DNA nanotechnology articles within Nature Communications

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  • Article
    | Open Access

    Podosomes are protrusive structures that coordinate diverse functions related to cell invasion, migration, bone resorption and immune surveillance. Here the authors integrate DNA nanotechnology with FLIM-FRET to demonstrate that podosomes apply pN integrin tensile forces to sense and respond to substrate mechanics.

    • Roxanne Glazier
    • , Joshua M. Brockman
    •  & Khalid Salaita

  • Article
    | Open Access

    A major bottleneck in using DNA as a data storage medium is the slowness of sequencing. Here the authors decode 1.67 megabytes of information using a portable nanopore platform with an assembly strategy for increased throughput.

    • Randolph Lopez
    • , Yuan-Jyue Chen
    •  & Luis Ceze

  • 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 hold great promise for drug delivery, but systemic administration is problematic. Here, the authors demonstrate that framework nucleic acids (FNAs) improve drug accumulation in tumours in topical application and that penetration depth is controllable through adjusting FNA size.

    • Christian Wiraja
    • , Ying Zhu
    •  & Chenjie Xu

  • 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

    Colloidal crystal engineering with DNA can be used to synthesize highly anisotropic hexagonal prismatic microcrystals. This manuscript introduces a plane multiplicity mechanism that can be used to deliberately design non-equilibrium Wulff shapes, a capability important in many areas, including optics and photocatalysis.

    • Soyoung E. Seo
    • , Martin Girard
    •  & Chad A. Mirkin

  • Article
    | Open Access

    Materials which change shape in response to a trigger are of interest for soft robotics and targeted therapeutic delivery. Here, the authors report on the development of DNA-crosslinked hydrogels which can expand upon the detection of different biomolecular inputs mediated by DNA strand-displacement.

    • Joshua Fern
    •  & Rebecca Schulman

  • 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

    Polymer knots are important for a range of biological systems and engineering applications, yet the variables influencing knotting probability are not well understood. Here the authors develop a nanofluidic device that can detect knots and provide a free energy formalism that can quantify knotting probability in their system.

    • Susan Amin
    • , Ahmed Khorshid
    •  & Walter Reisner

  • 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

    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

    BAR domain proteins feature a “banana-like” shape which is thought to aid membrane scaffolding and membrane tubulation. Here authors use DNA origami mimicking BAR domains, giant unilamellar vesicles and fluorescence imaging to study how different BAR domain shapes bind and deform membranes.

    • Henri G. Franquelim
    • , Alena Khmelinskaia
    •  & Petra Schwille

  • Article
    | Open Access

    Scaffolded DNA origami by folding single-stranded DNA into three-dimensional nanostructures holds promise for building functional nanomachines, yet their dynamic structures remain largely unknown. Here, Lei et al. address this issue using individual-particle electron tomography at 6–14 nm resolution.

    • Dongsheng Lei
    • , Alexander E. Marras
    •  & Gang Ren

  • Article
    | Open Access

    Self-propelled molecular entities enable studying swarm behavior on a macroscopic scale but programmability of interactions has yet not been achieved. Here the authors show reversible regulation of DNA-functionalized microtubules by DNA signals and switching between solitary and swarm behaviour by employing photoresponsive DNA strands.

    • Jakia Jannat Keya
    • , Ryuhei Suzuki
    •  & Akira Kakugo

  • Article
    | Open Access

    DNA based technology holds promise for non-volatile memory and computational tasks, yet the relatively slow hybridization kinetics remain a bottleneck. Here, Song et al. have developed an electric field-induced hybridization platform that can speed up multi-bit memory and logic operations.

    • Youngjun Song
    • , Sejung Kim
    •  & Xiaohua Huang

  • Article
    | Open Access

    FRET has been used to study protein conformational changes but has never been applied to RNA aptamers. Here the authors develop a genetically encodable RNA aptamer-based FRET system on single-stranded RNA origami scaffolds, and demonstrate it can be used to study RNA conformational changes.

    • Mette D. E. Jepsen
    • , Steffen M. Sparvath
    •  & Ebbe S. Andersen

  • Article
    | Open Access

    DNA nanostructures can cage enzymes but currently fall short of controlling their reactions with substrates. Here, the authors enclose an enzyme inside a dynamic DNA vault, which regulates its access to substrate molecules—and thus its enzymatic activity—through a multi-lock mechanism.

    • Guido Grossi
    • , Mette Dalgaard Ebbesen Jepsen
    •  & Ebbe Sloth Andersen

  • Article
    | Open Access

    Integration of semiconducting properties into the basic topological motif of DNA remains challenging. Here, the authors show a coordination polymer derived from 6-thioguanosine that complexes with Au(I) ions to form a wire-like material that can also integrate semiconducting sequences into the framework of DNA materials.

    • Lamia L. G. Al-Mahamad
    • , Osama El-Zubir
    •  & Andrew Houlton

  • 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

    Atomic force microscopy allows for the imaging of molecules at a nanometre resolution. Here the authors combine AFM with self-assembling DNA origami structures to detect single-nucleotide polymorphisms and determine haplotypes.

    • Honglu Zhang
    • , Jie Chao
    •  & Chunhai Fan

  • Article
    | Open Access

    Although DNA nanopores are widely explored as synthetic membrane proteins, it is still unclear how the anionic DNA assemblies stably reside within the hydrophobic core of a lipid bilayer. Here, the authors use molecular dynamics simulations to reveal the key dynamic interactions and energetics stabilizing the nanopore-membrane interaction.

    • Vishal Maingi
    • , Jonathan R. Burns
    •  & Mark S. P. Sansom

  • Article
    | Open Access

    Techniques for structural characterization and quantification of DNA origami are still poorly developed, despite advances in other aspects of DNA nanotechnology. Here, the authors combine barcoding and next generation sequencing to simultaneously image and quantify self-assembled DNA nanostructures.

    • Cameron Myhrvold
    • , Michael Baym
    •  & Peng Yin

  • 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

    Existing DNA based circuits, designed to perform logic operations and signal processing, are generally responsive to DNA or RNA inputs. Here, the authors show that antibodies can actuate DNA logic gates, opening the way to applications of DNA computing in diagnostics and biomedicine.

    • Wouter Engelen
    • , Lenny H. H. Meijer
    •  & Maarten Merkx

  • Article
    | Open Access

    Artificial DNA membrane channels are promising molecular devices for biotechnology but suffer from low affinity for lipid bilayers. Here, the authors report a large DNA nanopore that spontaneously inserts into a flat lipid membrane, driven by engineered hydrophobic or streptavidin-biotin interactions.

    • Swati Krishnan
    • , Daniela Ziegler
    •  & Friedrich C. Simmel

  • Article
    | Open Access

    Bottom-up synthesis of colloidal metallic nanomaterials with a designable structure is challenging. Here, the authors report the directed crystallisation of gold by a single DNA molecular regulator, using it to synthesise gold nanocrystals with defined complex morphologies.

    • Xingyi Ma
    • , June Huh
    •  & Sang Jun Sim

  • 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

  • Article
    | Open Access

    DNA nanostructures with interlocked topologies will tend to display different behaviour to the linear counterparts. Here, the authors show a DNA catenane that is inactive for rolling circle amplification but is activated upon cleavage of one ring, and exploit this for the development of a biosensing system.

    • Meng Liu
    • , Qiang Zhang
    •  & Yingfu Li

  • Article
    | Open Access

    Cellular DNA is often torsionally constrained, but the topologies that such DNA can adopt under tensile strain have remained largely untested. Here, the authors use single-molecule optical tweezers to illustrate the structural plasticity of torsionally constrained DNA under mechanical force.

    • Graeme A. King
    • , Erwin J. G. Peterman
    •  & Gijs J. L. Wuite

  • Article
    | Open Access

    DNA nanostructures have the potential to be powerful tools in many areas of biology however they are difficult to manufacture completely in vivo. Here the authors combine RNA hairpins and reverse transcription to generate and assemble a complex DNA structure inside the cellular environment.

    • Johann Elbaz
    • , Peng Yin
    •  & Christopher A. Voigt

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