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      DNA-origami-directed virus capsid polymorphism

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          Abstract

          Viral capsids can adopt various geometries, most iconically characterized by icosahedral or helical symmetries. Importantly, precise control over the size and shape of virus capsids would have advantages in the development of new vaccines and delivery systems. However, current tools to direct the assembly process in a programmable manner are exceedingly elusive. Here we introduce a modular approach by demonstrating DNA-origami-directed polymorphism of single-protein subunit capsids. We achieve control over the capsid shape, size and topology by employing user-defined DNA origami nanostructures as binding and assembly platforms, which are efficiently encapsulated within the capsid. Furthermore, the obtained viral capsid coatings can shield the encapsulated DNA origami from degradation. Our approach is, moreover, not limited to a single type of capsomers and can also be applied to RNA–DNA origami structures to pave way for next-generation cargo protection and targeting strategies.

          Abstract

          DNA and RNA origami nanostructures direct the size, shape and topology of different virus capsids in a user-defined manner while shielding encapsulated origamis from degradation.

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          Most cited references74

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          UCSF ChimeraX : Structure visualization for researchers, educators, and developers

          UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.
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            CTFFIND4: Fast and accurate defocus estimation from electron micrographs.

            CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope's contrast transfer function (CTF) to an image's amplitude spectrum. Here we describe modifications to the algorithm which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates. We show that this new version preserves the accuracy of the original algorithm while allowing for higher throughput. We also describe a measure of the quality of the fit as a function of spatial frequency and suggest this can be used to define the highest resolution at which CTF oscillations were successfully modeled.
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              Real-space refinement in PHENIX for cryo-EM and crystallography

              A description is provided of the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite and its application to the re-refinement of cryo-EM-derived models.
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                Author and article information

                Contributors
                juha.huiskonen@helsinki.fi
                mauri.kostiainen@aalto.fi
                Journal
                Nat Nanotechnol
                Nat Nanotechnol
                Nature Nanotechnology
                Nature Publishing Group UK (London )
                1748-3387
                1748-3395
                17 July 2023
                17 July 2023
                2023
                : 18
                : 10
                : 1205-1212
                Affiliations
                [1 ]Department of Bioproducts and Biosystems, Aalto University, ( https://ror.org/020hwjq30) Aalto, Finland
                [2 ]Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, ( https://ror.org/040af2s02) Helsinki, Finland
                [3 ]Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, ( https://ror.org/02sc3r913) Nathan, Queensland Australia
                [4 ]Faculty of Medicine and Health Technology, Tampere University, ( https://ror.org/033003e23) Tampere, Finland
                [5 ]Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, ( https://ror.org/006hf6230) Enschede, Netherlands
                [6 ]LIBER Center of Excellence, Aalto University, ( https://ror.org/020hwjq30) Aalto, Finland
                [7 ]Institute of Technology, University of Tartu, ( https://ror.org/03z77qz90) Tartu, Estonia
                Author information
                http://orcid.org/0000-0001-6552-9894
                http://orcid.org/0000-0003-0335-5993
                http://orcid.org/0000-0002-3342-3216
                http://orcid.org/0000-0003-2153-6149
                http://orcid.org/0000-0001-8152-3820
                http://orcid.org/0000-0002-9728-5043
                http://orcid.org/0000-0003-2762-1555
                http://orcid.org/0000-0002-0348-7323
                http://orcid.org/0000-0002-8282-2379
                Article
                1443
                10.1038/s41565-023-01443-x
                10575778
                37460794
                d6edeb12-fc59-4003-9dde-a1d338f8f6dd
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 25 October 2022
                : 6 June 2023
                Funding
                Funded by: FundRef https://doi.org/10.13039/100010663, EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council);
                Award ID: 101002258
                Award ID: 85670
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100005877, Suomen Akatemia | Luonnontieteiden ja Tekniikan Tutkimuksen Toimikunta (Research Council for Natural Sciences and Engineering);
                Award ID: 346110
                Award Recipient :
                Categories
                Article
                Custom metadata
                © Springer Nature Limited 2023

                Nanotechnology
                nanostructures,nanoparticles,nanobiotechnology
                Nanotechnology
                nanostructures, nanoparticles, nanobiotechnology

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