1
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Shi Z, Li Y, Du X, Liu D, Dong Y. Constructing Stiffness Tunable DNA Hydrogels Based on DNA Modules with Adjustable Rigidity. NANO LETTERS 2024; 24:8634-8641. [PMID: 38950146 DOI: 10.1021/acs.nanolett.4c01870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
DNA hydrogel represents a potent material for crafting biological scaffolds, but the toolbox to systematically regulate the mechanical property is still limited. Herein, we have provided a strategy to tune the stiffness of DNA hydrogel through manipulating the rigidity of DNA modules. By introducing building blocks with higher molecular rigidity and proper connecting fashion, DNA hydrogel stiffness could be systematically elevated. These hydrogels showed excellent dynamic properties and biocompatibility, thus exhibiting great potential in three-dimensional (3D) cell culture. This study has offered a systematic method to explore the structure-property relationship, which may contribute to the development of more intelligent and personalized biomedical platforms.
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Affiliation(s)
- Ziwei Shi
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yujie Li
- Engineering Research Center of Advanced Rare Earth Materials, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xiuji Du
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Dongsheng Liu
- Engineering Research Center of Advanced Rare Earth Materials, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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2
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Wang H, Yin F, Li L, Li M, Fang Z, Sun C, Li B, Shi J, Li J, Wang L, Song S, Zuo X, Liu X, Fan C. Twisted DNA Origami-Based Chiral Monolayers for Spin Filtering. J Am Chem Soc 2024; 146:5883-5893. [PMID: 38408317 DOI: 10.1021/jacs.3c11566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
DNA monolayers with inherent chirality play a pivotal role across various domains including biosensors, DNA chips, and bioelectronics. Nonetheless, conventional DNA chiral monolayers, typically constructed from single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), often lack structural orderliness and design flexibility at the interface. Structural DNA nanotechnology has emerged as a promising solution to tackle these challenges. In this study, we present a strategy for crafting highly adaptable twisted DNA origami-based chiral monolayers. These structures exhibit distinct interfacial assembly characteristics and effectively mitigate the structural disorder of dsDNA monolayers, which is constrained by a limited persistence length of ∼50 nm of dsDNA. We highlight the spin-filtering capabilities of seven representative DNA origami-based chiral monolayers, demonstrating a maximal one-order-of-magnitude increase in spin-filtering efficiency per unit area compared with conventional dsDNA chiral monolayers. Intriguingly, our findings reveal that the higher-order tertiary chiral structure of twisted DNA origami further enhances the spin-filtering efficiency. This work paves the way for the rational design of DNA chiral monolayers.
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Affiliation(s)
- Haozhi 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
| | - Fangfei Yin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lingyun 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
| | - 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
| | - Zheng Fang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chenyun Sun
- 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
| | - Jiye Shi
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiang Li
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Lihua Wang
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Shiping Song
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, 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
| | - Chunhai Fan
- 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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Lee JY, Koh H, Kim DN. A computational model for structural dynamics and reconfiguration of DNA assemblies. Nat Commun 2023; 14:7079. [PMID: 37925463 PMCID: PMC10625641 DOI: 10.1038/s41467-023-42873-4] [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: 06/18/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023] Open
Abstract
Recent advances in constructing a structured DNA assembly whose configuration can be dynamically changed in response to external stimuli have demanded the development of an efficient computational modeling approach to expedite its design process. Here, we present a computational framework capable of analyzing both equilibrium and non-equilibrium dynamics of structured DNA assemblies at the molecular level. The framework employs Langevin dynamics with structural and hydrodynamic finite element models that describe mechanical, electrostatic, base stacking, and hydrodynamic interactions. Equilibrium dynamic analysis for various problems confirms the solution accuracy at a near-atomic resolution, comparable to molecular dynamics simulations and experimental measurements. Furthermore, our model successfully simulates a long-time-scale close-to-open-to-close dynamic reconfiguration of the switch structure in response to changes in ion concentration. We expect that the proposed model will offer a versatile way of designing responsive and reconfigurable DNA machines.
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Affiliation(s)
- Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Heeyuen Koh
- Soft Foundry Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Soft Foundry Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Department of Mechanical Engineering, 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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4
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Lee AJ, Rackers JA, Bricker WP. Predicting accurate ab initio DNA electron densities with equivariant neural networks. Biophys J 2022; 121:3883-3895. [PMID: 36057785 PMCID: PMC9674991 DOI: 10.1016/j.bpj.2022.08.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/22/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022] Open
Abstract
One of the fundamental limitations of accurately modeling biomolecules like DNA is the inability to perform quantum chemistry calculations on large molecular structures. We present a machine learning model based on an equivariant Euclidean neural network framework to obtain accurate ab initio electron densities for arbitrary DNA structures that are much too large for conventional quantum methods. The model is trained on representative B-DNA basepair steps that capture both base pairing and base stacking interactions. The model produces accurate electron densities for arbitrary B-DNA structures with typical errors of less than 1%. Crucially, the error does not increase with system size, which suggests that the model can extrapolate to large DNA structures with negligible loss of accuracy. The model also generalizes reasonably to other DNA structural motifs such as the A- and Z-DNA forms, despite being trained on only B-DNA configurations. The model is used to calculate electron densities of several large-scale DNA structures, and we show that the computational scaling for this model is essentially linear. We also show that this machine learning electron density model can be used to calculate accurate electrostatic potentials for DNA. These electrostatic potentials produce more accurate results compared with classical force fields and do not show the usual deficiencies at short range.
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Affiliation(s)
- Alex J Lee
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico
| | - Joshua A Rackers
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico.
| | - William P Bricker
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico.
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5
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Adendorff MR, Tang GQ, Millar D, Bathe M, Bricker W. Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics. Nucleic Acids Res 2022; 50:717-730. [PMID: 34935970 PMCID: PMC8789063 DOI: 10.1093/nar/gkab1246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 11/28/2021] [Accepted: 12/06/2021] [Indexed: 12/19/2022] Open
Abstract
Immobile four-way junctions (4WJs) are core structural motifs employed in the design of programmed DNA assemblies. Understanding the impact of sequence on their equilibrium structure and flexibility is important to informing the design of complex DNA architectures. While core junction sequence is known to impact the preferences for the two possible isomeric states that junctions reside in, previous investigations have not quantified these preferences based on molecular-level interactions. Here, we use all-atom molecular dynamics simulations to investigate base-pair level structure and dynamics of four-way junctions, using the canonical Seeman J1 junction as a reference. Comparison of J1 with equivalent single-crossover topologies and isolated nicked duplexes reveal conformational impact of the double-crossover motif. We additionally contrast J1 with a second junction core sequence termed J24, with equal thermodynamic preference for each isomeric configuration. Analyses of the base-pair degrees of freedom for each system, free energy calculations, and reduced-coordinate sampling of the 4WJ isomers reveal the significant impact base sequence has on local structure, isomer bias, and global junction dynamics.
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Affiliation(s)
- Matthew R Adendorff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guo Qing Tang
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - David P Millar
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131, USA
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6
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Jun H, Wang X, Parsons M, Bricker W, John T, Li S, Jackson S, Chiu W, Bathe M. Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami. Nucleic Acids Res 2021; 49:10265-10274. [PMID: 34508356 PMCID: PMC8501967 DOI: 10.1093/nar/gkab762] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/11/2021] [Accepted: 08/24/2021] [Indexed: 01/05/2023] Open
Abstract
Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.
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Affiliation(s)
- Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Division of Mechanical System Engineering, Jeonbuk National University, Jeonju-si, Jellabuk-do 54896, Republic of Korea
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Torsten John
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shanshan Li
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Steve Jackson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wah Chiu
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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7
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Crocker K, Johnson J, Pfeifer W, Castro C, Bundschuh R. A quantitative model for a nanoscale switch accurately predicts thermal actuation behavior. NANOSCALE 2021; 13:13746-13757. [PMID: 34477649 DOI: 10.1039/d1nr02873a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Manipulation of temperature can be used to actuate DNA origami nano-hinges containing gold nanoparticles. We develop a physical model of this system that uses partition function analysis of the interaction between the nano-hinge and nanoparticle to predict the probability that the nano-hinge is open at a given temperature. The model agrees well with experimental data and predicts experimental conditions that allow the actuation temperature of the nano-hinge to be tuned over a range of temperatures from 30 °C to 45 °C. Additionally, the model identifies microscopic interactions that are important to the macroscopic behavior of the system, revealing surprising features of the system. This combination of physical insight and predictive potential is likely to inform future designs that integrate nanoparticles into dynamic DNA origami structures or use strand binding interactions to control dynamic DNA origami behavior. Furthermore, our modeling approach could be expanded to consider the incorporation, stability, and actuation of other types of functional elements or actuation mechanisms integrated into nucleic acid devices.
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Affiliation(s)
- Kyle Crocker
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA.
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8
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Green CM, Hughes WL, Graugnard E, Kuang W. Correlative Super-Resolution and Atomic Force Microscopy of DNA Nanostructures and Characterization of Addressable Site Defects. ACS NANO 2021; 15:11597-11606. [PMID: 34137595 DOI: 10.1021/acsnano.1c01976] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To bring real-world applications of DNA nanostructures to fruition, advanced microscopy techniques are needed to shed light on factors limiting the availability of addressable sites. Correlative microscopy, where two or more microscopies are combined to characterize the same sample, is an approach to overcome the limitations of individual techniques, yet it has seen limited use for DNA nanotechnology. We have developed an accessible strategy for high resolution, correlative DNA-based points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution and atomic force microscopy (AFM) of DNA nanostructures, enabled by a simple and robust method to selectively bind DNA origami to cover glass. Using this technique, we examined addressable "docking" sites on DNA origami to distinguish between two defect scenarios-structurally incorporated but inactive docking sites, and unincorporated docking sites. We found that over 75% of defective docking sites were incorporated but inactive, suggesting unincorporated strands played a minor role in limiting the availability of addressable sites. We further explored the effects of strand purification, UV irradiation, and photooxidation on availability, providing insight on potential sources of defects and pathways toward improving the fidelity of DNA nanostructures.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, D.C. 20375, United States
- National Research Council, 500 fifth St NW, Washington, D.C. 20001, United States
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9
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Kube M, Kohler F, Feigl E, Nagel-Yüksel B, Willner EM, Funke JJ, Gerling T, Stömmer P, Honemann MN, Martin TG, Scheres SHW, Dietz H. Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution. Nat Commun 2020; 11:6229. [PMID: 33277481 PMCID: PMC7718922 DOI: 10.1038/s41467-020-20020-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 11/11/2020] [Indexed: 11/25/2022] Open
Abstract
The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions. Precision design of DNA origami needs precision validation. Here, the authors developed cryo-EM methods for obtaining high resolution structural data and for constructing pseudo-atomic models in a semi-automated fashion, allowing for iterative nanodevice inspection and refinement.
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Affiliation(s)
- Massimo Kube
- Physik Department, Technische Universität München, Garching, Germany
| | - Fabian Kohler
- Physik Department, Technische Universität München, Garching, Germany
| | - Elija Feigl
- Physik Department, Technische Universität München, Garching, Germany
| | - Baki Nagel-Yüksel
- Physik Department, Technische Universität München, Garching, Germany
| | - Elena M Willner
- Physik Department, Technische Universität München, Garching, Germany
| | - Jonas J Funke
- Physik Department, Technische Universität München, Garching, Germany
| | - Thomas Gerling
- Physik Department, Technische Universität München, Garching, Germany
| | - Pierre Stömmer
- Physik Department, Technische Universität München, Garching, Germany
| | | | | | | | - Hendrik Dietz
- Physik Department, Technische Universität München, Garching, Germany.
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10
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Lee JY, Kim YJ, Lee C, Lee JG, Yagyu H, Tabata O, Kim DN. Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design. Nucleic Acids Res 2019; 47:93-102. [PMID: 30476210 PMCID: PMC6326809 DOI: 10.1093/nar/gky1189] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/09/2018] [Indexed: 01/09/2023] Open
Abstract
DNA nick can be used as a design motif in programming the shape and reconfigurable deformation of synthetic DNA nanostructures, but its mechanical properties have rarely been systematically characterized at the level of base sequences. Here, we investigated sequence-dependent mechanical properties of DNA nicks through molecular dynamics simulation for a comprehensive set of distinct DNA oligomers constructed using all possible base-pair steps with and without a nick. We found that torsional rigidity was reduced by 28–82% at the nick depending on its sequence and location although bending and stretching rigidities remained similar to those of regular base-pair steps. No significant effect of a nick on mechanically coupled deformation such as the twist-stretch coupling was observed. These results suggest that the primary structural role of nick is the relaxation of torsional constraint by backbones known to be responsible for relatively high torsional rigidity of DNA. Moreover, we experimentally demonstrated the usefulness of quantified nick properties in self-assembling DNA nanostructure design by constructing twisted DNA origami structures to show that sequence design of nicks successfully controls the twist angle of structures. Our study illustrates the importance as well as the opportunities of considering sequence-dependent properties in structural DNA nanotechnology.
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Affiliation(s)
- Jae Young Lee
- Department of Mechanical and Aerospace Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Young-Joo Kim
- Department of Mechanical and Aerospace Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Chanseok Lee
- Department of Mechanical and Aerospace Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jae Gyung Lee
- Department of Mechanical and Aerospace Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hiromasa Yagyu
- Department of Mechanical Engineering, Kanto Gakuin University, Yokohama 236-8501, Japan
| | - Osamu Tabata
- Department of Micro Engineering, Kyoto University, Kyoto Daigaku-Katsura, Kyoto 615-8540, Japan
| | - Do-Nyun Kim
- Department of Mechanical and Aerospace Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea.,Institute of Advanced Machines and Design, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Republic of Korea
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11
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Wamhoff EC, Banal JL, Bricker WP, Shepherd TR, Parsons MF, Veneziano R, Stone MB, Jun H, Wang X, Bathe M. Programming Structured DNA Assemblies to Probe Biophysical Processes. Annu Rev Biophys 2019; 48:395-419. [PMID: 31084582 PMCID: PMC7035826 DOI: 10.1146/annurev-biophys-052118-115259] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Rémi Veneziano
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Matthew B Stone
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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12
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Programming chain-growth copolymerization of DNA hairpin tiles for in-vitro hierarchical supramolecular organization. Nat Commun 2019; 10:1006. [PMID: 30824698 PMCID: PMC6397255 DOI: 10.1038/s41467-019-09004-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/21/2019] [Indexed: 12/12/2022] Open
Abstract
Formation of biological filaments via intracellular supramolecular polymerization of proteins or protein/nucleic acid complexes is under programmable and spatiotemporal control to maintain cellular and genomic integrity. Here we devise a bioinspired, catassembly-like isothermal chain-growth approach to copolymerize DNA hairpin tiles (DHTs) into nanofilaments with desirable composition, chain length and function. By designing metastable DNA hairpins with shape-defining intramolecular hydrogen bonds, we generate two types of DHT monomers for copolymerization with high cooperativity and low dispersity indexes. Quantitative single-molecule dissection methods reveal that catalytic opening of a DHT motif harbouring a toehold triggers successive branch migration, which autonomously propagates to form copolymers with alternate tile units. We find that these shape-defined supramolecular nanostructures become substrates for efficient endocytosis by living mammalian cells in a stiffness-dependent manner. Hence, this catassembly-like in-vitro reconstruction approach provides clues for understanding structure-function relationship of biological filaments under physiological and pathological conditions.
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13
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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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14
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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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15
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Reshetnikov RV, Stolyarova AV, Zalevsky AO, Panteleev DY, Pavlova GV, Klinov DV, Golovin AV, Protopopova AD. A coarse-grained model for DNA origami. Nucleic Acids Res 2018; 46:1102-1112. [PMID: 29267876 PMCID: PMC5814798 DOI: 10.1093/nar/gkx1262] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/14/2017] [Accepted: 12/07/2017] [Indexed: 01/20/2023] Open
Abstract
Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version.
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Affiliation(s)
- Roman V Reshetnikov
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str., 34/5, 119334 Moscow, Russia
- A.N.Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Leninskye gory, 1-40, 119992 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, 1-73, 119234 Moscow, Russia
| | - Anastasia V Stolyarova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, 1-73, 119234 Moscow, Russia
- Skolkovo Institute of Science and Technology, Nobel Street 3, 143026 Moscow, Russia
| | - Arthur O Zalevsky
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, 1-73, 119234 Moscow, Russia
| | - Dmitry Y Panteleev
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str., 34/5, 119334 Moscow, Russia
| | - Galina V Pavlova
- Institute of Gene Biology, Russian Academy of Sciences, Vavilova str., 34/5, 119334 Moscow, Russia
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya str. 1a, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy per. Dolgoprudny, 141700 Moscow Region, Russia
| | - Andrey V Golovin
- A.N.Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Leninskye gory, 1-40, 119992 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, 1-73, 119234 Moscow, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str. 8-2, 119991 Moscow, Russia
| | - Anna D Protopopova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya str. 1a, 119435 Moscow, Russia
- Department of Cell & Developmental Biology, Perelman School of Medicine, University of Pennsylvania, BRB II/III 421 Curie Boulevard, Philadelphia, PA 19104, USA
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16
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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