DNA nanotechnology articles within Nature Communications

Featured

  • 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

    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

    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

    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 development of RNA technologies demands accurate assessment of transcript size and heterogeneity. Here, authors report a nanopore-based approach to study full-length RNA transcripts at the single-molecule level, identify premature transcription termination and study rolling-circle transcription.

    • Gerardo Patiño-Guillén
    • , Jovan Pešović
    •  & Ulrich Felix Keyser

  • Article
    | Open Access

    Three-dimensional DNA origami constructs can be used to deliver vaccine antigens in a multi-valent form. Here the authors design a DNA origami system for SARS-CoV-2 proteins and characterize in mice the immune response and protective capacity of generated antibodies, finding that the construct itself is not immunogenic.

    • Eike-Christian Wamhoff
    • , Larance Ronsard
    •  & Mark Bathe

  • 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 gene networks in mammalian cells are currently limited to either transcription factors or RNA regulators. Here, the authors develop a regulatory approach based on circular single-stranded DNA, which can be used as a conformationally switchable genetic vector in mammalian cells.

    • Linlin Tang
    • , Zhijin Tian
    •  & Jie Song

  • Article
    | Open Access

    Concentration polarization electroosmosis (CPEO) has recently been found to produce similar flow patterns around spheres in an AC electric field as induced charge electroosmosis. Katzmeier and Simmel study the flow around the asymmetric particle dimers caused by CPEO and design a microrobot that can be steered with a joystick and facilitates the transport of cargo particles.

    • Florian Katzmeier
    •  & Friedrich C. Simmel

  • Comment
    | Open Access

    The commercialization of DNA tagging is a growing trend that demonstrates the increasing practicality of this novel approach. This interdisciplinary technology is based on the distinctive characteristics of DNA as a molecule that can remain stable in varying environmental conditions and store data following appropriate preparation. Moreover, newly developed technologies could simplify DNA synthesis and the encoding of data within DNA. The implementation of DNA tagging presents distinctive benefits in comparison to conventional labelling techniques, including universal product code (UPC) barcoding, radio-frequency identification (RFID), quick response (QR) codes, and Bluetooth technologies, by surmounting the limitations encountered by these systems. The discourse pertains to extant DNA-tagging mechanisms along with prospective implementations in a wide range of domains, including but not limited to art, the metaverse, forensics, wildlife monitoring, and the military. The potential of DNA labelling in various contexts underscores the importance of continued research and development in this rapidly evolving field.

    • Adam Kuzdraliński
    • , Marek Miśkiewicz
    •  & Bogdan Księżopolski

  • 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 development of dynamic DNA nanodevices, whose configuration and function are regulated by specific chemical inputs, represents a rapidly growing area in molecular science. Herein, the authors report the concept of metal-mediated base-pair switching to induce inter- and intramolecular DNA strand displacement in a metal-responsive manner.

    • Yusuke Takezawa
    • , Keita Mori
    •  & Mitsuhiko Shionoya

  • Article
    | Open Access

    Conformational cooperativity is a universal molecular effect mechanism and plays a critical role in signalling pathways. Here the authors present a programmable conformational cooperativity strategy to construct the oligo-protein signal transduction platform for logic operations and gene regulations which can be cooperatively regulated by conformational signals.

    • Yuan Liang
    • , Yunkai Qie
    •  & Cheng Zhang

  • 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

    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

    Controlled delivery of small molecule therapeutics is challenging. Here the authors report a simple and effective aptamer-based depot system where the formation of aptamer/drug complexes leads to sustained release, and using this approach demonstrate improved in vivo delivery of channel blockers.

    • Dali Wang
    • , Yang Li
    •  & Christopher B. Weldon

  • Article
    | Open Access

    Efforts to convert aptamers into molecular switches using rational design are often unsuccessful. Here the authors describe a massively parallel screening-based strategy whereby millions of potential aptamer switches are synthesised, sequenced and screened directly on a flow-cell.

    • Alex M. Yoshikawa
    • , Alexandra E. Rangel
    •  & H. Tom Soh

  • Article
    | Open Access

    Resolving the stoichiometry of membrane protein interactions is challenging but is vital to understand cell signalling. Using lipid-bound DNA receptors as a model for membrane proteins, the authors present a platform to achieve stoichiometric, spatial and temporal control over their interactions.

    • Vishal Maingi
    • , Zhao Zhang
    •  & Paul W. K. Rothemund

  • 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

    DNA origami may enable more versatile gene delivery applications through its ability to create custom nanoscale objects. Here the authors show that genes folded in DNA origami with custom scaffolds express efficiently when delivered to mammalian cells and can be assembled into multimeric arrays to deliver and express defined ratios of multiple genes simultaneously.

    • Jessica A. Kretzmann
    • , Anna Liedl
    •  & Hendrik Dietz

  • Article
    | Open Access

    Hybrid nucleic acid origami has potential for biomedical delivery of mRNA and fabrication of artificial ribozymes. Here, the authors use chemical footprinting and cryo-electron microscopy to reveal insights into nucleic acid origami used to fold messenger and ribosomal RNA into 3D polyhedral structures.

    • Molly F. Parsons
    • , Matthew F. Allan
    •  & Mark Bathe

  • Article
    | Open Access

    Artificial organelles can potentially be used support cellular functions, but there is a trade-off between cellular uptake and cellular retention. Here, the authors report the dynamic assembly of DNA-ceria-based artificial peroxisomes in cells, and show they can be used to reduce intracellular ROS.

    • Chi Yao
    • , Yuwei Xu
    •  & Dayong Yang

  • Article
    | Open Access

    Natural buffer molecules ensure the controlled and precise delivery of specific molecules in biology. Here, the authors replicate the natural buffer systems using aptamers with controlled binding efficiency to control and maintain the levels of free drugs both in vitro and in vivo.

    • Arnaud Desrosiers
    • , Rabeb Mouna Derbali
    •  & Alexis Vallée-Bélisle

  • 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

    Programming the 3D spatial organization of quantum dots requires precise control over their individual valence, but this is challenging due to the possible presence of multiple binding sites. Here, authors develop a general approach that uses highly programmable wireframe DNA origami structures to control the 3D spatial relationships between QDs and other non-nucleic-acid molecules.

    • Chi Chen
    • , Xingfei Wei
    •  & Mark Bathe

  • Article
    | Open Access

    Next-generation lipid nanoparticles that target non-hepatocytes could be important clinical tools. Using in vivo DNA barcoding, the authors identify piperazine-containing lipids deliver mRNA to immune cells without targeting ligands.

    • Huanzhen Ni
    • , Marine Z. C. Hatit
    •  & James E. Dahlman

  • 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

    A quantitative prediction of DNA-mediated interactions between colloids is crucial to the design of colloidal structures for optical applications. Cui et al. measure the interaction potential with nanometer resolution and propose a theory to accurately predict adhesion and melting at a molecular level.

    • Fan Cui
    • , Sophie Marbach
    •  & David J. Pine

  • 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

    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

Browse broader subjects

Browse narrower subjects

Browse DNA nanotechnology across other nature.com journals