Mechanical Design in DNA Nanotechnology

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Nanotechnology and Applied Nanosciences".

Deadline for manuscript submissions: closed (20 January 2022) | Viewed by 35126

Special Issue Editor

Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
Interests: DNA nanostructures; bionanotechnology; polyelectrolyte complexation; self-assembly; mechanical design; soft matter characterization; polymers

Special Issue Information

Dear Colleagues,

As DNA nanotechnology pushes the limits of geometric resolution and mechanical programmability in soft materials, diverse applications employing structurally distinct DNA-based devices and materials are emerging, including recent progress in sensing, drug delivery, dynamic devices, imaging, and more. New software and fabrication methods remove design and cost barriers, enabling implementation of structural DNA nanotechnology into areas with emerging synergies. This Special Issue of Applied Sciences is intended to broadly cover utilization and strengths of predefined shape, structure, and mechanical properties in DNA-based, or DNA-hybrid, structures and materials and can include experimental, simulation, and modeling work.

Dr. Alexander E. Marras
Guest Editor

Manuscript Submission Information

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Keywords

  • DNA nanotechnology
  • bionanotechnology
  • DNA origami
  • wireframe DNA nanostructures
  • DNA tiles
  • self-assembly
  • mechanical design
  • structural design
  • biohybrid materials
  • simulations and modeling

Published Papers (8 papers)

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Research

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15 pages, 2188 KiB  
Article
Mechanical Design of DNA Origami in the Classroom
by Yuchen Wang, Anjelica Kucinic, Lilly Des Rosiers, Peter E. Beshay, Nicholas Wile, Michael W. Hudoba and Carlos E. Castro
Appl. Sci. 2023, 13(5), 3208; https://doi.org/10.3390/app13053208 - 02 Mar 2023
Viewed by 2156
Abstract
DNA origami (DO) nanotechnology has strong potential for applications including molecular sensing, drug delivery, and nanorobotics that rely on nanoscale structural precision and the ability to tune mechanical and dynamic properties. Given these emerging applications, there is a need to broaden access to [...] Read more.
DNA origami (DO) nanotechnology has strong potential for applications including molecular sensing, drug delivery, and nanorobotics that rely on nanoscale structural precision and the ability to tune mechanical and dynamic properties. Given these emerging applications, there is a need to broaden access to and training on DO concepts, which would also provide an avenue to demonstrate engineering concepts such as kinematic motion and mechanical deformation as applied to nanotechnology and molecular systems. However, broader use in educational settings is hindered by the excessive cost and time of fabrication and analysis. Compliant, or deformable, DO is especially difficult to design and characterize in a cost-effective manner, because analysis often relies on advanced imaging methods to quantify structure conformations. Building on recent work establishing classroom-ready methods for DO fabrication and analysis, we developed an experiment module for classroom implementation focused on a DO compliant hinge joint. The module consists of folding three distinct joint conformations that can be evaluated via gel electrophoresis using portable and cost-effective equipment within ~120 min. To highlight the mechanical design, we present two beam-based models for describing the deformation that controls the joint angle. We envision that this module can broaden access to and interest in the mechanical design of DO. Full article
(This article belongs to the Special Issue Mechanical Design in DNA Nanotechnology)
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11 pages, 22423 KiB  
Article
The Free-Energy Landscape of a Mechanically Bistable DNA Origami
by Chak Kui Wong and Jonathan P. K. Doye
Appl. Sci. 2022, 12(12), 5875; https://doi.org/10.3390/app12125875 - 09 Jun 2022
Viewed by 2132
Abstract
Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed to exhibit two mechanically stable states and for which [...] Read more.
Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed to exhibit two mechanically stable states and for which a bistable landscape has been inferred from ensembles of structures visualized by electron microscopy. Surprisingly, simulations using the oxDNA model predict that the defect-free origami has a single free-energy minimum. The expected second state is not stable because the hinge joints do not simply allow free angular motion but instead lead to increasing free-energetic penalties as the joint angles relevant to the second state are approached. This raises interesting questions about the cause of this difference between simulations and experiment, such as how assembly defects might affect the ensemble of structures observed experimentally. Full article
(This article belongs to the Special Issue Mechanical Design in DNA Nanotechnology)
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19 pages, 10531 KiB  
Article
Generating DNA Origami Nanostructures through Shape Annealing
by Bolutito Babatunde, D. Sebastian Arias, Jonathan Cagan and Rebecca E. Taylor
Appl. Sci. 2021, 11(7), 2950; https://doi.org/10.3390/app11072950 - 25 Mar 2021
Cited by 4 | Viewed by 10359
Abstract
Structural DNA nanotechnology involves the design and self-assembly of DNA-based nanostructures. As a field, it has progressed at an exponential rate over recent years. The demand for unique DNA origami nanostructures has driven the development of design tools, but current CAD tools for [...] Read more.
Structural DNA nanotechnology involves the design and self-assembly of DNA-based nanostructures. As a field, it has progressed at an exponential rate over recent years. The demand for unique DNA origami nanostructures has driven the development of design tools, but current CAD tools for structural DNA nanotechnology are limited by requiring users to fully conceptualize a design for implementation. This article introduces a novel formal approach for routing the single-stranded scaffold DNA that defines the shape of DNA origami nanostructures. This approach for automated scaffold routing broadens the design space and generates complex multilayer DNA origami designs in an optimally driven way, based on a set of constraints and desired features. This technique computes unique designs of DNA origami assemblies by utilizing shape annealing, which is an integration of shape grammars and the simulated annealing algorithm. The results presented in this article illustrate the potential of the technique to code desired features into DNA nanostructures. Full article
(This article belongs to the Special Issue Mechanical Design in DNA Nanotechnology)
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15 pages, 3221 KiB  
Article
Elucidating the Mechanical Energy for Cyclization of a DNA Origami Tile
by Ruixin Li, Haorong Chen, Hyeongwoon Lee and Jong Hyun Choi
Appl. Sci. 2021, 11(5), 2357; https://doi.org/10.3390/app11052357 - 06 Mar 2021
Cited by 5 | Viewed by 2250
Abstract
DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, [...] Read more.
DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn, which is slightly different from that of native B-form DNA (~10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption. Full article
(This article belongs to the Special Issue Mechanical Design in DNA Nanotechnology)
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15 pages, 4501 KiB  
Article
Mechanical and Electrical Properties of DNA Hydrogel-Based Composites Containing Self-Assembled Three-Dimensional Nanocircuits
by Ming Gao, Abhichart Krissanaprasit, Austin Miles, Lilian C. Hsiao and Thomas H. LaBean
Appl. Sci. 2021, 11(5), 2245; https://doi.org/10.3390/app11052245 - 03 Mar 2021
Cited by 4 | Viewed by 2717
Abstract
Molecular self-assembly of DNA has been developed as an effective construction strategy for building complex materials. Among them, DNA hydrogels are known for their simple fabrication process and their tunable properties. In this study, we have engineered, built, and characterized a variety of [...] Read more.
Molecular self-assembly of DNA has been developed as an effective construction strategy for building complex materials. Among them, DNA hydrogels are known for their simple fabrication process and their tunable properties. In this study, we have engineered, built, and characterized a variety of pure DNA hydrogels using DNA tile-based crosslinkers and different sizes of linear DNA spacers, as well as DNA hydrogel/nanomaterial composites using DNA/nanomaterial conjugates with carbon nanotubes and gold nanoparticles as crosslinkers. We demonstrate the ability of this system to self-assemble into three-dimensional percolating networks when carbon nanotubes and gold nanoparticles are incorporated into the DNA hydrogel. These hydrogel composites showed interesting non-linear electrical properties. We also demonstrate the tuning of rheological properties of hydrogel-based composites using different types of crosslinkers and spacers. The viscoelasticity of DNA hydrogels is shown to dramatically increase by the use of a combination of interlocking DNA tiles and DNA/carbon nanotube crosslinkers. Finally, we present measurements and discuss electrically conductive nanomaterials for applications in nanoelectronics. Full article
(This article belongs to the Special Issue Mechanical Design in DNA Nanotechnology)
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Review

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28 pages, 10516 KiB  
Review
3D DNA Nanostructures: The Nanoscale Architect
by Daniel Fu and John Reif
Appl. Sci. 2021, 11(6), 2624; https://doi.org/10.3390/app11062624 - 16 Mar 2021
Cited by 6 | Viewed by 5027
Abstract
Structural DNA nanotechnology is a pioneering biotechnology that presents the opportunity to engineer DNA-based hardware that will mediate a profound interface to the nanoscale. To date, an enormous library of shaped 3D DNA nanostructures have been designed and assembled. Moreover, recent research has [...] Read more.
Structural DNA nanotechnology is a pioneering biotechnology that presents the opportunity to engineer DNA-based hardware that will mediate a profound interface to the nanoscale. To date, an enormous library of shaped 3D DNA nanostructures have been designed and assembled. Moreover, recent research has demonstrated DNA nanostructures that are not only static but can exhibit specific dynamic motion. DNA nanostructures have thus garnered significant research interest as a template for pursuing shape and motion-dependent nanoscale phenomena. Potential applications have been explored in many interdisciplinary areas spanning medicine, biosensing, nanofabrication, plasmonics, single-molecule chemistry, and facilitating biophysical studies. In this review, we begin with a brief overview of general and versatile design techniques for 3D DNA nanostructures as well as some techniques and studies that have focused on improving the stability of DNA nanostructures in diverse environments, which is pivotal for its reliable utilization in downstream applications. Our main focus will be to compile a wide body of existing research on applications of 3D DNA nanostructures that demonstrably rely on the versatility of their mechanical design. Furthermore, we frame reviewed applications into three primary categories, namely encapsulation, surface templating, and nanomechanics, that we propose to be archetypal shape- or motion-related functions of DNA nanostructures found in nanoscience applications. Our intent is to identify core concepts that may define and motivate specific directions of progress in this field as we conclude the review with some perspectives on the future. Full article
(This article belongs to the Special Issue Mechanical Design in DNA Nanotechnology)
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20 pages, 2252 KiB  
Review
Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials
by Joshua Bush, Chih-Hsiang Hu and Remi Veneziano
Appl. Sci. 2021, 11(4), 1885; https://doi.org/10.3390/app11041885 - 21 Feb 2021
Cited by 27 | Viewed by 4944
Abstract
DNA hydrogels are self-assembled biomaterials that rely on Watson–Crick base pairing to form large-scale programmable three-dimensional networks of nanostructured DNA components. The unique mechanical and biochemical properties of DNA, along with its biocompatibility, make it a suitable material for the assembly of hydrogels [...] Read more.
DNA hydrogels are self-assembled biomaterials that rely on Watson–Crick base pairing to form large-scale programmable three-dimensional networks of nanostructured DNA components. The unique mechanical and biochemical properties of DNA, along with its biocompatibility, make it a suitable material for the assembly of hydrogels with controllable mechanical properties and composition that could be used in several biomedical applications, including the design of novel multifunctional biomaterials. Numerous studies that have recently emerged, demonstrate the assembly of functional DNA hydrogels that are responsive to stimuli such as pH, light, temperature, biomolecules, and programmable strand-displacement reaction cascades. Recent studies have investigated the role of different factors such as linker flexibility, functionality, and chemical crosslinking on the macroscale mechanical properties of DNA hydrogels. In this review, we present the existing data and methods regarding the mechanical design of pure DNA hydrogels and hybrid DNA hydrogels, and their use as hydrogels for cell culture. The aim of this review is to facilitate further study and development of DNA hydrogels towards utilizing their full potential as multifeatured and highly programmable biomaterials with controlled mechanical properties. Full article
(This article belongs to the Special Issue Mechanical Design in DNA Nanotechnology)
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Other

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18 pages, 4254 KiB  
Perspective
DNA Nanodevices as Mechanical Probes of Protein Structure and Function
by Nicholas Stephanopoulos and Petr Šulc
Appl. Sci. 2021, 11(6), 2802; https://doi.org/10.3390/app11062802 - 21 Mar 2021
Cited by 6 | Viewed by 3543
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Mechanical Design in DNA Nanotechnology)
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