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      Programmable self-assembly of three-dimensional nanostructures from 10 4 unique components

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          Abstract

          Nucleic acids (DNA and RNA) are widely used to construct nanoscale structures with ever increasing complexity 114 for possible applications in fields as diverse as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early examples typically containing on the order of 10 unique DNA strands. The introduction of DNA origami 4 , which uses many staple strands to fold one long scaffold strand into a desired structure, gave access to kilo- to mega-dalton nanostructures containing about 10 2 unique DNA strands 6, 7, 10, 13 . Aiming for even larger DNA origami structures is in principle possible 15, 16 , but faces the challenge of having to manufacture and route an increasingly long scaffold strand. An alternative and in principle more readily scalable approach uses DNA brick assembly 8, 9 , which doesn’t need a scaffold and instead uses hundreds of short DNA brick strands that self-assemble according to specific inter-brick interactions. First-generation bricks used to create 3D structures are 32-nt long with four 8-nt binding domains that directed 10 2 distinct bricks into well-formed assemblies, but attempts to create larger structures encountered practical challenges and had limited success. 9 Here we show that a new generation of DNA bricks with longer binding domains makes it possible to self-assemble 0.1 – 1 giga-dalton three-dimensional nanostructures from 10 4 unique components, including a 0.5 giga-dalton cuboid containing 30,000 unique bricks and a 1 giga-dalton rotationally symmetric tetramer. We also assemble a cuboid containing 10,000 bricks and 20,000 uniquely addressable ‘nano-voxels’ that serves as a molecular canvas for three-dimensional sculpting, with introduction of sophisticated user-prescribed 3D cavities yielding structures such as letters, a complex helicoid and a teddy bear. We anticipate that, with further optimization, even larger assemblies might be accessible and prove useful as scaffolds or for positioning functional components.

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          Most cited references 39

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          Fiji: an open-source platform for biological-image analysis.

          Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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            NIH Image to ImageJ: 25 years of image analysis.

            For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
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              Folding DNA to create nanoscale shapes and patterns.

              'Bottom-up fabrication', which exploits the intrinsic properties of atoms and molecules to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of DNA molecules provides an attractive route towards this goal. Here I describe a simple method for folding long, single-stranded DNA molecules into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diameter and approximate desired shapes such as squares, disks and five-pointed stars with a spatial resolution of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex).
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                26 October 2017
                06 December 2017
                06 June 2018
                : 552
                : 7683
                : 72-77
                Affiliations
                [1 ]Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
                [2 ]Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
                [3 ]Max Planck Institute of Biochemistry, 82152 Martinsried Munich, Germany
                [4 ]Department of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany
                [5 ]Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, F-34000 Montpellier, France
                [6 ]Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
                [7 ]Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA 30322, USA
                [8 ]Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
                [9 ]Institut de Génomique Fonctionnelle, CNRS UMR 5203, INSERM U1191, F-34000 Montpellier, France
                [10 ]Department of Chemistry, Emory University, Atlanta, GA 30322, USA
                Article
                NIHMS913984
                10.1038/nature24648
                5786436
                29219968

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