DNA and RNA articles within Nature Communications

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  • 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

    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

    Gene delivery to fibroblasts for liver fibrosis treatment remains challenging. Here the authors develop a combinatorial library of ligand-tethered lipidoids via a modular synthetic method and adopt a 2-round screening strategy to identify lipidoids for potent and selective gene delivery to fibroblasts.

    • Xuexiang Han
    • , Ningqiang Gong
    •  & Michael J. Mitchell

  • 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

    The authors present an approach to connect polymer dynamics to force response by integrating optical tweezers with differential dynamic microscopy. They measure blends of ring and linear DNA and observe a resonant response, which is suppressed by the presence of microtubules.

    • Karthik R. Peddireddy
    • , Ryan Clairmont
    •  & Rae M. Robertson-Anderson

  • Article
    | Open Access

    Methods for fluorescently labelling DNAs are expensive and labour-intensive. Here the authors report an in situ DNA labelling strategy for oligonucleotides as well as dsDNA that makes use of aldehyde-reactive rotor dyes to trap AP sites resulting from excision of deaminated DNA bases.

    • Yong Woong Jun
    • , Emily M. Harcourt
    •  & Eric T. Kool

  • Article
    | Open Access

    Understanding and controlling the rheology of polymeric complex fluids is of fundamental importance in both industry and biology. Here, Michieletto et al. show how to achieve time-dependent rheology of DNA solutions via enzymatically-driven architectural alterations by restriction endonucleases.

    • D. Michieletto
    • , P. Neill
    •  & R. M. Robertson-Anderson

  • Article
    | Open Access

    G-wire structures have potential applications in bio-nanotechnology, however, this is limited by a lack of understanding about the assembly process and structures formed. Here, the authors use nuclear magnetic resonance and molecular dynamic simulations to understand the guiding principles of G-wire assembly.

    • Daša Pavc
    • , Nerea Sebastian
    •  & Primož Šket

  • 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

  • Comment
    | Open Access

    RNA therapeutics have benefited significantly from decades of research on lipid nanoparticles, specifically its key component—the ionizable lipid. This comment discusses the major ionizable lipid types, and provides perspectives for future development.

    • Xuexiang Han
    • , Hanwen Zhang
    •  & Michael J. Mitchell

  • Article
    | Open Access

    Experimental realization of cluster crystals- periodic structures with lattice sites occupied by several, overlapping building blocks, has been elusive. Here, the authors show the existence of well-controlled soft matter cluster crystals composed of a thermosensitive water-soluble polymer and nanometer-scale all-DNA dendrons.

    • Emmanuel Stiakakis
    • , Niklas Jung
    •  & Christos N. Likos

  • Article
    | Open Access

    While immunotherapy is a promising cancer treatment option, durable benefits are often rare due to immune escape. Here, the authors combine epigenetic regulation with gene therapy-mediated immune checkpoint blockade and show efficient anti-tumour effects and immune response in vivo.

    • Huapan Fang
    • , Zhaopei Guo
    •  & Xuesi Chen

  • Article
    | Open Access

    The therapeutic application of small interfering RNA (siRNA) is challenging due to its non-specific targeting and delivery issues. Here, the authors report an endogenous micro-RNA guided and hybridisation chain reaction-promoted siRNA delivery system encapsulated in tumour-derived extracellular vesicles, with cancer-specific activation, and achieve silencing of hypoxia-related genes.

    • Xue Gong
    • , Haizhou Wang
    •  & Fuan Wang

  • Article
    | Open Access

    In cells, DNA is arranged into topologically-constrained (supercoiled) structures, but how this supercoiling affects the detailed double-helical structure of DNA remains unclear. Here authors use atomic force microscopy and atomistic molecular dynamics simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution.

    • Alice L. B. Pyne
    • , Agnes Noy
    •  & Sarah A. Harris

  • Article
    | Open Access

    Previous design strategies for pH sensitive aptamers were not readily tunable across pH ranges. Here the authors present a general method to convert aptamers into pH-responsive switches using two orthogonal motifs.

    • Ian A. P. Thompson
    • , Liwei Zheng
    •  & H. Tom Soh

  • Article
    | Open Access

    Artificial nanopores can perform selective gating of molecules analogous to transmembrane proteins. Here, the authors design a DNA origami pore with a controllable lid for size-selective gating and translocation of macromolecules and evaluate its biosensing properties by single particle assay.

    • Rasmus P. Thomsen
    • , Mette Galsgaard Malle
    •  & Jørgen Kjems

  • Article
    | Open Access

    Increasing the complexity of engineered nucleic acid constructs and interfacing the microscopic with the macroscopic requires a multifaceted and programmable fabrication approach. Here the authors demonstrate multi-level photolithographic patterning for highly complex patterns at micrometer resolution.

    • Kathrin Hölz
    • , Erika Schaudy
    •  & Mark M. Somoza

  • Article
    | Open Access

    DNA is a biological building block which has drawn much attention as a structural material for a range of applications. Here, the authors report that DNA structures can be templated using shear-induced flow and microposts for controllable DNA patterning.

    • Yun Jeong Cha
    • , Soon Mo Park
    •  & Dong Ki Yoon

  • 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

    Interfering RNA have a range of therapeutic and research based applications, issues with delivery have made systems that make siRNA in situ of interest. Here, the author report on the creation of a DNA hydrogel with improved stability and transcription efficiency over plasmid DNA.

    • Jaejung Song
    • , Minhyuk Lee
    •  & Nokyoung Park

  • 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

    Complex assembly pathways often involve transient, partly-formed intermediates that are challenging to characterize. Here, the authors present a simple and rapid spectroscopic thermal hysteresis method for mapping the energy landscapes of supramolecular assembly.

    • Robert W. Harkness V
    • , Nicole Avakyan
    •  & Anthony K. Mittermaier

  • Article
    | Open Access

    Diffusion of molecules in crowded environment is important for various living systems, but the dynamics of charged molecules in charged matrices remains still unexplored. Here the authors report a dynamics of DNA and polyelectrolytes in a charged hydrogel where the guest molecules do not diffuse but experience topologically frustrated dynamics.

    • Di Jia
    •  & Murugappan Muthukumar

  • Article
    | Open Access

    DNA and RNA G-quadruplexes can stack to form higher-order structures called G-wires. Here the authors report high-resolution AFM images of higher-order DNA G-quadruplexes in aqueous solution that could impact the design of G-wire based nanodevices and the understanding of G-wires in biology.

    • Krishnashish Bose
    • , Christopher J. Lech
    •  & Anh Tuân Phan

  • 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

    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

    The mechanics and structural transitions of DNA are important to many essential processes inside living cells. Here the authors combine theory and single-molecule experiments to show that intercalator binding stabilises a new structural state of DNA: hyperstretched DNA.

    • Koen Schakenraad
    • , Andreas S. Biebricher
    •  & Paul van der Schoot

  • Article
    | Open Access

    The development of nanomaterials for imaging and drug delivery has been of great interest to the field. Here, the authors synthesized multifunctional enzyme-responsive hydrogels with self-assembling quantum dots for nucleic acid and drug delivery as well as having imaging capability.

    • Libing Zhang
    • , Sae Rin Jean
    •  & Shana O. Kelley

  • 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

    MicroRNAs regulate a wide range of biological processes and being able to inhibit their function could allow the development of therapeutic options. Here the authors describe a ‘small RNA zipper’ that sequesters miRNAs by forming a chain of DNA:RNA duplexes.

    • Lingyu Meng
    • , Cuicui Liu
    •  & Zuoren Yu

  • Article
    | Open Access

    Controlling self-assembly of nanoparticles into superlattices is an important approach to build functional materials. Here, Lu et al. use directional binding provided by DNA-encoded polyhedral blocks—cubes or octahedrons—to guide spherical nanoparticles into clusters and three-dimensional lattices.

    • Fang Lu
    • , Kevin G. Yager
    •  & Oleg Gang

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