DNA nanomachines articles within Nature Communications

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  • Article
    | Open Access

    Molecular switches are ubiquitous in the biochemistry regulatory network. Here, the authors construct synthetic molecular switches controlled by DNA-modifying enzymes such as DNA polymerase and nicking endonuclease to control and cascade assembly and disassembly.

    • Hong Kang
    • , Yuexuan Yang
    •  & Bryan Wei

  • Article
    | Open Access

    Various methods, using DNA, have been reported for the recording of biomolecular interactions, but most are either destructive in nature or are limited to reporting pairwise interactions. Here the authors develop DNA-based motors, termed ‘crawlers’, that roam around and record their trajectories to allow the examination of molecular environments.

    • Sungwook Woo
    • , Sinem K. Saka
    •  & Peng Yin

  • Article
    | Open Access

    Contractile rings are formed from cytoskeletal filaments, specific crosslinkers and motor proteins during cell division. Here, authors form micron-scale contractile DNA rings from DNA nanotubes and synthetic crosslinkers, with both simulations and experiments showing ring contraction without motor proteins, offering a potential first step towards synthetic cell division machinery.

    • Maja Illig
    • , Kevin Jahnke
    •  & Kerstin Göpfrich

  • 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

    Artificial molecular machines have captured the imagination of researchers, given their clear potential to mimic and influence human life. Here, the authors use a DNA cube framework for the design of a dice device at the nanoscale to reproduce probabilistic events in different situations such as equal probability, high probability, and low probability.

    • Xiaochen Tang
    • , Tianshu Chen
    •  & Xiaoli Zhu

  • Article
    | Open Access

    Building synthetic protocells and prototissues hinges on the formation of biomimetic skeletal frameworks. Here, the authors harness simplicity to create complexity by assembling DNA subunits into structural frameworks which support membrane-based protocells and prototissues.

    • Nishkantha Arulkumaran
    • , Mervyn Singer
    •  & Jonathan R. Burns

  • 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

    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

    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

    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

    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

    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

    DNA molecular machines hold promise for biological nanotechnology, but how to actuate them in a fast and programmable manner remains challenging. Here, Lauback et al. demonstrate direct manipulation of DNA origami assemblies via a micrometer-long stiff mechanical lever controlled by a magnetic field.

    • Stephanie Lauback
    • , Kara R. Mattioli
    •  & Carlos E. Castro

  • 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

  • Article
    | Open Access

    The spatial organisation of nanostructures is fundamental to their function. Here, the authors develop a non-destructive, proximity-based method to record extensive spatial organization information in DNA molecules for later readout.

    • Thomas E. Schaus
    • , Sungwook Woo
    •  & Peng Yin

  • Article
    | Open Access

    Responsive molecular machines can perform specific tasks triggered by environmental or chemical stimuli. Here, the authors show that antibodies can be used as inputs to modulate the binding of a molecular cargo to a designed DNA-based nanomachine, with potential applications in diagnostics and drug delivery.

    • Simona Ranallo
    • , Carl Prévost-Tremblay
    •  & Francesco Ricci

  • Article
    | Open Access

    Synthetic DNA nanomachines have been designed to perform a variety of tasksin vitro. Here, the authors build a nanomotor system that integrates a DNAzyme and DNA track on a gold nanoparticle, to facilitate cellular uptake, and apply it as a real-time miRNA imaging tool in living cells.

    • Hanyong Peng
    • , Xing-Fang Li
    •  & X. Chris Le

  • Article
    | Open Access

    DNA circuits hold promise for advancing information-based molecular technologies, yet it is challenging to design and construct them in practice. Thubagereet al. build DNA strand displacement circuits using unpurified strands whose sequences are automatically generated from a user-friendly compiler.

    • Anupama J. Thubagere
    • , Chris Thachuk
    •  & Lulu Qian

  • Article
    | Open Access

    Rotaxanes are interlocked molecules that can undergo sliding and rotational movements and can be used in artificial molecular machines and motors. Here, Simmel and co-workers show a rigid rotaxane structures consisting of DNA origami subunits that can slide over several hundreds of nanometres.

    • Jonathan List
    • , Elisabeth Falgenhauer
    •  & Friedrich C. Simmel

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