1
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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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2
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Liu Y, Li B, Wang F, Li Q, Jia S, Liu X, Li M. Quantitative Analysis of Resistance to Deformation of the DNA Origami Framework Supported by Struts. ACS APPLIED BIO MATERIALS 2024; 7:1311-1316. [PMID: 38303492 DOI: 10.1021/acsabm.3c01270] [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: 02/03/2024]
Abstract
Nanostructures with controlled shapes are of particular interest due to their consistent physical and chemical properties and their potential for assembly into complex superstructures. The use of supporting struts has proven to be effective in the construction of precise DNA polyhedra. However, the influence of struts on the structure of DNA origami frameworks on the nanoscale remains unclear. In this study, we developed a flexible square DNA origami (SDO) framework and enhanced its structural stability by incorporating interarm supporting struts (SDO-s). Comparing the framework with and without such struts, we found that SDO-s demonstrated a significantly improved resistance to deformation. We assessed the deformability of these two DNA origami structures through the statistical analysis of interior angles of polygons based on atomic force microscopy and transmission electron microscopy data. Our results showed that SDO-s exhibited more centralized interior angle distributions compared to SDO, reducing from 30-150° to 60-120°. Furthermore, molecular dynamics simulations indicated that supporting struts significantly decreased the thermodynamic fluctuations of the SDO-s, as described by the root-mean-square fluctuation parameter. Finally, we experimentally demonstrated that the 2D arrays assembled from SDO-s exhibited significantly higher quality than those assembled from SDO. These quantitative analyses provide an understanding of how supporting struts can enhance the structural integrity of DNA origami frameworks.
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Affiliation(s)
- Yongjun Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bochen Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sisi Jia
- Zhangjiang Laboratory, Shanghai 201210, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Wang Y, Jin X, Castro C. Accelerating the characterization of dynamic DNA origami devices with deep neural networks. Sci Rep 2023; 13:15196. [PMID: 37709771 PMCID: PMC10502017 DOI: 10.1038/s41598-023-41459-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/27/2023] [Indexed: 09/16/2023] Open
Abstract
Mechanical characterization of dynamic DNA nanodevices is essential to facilitate their use in applications like molecular diagnostics, force sensing, and nanorobotics that rely on device reconfiguration and interactions with other materials. A common approach to evaluate the mechanical properties of dynamic DNA nanodevices is by quantifying conformational distributions, where the magnitude of fluctuations correlates to the stiffness. This is generally carried out through manual measurement from experimental images, which is a tedious process and a critical bottleneck in the characterization pipeline. While many tools support the analysis of static molecular structures, there is a need for tools to facilitate the rapid characterization of dynamic DNA devices that undergo large conformational fluctuations. Here, we develop a data processing pipeline based on Deep Neural Networks (DNNs) to address this problem. The YOLOv5 and Resnet50 network architecture were used for the two key subtasks: particle detection and pose (i.e. conformation) estimation. We demonstrate effective network performance (F1 score 0.85 in particle detection) and good agreement with experimental distributions with limited user input and small training sets (~ 5 to 10 images). We also demonstrate this pipeline can be applied to multiple nanodevices, providing a robust approach for the rapid characterization of dynamic DNA devices.
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Affiliation(s)
- Yuchen Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA.
| | - Xin Jin
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA.
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4
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Umapathy VR, Natarajan PM, Swamikannu B. Review of the Role of Nanotechnology in Overcoming the Challenges Faced in Oral Cancer Diagnosis and Treatment. Molecules 2023; 28:5395. [PMID: 37513267 PMCID: PMC10385509 DOI: 10.3390/molecules28145395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Throughout the world, oral cancer is a common and aggressive malignancy with a high risk of morbidity, mortality, and recurrence. The importance of early detection in cancer prevention and disease treatment cannot be overstated. Conventional therapeutic strategies have minor difficulties but considerable side effects and unfavourable consequences in clinical applications. Hence, there is a requirement for effective ways for early detection and treatment of oral cancer. At present, numerous forms of nanoparticles have piqued researchers' interest as a potentially useful tool for diagnostic probes and medicinal devices. Because of their inherent physicochemical properties and customizable surface modification, they are able to circumvent some of restrictions and accomplish the intended diagnostic and therapeutic impact. Nanotechnology is a unique field that has revolutionised the industry and is paving the way for new treatments for oral cancer. It can help with a better diagnosis with less harmful substances and is setting current guidelines for treatment. The use of nanotechnology in cancer diagnosis, therapy, and care improves clinical practise dramatically. The different types of nanoparticles that have been developed for the diagnosis and therapy of oral cancers will be covered in this study. The difficulties and potential uses of nanoparticles in the treatment and diagnosis of oral cancer are then highlighted. In order to emphasise existing difficulties and potential remedies for oral cancer, a prospective view of the future is also provided.
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Affiliation(s)
- Vidhya Rekha Umapathy
- Department of Public Health Dentistry, Thai Moogambigai Dental College and Hospital, Dr. M.G.R. Educational and Research Institute, Chennai 600107, Tamil Nadu, India
| | - Prabhu Manickam Natarajan
- Department of Clinical Sciences, Centre of Medical and Bio-Allied Health Sciences and Research, Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Bhuminathan Swamikannu
- Department of Prosthodontics, Sree Balaji Dental College and Hospital, BIHER University, Pallikaranai, Chennai 600100, Tamil Nadu, India
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5
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Wang Y, Sensale S, Pedrozo M, Huang CM, Poirier MG, Arya G, Castro CE. Steric Communication between Dynamic Components on DNA Nanodevices. ACS NANO 2023; 17:8271-8280. [PMID: 37072126 PMCID: PMC10173695 DOI: 10.1021/acsnano.2c12455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Biomolecular nanotechnology has helped emulate basic robotic capabilities such as defined motion, sensing, and actuation in synthetic nanoscale systems. DNA origami is an attractive approach for nanorobotics, as it enables creation of devices with complex geometry, programmed motion, rapid actuation, force application, and various kinds of sensing modalities. Advanced robotic functions like feedback control, autonomy, or programmed routines also require the ability to transmit signals among subcomponents. Prior work in DNA nanotechnology has established approaches for signal transmission, for example through diffusing strands or structurally coupled motions. However, soluble communication is often slow and structural coupling of motions can limit the function of individual components, for example to respond to the environment. Here, we introduce an approach inspired by protein allostery to transmit signals between two distal dynamic components through steric interactions. These components undergo separate thermal fluctuations where certain conformations of one arm will sterically occlude conformations of the distal arm. We implement this approach in a DNA origami device consisting of two stiff arms each connected to a base platform via a flexible hinge joint. We demonstrate the ability for one arm to sterically regulate both the range of motion and the conformational state (latched or freely fluctuating) of the distal arm, results that are quantitatively captured by mesoscopic simulations using experimentally informed energy landscapes for hinge-angle fluctuations. We further demonstrate the ability to modulate signal transmission by mechanically tuning the range of thermal fluctuations and controlling the conformational states of the arms. Our results establish a communication mechanism well-suited to transmit signals between thermally fluctuating dynamic components and provide a path to transmitting signals where the input is a dynamic response to parameters like force or solution conditions.
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Affiliation(s)
- Yuchen Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sebastian Sensale
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Miguel Pedrozo
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
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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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Mao D, Paluzzi VE, Zhang C, Mao C. DNA conformational equilibrium enables continuous changing of curvatures. NANOSCALE 2023; 15:470-475. [PMID: 36515101 DOI: 10.1039/d2nr05404c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Assembly of complex structures from a small set of tiles is a common theme in biology. For example, many copies of identical proteins make up polyhedron-shaped, viral capsids and tubulin can make long microtubules. This inspired the development of tile-based DNA self-assembly for nanoconstruction, particularly for structures with high symmetries. In the final structure, each type of motif will adopt the same conformation, either rigid or with defined flexibility. For structures that have no symmetry, their assembly remains a challenge from a small set of tiles. To meet this challenge, algorithmic self-assembly has been explored driven by computational science, but it is not clear how to implement this approach to one-dimensional (1D) structures. Here, we have demonstrated that a constant shift of a conformational equilibrium could allow 1D structures to evolve. As shown by atomic force microscopy imaging, one type of DNA tile successfully assembled into DNA spirals and concentric circles, which became less and less curved from the structure's center outward. This work points to a new direction for tile-based DNA assembly.
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Affiliation(s)
- Dake Mao
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Victoria E Paluzzi
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Cuizheng Zhang
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Chengde Mao
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
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8
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Chattha GM, Arshad S, Kamal Y, Chattha MA, Asim MH, Raza SA, Mahmood A, Manzoor M, Dar UI, Arshad A. Nanorobots: An innovative approach for DNA-based cancer treatment. J Drug Deliv Sci Technol 2023. [DOI: 10.1016/j.jddst.2023.104173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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9
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Büchl A, Kopperger E, Vogt M, Langecker M, Simmel FC, List J. Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking. Biophys J 2022; 121:4849-4859. [PMID: 36071662 PMCID: PMC9808541 DOI: 10.1016/j.bpj.2022.08.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/12/2022] [Accepted: 08/30/2022] [Indexed: 01/07/2023] Open
Abstract
Biomolecular nanomechanical devices are of great interest as tools for the processing and manipulation of molecules, thereby mimicking the function of nature's enzymes. DNA nanotechnology provides the capability to build molecular analogs of mechanical machine elements such as joints and hinges via sequence-programmable self-assembly, which are otherwise known from traditional mechanical engineering. Relative to their size, these molecular machine elements typically do not reach the same relative precision and reproducibility that we know from their macroscopic counterparts; however, as they are scaled down to molecular sizes, physical effects typically not considered by mechanical engineers such as Brownian motion, intramolecular forces, and the molecular roughness of the devices begin to dominate their behavior. In order to investigate the effect of different design choices on the roughness of the mechanical energy landscapes of DNA nanodevices in greater detail, we here study an exemplary DNA origami-based structure, a modularly designed rotor-stator arrangement, which resembles a rotatable nanorobotic arm. Using fluorescence tracking microscopy, we follow the motion of individual rotors and record their corresponding energy landscapes. We then utilize the modular construction of the device to exchange its constituent parts individually and systematically test the effect of different design variants on the movement patterns. This allows us to identify the design parameters that most strongly affect the shape of the energy landscapes of the systems. Taking into account these insights, we are able to create devices with significantly flatter energy landscapes, which translates to mechanical nanodevices with improved performance and behaviors more closely resembling those of their macroscopic counterparts.
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Affiliation(s)
- Adrian Büchl
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Enzo Kopperger
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Matthias Vogt
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Martin Langecker
- Physics Department E14, Technical University of Munich, Garching, Germany
| | - Friedrich C Simmel
- Physics Department E14, Technical University of Munich, Garching, Germany.
| | - Jonathan List
- Physics Department E14, Technical University of Munich, Garching, Germany.
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10
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Majikes JM, Liddle JA. Synthesizing the biochemical and semiconductor worlds: the future of nucleic acid nanotechnology. NANOSCALE 2022; 14:15586-15595. [PMID: 36268635 PMCID: PMC10949957 DOI: 10.1039/d2nr04040a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Since its inception nearly 40 years ago [Kallenbach, et al., Nature, 1983, 305, 829; N. C. Seeman, J. Theoretical Biology, 1982, 99, 237], Nucleic Acid Nanotechnology (NAN) has matured and is beginning to find commercial applications. For the last 20 years, it has been suggested that NAN might be an effective replacement for parts of the semiconductor lithography or protein engineering workflows. However, in that time, these incumbent technologies have made significant advances, and our understanding of NAN's strengths and weaknesses has progressed, suggesting that the greatest opportunities in fact lie elsewhere. Given the commitment of resources necessary to bring new technologies to the market and the desire to use those resources as wisely as possible, we conduct a critical examination of where NAN may benefit from, and provide benefit to, adjacent technologies and compete least with market incumbents. While the accuracy of our conclusions may be limited by our ability to extrapolate from the current state of NAN to its future commercial success, we conclude that the next promising direction is to create a bridge between biology and semiconductor technology. We also hope to stimulate a robust conversation around this technology's capabilities with the goal of building consensus on those research and development efforts that would advance NAN to the greatest effect in real-world applications.
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Affiliation(s)
- Jacob M Majikes
- Physical Measurement Laboratory, National Institute Standards and Technology, 100 Bureau drive, Gaithersburg, MD, 20878, USA.
| | - J Alexander Liddle
- Physical Measurement Laboratory, National Institute Standards and Technology, 100 Bureau drive, Gaithersburg, MD, 20878, USA.
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11
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Three-dimensional electron ptychography of organic-inorganic hybrid nanostructures. Nat Commun 2022; 13:4787. [PMID: 35970924 PMCID: PMC9378626 DOI: 10.1038/s41467-022-32548-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/04/2022] [Indexed: 11/22/2022] Open
Abstract
Three dimensional scaffolded DNA origami with inorganic nanoparticles has been used to create tailored multidimensional nanostructures. However, the image contrast of DNA is poorer than those of the heavy nanoparticles in conventional transmission electron microscopy at high defocus so that the biological and non-biological components in 3D scaffolds cannot be simultaneously resolved using tomography of samples in a native state. We demonstrate the use of electron ptychography to recover high contrast phase information from all components in a DNA origami scaffold without staining. We further quantitatively evaluate the enhancement of contrast in comparison with conventional transmission electron microscopy. In addition, We show that for ptychography post-reconstruction focusing simplifies the workflow and reduces electron dose and beam damage. The authors demonstrate electron ptychographic computed tomography by simultaneously recording high contrast data from both the organic- and inorganic components in a 3D DNA-origami framework hybrid nanostructure.
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12
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A modular spring-loaded actuator for mechanical activation of membrane proteins. Nat Commun 2022; 13:3182. [PMID: 35902570 PMCID: PMC9334261 DOI: 10.1038/s41467-022-30745-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
How cells respond to mechanical forces by converting them into biological signals underlie crucial cellular processes. Our understanding of mechanotransduction has been hindered by technical barriers, including limitations in our ability to effectively apply low range piconewton forces to specific mechanoreceptors on cell membranes without laborious and repetitive trials. To overcome these challenges we introduce the Nano-winch, a robust, easily assembled, programmable DNA origami-based molecular actuator. The Nano-winch is designed to manipulate multiple mechanoreceptors in parallel by exerting fine-tuned, low- piconewton forces in autonomous and remotely activated modes via adjustable single- and double-stranded DNA linkages, respectively. Nano-winches in autonomous mode can land and operate on the cell surface. Targeting the device to integrin stimulated detectable downstream phosphorylation of focal adhesion kinase, an indication that Nano-winches can be applied to study cellular mechanical processes. Remote activation mode allowed finer extension control and greater force exertion. We united remotely activated Nano-winches with single-channel bilayer experiments to directly observe the opening of a channel by mechanical force in the force responsive gated channel protein, BtuB. This customizable origami provides an instrument-free approach that can be applied to control and explore a diversity of mechanotransduction circuits on living cells. Studies on mechanotransduction are limited by our ability to apply low range forces to specific mechanoreceptors on cell membranes. Here the authors report the Nano-winch, a programmable DNA origami-based molecular actuator, to manipulate multiple mechanoreceptors in parallel by exerting piconewton forces.
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13
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Kaufhold WT, Pfeifer W, Castro CE, Di Michele L. Probing the Mechanical Properties of DNA Nanostructures with Metadynamics. ACS NANO 2022; 16:8784-8797. [PMID: 35580231 PMCID: PMC9245350 DOI: 10.1021/acsnano.1c08999] [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: 05/05/2023]
Abstract
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, the convergence of distributions from unbiased simulation is slow, limiting applications to equilibrium structural properties. Given the increasing interest in dynamic, reconfigurable, and deformable devices, methods that enable efficient quantification of large ranges of motion, conformational transitions, and mechanical deformation are critically needed. Metadynamics is an automated biasing technique that enables the rapid acquisition of molecular conformational distributions by flattening free energy landscapes. Here we leveraged this approach to sample the free energy landscapes of DNA nanostructures whose unbiased dynamics are nonergodic, including bistable Holliday junctions and part of a bistable DNA origami structure. Taking a DNA origami-compliant joint as a case study, we further demonstrate that metadynamics can predict the mechanical response of a full DNA origami device to an applied force, showing good agreement with experiments. Our results exemplify the efficient computation of free energy landscapes and force response in DNA nanodevices, which could be applied for rapid feedback in iterative design workflows and generally facilitate the integration of simulation and experiments. Metadynamics will be particularly useful to guide the design of dynamic devices for nanorobotics, biosensing, or nanomanufacturing applications.
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Affiliation(s)
- Will T. Kaufhold
- Department
of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
- Department
of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Wolfgang Pfeifer
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Carlos E. Castro
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Lorenzo Di Michele
- Department
of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
- Department
of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
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14
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Kaufhold WT, Pfeifer W, Castro CE, Di Michele L. Probing the Mechanical Properties of DNA Nanostructures with Metadynamics. ACS NANO 2022; 16:8784-8797. [PMID: 35580231 DOI: 10.48550/arxiv.2110.01477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, the convergence of distributions from unbiased simulation is slow, limiting applications to equilibrium structural properties. Given the increasing interest in dynamic, reconfigurable, and deformable devices, methods that enable efficient quantification of large ranges of motion, conformational transitions, and mechanical deformation are critically needed. Metadynamics is an automated biasing technique that enables the rapid acquisition of molecular conformational distributions by flattening free energy landscapes. Here we leveraged this approach to sample the free energy landscapes of DNA nanostructures whose unbiased dynamics are nonergodic, including bistable Holliday junctions and part of a bistable DNA origami structure. Taking a DNA origami-compliant joint as a case study, we further demonstrate that metadynamics can predict the mechanical response of a full DNA origami device to an applied force, showing good agreement with experiments. Our results exemplify the efficient computation of free energy landscapes and force response in DNA nanodevices, which could be applied for rapid feedback in iterative design workflows and generally facilitate the integration of simulation and experiments. Metadynamics will be particularly useful to guide the design of dynamic devices for nanorobotics, biosensing, or nanomanufacturing applications.
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Affiliation(s)
- Will T Kaufhold
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
- Department of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
| | - Wolfgang Pfeifer
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Lorenzo Di Michele
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
- Department of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
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15
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Yu L, Cheng J, Wang D, Pan V, Chang S, Song J, Ke Y. Stress in DNA Gridiron Facilitates the Formation of Two-Dimensional Crystalline Structures. J Am Chem Soc 2022; 144:9747-9752. [PMID: 35578912 DOI: 10.1021/jacs.2c02009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Programmable DNA nanotechnology has generated some of the most intricate self-assembled nanostructures and has been employed in a growing number of applications, including functional nanomaterials, nanofabrication, biophysics, photonics, molecular machines, and drug delivery. An important design rule for DNA nanostructures is to minimize the mechanical stress to reduce the potential energy in these nanostructures whenever it is possible. This work revisits the DNA gridiron design consisting of Holliday junctions and compares the self-assembly of the canonical DNA gridiron with a new design of DNA gridiron, which has a higher degree of mechanical stress because of the interweaving of DNA helices. While the interweaving DNA gridiron indeed exhibits lower yield, compared to its canonical counterpart of a similar size, we discover that the mechanical stress within the interweaving gridiron can promote the formation of the two-dimensional crystalline lattice instead of nanotubes. Furthermore, tuning the design of interweaving gridiron leads to the change of overall crystal size and regularity of geometry. Interweaving DNA double helices represents a new design strategy in the self-assembly of DNA nanostructures. Furthermore, the discovery of the new role of mechanical stress in the self-assembly of DNA nanostructures provides useful knowledge to DNA nanotechnology practitioners: a more balanced view regarding mechanical stress can be considered when designing future DNA nanostructures.
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Affiliation(s)
- Lei Yu
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongfang Wang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences; The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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16
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Xin Y, Piskunen P, Suma A, Li C, Ijäs H, Ojasalo S, Seitz I, Kostiainen MA, Grundmeier G, Linko V, Keller A. Environment-Dependent Stability and Mechanical Properties of DNA Origami Six-Helix Bundles with Different Crossover Spacings. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107393. [PMID: 35363419 DOI: 10.1002/smll.202107393] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/14/2022] [Indexed: 05/25/2023]
Abstract
The internal design of DNA nanostructures defines how they behave in different environmental conditions, such as endonuclease-rich or low-Mg2+ solutions. Notably, the inter-helical crossovers that form the core of such DNA objects have a major impact on their mechanical properties and stability. Importantly, crossover design can be used to optimize DNA nanostructures for target applications, especially when developing them for biomedical environments. To elucidate this, two otherwise identical DNA origami designs are presented that have a different number of staple crossovers between neighboring helices, spaced at 42- and 21- basepair (bp) intervals, respectively. The behavior of these structures is then compared in various buffer conditions, as well as when they are exposed to enzymatic digestion by DNase I. The results show that an increased number of crossovers significantly improves the nuclease resistance of the DNA origami by making it less accessible to digestion enzymes but simultaneously lowers its stability under Mg2+ -free conditions by reducing the malleability of the structures. Therefore, these results represent an important step toward rational, application-specific DNA nanostructure design.
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Affiliation(s)
- Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Antonio Suma
- Dipartimento di Fisica, Università di Bari and Sezione INFN di Bari, Bari, 70126, Italy
| | - Changyong Li
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Sofia Ojasalo
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Iris Seitz
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
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17
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Chang X, Yang Q, Lee J, Zhang F. Self-Assembled Nucleic Acid Nanostructures for Biomedical Applications. Curr Top Med Chem 2022; 22:652-667. [PMID: 35319373 DOI: 10.2174/1568026622666220321140729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 01/20/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
Structural DNA nanotechnology has been developed into a powerful method for creating self-assembled nanomaterials. Their compatibility with biosystems, nanoscale addressability, and programmable dynamic features make them appealing candidates for biomedical research. This review paper focuses on DNA self-assembly strategies and designer nanostructures with custom functions for biomedical applications. Specifically, we review the development of DNA self-assembly methods, from simple DNA motifs consisting of a few DNA strands to complex DNA architectures assembled by DNA origami. Three advantages are discussed using structural DNA nanotechnology for biomedical applications: (1) precise spatial control, (2) molding and guiding other biomolecules, and (3) using reconfigurable DNA nanodevices to overcome biomedical challenges. Finally, we discuss the challenges and opportunities of employing DNA nanotechnology for biomedical applications, emphasizing diverse assembly strategies to create a custom DNA nanostructure with desired functions.
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Affiliation(s)
- Xu Chang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Qi Yang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Jungyeon Lee
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
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18
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Lee C, Kim YJ, Kim KS, Lee JY, Kim DN. Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules. Nucleic Acids Res 2021; 49:12591-12599. [PMID: 34850119 PMCID: PMC8643692 DOI: 10.1093/nar/gkab1119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/06/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
Recent advances in DNA nanotechnology led the fabrication and utilization of various DNA assemblies, but the development of a method to control their global shapes and mechanical flexibilities with high efficiency and repeatability is one of the remaining challenges for the realization of the molecular machines with on-demand functionalities. DNA-binding molecules with intercalation and groove binding modes are known to induce the perturbation on the geometrical and mechanical characteristics of DNA at the strand level, which might be effective in structured DNA assemblies as well. Here, we demonstrate that the chemo-mechanical response of DNA strands with binding ligands can change the global shape and stiffness of DNA origami nanostructures, thereby enabling the systematic modulation of them by selecting a proper ligand and its concentration. Multiple DNA-binding drugs and fluorophores were applied to straight and curved DNA origami bundles, which demonstrated a fast, recoverable, and controllable alteration of the bending persistence length and the radius of curvature of DNA nanostructures. This chemo-mechanical modulation of DNA nanostructures would provide a powerful tool for reconfigurable and dynamic actuation of DNA machineries.
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Affiliation(s)
- Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Young-Joo Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Kyung Soo Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea.,Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea.,Institute of Engineering Research, Seoul National University, Seoul 08826, Korea
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19
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Su H, Brockman JM, Duan Y, Sen N, Chhabra H, Bazrafshan A, Blanchard AT, Meyer T, Andrews B, Doye JPK, Ke Y, Dyer RB, Salaita K. Massively Parallelized Molecular Force Manipulation with On-Demand Thermal and Optical Control. J Am Chem Soc 2021; 143:19466-19473. [PMID: 34762807 DOI: 10.1021/jacs.1c08796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In single-molecule force spectroscopy (SMFS), a tethered molecule is stretched using a specialized instrument to study how macromolecules extend under force. One problem in SMFS is the serial and slow nature of the measurements, performed one molecule at a time. To address this long-standing challenge, we report on the origami polymer force clamp (OPFC) which enables parallelized manipulation of the mechanical forces experienced by molecules without the need for dedicated SMFS instruments or surface tethering. The OPFC positions target molecules between a rigid nanoscale DNA origami beam and a responsive polymer particle that shrinks on demand. As a proof-of-concept, we record the steady state and time-resolved mechanical unfolding dynamics of DNA hairpins using the fluorescence signal from ensembles of molecules and confirm our conclusion using modeling.
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Affiliation(s)
- Hanquan Su
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Joshua M Brockman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Navoneel Sen
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Hemani Chhabra
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Alisina Bazrafshan
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Aaron T Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Travis Meyer
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Brooke Andrews
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Yonggang Ke
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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20
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KOH HEEYUEN, LEE JAEGYUNG, LEE JAEYOUNG, KIM RYAN, TABATA OSAMU, JIN-WOO KIM, KIM DONYUN. Design Approaches and Computational Tools for DNA Nanostructures. IEEE OPEN JOURNAL OF NANOTECHNOLOGY 2021; 2:86-100. [PMID: 35756857 PMCID: PMC9232119 DOI: 10.1109/ojnano.2021.3119913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Designing a structure in nanoscale with desired shape and properties has been enabled by structural DNA nanotechnology. Design strategies in this research field have evolved to interpret various aspects of increasingly more complex nanoscale assembly and to realize molecular-level functionality by exploring static to dynamic characteristics of the target structure. Computational tools have naturally been of significant interest as they are essential to achieve a fine control over both shape and physicochemical properties of the structure. Here, we review the basic design principles of structural DNA nanotechnology together with its computational analysis and design tools.
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Affiliation(s)
- HEEYUEN KOH
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Republic of Korea
| | - JAE GYUNG LEE
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - JAE YOUNG LEE
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Republic of Korea
| | - RYAN KIM
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 USA
- Bio/Nano Technology Group, Institute for Nanoscience and Engineering, University of Arkansas, Fayetteville, AR 72701 USA
| | - OSAMU TABATA
- Faculty of Engineering, Kyoto University of Advanced Science, Kyoto 621-8555, Japan
| | - KIM JIN-WOO
- Bio/Nano Technology Group, Institute for Nanoscience and Engineering, University of Arkansas, Fayetteville, AR 72701 USA
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701 USA
- Materials Science and Engineering Program, University of Arkansas, Fayetteville, AR 72701 USA
| | - DO-NYUN KIM
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Republic of Korea
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Engineering Research, Seoul National University, Seoul 08826, Republic of Korea
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21
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Wang Y, Le JV, Crocker K, Darcy MA, Halley PD, Zhao D, Andrioff N, Croy C, Poirier MG, Bundschuh R, Castro CE. A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules. Nucleic Acids Res 2021; 49:8987-8999. [PMID: 34358322 PMCID: PMC8421221 DOI: 10.1093/nar/gkab656] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/30/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
Single molecule force spectroscopy is a powerful approach to probe the structure, conformational changes, and kinetic properties of biological and synthetic macromolecules. However, common approaches to apply forces to biomolecules require expensive and cumbersome equipment and relatively large probes such as beads or cantilevers, which limits their use for many environments and makes integrating with other methods challenging. Furthermore, existing methods have key limitations such as an inability to apply compressive forces on single molecules. We report a nanoscale DNA force spectrometer (nDFS), which is based on a DNA origami hinge with tunable mechanical and dynamic properties. The angular free energy landscape of the nDFS can be engineered across a wide range through substitution of less than 5% of the strand components. We further incorporate a removable strut that enables reversible toggling of the nDFS between open and closed states to allow for actuated application of tensile and compressive forces. We demonstrate the ability to apply compressive forces by inducing a large bend in a 249bp DNA molecule, and tensile forces by inducing DNA unwrapping of a nucleosome sample. These results establish a versatile tool for force spectroscopy and robust methods for designing nanoscale mechanical devices with tunable force application.
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Affiliation(s)
- Yuchen Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Jenny V Le
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Kyle Crocker
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Michael A Darcy
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick D Halley
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Dengke Zhao
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Nick Andrioff
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Cassie Croy
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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22
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Kim YJ, Park J, Lee JY, Kim DN. Programming ultrasensitive threshold response through chemomechanical instability. Nat Commun 2021; 12:5177. [PMID: 34462430 PMCID: PMC8405678 DOI: 10.1038/s41467-021-25406-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 08/03/2021] [Indexed: 11/09/2022] Open
Abstract
The ultrasensitive threshold response is ubiquitous in biochemical systems. In contrast, achieving ultrasensitivity in synthetic molecular structures in a controllable way is challenging. Here, we propose a chemomechanical approach inspired by Michell's instability to realize it. A sudden reconfiguration of topologically constrained rings results when the torsional stress inside reaches a critical value. We use DNA origami to construct molecular rings and then DNA intercalators to induce torsional stress. Michell's instability is achieved successfully when the critical concentration of intercalators is applied. Both the critical point and sensitivity of this ultrasensitive threshold reconfiguration can be controlled by rationally designing the cross-sectional shape and mechanical properties of DNA rings.
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Affiliation(s)
- Young-Joo Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea
| | - Junho Park
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Jae Young Lee
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea. .,Department of Mechanical Engineering, Seoul National University, Seoul, Korea. .,Institute of Engineering Research, Seoul National University, Seoul, Korea.
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23
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Dastorani S, Ghasemi RH, Soheilifard R. A Study on the Bending Stiffness of a New DNA Origami Nano-Joint. Mol Biotechnol 2021; 63:1057-1067. [PMID: 34224047 DOI: 10.1007/s12033-021-00367-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 06/28/2021] [Indexed: 11/29/2022]
Abstract
The present article aims to investigate the mechanical properties of a new DNA origami nano-joint using the steered molecular dynamics (SMD) simulation. Since the analysis of mechanical properties is of great importance in bending conditions for a nano-joint, the forces are selected to achieve angular changes in the joint by the resultant torque. In this study, the nano-joint is considered as a beam in order to use mechanical equations to extract the mechanical properties of the designed nano-joint. In addition, the bending stiffness of the beam is investigated in different modes of deflection using the Euler-Bernoulli beam theory. The results revealed that the value of bending stiffness increases with increasing deflection, and the changes in the bending stiffness relative to the deflection is linear. The proposed DNA origami nano-joint can be used as a joint in nanorobots and can be effectively applied in nanorobotic systems to move different components.
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Affiliation(s)
- Sadegh Dastorani
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
| | | | - Reza Soheilifard
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
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24
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Johnson JA, Kolliopoulos V, Castro CE. Co-self-assembly of multiple DNA origami nanostructures in a single pot. Chem Commun (Camb) 2021; 57:4795-4798. [PMID: 33982710 DOI: 10.1039/d1cc00049g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simultaneous self-assembly of two distinct DNA origami nanostructures folded with the same scaffold strand was achieved in a single pot. Relative yields were tuned by adjusting concentrations of the competing strands, correlating well with folding kinetics of individual structures. These results can faciliate efficient fabrication of multi-structure systems and materials.
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Affiliation(s)
- Joshua A Johnson
- Biophysics Graduate Program, The Ohio State University, 281 W Lane Ave, Columbus, OH 43210, USA.
| | - Vasiliki Kolliopoulos
- Department of Chemical and Biomolecular Engineering, The Ohio State University, 281 W Lane Ave, Columbus, OH 43210, USA
| | - Carlos E Castro
- Biophysics Graduate Program, The Ohio State University, 281 W Lane Ave, Columbus, OH 43210, USA. and Department of Mechanical and Aerospace Engineering, The Ohio State University, 281 W Lane Ave, Columbus, OH 43210, USA
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25
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Benson E, Carrascosa Marzo R, Bath J, Turberfield AJ. Strategies for Constructing and Operating DNA Origami Linear Actuators. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007704. [PMID: 33942502 DOI: 10.1002/smll.202007704] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Linear actuators are ubiquitous components at all scales of engineering. DNA nanotechnology offers a unique opportunity for bottom-up assembly at the molecular scale, providing nanoscale precision with multiple methods for constructing and operating devices. In this paper, DNA origami linear actuators with up to 200 nm travel, based on a rail threading a topologically locked slider, are demonstrated. Two strategies, one- and two-pot assembly, are demonstrated whereby the two components are folded from one or two DNA scaffold strands, respectively. In order to control the position of the slider on the rail, the rail and the inside of the slider are decorated with single-stranded oligonucleotides with distinct sequences. Two positioning strategies, based on diffusion and capture of signaling strands, are used to link the slider reversibly to determined positions on the rail with high yield and precision. These machine components provide a basis for applications in molecular machinery and nanoscale manufacture including programmed chemical synthesis.
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Affiliation(s)
- Erik Benson
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | | | - Jonathan Bath
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
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26
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Aksakal R, Mertens C, Soete M, Badi N, Du Prez F. Applications of Discrete Synthetic Macromolecules in Life and Materials Science: Recent and Future Trends. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004038. [PMID: 33747749 PMCID: PMC7967060 DOI: 10.1002/advs.202004038] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/22/2020] [Indexed: 05/19/2023]
Abstract
In the last decade, the field of sequence-defined polymers and related ultraprecise, monodisperse synthetic macromolecules has grown exponentially. In the early stage, mainly articles or reviews dedicated to the development of synthetic routes toward their preparation have been published. Nowadays, those synthetic methodologies, combined with the elucidation of the structure-property relationships, allow envisioning many promising applications. Consequently, in the past 3 years, application-oriented papers based on discrete synthetic macromolecules emerged. Hence, material science applications such as macromolecular data storage and encryption, self-assembly of discrete structures and foldamers have been the object of many fascinating studies. Moreover, in the area of life sciences, such structures have also been the focus of numerous research studies. Here, it is aimed to highlight these recent applications and to give the reader a critical overview of the future trends in this area of research.
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Affiliation(s)
- Resat Aksakal
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Chiel Mertens
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Matthieu Soete
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Nezha Badi
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
| | - Filip Du Prez
- Polymer Chemistry Research GroupCentre of Macromolecular Chemistry (CMaC)Department of Organic and Macromolecular ChemistryGhent UniversityKrijgslaan 281 S4‐bisGhentB‐9000Belgium
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27
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Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041885] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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 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.
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28
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Lee JY, Lee JG, Yun G, Lee C, Kim YJ, Kim KS, Kim TH, Kim DN. Rapid Computational Analysis of DNA Origami Assemblies at Near-Atomic Resolution. ACS NANO 2021; 15:1002-1015. [PMID: 33410664 DOI: 10.1021/acsnano.0c07717] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Structural DNA nanotechnology plays an ever-increasing role in advanced biomolecular applications. Here, we present a computational method to analyze structured DNA assemblies rapidly at near-atomic resolution. Both high computational efficiency and molecular-level accuracy are achieved by developing a multiscale analysis framework. The sequence-dependent relative geometry and mechanical properties of DNA motifs are characterized by the all-atom molecular dynamics simulation and incorporated into the structural finite element model successfully without significant loss of atomic information. The proposed method can predict the three-dimensional shape, equilibrium dynamic properties, and mechanical rigidities of monomeric to hierarchically assembled DNA structures at near-atomic resolution without adjusting any model parameters. The calculation takes less than only 15 min for most origami-scale DNA nanostructures consisting of 7000-8000 base-pairs. Hence, it is expected to be highly utilized in an iterative design-analysis-revision process for structured DNA assemblies.
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Affiliation(s)
- Jae Young Lee
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Jae Gyung Lee
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Giseok Yun
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Young-Joo Kim
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Kyung Soo Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Tae Hwi Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Do-Nyun Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
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29
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Dansuk KC, Keten S. Self-strengthening biphasic nanoparticle assemblies with intrinsic catch bonds. Nat Commun 2021; 12:85. [PMID: 33397979 PMCID: PMC7782701 DOI: 10.1038/s41467-020-20344-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 11/23/2020] [Indexed: 01/06/2023] Open
Abstract
Protein-ligand complexes with catch bonds exhibit prolonged lifetimes when subject to tensile force, which is a desirable yet elusive attribute for man-made nanoparticle interfaces and assemblies. Most designs proposed so far rely on macromolecular linkers with complicated folds rather than particles exhibiting simple dynamic shapes. Here, we establish a scissor-type X-shaped particle design for achieving intrinsic catch bonding ability with tunable force-enhanced lifetimes under thermal excitations. Molecular dynamics simulations are carried out to illustrate equilibrium self-assembly and force-enhanced bond lifetime of dimers and fibers facilitated by secondary interactions that form under tensile force. The non-monotonic force dependence of the fiber breaking kinetics is well-estimated by an analytical model. Our design concepts for shape-changing particles illuminates a path towards novel nanoparticle or colloidal assemblies that have the passive ability to tune the strength of their interfaces with applied force, setting the stage for self-assembling materials with novel mechanical functions and rheological properties.
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Affiliation(s)
- Kerim C Dansuk
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Sinan Keten
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
- Department of Civil & Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
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30
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Jung WH, Chen E, Veneziano R, Gaitanaros S, Chen Y. Stretching DNA origami: effect of nicks and Holliday junctions on the axial stiffness. Nucleic Acids Res 2020; 48:12407-12414. [PMID: 33152066 PMCID: PMC7708044 DOI: 10.1093/nar/gkaa985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/09/2020] [Accepted: 10/15/2020] [Indexed: 12/25/2022] Open
Abstract
The axial stiffness of DNA origami is determined as a function of key nanostructural characteristics. Different constructs of two-helix nanobeams with specified densities of nicks and Holliday junctions are synthesized and stretched by fluid flow. Implementing single particle tracking to extract force–displacement curves enables the measurement of DNA origami stiffness values at the enthalpic elasticity regime, i.e. for forces larger than 15 pN. Comparisons between ligated and nicked helices show that the latter exhibit nearly a two-fold decrease in axial stiffness. Numerical models that treat the DNA helices as elastic rods are used to evaluate the local loss of stiffness at the locations of nicks and Holliday junctions. It is shown that the models reproduce the experimental data accurately, indicating that both of these design characteristics yield a local stiffness two orders of magnitude smaller than the corresponding value of the intact double-helix. This local degradation in turn leads to a macroscopic loss of stiffness that is evaluated numerically for multi-helix DNA bundles.
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Affiliation(s)
- Wei-Hung Jung
- Department of Mechanical Engineering, Johns Hopkins University, USA.,Institute for NanoBioTechnology, Johns Hopkins University, USA.,Center for Cell Dynamics, Johns Hopkins University, USA
| | - Enze Chen
- Department of Civil and Systems Engineering, Johns Hopkins University, USA
| | - Remi Veneziano
- Department of Bioengineering, George Mason University, USA.,Institute for Advanced Biomedical Research, George Mason University, USA
| | - Stavros Gaitanaros
- Department of Civil and Systems Engineering, Johns Hopkins University, USA
| | - Yun Chen
- Department of Mechanical Engineering, Johns Hopkins University, USA.,Institute for NanoBioTechnology, Johns Hopkins University, USA.,Center for Cell Dynamics, Johns Hopkins University, USA
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31
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Chhabra H, Mishra G, Cao Y, Prešern D, Skoruppa E, Tortora MMC, Doye JPK. Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures. J Chem Theory Comput 2020; 16:7748-7763. [PMID: 33164531 DOI: 10.1021/acs.jctc.0c00661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
To study the elastic properties of rodlike DNA nanostructures, we perform long simulations of these structures using the oxDNA coarse-grained model. By analyzing the fluctuations in these trajectories, we obtain estimates of the bend and twist persistence lengths and the underlying bend and twist elastic moduli and couplings between them. Only on length scales beyond those associated with the spacings between the interhelix crossovers do the bending fluctuations behave like those of a wormlike chain. The obtained bending persistence lengths are much larger than that for double-stranded DNA and increase nonlinearly with the number of helices, whereas the twist moduli increase approximately linearly. To within the numerical error in our data, the twist-bend coupling constants are of order zero. That the bending persistence lengths that we obtain are generally somewhat higher than in experiment probably reflects both that the simulated origamis have no assembly defects and that the oxDNA extensional modulus for double-stranded DNA is too large.
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Affiliation(s)
- Hemani Chhabra
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Garima Mishra
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Yijing Cao
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Domen Prešern
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Maxime M C Tortora
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.,Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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32
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Ding Z, Sigdel K, Yang L, Liu Y, Xuan M, Wang X, Gu Z, Wu J, Xie H. Nanotechnology-based drug delivery systems for enhanced diagnosis and therapy of oral cancer. J Mater Chem B 2020; 8:8781-8793. [PMID: 33026383 DOI: 10.1039/d0tb00957a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Oral cancer is a common malignant life-threatening tumor. Despite some advances in traditional therapy, mortality and mobidity rates are high due to delayed diagnosis and ineffective treatment. Additionally, some patients inevitably suffer from various fatal adverse effects during the course of therapy. Therefore, it is imperative to develop novel methods to eradicate oral cancer cells with minimal adverse effects on normal cells. Nanotechnology is a promising and novel vehicle for the diagnosis and treatment of oral cancer with encouraging recent achievements. In this review, we present state-of-the-art nanotechnology-based drug delivery systems employed in the domain of oral cancer, especially for its enhanced diagnosis and therapy. We describe in detail the types of nanotechnology used in the management of oral cancer and summarize administration routes of nanodrugs. Finally, the potential and prospects of nanotechnology-based drug delivery systems as promising modalities of diagnosis and therapy of oral cancer are highlighted.
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Affiliation(s)
- Zhangfan Ding
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China.
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33
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Du F, Qiao B, Nguyen TD, Vincent MP, Bobbala S, Yi S, Lescott C, Dravid VP, Olvera de la Cruz M, Scott EA. Homopolymer self-assembly of poly(propylene sulfone) hydrogels via dynamic noncovalent sulfone-sulfone bonding. Nat Commun 2020; 11:4896. [PMID: 32994414 PMCID: PMC7525563 DOI: 10.1038/s41467-020-18657-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 08/25/2020] [Indexed: 01/08/2023] Open
Abstract
Natural biomolecules such as peptides and DNA can dynamically self-organize into diverse hierarchical structures. Mimicry of this homopolymer self-assembly using synthetic systems has remained limited but would be advantageous for the design of adaptive bio/nanomaterials. Here, we report both experiments and simulations on the dynamic network self-assembly and subsequent collapse of the synthetic homopolymer poly(propylene sulfone). The assembly is directed by dynamic noncovalent sulfone–sulfone bonds that are susceptible to solvent polarity. The hydration history, specified by the stepwise increase in water ratio within lower polarity water-miscible solvents like dimethylsulfoxide, controls the homopolymer assembly into crystalline frameworks or uniform nanostructured hydrogels of spherical, vesicular, or cylindrical morphologies. These electrostatic hydrogels have a high affinity for a wide range of organic solutes, achieving >95% encapsulation efficiency for hydrophilic small molecules and biologics. This system validates sulfone–sulfone bonding for dynamic self-assembly, presenting a robust platform for controllable gelation, nanofabrication, and molecular encapsulation. Natural biomolecules such as peptides and DNA can dynamically self-organize into diverse hierarchical structures. Here the authors report experiments and simulations on the dynamic network self-assembly and subsequent collapse of the synthetic homopolymer poly(propylene sulfone).
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Affiliation(s)
- Fanfan Du
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.,Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Baofu Qiao
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Trung Dac Nguyen
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Michael P Vincent
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Sharan Bobbala
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Sijia Yi
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Chamille Lescott
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, 60208, USA.,Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
| | - Evan Alexander Scott
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA. .,Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA. .,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA.
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34
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Abstract
Over the past decade, DNA nanotechnology has spawned a broad variety of functional nanostructures tailored toward the enabled state at which applications are coming increasingly in view. One of the branches of these applications is in synthetic biology, where the intrinsic programmability of the DNA nanostructures may pave the way for smart task-specific molecular robotics. In brief, the synthesis of the user-defined artificial DNA nano-objects is based on employing DNA molecules with custom lengths and sequences as building materials that predictably assemble together by obeying Watson-Crick base pairing rules. The general workflow of creating DNA nanoshapes is getting more and more straightforward, and some objects can be designed automatically from the top down. The versatile DNA nano-objects can serve as synthetic tools at the interface with biology, for example, in therapeutics and diagnostics as dynamic logic-gated nanopills, light-, pH-, and thermally driven devices. Such diverse apparatuses can also serve as optical polarizers, sensors and capsules, autonomous cargo-sorting robots, rotary machines, precision measurement tools, as well as electric and magnetic-field directed robotic arms. In this review, we summarize the recent progress in robotic DNA nanostructures, mechanics, and their various implementations.
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Affiliation(s)
- Sami Nummelin
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Boxuan Shen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Petteri Piskunen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Qing Liu
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
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35
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Dastorani S, Mogheiseh M, Ghasemi RH, Soheilifard R. Modelling and structural investigation of a new DNA Origami based flexible bio-nano joint. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1797019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Sadegh Dastorani
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
| | - Maryam Mogheiseh
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
| | | | - Reza Soheilifard
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
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36
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Shi Z, Arya G. Free energy landscape of salt-actuated reconfigurable DNA nanodevices. Nucleic Acids Res 2020; 48:548-560. [PMID: 31799631 PMCID: PMC6954428 DOI: 10.1093/nar/gkz1137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/15/2019] [Accepted: 12/02/2019] [Indexed: 12/11/2022] Open
Abstract
Achieving rapid, noninvasive actuation of DNA structures is critical to expanding the functionality of DNA nanotechnology. A promising actuation approach involves introducing multiple, short pairs of single-stranded DNA overhangs to components of the structure and triggering hybridization or dissociation of the overhangs via changes in solution ionic conditions to drive structural transitions. Here, we reveal the underlying basis of this new approach by computing via molecular simulations the free energy landscape of DNA origami hinges actuated between open and closed states. Our results reveal how the overhangs collectively introduce a sharp free-energy minimum at the closed state and a broad energy barrier between open and closed states and how changes in ionic conditions modulate these features of the landscape to drive actuation towards the open or closed state. We demonstrate the critical role played by hinge confinement in stabilizing the hybridized state of the overhangs and magnifying the energy barrier to dissociation. By analyzing how the distribution of overhangs and their length and sequence modulate the energy landscape, we obtain design rules for tuning the actuation behavior. The molecular insights obtained here should be applicable to a broad range of systems involving DNA hybridization within confined systems.
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Affiliation(s)
- Ze Shi
- Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
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37
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Johnson JA, Dehankar A, Winter JO, Castro CE. Reciprocal Control of Hierarchical DNA Origami-Nanoparticle Assemblies. NANO LETTERS 2019; 19:8469-8475. [PMID: 31664841 DOI: 10.1021/acs.nanolett.9b02786] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
DNA origami mechanisms offer promising tools for precision nanomanipulation of molecules or nanomaterials. Recent advances have extended the function of individual DNA origami devices to material scales via hierarchical assemblies. However, achieving rapid and precise control of large conformational changes in hierarchical assemblies remains a critical challenge. Here, we demonstrate a method for controlling DNA origami-nanoparticle assemblies through a multiscale approach, in which nanoparticles impart control on the conformation of individual DNA origami mechanisms, whereas DNA origami assemblies control the conformation of nanoparticle arrays. Specifically, we show that the angular distributions of DNA origami hinge mechanisms are tunable as a function of nanoparticle size and distance from the hinge vertex. We selectively adjust the affinity of nanoparticle binding sites, resulting in hinge actuation via DNA melting without releasing the nanoparticle, thereby enabling rapid and reversible temperature-based actuation. Finally, we demonstrate this rapid actuation in DNA origami-nanoparticle arrays of length scales extending over a micron. These results provide guiding principles toward the design of dynamic, DNA-origami hierarchical materials capable of storing and releasing mechanical energy.
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38
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Blanchard AT, Bazrafshan AS, Yi J, Eisman JT, Yehl KM, Bian T, Mugler A, Salaita K. Highly Polyvalent DNA Motors Generate 100+ pN of Force via Autochemophoresis. NANO LETTERS 2019; 19:6977-6986. [PMID: 31402671 DOI: 10.1021/acs.nanolett.9b02311] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Motor proteins such as myosin, kinesin, and dynein are essential to eukaryotic life and power countless processes including muscle contraction, wound closure, cargo transport, and cell division. The design of synthetic nanomachines that can reproduce the functions of these motors is a longstanding goal in the field of nanotechnology. DNA walkers, which are programmed to "walk" along defined tracks via the burnt bridge Brownian ratchet mechanism, are among the most promising synthetic mimics of these motor proteins. While these DNA-based motors can perform useful tasks such as cargo transport, they have not been shown to be capable of cooperating to generate large collective forces for tasks akin to muscle contraction. In this work, we demonstrate that highly polyvalent DNA motors (HPDMs), which can be viewed as cooperative teams of thousands of DNA walkers attached to a microsphere, can generate and sustain substantial forces in the 100+ pN regime. Specifically, we show that HPDMs can generate forces that can unzip and shear DNA duplexes (∼12 and ∼50 pN, respectively) and rupture biotin-streptavidin bonds (∼100-150 pN). To help explain these results, we present a variant of the burnt-bridge Brownian ratchet mechanism that we term autochemophoresis, wherein many individual force generating units generate a self-propagating chemomechanical gradient that produces large collective forces. In addition, we demonstrate the potential of this work to impact future engineering applications by harnessing HPDM autochemophoresis to deposit "molecular ink" via mechanical bond rupture. This work expands the capabilities of synthetic DNA motors to mimic the force-generating functions of biological motors. Our work also builds upon previous observations of autochemophoresis in bacterial transport processes, indicating that autochemophoresis may be a fundamental mechanism of pN-scale force generation in living systems.
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Affiliation(s)
- Aaron T Blanchard
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
| | - Alisina S Bazrafshan
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Jacob Yi
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Julia T Eisman
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Kevin M Yehl
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Teng Bian
- Department of Physics , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Andrew Mugler
- Department of Physics , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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39
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Abstract
DNA mechanotechnology has applications in biological research and materials science
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Affiliation(s)
- Aaron T Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA.
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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40
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Lee C, Kim KS, Kim YJ, Lee JY, Kim DN. Tailoring the Mechanical Stiffness of DNA Nanostructures Using Engineered Defects. ACS NANO 2019; 13:8329-8336. [PMID: 31291091 DOI: 10.1021/acsnano.9b03770] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
As scaffolded DNA origami enables the construction of diverse DNA nanostructures with predefined shapes, precise modulation of their mechanical stiffness remains challenging. We demonstrate a modular design method to widely and precisely control the mechanical flexibility of scaffolded DNA origami nanostructures while maintaining their overall structural integrity and geometric characteristics. Individually engineered defects that are short single-stranded DNA (ssDNA) gaps could reduce up to 70% of the bending stiffness of DNA origami constructs with different cross-sectional shapes. We further developed a computational analysis platform predicting the bending stiffness of a defect-engineered DNA nanostructure quickly during the design process, to offer an efficient way of designing various DNA constructs with required mechanical stiffness in a desired shape for a targeted function.
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Affiliation(s)
- Chanseok Lee
- Department of Mechanical and Aerospace Engineering , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Korea
| | - Kyung Soo Kim
- Department of Mechanical and Aerospace Engineering , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Korea
| | - Young-Joo Kim
- Department of Mechanical and Aerospace Engineering , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Korea
| | - Jae Young Lee
- Department of Mechanical and Aerospace Engineering , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Korea
| | - Do-Nyun Kim
- Department of Mechanical and Aerospace Engineering , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Korea
- Institute of Advanced Machines and Design , Seoul National University , 1 Gwanak-ro , Gwanak-gu , Seoul 08826 , Korea
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41
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A programmable DNA-origami platform for studying lipid transfer between bilayers. Nat Chem Biol 2019; 15:830-837. [PMID: 31320758 PMCID: PMC6650167 DOI: 10.1038/s41589-019-0325-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 06/14/2019] [Indexed: 02/07/2023]
Abstract
Non-vesicular lipid transport between bilayers at membrane contact sites plays important physiological roles. Mechanistic insight into the action of lipid transport proteins localized at these sites (bridge/tunnel versus shuttle models) requires a determination of the distance between bilayers at which this transport can occur. Here, we developed DNA-origami nanostructures to organize size-defined liposomes at precise distances and used them to study lipid transfer by the SMP domain of E-Syt1. Pairs of DNA-ring-templated donor and acceptor liposomes were docked through DNA pillars, which determined their distance. The SMP domain was anchored to donor liposomes via an unstructured linker and lipid transfer was assessed via a FRET-based assay. We show that lipid transfer can occur over distances that exceed the length of SMP dimer, compatible with a shuttle model. The DNA nanostructures developed here can be adapted to study other processes occurring where two membranes are closely apposed to each other.
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42
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Grome M, Zhang Z, Lin C. Stiffness and Membrane Anchor Density Modulate DNA-Nanospring-Induced Vesicle Tubulation. ACS APPLIED MATERIALS & INTERFACES 2019; 11:22987-22992. [PMID: 31252462 PMCID: PMC6613048 DOI: 10.1021/acsami.9b05401] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
DNA nanotechnology provides an avenue for the construction of rationally designed artificial assemblages with well-defined and tunable architectures. Shaped to mimic natural membrane-deforming proteins and equipped with membrane anchoring molecules, curved DNA nanostructures can reproduce subcellular membrane remodeling events such as vesicle tubulation in vitro. To systematically analyze how structural stiffness and membrane affinity of DNA nanostructures affect the membrane remodeling outcome, here we build DNA-origami curls with varying thickness and amphipathic peptide density, and have them polymerize into nanosprings on the surface of liposomes. We find that modestly reducing rigidity and maximizing the number of membrane anchors not only promote membrane binding and remodeling but also lead to the formation of lipid tubules with better defined diameters, highlighting the ability of programmable DNA-based constructs to controllably deform the membrane.
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43
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Matthies M, Agarwal NP, Poppleton E, Joshi FM, Šulc P, Schmidt TL. Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles. ACS NANO 2019; 13:1839-1848. [PMID: 30624898 DOI: 10.1021/acsnano.8b08009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The field of structural DNA nanotechnology offers a wide range of design strategies with which to build structures with a desired aspect ratio, size, and shape. Compared with traditional close-packed DNA structures, triangulated wireframe structures require less material per surface or volume unit and improve the stability in biologically relevant conditions due to the reduced electrostatic repulsion. Herein, we expand the design space of the DNA single-stranded tile method to cover a range of anisotropic, finite, triangulated wireframe structures as well as a number of one-dimensional crystalline assemblies. These structures are composed of six-arm junctions with a single double helix as connecting edges that assemble in physiologically relevant salinities. For a reliable folding of the structures, single-stranded spacers 2-4 nucleotides long have to be introduced in the junction connecting neighboring arms. Coarse-grained molecular dynamics simulations using the oxDNA model suggests that the spacers prevent the stacking of DNA helices, thereby facilitating the assembly of planar geometries.
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Affiliation(s)
| | | | - Erik Poppleton
- Center for Molecular Design and Biomimetics, The Biodesign Institute , Arizona State University , 1001 South McAllister Avenue , Tempe , Arizona 85281 , United States
| | | | - Petr Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute , Arizona State University , 1001 South McAllister Avenue , Tempe , Arizona 85281 , United States
- School of Molecular Sciences Arizona State University , Physical Sciences Building, Room D-102 , PO Box 871604, Tempe , Arizona 85287-1604 , United States
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Jun H, Shepherd TR, Zhang K, Bricker WP, Li S, Chiu W, Bathe M. Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges. ACS NANO 2019; 13:2083-2093. [PMID: 30605605 PMCID: PMC6679942 DOI: 10.1021/acsnano.8b08671] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
3D polyhedral wireframe DNA nanoparticles (DNA-NPs) fabricated using scaffolded DNA origami offer complete and independent control over NP size, structure, and asymmetric functionalization on the 10-100 nm scale. However, the complex DNA sequence design needed for the synthesis of these versatile DNA-NPs has limited their widespread use to date. While the automated sequence design algorithms DAEDALUS and vHelix-BSCOR apply to DNA-NPs synthesized using either uniformly dual or hybrid single-dual duplex edges, respectively, these DNA-NPs are relatively compliant mechanically and are therefore of limited utility for some applications. Further, these algorithms are incapable of handling DNA-NP edge designs composed of more than two duplexes, which are needed to enhance DNA-NP mechanical stiffness. As an alternative, here we introduce the scaffolded DNA origami sequence design algorithm TALOS, which is a generalized procedure for the fully automated design of wireframe 3D polyhedra composed of edges of any cross section with an even number of duplexes, and apply it to DNA-NPs composed uniformly of single honeycomb edges. We also introduce a multiway vertex design that enables the fabrication of DNA-NPs with arbitrary edge lengths and vertex angles and apply it to synthesize a highly asymmetric origami object. Sequence designs are demonstrated to fold robustly into target DNA-NP shapes with high folding efficiency and structural fidelity that is verified using single particle cryo-electron microscopy and 3D reconstruction. In order to test its generality, we apply TALOS to design an in silico library of over 200 DNA-NPs of distinct symmetries and sizes, and for broad impact, we also provide the software as open source for the generation of custom NP designs.
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Affiliation(s)
- Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Tyson R. Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kaiming Zhang
- Department of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - William P. Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Shanshan Li
- Department of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Wah Chiu
- Department of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Corresponding Author
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Simmel FC, Yurke B, Singh HR. Principles and Applications of Nucleic Acid Strand Displacement Reactions. Chem Rev 2019; 119:6326-6369. [PMID: 30714375 DOI: 10.1021/acs.chemrev.8b00580] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.
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Affiliation(s)
| | - Bernard Yurke
- Micron School of Materials Science and Engineering , Boise State University , Boise , ID 83725 , United States
| | - Hari R Singh
- Physics Department , TU München , 85748 Garching , Germany
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Huang CM, Kucinic A, Le JV, Castro CE, Su HJ. Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis. NANOSCALE 2019; 11:1647-1660. [PMID: 30519693 DOI: 10.1039/c8nr06377j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Significant advances have been made towards the design, fabrication, and actuation of dynamic DNA nanorobots including the development of DNA origami mechanisms. These DNA origami mechanisms integrate relatively stiff links made of bundles of double-stranded DNA and relatively flexible joints made of single-stranded DNA to mimic the design of macroscopic machines and robots. Despite reproducing the complex configurations of macroscopic machines, these DNA origami mechanisms exhibit significant deviations from their intended motion behavior since nanoscale mechanisms are subject to significant thermal fluctuations that lead to variations in the geometry of the underlying DNA origami components. Understanding these fluctuations is critical to assess and improve the performance of DNA origami mechanisms and to enable precise nanoscale robotic functions. Here, we report a hybrid computational framework combining coarse-grained modeling with kinematic variance analysis to predict uncertainties in the motion pathway of a multi-component DNA origami mechanism. Coarse-grained modeling was used to evaluate the variation in geometry of individual components due to thermal fluctuations. This variation was incorporated in kinematic analyses to predict the motion pathway uncertainty of the entire mechanism, which agreed well with experimental characterization of motion. We further demonstrated the ability to predict the probability density of DNA origami mechanism conformations based on analysis of mechanical properties of individual joints. This integration of computational analysis, modeling tools, and experimental methods establish the foundation to predict and manage motion uncertainties of general DNA origami mechanisms to guide the design of DNA-based nanoscale machines and robots.
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Affiliation(s)
- Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, USA.
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Kroener F, Traxler L, Heerwig A, Rant U, Mertig M. Magnesium-Dependent Electrical Actuation and Stability of DNA Origami Rods. ACS APPLIED MATERIALS & INTERFACES 2019; 11:2295-2301. [PMID: 30584763 DOI: 10.1021/acsami.8b18611] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Dynamic methods of biosensing based on electrical actuation of surface-tethered nanolevers require the use of levers whose movement in ionic liquids is well controllable and stable. In particular, mechanical integrity of the nanolevers in a wide range of ionic strengths will enable to meet the chemical conditions of a large variety of applications where the specific binding of biomolecular analytes is analyzed. Herein, we study the electrically induced switching behavior of different rodlike DNA origami nanolevers and compare to the actuation of simply double-stranded DNA nanolevers. Our measurements reveal a significantly stronger response of the DNA origami to switching of electrode potential, leading to a smaller potential change necessary to actuate the origami and subsequently to a long-term stable movement. Dynamic measurements in buffer solutions with different Mg2+ contents show that the levers do not disintegrate even at very low ion concentrations and constant switching stress and thus provide stable actuation performance. The latter will pave the way for many new applications without largely restricting application-specific environments.
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Affiliation(s)
- Felix Kroener
- Professur für Physikalische Chemie, Mess- und Sensortechnik , Technische Universität Dresden , 01062 Dresden , Germany
- Dynamic Biosensors GmbH , 82152 Planegg , Germany
| | | | - Andreas Heerwig
- Kurt-Schwabe-Institut für Mess- und Sensortechnik e.V. Meinsberg , 04736 Waldheim , Germany
| | - Ulrich Rant
- Dynamic Biosensors GmbH , 82152 Planegg , Germany
| | - Michael Mertig
- Professur für Physikalische Chemie, Mess- und Sensortechnik , Technische Universität Dresden , 01062 Dresden , Germany
- Kurt-Schwabe-Institut für Mess- und Sensortechnik e.V. Meinsberg , 04736 Waldheim , Germany
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Cumberworth A, Reinhardt A, Frenkel D. Lattice models and Monte Carlo methods for simulating DNA origami self-assembly. J Chem Phys 2018; 149:234905. [DOI: 10.1063/1.5051835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Alexander Cumberworth
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Aleks Reinhardt
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Tian T, Zhang T, Zhou T, Lin S, Shi S, Lin Y. Synthesis of an ethyleneimine/tetrahedral DNA nanostructure complex and its potential application as a multi-functional delivery vehicle. NANOSCALE 2018; 9:18402-18412. [PMID: 29147695 DOI: 10.1039/c7nr07130b] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Nowadays, DNA nanostructures are extensively researched for their biocompatibility, editable functionality, and structural stability. Tetrahedral DNA nanostructures (TDNs), widely known for their membrane permeability, are regarded as potential candidates for drug delivery. However, the stability and membrane permeability of TDNs call for further enhancement if in vivo usage is ascribed. To overcome the drawbacks of TDNs, ethylene imine (PEI, 25 kDa, branched)-a classic cationic polymer in the field of gene delivery-was applied. Via a facile one-pot synthesis method, a PEI/TDNs complex was formed. Subsequently, a DNase protection assay, a cytotoxicity assay, endocytosis-related experiments, and lysosome staining were performed to examine the potential of PEI/TDNs as a delivery vehicle. The combination of PEI and TDNs not only overcame the drawbacks of each substance but also retained their individual merits. Traditionally, drug-delivery vehicles that enable enhanced cell entry and lysosome escape are often compromised by their toxicity and poor multifunctionality. We believe this novel PEI/TDNs complex with enhanced systemic stability, biocompatibility, cell-entry ability, and lysosome-escape ability and unsurpassed editable functionality could be a powerful tool as a multi-functional delivery vehicle in targeted drug delivery, in vivo imaging, and other related fields.
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Affiliation(s)
- Taoran Tian
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P.R. China.
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Zhou L, Marras AE, Huang CM, Castro CE, Su HJ. Paper Origami-Inspired Design and Actuation of DNA Nanomachines with Complex Motions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802580. [PMID: 30369060 DOI: 10.1002/smll.201802580] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/19/2018] [Indexed: 05/26/2023]
Abstract
Significant progress in DNA nanotechnology has accelerated the development of molecular machines with functions like macroscale machines. However, the mobility of DNA self-assembled nanorobots is still dramatically limited due to challenges with designing and controlling nanoscale systems with many degrees of freedom. Here, an origami-inspired method to design transformable DNA nanomachines is presented. This approach integrates stiff panels formed by bundles of double-stranded DNA connected with foldable creases formed by single-stranded DNA. To demonstrate the method, a DNA version of the paper origami mechanism called a waterbomb base (WBB) consisting of six panels connected by six joints is constructed. This nanoscale WBB can follow four distinct motion paths to transform between five distinct configurations including a flat square, two triangles, a rectangle, and a fully compacted trapezoidal shape. To achieve this, the sequence specificity of DNA base-pairing is leveraged for the selective actuation of joints and the ion-sensitivity of base-stacking interactions is employed for the flattening of joints. In addition, higher-order assembly of DNA WBBs into reconfigurable arrays is achieved. This work establishes a foundation for origami-inspired design for next generation synthetic molecular robots and reconfigurable nanomaterials enabling more complex and controllable motion.
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Affiliation(s)
- Lifeng Zhou
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Alexander E Marras
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Hai-Jun Su
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
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