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| Open AccessMechanism of DNA origami folding elucidated by mesoscopic simulations
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
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Article
| Open AccessRectifying artificial nanochannels with multiple interconvertible permeability states
Transmembrane channels have inspired the development of biomimetic channels. Here, the authors present a class of artificial nanochannels based on DNAzyme-functionalized glass nanopipettes to allow for the control of channel permeability.
- Ruocan Qian
- , Mansha Wu
- & Yi Lu
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Article
| Open AccessDynamic control of DNA condensation
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
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| Open AccessDNA mechanocapsules for programmable piconewton responsive drug delivery
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
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Article
| Open AccessDNA T-shaped crossover tiles for 2D tessellation and nanoring reconfiguration
DNA tiles lay the foundation for programmable self-assembly of diverse DNA nanostructures. Here, the authors present a set of T-shaped crossover DNA tiles for various 2D tessellation and nanoring reconfiguration.
- Qi Yang
- , Xu Chang
- & Fei Zhang
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| Open AccessA computational model for structural dynamics and reconfiguration of DNA assemblies
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
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Article
| Open AccessDNA nanopores as artificial membrane channels for bioprotonics
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
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Article
| Open AccessFunctionalization and higher-order organization of liposomes with DNA nanostructures
Liposomes are indispensable model membranes and drug carriers. Here, the authors use DNA nanostructures to coat, cluster, and pattern sub-100-nm liposomes, enabling attachment of proteins and temporal control of membrane fusion.
- Zhao Zhang
- , Zhaomeng Feng
- & Edwin R. Chapman
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Article
| Open AccessEnabling programmable dynamic DNA chemistry using small-molecule DNA binders
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
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Article
| Open AccessIn situ continuous Dopa supply by responsive artificial enzyme for the treatment of Parkinson’s disease
Oral dihydroxyphenylalanine (Dopa) administration to replenish neuronal dopamine is a treatment for Parkinson’s disease but induces fluctuations in plasma Dopa levels. Here the authors report a nucleic acid-based responsive artificial enzyme (FNA-Fe3O4) for in situ continuous Dopa production.
- Xiao Fang
- , Meng Yuan
- & Huanghao Yang
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Article
| Open AccessLong-term whole blood DNA preservation by cost-efficient cryosilicification
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
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| Open AccessIn situ small-angle X-ray scattering reveals strong condensation of DNA origami during silicification
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
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Article
| Open AccessAdenine oligomer directed synthesis of chiral gold nanoparticles
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
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| Open AccessSizing up DNA nanostructure assembly with native mass spectrometry and ion mobility
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
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Article
| Open AccessThe influence of Holliday junction sequence and dynamics on DNA crystal self-assembly
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
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| Open AccessSuppressing high-dimensional crystallographic defects for ultra-scaled DNA arrays
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
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Article
| Open AccessA reversibly gated protein-transporting membrane channel made of DNA
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
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Article
| Open AccessFast microwave heating-based one-step synthesis of DNA and RNA modified gold nanoparticles
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
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| Open AccessSupercoiling and looping promote DNA base accessibility and coordination among distant sites
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
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Article
| Open AccessDigital immunoassay for biomarker concentration quantification using solid-state nanopores
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
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| Open AccessProgramming ultrasensitive threshold response through chemomechanical instability
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
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| Open AccessAutonomous DNA nanostructures instructed by hierarchically concatenated chemical reaction networks
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
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| Open AccessDNA dynamics and computation based on toehold-free strand displacement
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
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| Open AccessResponsive core-shell DNA particles trigger lipid-membrane disruption and bacteria entrapment
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
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Article
| Open AccessProton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells
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
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| Open AccessDynamic self-assembly of compartmentalized DNA nanotubes
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
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Article
| Open AccessDNA origami single crystals with Wulff shapes
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
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Article
| Open AccessAn alternative approach to nucleic acid memory
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
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| Open AccessRobust nucleation control via crisscross polymerization of highly coordinated DNA slats
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
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Article
| Open AccessAddressable nanoantennas with cleared hotspots for single-molecule detection on a portable smartphone microscope
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
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Article
| Open AccessFeedback regulation of crystal growth by buffering monomer concentration
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
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| Open AccessComplex multicomponent patterns rendered on a 3D DNA-barrel pegboard
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
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Article
| Open AccessRational design of DNA nanostructures for single molecule biosensing
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
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| Open AccessEncoding quantized fluorescence states with fractal DNA frameworks
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
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Article
| Open AccessSynthetic protein-conductive membrane nanopores built with DNA
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
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| Open AccessActive generation of nanoholes in DNA origami scaffolds for programmed catalysis in nanocavities
DNA origami provide scaffolds for spatial and temporal control of catalytic functions in confined nanocavities. Here the authors engineer nanoholes in DNA origami scaffolds.
- Jianbang Wang
- , Liang Yue
- & Itamar Willner
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| Open AccessNanomechanical DNA resonators for sensing and structural analysis of DNA-ligand complexes
Intercalating molecules can significantly change the conformation of DNA. Here, the authors fabricated resonators fully composed of DNA forming bundles between microfabricated pillars to study the vibration property of the DNA bundles with/without intercalant molecules.
- Stefano Stassi
- , Monica Marini
- & Enzo Di Fabrizio
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| Open AccessDirecting curli polymerization with DNA origami nucleators
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
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| Open AccessComplex wireframe DNA nanostructures from simple building blocks
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
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| Open AccessSites of high local frustration in DNA origami
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
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| Open AccessProgramming chain-growth copolymerization of DNA hairpin tiles for in-vitro hierarchical supramolecular organization
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
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Article
| Open AccessConformations and cryo-force spectroscopy of spray-deposited single-strand DNA on gold
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
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| Open AccessVersatile kit of robust nanoshapes self-assembling from RNA and DNA modules
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
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Article
| Open AccessInformation-based autonomous reconfiguration in systems of interacting DNA nanostructures
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
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Article
| Open AccessProgramming molecular topologies from single-stranded nucleic acids
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
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Article
| Open AccessA synthetic enzyme built from DNA flips 107 lipids per second in biological membranes
Mimicking enzyme function and improving upon it is a challenge facing nanotechnology. Here the authors design a DNA nanostructure that catalyzes the transport of lipids between bilayers at a rate three orders of magnitude higher than biological enzymes.
- Alexander Ohmann
- , Chen-Yu Li
- & Aleksei Aksimentiev
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Article
| Open AccessQuantifying absolute addressability in DNA origami with molecular resolution
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
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Article
| Open AccessMulti-functional DNA nanostructures that puncture and remodel lipid membranes into hybrid materials
DNA nanopores can span lipid bilayers but how they interact with lipids is not known. Here the authors establish at single-molecule level the insertion mechanism and show that DNA nanopores can locally cluster and remodel membranes, and stabilize autonomously formed lipid nanotubes.
- Oliver Birkholz
- , Jonathan R. Burns
- & Jacob Piehler
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Article
| Open AccessGold nanocrystal-mediated sliding of doublet DNA origami filaments
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