DNA nanotechnology articles within Nature Chemistry

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  • Article
    | Open Access

    Advances in the development of cytoskeletal-like materials with modular structures and mechanics are pivotal for the engineering of synthetic cells. Now actin-mimetic supramolecular peptide networks have been designed using programmable peptide–DNA crosslinkers, giving rise to tunable tactoid-shaped bundles and mechanical properties that control spatial localization, the diffusion of payloads and shape changes within artificial cells.

    • Margaret L. Daly
    • , Kengo Nishi
    •  & Ronit Freeman

  • Article |

    The advantages and disadvantages of building a nanosystem using one, two or more molecular components are poorly understood. Now, using structural and catalytic DNA-based nanosystems and theoretical simulations, it has been shown that the assembly of trimeric nanosystems displays much higher levels of programmability and functionality than the monomeric or dimeric counterparts.

    • D. Lauzon
    •  & A. Vallée-Bélisle

  • News & Views |

    Molecular computing programmed with complementary nucleic acid strands allows the construction of sophisticated biomolecular circuits. Now, systems with partially complementary strands have been shown to enable more compact and faster molecular circuits, and may illuminate biological processes.

    • Philip Petersen
    •  & Grigory Tikhomirov

  • Article |

    A method has been developed to identify RNA transcript isoforms at the single-molecule level using solid-state nanopore microscopy. In this method, target RNA is refolded into RNA identifiers with designed sets of complementary DNA strands. Each reshaped molecule carries a unique sequence of structural (pseudo)colours that enables identification and quantification using solid-state nanopore microscopy.

    • Filip Bošković
    •  & Ulrich Felix Keyser

  • Article |

    Synthetic chemical networks with far-from-equilibrium dynamics akin to genetic regulatory networks in living cells could precisely regulate the kinetics of chemical synthesis or self-assembly. Now standardized excitable chemical regulatory elements, termed genelets, that enable predictive bottom-up construction of in vitro networks with designed temporal and multistable behaviour have been developed.

    • Samuel W. Schaffter
    • , Kuan-Lin Chen
    •  & Rebecca Schulman

  • Article
    | Open Access

    Cytoskeletons are essential components of cells that perform a variety of tasks, and artificial cytoskeletons that perform these functions are required for the bottom-up assembly of synthetic cells. Now, a multi-functional cytoskeleton mimic has been engineered from DNA, consisting of confined DNA filaments that are capable of reversible self-assembly and transport of gold nanoparticles and vesicular cargo.

    • Pengfei Zhan
    • , Kevin Jahnke
    •  & Kerstin Göpfrich

  • Review Article |

    The emerging field of dissipative DNA nanotechnology aims at developing synthetic devices and nanomaterials with life-like properties such as directional motion, transport, communication or adaptation. This Review surveys how dissipative DNA systems combine the programmability of nucleic-acid reactions with the consumption of energy stored in chemical fuel molecules to perform work and cyclical tasks.

    • Erica Del Grosso
    • , Elisa Franco
    •  & Francesco Ricci

  • News & Views |

    Self-organization — ubiquitous in living systems — occurs out-of-equilibrium, with dissipation of energy and matter. Researchers have now shown that slow proton dissipation switches the assembly of DNA-based fibres to a growth mechanism that heals their gaps, yielding tight nanocable architectures.

    • Mathieu Surin

  • Article |

    Nature uses out-of-equilibrium systems to control hierarchical assembly. Now, a dissipative chemical system has been shown to slowly release monomer DNA strands from a high-energy reservoir, regulating self-assembly by switching the mechanism of supramolecular polymerization at the single-molecule level. This process heals fibre defects, converting branched, heterogeneous networks into nanocable superstructures.

    • Felix J. Rizzuto
    • , Casey M. Platnich
    •  & Hanadi F. Sleiman

  • Article |

    RNA origami can be used for the modular design of RNA nanoscaffolds but can be challenging to design. Newly developed computer-aided design software has now been shown to improve the folding yield of kilobase-sized RNA origami. These structures fold from a single strand during transcription by an RNA polymerase, and are able to position small molecules and protein components with nanoscale precision.

    • Cody Geary
    • , Guido Grossi
    •  & Ebbe S. Andersen

  • News & Views |

    Modelling the structure and behaviour of vesicles in cells requires liposomes with precise sizes, but producing liposomes with a narrow size distribution is challenging. An approach has now been developed to accurately size-sort liposomes in a scalable way by coating them with customized structures based on DNA nanotechnology.

    • Silvia Hernández-Ainsa

  • Article |

    Small liposomes of uniform sizes are valuable tools for studying membrane biology and developing drug-delivery vehicles. Now, a DNA-assisted sorting technique has been shown to produce multiple species of monodispersed liposomes with mean diameters below 150 nm in a scalable manner. This approach has enabled the high-resolution analyses of curvature-dependent membrane protein activities.

    • Yang Yang
    • , Zhenyong Wu
    •  & Chenxiang Lin

  • Article |

    Stimuli-responsive control of drug activation can mitigate issues caused by poor drug selectivity. Now, it has been shown that mechanical force—induced by ultrasound—can be used to activate drugs in three different systems. This approach has enabled the activation of antibiotics or a cytotoxic anticancer agent from synthetic polymers, polyaptamers and nanoparticle assemblies.

    • Shuaidong Huo
    • , Pengkun Zhao
    •  & Andreas Herrmann

  • Article |

    A six-helix bundle DNA structure called meta-DNA has now been assembled and shown to possess some structural properties similar to those of single-stranded DNA. Two meta-DNAs containing complementary ‘meta-base pairs’ are shown to form double helices. Meta-DNA building blocks are also used to construct a series of DNA architectures and to perform a hierarchical strand-displacement reaction.

    • Guangbao Yao
    • , Fei Zhang
    •  & Hao Yan

  • Article |

    Multivalent binding is a common strategy to enhance the interactions between weak binding partners. Now, following this principle, DNA origami scaffolds have been used to arrange DNA aptamers into specific geometries and to optimize linker spacings and flexibilities, which results in artificial binding sites with very high affinities for their corresponding ligands.

    • Ali Aghebat Rafat
    • , Sandra Sagredo
    •  & Friedrich C. Simmel

  • News & Views |

    RNA has multiple roles in biology, enabled by its structural diversity. Now, artificially grafted RNA motifs have been encoded in a single RNA strand to form self-assembling nanostructures with controlled geometry and function.

    • Qi Shen
    •  & Chenxiang Lin

  • Article |

    Homooligomerization systems can be used to construct nanoarchitectures and to aid understanding of natural analogues. But the formation of such artificial systems with structural diversity and complexity comparable to that of biological systems is challenging. Now, an artificial branched kissing-loop motif has been designed, which links tiles folded from a single strand of RNA to give diverse homooligomeric nanostructures.

    • Di Liu
    • , Cody W. Geary
    •  & Yossi Weizmann

  • Article |

    DNA is capable of self-assembling into a wide range of user-defined structures and so can be used as a scaffold to arrange binding motifs with nanometre precision. Now, DNA has been used to accurately display aptamers that fit the repeated epitope pattern of a dengue viral antigen to produce a nanostructure that can be a potent viral inhibitor or a fluorescent sensor.

    • Paul S. Kwon
    • , Shaokang Ren
    •  & Xing Wang

  • Article |

    Super-resolution microscopy has enabled optical imaging of individual biomolecules on the nanometre scale. Now, a new method has been developed that allows active manipulation of single-molecule targets on visualization in a sequential manner. This method, called ‘Action-PAINT’, combines real-time super-resolution microscopy (DNA-PAINT) and photoinducible crosslinking chemistry to deliver a single-molecule cargo with <30 nm selectivity.

    • Ninning Liu
    • , Mingjie Dai
    •  & Peng Yin

  • Article |

    The regulation of cellular response to stimuli by genetic regulatory networks (GRNs) suggests how in vitro chemical reaction networks might be used to direct the dynamics of synthetic materials or chemical reactions. Now, multiple functional in vitro transcriptional circuit modules have been integrated to form composite regulatory networks capable of complex features analogous to those found in cellular GRNs.

    • Samuel W. Schaffter
    •  & Rebecca Schulman

  • News & Views |

    In biological systems, order typically emerges from out-of-equilibrium molecular processes that control both static patterns and dynamic changes. Now, the self-regulating assembly and disassembly of a synthetic system has been achieved on the micrometre scale, by coupling the growth of a DNA nanotube to a biochemical oscillator.

    • Tim Liedl

  • Article |

    Nucleic acid nanotechnology offers a promising route towards the design and synthesis of reconfigurable biomolecular materials. Now, the combination of dynamic and structural DNA nanotechnology has enabled the dynamic control of the assembly and disassembly of DNA nanotubes. The process involves minimal synthetic gene systems, including an autonomous molecular oscillator.

    • Leopold N. Green
    • , Hari K. K. Subramanian
    •  & Elisa Franco

  • Article |

    Synthetic gene circuits encapsulated in lipid membrane compartments are often employed as artificial cell mimics, but these lack the complex behaviour of biological tissues. Now, spatial information based on chemical gradients has been used to engineer non-trivial dynamics such as signal propagation and differentiation in an artificial multicellular system.

    • Aurore Dupin
    •  & Friedrich C. Simmel

  • Article |

    Gene expression profiling remains cost-prohibitive and challenging to implement in a clinical setting. Now, a molecular computation strategy for classifying complex gene expression signatures has been developed. Classification occurs through a series of molecular interactions between RNA inputs and engineered DNA probes designed to implement a relevant linear classification model.

    • Randolph Lopez
    • , Ruofan Wang
    •  & Georg Seelig

  • Article |

    Primer exchange reaction (PER) cascades have now been used to grow nascent single-stranded DNA with user-specified sequences following prescribed reaction pathways. PER synthesis occurs in a programmable, autonomous, in situ and environmentally responsive fashion, providing a platform for engineering molecular circuits and devices with a wide range of sensing, monitoring, recording, signal processing and actuation capabilities.

    • Jocelyn Y. Kishi
    • , Thomas E. Schaus
    •  & Peng Yin

  • Review Article |

    DNA nanotechnology provides a versatile toolbox for engineering synthetic circuits in living cells. This Review discusses how nanostructures made from nucleic acids can enable biocomputation and also be readily interfaced with a variety of intracellular and in vivo components to facilitate synthetic biology applications.

    • Jiang Li
    • , Alexander A. Green
    •  & Chunhai Fan

  • News & Views |

    DNA double helical structures are supramolecular assemblies that are typically held together by classical Watson–Crick pairing. Now, nucleotide chelation of silver ions supports an extended silver–DNA hybrid duplex featuring an uninterrupted silver array.

    • Pascal Auffinger
    •  & Eric Ennifar

  • Article |

    A metallo–DNA hybrid nanowire composed only of silver-mediated base pairs has been prepared and its crystal structure resolved by X-ray diffraction. The nanowire, which is 2 nm wide and whose length reaches the μm to mm scale, holds silver ions into uninterrupted one-dimensional arrays along the DNA helical axis.

    • Jiro Kondo
    • , Yoshinari Tada
    •  & Yoshiyuki Tanaka

  • Article |

    Controlling liposome shape, arrangement and dynamics is important for biophysical studies and synthetic biology applications. Now, using a family of reconfigurable DNA nanocages as templates, spherical, tubular, toroidal and helical liposomes with predefined geometry have been produced. DNA-guided membrane fusion and bending is also demonstrated.

    • Zhao Zhang
    • , Yang Yang
    •  & Chenxiang Lin

  • Article |

    A DNA-based reaction network has now been developed that creates a French flag pattern with immobile and sharp borders from a shallow initial concentration gradient. The output pattern can be used to control the macroscopic organization of DNA-decorated particles thereby inducing a French flag pattern of colloidal aggregation.

    • Anton S. Zadorin
    • , Yannick Rondelez
    •  & André Estevez-Torres

  • Article |

    Although DNA nanotechnology has found many applications in developing functional structures, there has never been an independent device contained within a 3D crystal. Now, a self-assembled three-state device that can change the colour of its crystal by diffusion of DNA-ligated dyes has been reported, representing the potential to develop programmable nanomechanical devices.

    • Yudong Hao
    • , Martin Kristiansen
    •  & Nadrian C. Seeman

  • Article |

    Charge transfer in DNA is of fundamental interest in chemistry and biochemistry and has possible applications in nano-electronics. Now it has been shown, through a combined experimental and theoretical study, that the migration of positive charges through low-lying orbitals of nucleobases (deep-hole transfer) leads to charge transfer that is faster than previously considered transport regimes.

    • Nicolas Renaud
    • , Michelle A. Harris
    •  & Ferdinand C. Grozema

  • Article |

    The synthesis of topologically non-trivial compounds requires the manipulation of molecular recognition with an extraordinarily high level of control. Now, DNA four-way junctions have been configured to construct synthetic DNA knots and links, which can then be used to investigate important DNA-processing enzymes.

    • Di Liu
    • , Gang Chen
    •  & Yossi Weizmann

  • Article |

    The existence (or not) of electronic coherence in homopolymers is dependent on a balance between monomer–monomer interactions and environmental heterogeneity. Now, by understanding how even–odd orbital symmetry influences coherence and produces resistance oscillations as a function of distance—it is shown that DNA sequences can be designed to support coherent charge transport.

    • Chaoren Liu
    • , Limin Xiang
    •  & Nongjian Tao

  • Article |

    Dynamic nonlinear biochemical circuits are functionally rich; however, this nonlinear nature also makes programming them delicate and painstaking. Now a droplet microfluidic platform reveals precisely the bifurcations of two canonical systems: a bistable switch and a predator–prey oscillator, exposing optimal regions and mechanistic insights that inform the design of these systems.

    • A. J. Genot
    • , A. Baccouche
    •  & Y. Rondelez

  • Article |

    A broadly applicable strategy that can control the self-assembly of nanoparticles into a predefined structure has been reported. Integrating nanoparticles with DNA constructs creates individual modules that can be assembled into complex planar architectures. The approach combines nanoparticles with the selectivity and directionality of bonds provided by DNA.

    • Wenyan Liu
    • , Jonathan Halverson
    •  & Oleg Gang

  • Article |

    Molecular machines that assemble polymers in a programmed sequence are fundamental to life. Now, synthetic machinery built from DNA has been used to execute a molecular program that produces peptides, or olefin oligomers, with a defined sequence. The oligomeric product is linked to a double-stranded DNA product that records the sequence of reactions that were executed.

    • Wenjing Meng
    • , Richard A. Muscat
    •  & Andrew J. Turberfield

  • Article |

    Understanding the correlation between structure and charge transport properties of a DNA-based single molecule device is crucial to the creation of nanoscale functional devices. Now, a DNA-based molecular rectifier with a high rectification ratio has been constructed by site-specific intercalation of small molecules (coralyne) into native double-stranded DNA.

    • Cunlan Guo
    • , Kun Wang
    •  & Bingqian Xu

  • Article |

    Precise control of vesicle size is highly desirable both for basic biochemical research and biomedical applications. Now, monodispersed sub-100-nm vesicles with predefined sizes have been produced using a method based on membrane self-assembly within a DNA-nanostructure guide.

    • Yang Yang
    • , Jing Wang
    •  & Chenxiang Lin

  • Article |

    Cyanuric acid, a small molecule with three thymine-like faces, reprogrammes the assembly of unmodified poly(adenine) into long fibres with a unique internal structure. The association of adenine and cyanuric acid units into a hexameric rosette motif brings together poly(adenine) triplexes with subsequent cooperative polymerization.

    • Nicole Avakyan
    • , Andrea A. Greschner
    •  & Hanadi F. Sleiman

  • Article |

    DNA nanostructures are typically used as molecular scaffolds. Now, it has been shown that they can also act as reusable templates for ‘molecular printing’ of DNA strands onto gold nanoparticles. The products inherit the recognition elements of the parent template: number, orientation and sequence asymmetry of DNA strands. This converts isotropic nanoparticles into complex building blocks.

    • Thomas G. W. Edwardson
    • , Kai Lin Lau
    •  & Hanadi F. Sleiman

  • Article |

    DNA nanotubes are attractive building blocks for the assembly of complex arrays. An efficient solid-state synthesis for producing surface-grafted, robust nanotubes has now been devised. Rungs are incorporated in a stepwise manner so that each one is addressable. Using fluorescent tags, the nanotube growth was visualized at the single-molecule level.

    • Amani A. Hariri
    • , Graham D. Hamblin
    •  & Gonzalo Cosa

  • News & Views |

    DNA self-assembly has previously been used to create channel-like structures that can penetrate through lipid bilayer membranes. However, such assemblies have not been shown to cause cell death before. Now a DNA nanopore has been shown to exert a cytotoxic effect when administered to cells.

    • Swati Krishnan
    •  & Friedrich C. Simmel

  • Article |

    The programmed assembly of single DNA strands into bricks and ultimately micrometre-sized two-dimensional crystals with prescribed depths up to 80 nm is described. These crystals display intricate three-dimensional features including continuous or discontinuous cavities and channels with nanometre precision, and can pack DNA helices in parallel or perpendicularly to the plane of the crystals.

    • Yonggang Ke
    • , Luvena L. Ong
    •  & Peng Yin

  • Article |

    Conjugation of DNA to proteins often involves a choice between either expressing recombinant proteins with a specific handle, or labelling wild-type proteins with low site-selectivity. Now preorganization of a DNA–ligand complex to a metal-binding site enables site-selective conjugation of a DNA strand to lysine residues of wild-type proteins and antibodies.

    • Christian B. Rosen
    • , Anne L. B. Kodal
    •  & Kurt V. Gothelf

  • Article |

    Compartmentalization of complex chemical networks is an essential step towards the creation of cell-scale molecular systems. The encapsulation of a synthetic biochemical oscillating reaction system into cell-sized emulsion droplets is now demonstrated; a large variability in its oscillatory dynamics is observed, which is attributed to partitioning effects.

    • Maximilian Weitz
    • , Jongmin Kim
    •  & Friedrich C. Simmel

  • News & Views |

    Using chemical reactions and diffusion to control pattern formation requires the careful design of reaction networks and a balance of kinetics that is difficult to achieve. Now, it has been shown that DNA-based reaction networks provide a robust method for transforming patterns.

    • Dominic Scalise
    •  & Rebecca Schulman

  • Article |

    The programmable nature of chemical reactions enables the creation of complex networks; however, it can be difficult to redesign the underlying reactions. Here, systematic and quantitative control over the diffusivity and reactivity of DNA molecules yields highly programmable chemical reaction networks that execute macroscale pattern transformation algorithms, such as edge detection.

    • Steven M. Chirieleison
    • , Peter B. Allen
    •  & Xi Chen

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