DNA nanostructures articles within Nature Communications

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  • Article
    | Open Access

    The self-assembly process of DNA nanostructures is still not well understood, especially for DNA origami. Here, the authors present a mesoscopic model that uses a switchable force field to capture the mechanical behavior of single- and double-stranded DNA motifs and transition between them, allowing access to the long assembly timescales of DNA origami up to several kilobases in size.

    • Marcello DeLuca
    • , Daniel Duke
    •  & Gaurav Arya

  • Article
    | Open Access

    Artificial biomolecular condensates are valuable tools to study the design principles of phase separation. Here, the authors demonstrate and characterize a model system of artificial DNA condensates whose kinetic formation and dissolution depends on DNA inputs that activate or deactivate the phase separating DNA subunits.

    • Siddharth Agarwal
    • , Dino Osmanovic
    •  & Elisa Franco

  • Article
    | Open Access

    The mechanical dysregulation of cells is associated with several diseases and strategies to deliver drugs based on the “mechanical phenotype” of a cell are desirable. Here, the authors design and characterize DNA mechanocapsules comprised of DNA tetrahedrons that are force responsive, and showed they can encapsulate macromolecular cargo and release it upon application of force.

    • Arventh Velusamy
    • , Radhika Sharma
    •  & Khalid Salaita

  • Article
    | Open Access

    Computational frameworks for structural dynamics are in continuous need of being developed. Here the authors present a a computational framework based on Langevin dynamics to analyze structural dynamics and reconfiguration of DNA assemblies, offering a rational method for designing responsive and reconfigurable DNA machines

    • Jae Young Lee
    • , Heeyuen Koh
    •  & Do-Nyun Kim

  • Article
    | Open Access

    Synthetic membrane channels have many potential applications, but interfacing membrane channels with electronic devices for efficient information transfer is challenging. Here the authors integrate membrane spanning DNA nanopores with bioprotonic contacts to create programmable, modular, and efficient artificial ion-channel interfaces.

    • Le Luo
    • , Swathi Manda
    •  & Marco Rolandi

  • Article
    | Open Access

    The binding of small molecules to the double stranded DNA may significantly alter its stability and functionality, which is the basis for many therapeutic and sensing applications. Here, the authors report that DNA binders can be used to program reaction pathways of a dynamic DNA reaction, where DNA strand displacement can be tuned quantitatively according to the affinity, charge, and concentrations of a given DNA binder.

    • Junpeng Xu
    • , Guan Alex Wang
    •  & Feng Li

  • Article
    | Open Access

    Cost-effective methods for long-term storage of DNA are desired. Here the authors present a method for in situ cryosilicification of whole blood cells, allowing long-term and room temperature preservation of genomic information for only approximately $0.5 per sample.

    • Liang Zhou
    • , Qi Lei
    •  & Wei Zhu

  • Article
    | Open Access

    DNA origami can be coated in a layer of silica to improve chemical and thermal stability however; it is unclear if this is a surface or interpenetrating layer. Here, the authors use in situ small-angle X-ray scattering to study silica deposition and observe internal silica formation resulting in DNA origami condensation and structure shrinkage.

    • Martina F. Ober
    • , Anna Baptist
    •  & Bert Nickel

  • Article
    | Open Access

    Chiral plasmonic nanoparticles are of great interest in nanotechnology. Here, the authors demonstrate chiral shape guidance by single-stranded oligonucleotides during particle growth based on sequence-specific hydrogen bonding within the strand.

    • Nam Heon Cho
    • , Young Bi Kim
    •  & Ki Tae Nam

  • Article
    | Open Access

    Interest in oligonucleotide nanostructures has recently surged in basic and applied research. Here, the authors use native mass spectrometry and ion mobility to elucidate a prototypical hexameric DNA barrel structure as well as intermediates and byproducts of the assembly reaction.

    • Jeroen F. van Dyck
    • , Jonathan R. Burns
    •  & Frank Sobott

  • Article
    | Open Access

    Engineered crystal architectures from DNA have become a foundational goal for nanotechnological precise arrangement. Here, the authors systematically investigate the structures of 36 immobile Holliday junction sequences and identify the features allowing the crystallisation of most of them, while 6 are considered fatal.

    • Chad R. Simmons
    • , Tara MacCulloch
    •  & Hao Yan

  • Article
    | Open Access

    DNA nanofabrication techniques have huge potential for the patterning of electronic materials and devices but suffer from defects which become more significant at lower scales. Here, the authors report on a study into the causes of line defects and develop criteria for reducing defects demonstrating this technique.

    • Yahong Chen
    • , Chaoyong Yang
    •  & Wei Sun

  • Article
    | Open Access

    Artificial systems to control the transport of molecules across biomembranes can be useful for biosensing or drug delivery. Here, the authors assemble a DNA channel enabling the precisely timed, stimulus-controlled transport of functional proteins across bilayer membranes.

    • Swarup Dey
    • , Adam Dorey
    •  & Hao Yan

  • Article
    | Open Access

    Simple methods for attaching polynucleotides to gold nanoparticles are of interest for simplifying conjugation in a range of applications. Here, the authors report a microwave heating-based method for the fast, one-step attachment of a range of thiolated or non-thiolated DNA and RNA to gold nanoparticles.

    • Mengqi Huang
    • , Erhu Xiong
    •  & Xiaoming Zhou

  • 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

    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

    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

    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

    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

    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

    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

    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

    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

  • Article
    | Open Access

    Curli are bacterial functional amyloids that have gained interest as self-assembling biomaterial for biotechnology applications. Here, the authors show that DNA origami decorated with CsgB nucleator proteins induced the site-specific nucleation and subsequent fibrillization of CsgA proteins.

    • Xiuhai Mao
    • , Ke Li
    •  & Chao Zhong

  • Article
    | Open Access

    DNA nanostructures of increasing complexity have been designed using scaffolded origami or single-stranded tiles and bricks. Here the authors demonstrate the construction of complex structures using a wireframe approach that overcomes limitations of using scaffolding.

    • Wen Wang
    • , Silian Chen
    •  & Bryan Wei

  • Article
    | Open Access

    Self-assembly of DNA origami is a complex folding problem without a unified view of the energetic factors involved. Here the authors analyse identical structures that differ by nucleotide sequence and identify how mechanical stress at nucleation sites shapes the energy landscape.

    • Richard Kosinski
    • , Ann Mukhortava
    •  & Barbara Saccà

  • Article
    | Open Access

    Formation of biological filaments via intracellular supramolecular polymerization of proteins occurs under programmable and spatiotemporal control to maintain integrity. Here the authors devise a bioinspired isothermal chain-growth approach to programmably copolymerize DNA hairpin tiles into 1D nanofilaments.

    • Honglu Zhang
    • , Yu Wang
    •  & Chunhai Fan

  • Article
    | Open Access

    Cryo-electron microscopy can determine the structure but not the nanomechanics of biological matter. Here the authors combine force spectroscopy in cryogenic conditions with computer simulations to characterize the properties of DNA simultaneously down to the sub-nm level.

    • Rémy Pawlak
    • , J. G. Vilhena
    •  & Ernst Meyer

  • Article
    | Open Access

    DNA and RNA have been used for nanotechnology applications, though rarely in combination. Here the authors report the use of RNA motifs as structural joints with DNA building blocks for enhanced construction of small multi-component nanoshapes.

    • Alba Monferrer
    • , Douglas Zhang
    •  & Thomas Hermann

  • Article
    | Open Access

    Strand displacement is commonly used in DNA nanotechnology to program dynamic interactions between individual DNA strands. Here, the authors describe a tile displacement principle that is similar in concept but occurs on a larger structural level: the displacement reactions take place between DNA origami tiles, allowing reconfiguration of entire systems of interacting DNA structures.

    • Philip Petersen
    • , Grigory Tikhomirov
    •  & Lulu Qian

  • Article
    | Open Access

    Designing nucleic acid-based nanostructures with knots remains challenging. Here the authors present a general strategy to design and construct highly knotted 2D and 3D nanostructures from single-stranded DNA or RNA

    • Xiaodong Qi
    • , Fei Zhang
    •  & Hao Yan

  • Article
    | Open Access

    Self-assembled DNA nanostructures hold potential as nanomachines or platforms for organized chemical synthesis, but methods for assembly quality control are lacking. Here the authors use DNA-PAINT to quantify the incorporation and accessibility of individual strands in a DNA origami platform with molecular resolution.

    • Maximilian T. Strauss
    • , Florian Schueder
    •  & Ralf Jungmann

  • Article
    | Open Access

    Kinesin, a motor protein, moves along filaments in a walk-like fashion to transport cargo to specific places in the cell. Here, the authors developed an analogous, artificial system consisting of nanoparticles moving along DNA filaments.

    • Maximilian J. Urban
    • , Steffen Both
    •  & Na Liu

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