article
    | Open Access

    Integration and communication of distinct chemical reaction networks is a biological strategy for controlling dynamics of hierarchical structures. Here, the authors report ATP-fuelled autonomous DNA nanotube assembly regulated by DNA strand displacement reactions, which are induced and controlled by an upstream enzyme reaction network of concurrent ATP-mediated ligation and restriction of DNA components.

    • Jie Deng
    •  & Andreas Walther

  • Article
    | Open Access

    Synthetic DNA constructs can to used to recognise and respond to input signals. Here the authors present complex DNA nanostructures with toehold-free strand displacement for generation of ON/OFF switches and Boolean gates.

    • Hong Kang
    • , Tong Lin
    •  & Bryan Wei

  • Article
    | Open Access

    Lipid membrane disruption is often associated with disease but is also essential to a range of biosensing and therapeutic techniques. Here, the authors report on the development of DNA-based particles that, upon exposure to an external cue, can aggregate, disrupt lipid membranes, and arrest the motion of bacteria.

    • Michal Walczak
    • , Ryan A. Brady
    •  & Lorenzo Di Michele

  • Article
    | Open Access

    Ligand-oligonucleotide interactions can integrate both small molecules and proteins into nucleic acid-based circuits. Here the authors design ligand-aptamer complexes to control strand-displacement reactions for versatile ligand transduction.

    • Qiu-Long Zhang
    • , Liang-Liang Wang
    •  & Liang Xu

  • Article
    | Open Access

    The length of single-particle tracking experiments are limited due to photobleaching. Here the authors achieve long-term single-particle tracking with continuous fluorophore exchange in DNA-PAINT and use this to observe DNA origami on lipid bilayers for tens of minutes.

    • Florian Stehr
    • , Johannes Stein
    •  & Petra Schwille

  • Article
    | Open Access

    DNA origami can be used to control the movement of nanoscale assemblies. Here the authors construct multiple-micrometer-long hollow DNA filaments through which DNA pistons move with micrometer-per-second speeds.

    • Pierre Stömmer
    • , Henrik Kiefer
    •  & Hendrik Dietz

  • Article
    | Open Access

    Nucleic acid-based constitutional dynamic networks (CDNs) enable control of various catalytic processes, but it is challenging to achieve intercommunication between different CDNs and by that mimic complex cell biology networks. Here, the authors report two CDNs that control the integration of photochemical and dark-operating processes, and show their intercommunication afforded by environmental components.

    • Chen Wang
    • , Michael P. O’Hagan
    •  & Itamar Willner

  • Article
    | Open Access

    Controlled actuation is an important aspect of synthetic cellular systems. Here, the authors combine pH responsive DNA origami structures with light triggered proton pump engineered E. coli to trigger a change in pH and control the deformation of giant unilamellar vesicles by simple illumination.

    • Kevin Jahnke
    • , Noah Ritzmann
    •  & Kerstin Göpfrich

  • Article
    | Open Access

    Organising proteins in 2D and 3D is needed to develop complex bimolecular materials for a range of applications. Here, the authors report the encapsulation of ferritin and apoferritin in DNA-based voxels with programmed assembly to generate both 2D and 3D protein lattices and demonstrate the retention of protein function.

    • Shih-Ting Wang
    • , Brian Minevich
    •  & Oleg Gang

  • Article
    | Open Access

    A major goal in Engineering Biology and Materials Science is the development of active, autonomous scaffolds that mimic those present in biological cells. Here the authors report a toolkit for programming the dynamic behaviour of nucleic acid scaffolds in minimal cell-like compartments.

    • Siddharth Agarwal
    • , Melissa A. Klocke
    •  & Elisa Franco

  • Article
    | Open Access

    Creation of high-order architectures using DNA devices is of interest for increasing the complexity of synthetic systems. Here, the authors, inspired by biological oligomers, create DNA dimers and oligomers that combining rotation and walking to make high-order systems with more complex conformational changes.

    • Ling Xin
    • , Xiaoyang Duan
    •  & Na Liu

  • Article
    | Open Access

    DNA origami is a valuable tool for precise manipulation of molecules in a three dimensional manner, but the design and assembly of origami units into single crystals is challenging. Here, the authors report successful fabrication of DNA origami single crystals with Wulff shapes, and regulation of their shapes by changing the symmetry and binding modes of DNA origami building blocks.

    • Yong Wang
    • , Lizhi Dai
    •  & Ye Tian

  • Article
    | Open Access

    Encoding data in DNA is a promising approach to high density data storage. Here the authors present a prototype sequencing-free method that uses the spatial orientation of DNA strands with super-resolution microscopy readout.

    • George D. Dickinson
    • , Golam Md Mortuza
    •  & William L. Hughes

  • Article
    | Open Access

    Here, the authors experimentally demonstrate chiral transfer over large distances up to 100 nm. They realise the coupling with an achiral nanosphere situated between a pair of distant gold nanorods arranged in a chiral fashion using DNA origami, and observe enhanced circular dichroism signals.

    • Kevin Martens
    • , Felix Binkowski
    •  & Tim Liedl

  • Article
    | Open Access

    Investigation of spatial organization and relationships of biomolecules in cellular nanoenvironments is necessary to understand essential biological processes, but methodologically challenging. Here, the authors report cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments of DNA modifications around histone post-translational modifications, and explore the nanoenvironments in different cancer cell lines and clinical specimens.

    • Feng Chen
    • , Min Bai
    •  & Yongxi Zhao

  • Article
    | Open Access

    For programmable DNA self-assembly, it is desirable to suppress spontaneous nucleation to enable all-or-nothing assembly of nanostructures far larger than a single DNA origami. Here the authors introduce crisscross polymerization of elongated slat monomers that engage beyond nearest neighbors, providing strictly seed-initiated nucleation of crisscross ribbons with distinct widths and twists.

    • Dionis Minev
    • , Christopher M. Wintersinger
    •  & William M. Shih

  • Article
    | Open Access

    Single-molecule fluorescence currently requires specialized imaging equipment due to the low signal of a single emitter. Here the authors introduce NanoAntennas with Cleared HOtSpots (NACHOS) to boost the signal sufficient for detection of a single emitter by a smartphone, opening the door to point-of-care applications.

    • Kateryna Trofymchuk
    • , Viktorija Glembockyte
    •  & Philip Tinnefeld

  • Article
    | Open Access

    Catch bonds are protein–ligand interactions that exhibit enhancement of bond lifetime when subject to tensile force, which is a desirable yet elusive attribute for man-made nanoparticle interfaces. Here, the authors provide a nanoparticle design that can form catch bonds with tunable force-enhanced lifetimes under thermal excitations.

    • Kerim C. Dansuk
    •  & Sinan Keten

  • Article
    | Open Access

    DNA-templated synthesis takes advantage of sequence-specific hybridization to accelerate chemical reactions. Here, the authors present templated synthesis controlled through antibody-antigen interactions.

    • Lorena Baranda Pellejero
    • , Malihe Mahdifar
    •  & Francesco Ricci

  • Article
    | Open Access

    Precision design of DNA origami needs precision validation. Here, the authors developed cryo-EM methods for obtaining high resolution structural data and for constructing pseudo-atomic models in a semi-automated fashion, allowing for iterative nanodevice inspection and refinement.

    • Massimo Kube
    • , Fabian Kohler
    •  & Hendrik Dietz

  • Article
    | Open Access

    Gaining control over crystallization processes is challenging. Herein, the authors describe a protocol for the controlled growth of DNA nanotubes by feedback regulation: the coupling of a reversible bimolecular monomer buffering reaction delivers the optimal monomer concentration and leads to reliable crystal growth in a simple manner.

    • Samuel W. Schaffter
    • , Dominic Scalise
    •  & Rebecca Schulman

  • Article
    | Open Access

    The design and optimisation of 3D DNA-origami can be a barrier to rapid application. Here the authors design barrel structure of stacked 2D double helical rings with complex surface patterns.

    • Shelley F. J. Wickham
    • , Alexander Auer
    •  & William M. Shih

  • Article
    | Open Access

    Fabrication of superconducting 3D nanoarchitectures, using standard nanofabrication methods, is challenging. Here, the authors demonstrate the fabrication of a nanostructured 3D superconducting array of Josephson junctions, exploiting self-assembled DNA origami lattices as a template.

    • Lior Shani
    • , Aaron N. Michelson
    •  & Oleg Gang

  • Article
    | Open Access

    A key attribute for modern healthcare is the ability to detect low concentrations of biomarkers. Here, the authors use nanopores and DNA origami with target-specific aptamers for detection of CRP.

    • Mukhil Raveendran
    • , Andrew J. Lee
    •  & Paolo Actis

  • Article
    | Open Access

    Understanding antibody-antigen interactions is important to deepen the understanding of immunology. Here, the authors report on the application of DNA origami structures for the controlled presentation of antigens to study antibody binding behaviours at room temperature.

    • Ping Zhang
    • , Xiaoguo Liu
    •  & Chunhai Fan

  • Article
    | Open Access

    Previous design strategies for pH sensitive aptamers were not readily tunable across pH ranges. Here the authors present a general method to convert aptamers into pH-responsive switches using two orthogonal motifs.

    • Ian A. P. Thompson
    • , Liwei Zheng
    •  & H. Tom Soh

  • Article
    | Open Access

    Synthetic molecular systems require subtle control over their thermodynamics and reaction kinetics to implement features such as catalysis. Here the authors propose using mismatches in a DNA duplex to drive catalytic reactions forward whilst maintaining tight catalytic control.

    • Natalie E. C. Haley
    • , Thomas E. Ouldridge
    •  & Andrew J. Turberfield

  • Article
    | Open Access

    Colloidal crystals assembled from nanoscale building blocks are powerful designer materials with diverse functionalities. Here, the authors describe a colloidal crystal engineering strategy to prepare hierarchical structures from metal–organic framework nanoparticles and DNA which retain permanent porosity and catalytic activity.

    • Shunzhi Wang
    • , Sarah S. Park
    •  & Chad A. Mirkin

  • Article
    | Open Access

    Assembling nanoparticles into precise architectures by controlling their positions in three-dimensional space is a major challenge in nanoscience. Here, the authors construct complex, preprogrammed clusters of DNA-encoded nanoparticles by coordinating them onto a DNA mesh wireframe.

    • Sha Sun
    • , Shize Yang
    •  & Oleg Gang

  • Article
    | Open Access

    Though DNA framework-based scaffolds for biomolecular assembly are attractive for bioimaging applications, realizing super-multiplex fluorescent amplifiers remains a challenge. Here, the authors report a topological engineering approach to designing fractal DNA frameworks for multiplexed amplifiers.

    • Jiang Li
    • , Jiangbing Dai
    •  & Chunhai Fan

  • Article
    | Open Access

    DNA strand displacement reactions can be difficult to scale up for computational tasks. Here the authors develop DNA switching circuits that achieve high-speed computing with fewer molecules.

    • Fei Wang
    • , Hui Lv
    •  & Chunhai Fan

  • Article
    | Open Access

    Biomolecular cyptography that exploits specific interactions could be used for data encryption. Here the authors use the folding of M13 DNA to encrypt information for secure communication.

    • Yinan Zhang
    • , Fei Wang
    •  & Chunhai Fan

  • Article
    | Open Access

    Current DNA-assembled nanophotonic devices can only reconfigure among random or few defined states. Here, the authors demonstrate a DNA-assembled rotary plasmonic nanoclock in which a rotor gold nanorod carries out directional and reversible 360° rotation transitioning among 16 well-defined configurations.

    • Ling Xin
    • , Chao Zhou
    •  & Na Liu

  • Article
    | Open Access

    Aptamer switches are promising biotechnological tools but coupling of their affinity and temporal response limits their versatility. Here, the authors developed an intramolecular strand-displacement strategy that allows for independent fine-tuning of thermodynamics and kinetics of aptamer switches.

    • Brandon D. Wilson
    • , Amani A. Hariri
    •  & H. Tom Soh

  • Article
    | Open Access

    Nanopores have a wide range of applications in the field of sensing. Here the authors report on synthetic nanopores made of DNA and designed for the transit of folded proteins across membranes to allow for biosensing.

    • Tim Diederichs
    • , Genevieve Pugh
    •  & Stefan Howorka

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