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      A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads

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          Abstract

          Mechanosensitive biological nanomachines such as motor proteins and ion channels regulate diverse cellular behaviour. Combined optical trapping with single-molecule fluorescence imaging provides a powerful methodology to clearly characterize the mechanoresponse, structural dynamics and stability of such nanomachines. However, this system requires complicated experimental geometry, preparation and optics, and is limited by low data-acquisition efficiency. Here we develop a programmable DNA origami nanospring that overcomes these issues. We apply our nanospring to human myosin VI, a mechanosensory motor protein, and demonstrate nanometre-precision single-molecule fluorescence imaging of the individual motor domains (heads) under force. We observe force-induced transitions of myosin VI heads from non-adjacent to adjacent binding, which correspond to adapted roles for low-load and high-load transport, respectively. Our technique extends single-molecule studies under force and clarifies the effect of force on biological processes.

          Abstract

          Characterizing the mechanical response of molecular motors involves the use of methods such as optical trapping to apply force. Here the authors develop a DNA origami nanospring to apply progressive force to human myosin VI, and discover that it adopts different stepping modes when subjected to low load or high load.

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          Most cited references40

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          Self-assembly of DNA into nanoscale three-dimensional shapes

          Molecular self-assembly offers a ‘bottom-up’ route to fabrication with subnanometre precision of complex structures from simple components1. DNA has proven a versatile building block2–5 for programmable construction of such objects, including two-dimensional crystals6, nanotubes7–11, and three-dimensional wireframe nanopolyhedra12–17. Templated self-assembly of DNA18 into custom two-dimensional shapes on the megadalton scale has been demonstrated previously with a multiple-kilobase ‘scaffold strand’ that is folded into a flat array of antiparallel helices by interactions with hundreds of oligonucleotide ‘staple strands’19, 20. Here we extend this method to building custom three-dimensional shapes formed as pleated layers of helices constrained to a honeycomb lattice. We demonstrate the design and assembly of nanostructures approximating six shapes — monolith, square nut, railed bridge, genie bottle, stacked cross, slotted cross — with precisely controlled dimensions ranging from 10 to 100 nm. We also show hierarchical assembly of structures such as homomultimeric linear tracks and of heterotrimeric wireframe icosahedra. Proper assembly requires week-long folding times and calibrated monovalent and divalent cation concentrations. We anticipate that our strategy for self-assembling custom three-dimensional shapes will provide a general route to the manufacture of sophisticated devices bearing features on the nanometer scale.
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            Local force and geometry sensing regulate cell functions.

            The shapes of eukaryotic cells and ultimately the organisms that they form are defined by cycles of mechanosensing, mechanotransduction and mechanoresponse. Local sensing of force or geometry is transduced into biochemical signals that result in cell responses even for complex mechanical parameters such as substrate rigidity and cell-level form. These responses regulate cell growth, differentiation, shape changes and cell death. Recent tissue scaffolds that have been engineered at the micro- and nanoscale level now enable better dissection of the mechanosensing, transduction and response mechanisms.
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              Folding DNA into twisted and curved nanoscale shapes.

              We demonstrate the ability to engineer complex shapes that twist and curve at the nanoscale from DNA. Through programmable self-assembly, strands of DNA are directed to form a custom-shaped bundle of tightly cross-linked double helices, arrayed in parallel to their helical axes. Targeted insertions and deletions of base pairs cause the DNA bundles to develop twist of either handedness or to curve. The degree of curvature could be quantitatively controlled, and a radius of curvature as tight as 6 nanometers was achieved. We also combined multiple curved elements to build several different types of intricate nanostructures, such as a wireframe beach ball or square-toothed gears.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group
                2041-1723
                12 December 2016
                2016
                : 7
                : 13715
                Affiliations
                [1 ]Quantitative Biology Center, RIKEN , OLABB, 6-2-3, Furuedai, Suita, Osaka 5650874, Japan
                [2 ]Graduate School of Frontier Biosciences, Osaka University , Suita, Osaka 5650871, Japan
                [3 ]Department of Cancer Biology, Dana-Farber Cancer Institute , Boston, Massachusetts 02115, USA
                [4 ]Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, USA
                [5 ]Wyss Institute for Biologically Inspired Engineering, Harvard University , Boston, Massachusetts 02115, USA
                [6 ]School of Frontier Sciences, The University of Tokyo , Kashiwa, Chiba 2778561, Japan
                [7 ]Center for Information and Neural Networks, NICT , Suita, Osaka 5650874, Japan
                Author notes
                Author information
                http://orcid.org/0000-0002-8893-1103
                Article
                ncomms13715
                10.1038/ncomms13715
                5159853
                27941751
                e52ad5d3-ff92-469d-af43-d94ed4f6ee91
                Copyright © 2016, The Author(s)

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 02 June 2016
                : 26 October 2016
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