1
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Cristofaro S, Querciagrossa L, Soprani L, Fraccia TP, Bellini T, Berardi R, Arcioni A, Zannoni C, Muccioli L, Orlandi S. Simulating the Lyotropic Phase Behavior of a Partially Self-Complementary DNA Tetramer. Biomacromolecules 2024; 25:3920-3929. [PMID: 38826125 DOI: 10.1021/acs.biomac.3c01435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
DNA oligomers in solution have been found to develop liquid crystal phases via a hierarchical process that involves Watson-Crick base pairing, supramolecular assembly into columns of duplexes, and long-range ordering. The multiscale nature of this phenomenon makes it difficult to quantitatively describe and assess the importance of the various contributions, particularly for very short strands. We performed molecular dynamics simulations based on the coarse-grained oxDNA model, aiming to depict all of the assembly processes involved and the phase behavior of solutions of the DNA GCCG tetramers. We find good quantitative matching to experimental data at both levels of molecular association (thermal melting) and collective ordering (phase diagram). We characterize the isotropic state and the low-density nematic and high-density columnar liquid crystal phases in terms of molecular order, size of aggregates, and structure, together with their effects on diffusivity processes. We observe a cooperative aggregation mechanism in which the formation of dimers is less thermodynamically favored than the formation of longer aggregates.
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Affiliation(s)
- Silvia Cristofaro
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Lara Querciagrossa
- CINECA, Via Magnanelli 6/3, Casalecchio di Reno 40033, Italy
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Lorenzo Soprani
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Tommaso P Fraccia
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università di Milano, Via Balzaretti 9, Milano 20133, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, Via Vanvitelli 32, Milano 20129, Italy
| | - Roberto Berardi
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Alberto Arcioni
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Claudio Zannoni
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Luca Muccioli
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
| | - Silvia Orlandi
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna 40136, Italy
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2
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Novacek A, Ugaz B, Stephanopoulos N. Templating Peptide Chemistry with Nucleic Acids: Toward Artificial Ribosomes, Cell-Specific Therapeutics, and Novel Protein-Mimetic Architectures. Biomacromolecules 2024; 25:3865-3876. [PMID: 38860980 DOI: 10.1021/acs.biomac.4c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
In biology, nanomachines like the ribosome use nucleic acid templates to synthesize polymers in a sequence-specific, programmable fashion. Researchers have long been interested in using the programmable properties of nucleic acids to enhance chemical reactions via colocalization of reagents using complementary nucleic acid handles. In this review, we describe progress in using nucleic acid templates, handles, or splints to enhance the covalent coupling of peptides to other peptides or oligonucleotides. We discuss work in several areas: creating ribosome-mimetic systems, synthesizing bioactive peptides on DNA or RNA templates, linking peptides into longer molecules and bioactive antibody mimics, and scaffolding peptides to build protein-mimetic architectures. We close by highlighting the challenges that must be overcome in nucleic acid-templated peptide chemistry in two areas: making full-length, functional proteins from synthetic peptides and creating novel protein-mimetic architectures not possible through macromolecular folding alone.
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Affiliation(s)
- Alexandra Novacek
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
| | - Bryan Ugaz
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
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3
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DeLuca M, Sensale S, Lin PA, Arya G. Prediction and Control in DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2024; 7:626-645. [PMID: 36880799 DOI: 10.1021/acsabm.2c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Sebastian Sensale
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Po-An Lin
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
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4
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Xu Y, Zheng R, Prasad A, Liu M, Wan Z, Zhou X, Porter RM, Sample M, Poppleton E, Procyk J, Liu H, Li Y, Wang S, Yan H, Sulc P, Stephanopoulos N. High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558353. [PMID: 37790307 PMCID: PMC10542138 DOI: 10.1101/2023.09.18.558353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Multivalency enables nanostructures to bind molecular targets with high affinity. Although antibodies can be generated against a wide range of antigens, their shape and size cannot be tuned to match a given target. DNA nanotechnology provides an attractive approach for designing customized multivalent scaffolds due to the addressability and programmability of the nanostructure shape and size. Here, we design a nanoscale synthetic antibody ("nano-synbody") based on a three-helix bundle DNA nanostructure with one, two, or three identical arms terminating in a mini-binder protein that targets the SARS-CoV-2 spike protein. The nano-synbody was designed to match the valence and distance between the three receptor binding domains (RBDs) in the spike trimer, in order to enhance affinity. The protein-DNA nano-synbody shows tight binding to the wild-type, Delta, and several Omicron variants of the SARS-CoV-2 spike trimer, with affinity increasing as the number of arms increases from one to three. The effectiveness of the nano-synbody was also verified using a pseudovirus neutralization assay, with the three-arm nanostructure inhibiting two Omicron variants against which the structures with only one or two arms are ineffective. The structure of the three-arm nano-synbody bound to the Omicron variant spike trimer was solved by negative-stain transmission electron microscopy reconstruction, and shows the protein-DNA nanostructure with all three arms attached to the RBD domains, confirming the intended trivalent attachment. The ability to tune the size and shape of the nano-synbody, as well as its potential ability to attach two or more different binding ligands, will enable the high-affinity targeting of a range of proteins not possible with traditional antibodies.
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5
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Buchberger A, Al-Amin M, Simmons CR, Stephanopoulos N. Self-Assembly of Hybrid Peptide-DNA Nanostructures using Homotrimeric Coiled-Coil/Nucleic Acid Building Blocks. Chembiochem 2023; 24:e202300223. [PMID: 37099451 PMCID: PMC10789489 DOI: 10.1002/cbic.202300223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/22/2023] [Accepted: 04/26/2023] [Indexed: 04/27/2023]
Abstract
Peptides and DNA are two of the most commonly used self-assembling biological molecules for the construction of nanomaterials. However, there are only a few examples that combine these two self-assembly motifs as key structural elements in a nanostructure. We report on the synthesis of a peptide-DNA conjugate that self-assembles into a stable homotrimer based on the coiled-coil motif. The hybrid peptide-DNA trimer was then used as a novel three-way junction to link together either small DNA tile nanostructures, or to close up a triangular wireframe DNA structure. The resulting nanostructures were characterized by atomic force microscopy, and compared with a scrambled, non-assembling peptide as a control. These hybrid nanostructures enable the integration of peptide motifs and potentially bio-functionality with DNA nanostructures, and open the door to novel nano-materials that have the advantages of both molecules.
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Affiliation(s)
- Alex Buchberger
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Molecular Design and Biomimetics The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Md Al-Amin
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Molecular Design and Biomimetics The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Chad R Simmons
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Molecular Design and Biomimetics The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Molecular Design and Biomimetics The Biodesign Institute, Arizona State University, Tempe, AZ, USA
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6
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Mills A, Aissaoui N, Finkel J, Elezgaray J, Bellot G. Mechanical DNA Origami to Investigate Biological Systems. Adv Biol (Weinh) 2023; 7:e2200224. [PMID: 36509679 DOI: 10.1002/adbi.202200224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to self-assemble DNA nanodevices with programmed structural dynamics that can sense and respond to the local environment can enable transformative applications in fields including mechanobiology and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. In this review, the current state-of-the-art in constructing complex DNA geometries with dynamic and mechanical properties to enable a molecular scale force measurement is first summarized. Next, an overview of engineering modular DNA devices that interact with cell surfaces is highlighted detailing examples of mechanosensitive proteins and the force-induced dynamic molecular interaction on the downstream biochemical signaling. Finally, the challenges and an outlook on this promising class of DNA devices acting as nanomachines to operate at a low piconewton range suitable for a majority of biological effects or as hybrid materials to achieve higher tension exertion required for other biological investigations, are discussed.
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Affiliation(s)
- Allan Mills
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Nesrine Aissaoui
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, Paris, 75006, France
| | - Julie Finkel
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Juan Elezgaray
- CRPP, CNRS, UMR 5031, Université de Bordeaux, Pessac, 33600, France
| | - Gaëtan Bellot
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
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7
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Narayanan RP, Procyk J, Nandi P, Prasad A, Xu Y, Poppleton E, Williams D, Zhang F, Yan H, Chiu PL, Stephanopoulos N, Šulc P. Coarse-Grained Simulations for the Characterization and Optimization of Hybrid Protein-DNA Nanostructures. ACS NANO 2022; 16:14086-14096. [PMID: 35980981 PMCID: PMC9590280 DOI: 10.1021/acsnano.2c04013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We present here the combination of experimental and computational modeling tools for the design and characterization of protein-DNA hybrid nanostructures. Our work incorporates several features in the design of these nanostructures: (1) modeling of the protein-DNA linker identity and length; (2) optimizing the design of protein-DNA cages to account for mechanical stresses; (3) probing the incorporation efficiency of protein-DNA conjugates into DNA nanostructures. The modeling tools were experimentally validated using structural characterization methods like cryo-TEM and AFM. Our method can be used for fitting low-resolution electron density maps when structural insights cannot be deciphered from experiments, as well as enable in-silico validation of nanostructured systems before their experimental realization. These tools will facilitate the design of complex hybrid protein-DNA nanostructures that seamlessly integrate the two different biomolecules.
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Affiliation(s)
- Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Jonah Procyk
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Purbasha Nandi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Abhay Prasad
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Yang Xu
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Erik Poppleton
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Dewight Williams
- Eyring Materials Center, Office of Knowledge Enterprise Development, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Hao Yan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Po-Lin Chiu
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Petr Šulc
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
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8
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Design and simulation of DNA, RNA and hybrid protein-nucleic acid nanostructures with oxView. Nat Protoc 2022; 17:1762-1788. [PMID: 35668321 DOI: 10.1038/s41596-022-00688-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/18/2022] [Indexed: 11/08/2022]
Abstract
Molecular simulation has become an integral part of the DNA/RNA nanotechnology research pipeline. In particular, understanding the dynamics of structures and single-molecule events has improved the precision of nanoscaffolds and diagnostic tools. Here we present oxView, a design tool for visualization, design, editing and analysis of simulations of DNA, RNA and nucleic acid-protein nanostructures. oxView provides an accessible software platform for designing novel structures, tweaking existing designs, preparing them for simulation in the oxDNA/RNA molecular simulation engine and creating visualizations of simulation results. In several examples, we present procedures for using the tool, including its advanced features that couple the design capabilities with a coarse-grained simulation engine and scripting interface that can programmatically edit structures and facilitate design of complex structures from multiple substructures. These procedures provide a practical basis from which researchers, including experimentalists with limited computational experience, can integrate simulation and 3D visualization into their existing research programs.
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9
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Kuťák D, Melo L, Schroeder F, Jelic-Matošević Z, Mutter N, Bertoša B, Barišić I. CATANA: an online modelling environment for proteins and nucleic acid nanostructures. Nucleic Acids Res 2022; 50:W152-W158. [PMID: 35544315 PMCID: PMC9252799 DOI: 10.1093/nar/gkac350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022] Open
Abstract
In the last decade, significant advances have been made towards the rational design of proteins, DNA, and other organic nanostructures. The emerging possibility to precisely engineer molecular structures resulted in a wide range of new applications in fields such as biotechnology or medicine. The complexity and size of the artificial molecular systems as well as the number of interactions are greatly increasing and are manifesting the need for computational design support. In addition, a new generation of AI-based structure prediction tools provides researchers with completely new possibilities to generate recombinant proteins and functionalized DNA nanostructures. In this study, we present Catana, a web-based modelling environment suited for proteins and DNA nanostructures. User-friendly features were developed to create and modify recombinant fusion proteins, predict protein structures based on the amino acid sequence, and manipulate DNA origami structures. Moreover, Catana was jointly developed with the novel Unified Nanotechnology Format (UNF). Therefore, it employs a state-of-the-art coarse-grained data model, that is compatible with other established and upcoming applications. A particular focus was put on an effortless data export to allow even inexperienced users to perform in silico evaluations of their designs by means of molecular dynamics simulations. Catana is freely available at http://catana.ait.ac.at/.
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Affiliation(s)
- David Kuťák
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia.,Visitlab, Faculty of Informatics, Masaryk University, Brno 602 00, Czech Republic
| | - Lucas Melo
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
| | - Fabian Schroeder
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
| | - Zoe Jelic-Matošević
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Natalie Mutter
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
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10
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Poppleton E, Mallya A, Dey S, Joseph J, Šulc P. Nanobase.org: a repository for DNA and RNA nanostructures. Nucleic Acids Res 2022; 50:D246-D252. [PMID: 34747480 PMCID: PMC8728195 DOI: 10.1093/nar/gkab1000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
We introduce a new online database of nucleic acid nanostructures for the field of DNA and RNA nanotechnology. The database implements an upload interface, searching and database browsing. Each deposited nanostructures includes an image of the nanostructure, design file, an optional 3D view, and additional metadata such as experimental data, protocol or literature reference. The database accepts nanostructures in any preferred format used by the uploader for the nanostructure design. We further provide a set of conversion tools that encourage design file conversion into common formats (oxDNA and PDB) that can be used for setting up simulations, interactive editing or 3D visualization. The aim of the repository is to provide to the DNA/RNA nanotechnology community a resource for sharing their designs for further reuse in other systems and also to function as an archive of the designs that have been achieved in the field so far. Nanobase.org is available at https://nanobase.org/.
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Affiliation(s)
- Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Aatmik Mallya
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Swarup Dey
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- Wyss Institute, Harvard University, Boston, MA 02115, USA
| | - Joel Joseph
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
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11
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Kuťák D, Poppleton E, Miao H, Šulc P, Barišić I. Unified Nanotechnology Format: One Way to Store Them All. Molecules 2021; 27:63. [PMID: 35011301 PMCID: PMC8746876 DOI: 10.3390/molecules27010063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.
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Affiliation(s)
- David Kuťák
- Business Unit Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria
- Visualization Laboratory, Faculty of Informatics, Masaryk University, 60200 Brno, Czech Republic
| | - Erik Poppleton
- Center for Molecular Design and Biomimetics, The Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA; (E.P.); (P.Š.)
| | - Haichao Miao
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA;
| | - Petr Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA; (E.P.); (P.Š.)
| | - Ivan Barišić
- Business Unit Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria
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12
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Bernal-Chanchavac J, Al-Amin M, Stephanopoulos N. Nanoscale structures and materials from the self-assembly of polypeptides and DNA. Curr Top Med Chem 2021; 22:699-712. [PMID: 34911426 DOI: 10.2174/1568026621666211215142916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/22/2022]
Abstract
The use of biological molecules with programmable self-assembly properties is an attractive route to functional nanomaterials. Proteins and peptides have been used extensively for these systems due to their biological relevance and large number of supramolecular motifs, but it is still difficult to build highly anisotropic and programmable nanostructures due to their high complexity. Oligonucleotides, by contrast, have the advantage of programmability and reliable assembly, but lack biological and chemical diversity. In this review, we discuss systems that merge protein or peptide self-assembly with the addressability of DNA. We outline the various self-assembly motifs used, the chemistry for linking polypeptides with DNA, and the resulting nanostructures that can be formed by the interplay of these two molecules. Finally, we close by suggesting some interesting future directions in hybrid polypeptide-DNA nanomaterials, and potential applications for these exciting hybrids.
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Affiliation(s)
- Julio Bernal-Chanchavac
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
| | - Md Al-Amin
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ 85251. United States
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13
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Poblete S, Guzman HV. Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models. Viruses 2021; 13:1555. [PMID: 34452420 PMCID: PMC8402887 DOI: 10.3390/v13081555] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based on secondary structures from experimental techniques. Despite the amount of sampling involved in the folded and also unfolded RNA molecules, advanced microscope techniques can provide points of anchoring, which enhance our model to include interactions between capsid pentamers and RNA subdomains. To test our method, we tackle the satellite tobacco mosaic virus (STMV) genome, which has been widely studied by both experimental and computational communities. We provide not only a methodology to structurally analyze the tertiary conformations of the RNA genome inside capsids, but a flexible platform that allows the easy implementation of features/descriptors coming from both theoretical and experimental approaches.
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Affiliation(s)
- Simón Poblete
- Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5091000, Chile
- Chile and Computational Biology Lab, Fundación Ciencia & Vida, Santiago 7780272, Chile
| | - Horacio V. Guzman
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
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Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021; 8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.
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Affiliation(s)
- A. Sengar
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - T. E. Ouldridge
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - O. Henrich
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
| | - L. Rovigatti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- CNR Institute of Complex Systems, Sapienza University of Rome, Rome, Italy
| | - P. Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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15
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DNA Nanodevices as Mechanical Probes of Protein Structure and Function. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11062802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology has reported a wide range of structurally tunable scaffolds with precise control over their size, shape and mechanical properties. One promising application of these nanodevices is as probes for protein function or determination of protein structure. In this perspective we cover several recent examples in this field, including determining the effect of ligand spacing and multivalency on cell activation, applying forces at the nanoscale, and helping to solve protein structure by cryo-EM. We also highlight some future directions in the chemistry necessary for integrating proteins with DNA nanoscaffolds, as well as opportunities for computational modeling of hybrid protein-DNA nanomaterials.
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