1
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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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2
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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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3
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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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4
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Glaser M, Deb S, Seier F, Agrawal A, Liedl T, Douglas S, Gupta MK, Smith DM. The Art of Designing DNA Nanostructures with CAD Software. Molecules 2021; 26:molecules26082287. [PMID: 33920889 PMCID: PMC8071251 DOI: 10.3390/molecules26082287] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022] Open
Abstract
Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.
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Affiliation(s)
- Martin Glaser
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany;
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
| | - Sourav Deb
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
| | - Florian Seier
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
| | - Amay Agrawal
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
| | - Tim Liedl
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany;
| | - Shawn Douglas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA;
| | - Manish K. Gupta
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
- Correspondence: (M.K.G.); (D.M.S.)
| | - David M. Smith
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany;
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
- Institute of Clinical Immunology, University of Leipzig Medical Faculty, 04103 Leipzig, Germany
- Correspondence: (M.K.G.); (D.M.S.)
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5
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Snodin BEK, Schreck JS, Romano F, Louis AA, Doye JPK. Coarse-grained modelling of the structural properties of DNA origami. Nucleic Acids Res 2019; 47:1585-1597. [PMID: 30605514 PMCID: PMC6379721 DOI: 10.1093/nar/gky1304] [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: 09/27/2018] [Revised: 11/17/2018] [Accepted: 12/20/2018] [Indexed: 01/12/2023] Open
Abstract
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origami, focussing on archetypal 2D and 3D origami. The model reproduces well the characteristic pattern of helix bending in a 2D origami, showing that it stems from the intrinsic tendency of anti-parallel four-way junctions to splay apart, a tendency that is enhanced both by less screened electrostatic interactions and by increased thermal motion. We also compare to the structure of a 3D origami whose structure has been determined by cryo-electron microscopy. The oxDNA average structure has a root-mean-square deviation from the experimental structure of 8.4 Å, which is of the order of the experimental resolution. These results illustrate that the oxDNA model is capable of providing detailed and accurate insights into the structure of DNA origami, and has the potential to be used to routinely pre-screen putative origami designs and to investigate the molecular mechanisms that regulate the properties of DNA origami.
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Affiliation(s)
- Benedict E K Snodin
- Physical, and Theoretical Chemistry Laboratory, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - John S Schreck
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Universit Ca' Foscari, Via Torino 155, 30172 Venezia Mestre, Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK
| | - Jonathan P K Doye
- Physical, and Theoretical Chemistry Laboratory, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
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6
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A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems. Methods Mol Biol 2019. [PMID: 29926456 DOI: 10.1007/978-1-4939-8582-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The DNA origami method exploits the self-assembly property of nucleic acids to build diverse nanoscale systems. The all-atom molecular dynamics (MD) method has emerged as a powerful computational tool for atomic-resolution characterization of the in situ structure and physical properties of DNA origami objects. This chapter provides step-by-step instructions for building atomic-scale models of DNA origami systems, using the MD method to simulate the models, and performing basic analyses of the resulting MD trajectories.
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7
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Sharma R, Schreck JS, Romano F, Louis AA, Doye JPK. Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model. ACS NANO 2017; 11:12426-12435. [PMID: 29083876 DOI: 10.1021/acsnano.7b06470] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
As detailed structural characterizations of large complex DNA nanostructures are hard to obtain experimentally, particularly if they have substantial flexibility, coarse-grained modeling can potentially provide an important complementary role. Such modeling can provide a detailed view of both the average structure and the structural fluctuations, as well as providing insight into how the nanostructure's design determines its structural properties. Here, we present a case study of jointed DNA nanostructures using the oxDNA model. In particular, we consider archetypal hinge and sliding joints, as well as more complex structures involving a number of such coupled joints. Our results highlight how the nature of the motion in these structures can sensitively depend on the precise details of the joints. Furthermore, the generally good agreement with experiments illustrates the power of this approach and suggests the use of such modeling to prescreen the properties of putative designs.
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Affiliation(s)
- Rahul Sharma
- Department of Chemistry, Indian Institute of Technology Roorkee , Roorkee, 247667, India
| | - John S Schreck
- Department of Chemical Engineering, Columbia University , New York, New York 10027, United States
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca' Foscari Venezia , I-30123 Venezia, Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford , 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
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8
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Pan K, Bricker WP, Ratanalert S, Bathe M. Structure and conformational dynamics of scaffolded DNA origami nanoparticles. Nucleic Acids Res 2017; 45:6284-6298. [PMID: 28482032 PMCID: PMC5499760 DOI: 10.1093/nar/gkx378] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 04/25/2017] [Indexed: 12/22/2022] Open
Abstract
Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fully determined by underlying Watson–Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5–100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost. We apply all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanoparticles to elucidate their fine-scale and global conformational structure and dynamics. We use our coarse-grained model with a set of secondary structural motifs to predict the equilibrium solution structures of 45 DX-based DNA origami nanoparticles including a tetrahedron, octahedron, icosahedron, cuboctahedron and reinforced cube. Coarse-grained models are compared with 3D cryo-electron microscopy density maps for these five DNA nanoparticles and with all-atom molecular dynamics simulations for the tetrahedron and octahedron. Our results elucidate non-intuitive atomic-level structural details of DX-based DNA nanoparticles, and offer a general framework for efficient computational prediction of global and local structural and mechanical properties of DX-based assemblies that are inaccessible to all-atom based models alone.
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Affiliation(s)
- Keyao Pan
- 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
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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9
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Shi Z, Castro CE, Arya G. Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations. ACS NANO 2017; 11:4617-4630. [PMID: 28423273 DOI: 10.1021/acsnano.7b00242] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically compliant nanostructures with tunable equilibrium conformations and conformational distributions. Here we use coarse-grained molecular dynamics simulations to provide insights into the conformational dynamics of a set of mechanically compliant DNA nanostructures-DNA hinges that use single-stranded DNA "springs" to tune the equilibrium conformation of a layered double-stranded DNA "joint" connecting two stiff "arms" constructed from DNA helix bundles. The simulations reproduce the experimentally measured equilibrium angles between hinge arms for a range of hinge designs. The hinges are found to be structurally stable, except for some fraying of the open ends of the DNA helices comprising the hinge arms and some loss of base-pairing interactions in the joint regions coinciding with the crossover junctions, especially in hinges designed to exhibit a small bending angle that exhibit large local stresses resulting in strong kinks in their joints. Principal component analysis reveals that while the hinge dynamics are dominated by bending motion, some twisting and sliding of hinge arms relative to each other also exists. Forced deformation of the hinges reveals distinct bending mechanisms for hinges with short, inextensible springs versus those with longer, more extensible springs. Lastly, we introduce an approach for rapidly predicting equilibrium hinge angles from individual force-deformation behaviors of its single- and double-stranded DNA components. Taken together, these results demonstrate that coarse-grained modeling is a promising approach for designing, predicting, and studying the dynamics of compliant DNA nanostructures, where conformational fluctuations become important, multiple deformation mechanisms exist, and continuum approaches may not yield accurate properties.
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Affiliation(s)
- Ze Shi
- Department of NanoEngineering, University of California, San Diego , La Jolla, California 92093, United States
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| | - Gaurav Arya
- Department of NanoEngineering, University of California, San Diego , La Jolla, California 92093, United States
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10
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Liang B, Nagarajan A, Hudoba MW, Alvarez R, Castro CE, Soghrati S. Automated Quantification of the Impact of Defects on the Mechanical Behavior of Deoxyribonucleic Acid Origami Nanoplates. J Biomech Eng 2017; 139:2607051. [DOI: 10.1115/1.4036022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Indexed: 12/22/2022]
Abstract
Deoxyribonucleic acid (DNA) origami is a method for the bottom-up self-assembly of complex nanostructures for applications, such as biosensing, drug delivery, nanopore technologies, and nanomechanical devices. Effective design of such nanostructures requires a good understanding of their mechanical behavior. While a number of studies have focused on the mechanical properties of DNA origami structures, considering defects arising from molecular self-assembly is largely unexplored. In this paper, we present an automated computational framework to analyze the impact of such defects on the structural integrity of a model DNA origami nanoplate. The proposed computational approach relies on a noniterative conforming to interface-structured adaptive mesh refinement (CISAMR) algorithm, which enables the automated transformation of a binary image of the nanoplate into a high fidelity finite element model. We implement this technique to quantify the impact of defects on the mechanical behavior of the nanoplate by performing multiple simulations taking into account varying numbers and spatial arrangements of missing DNA strands. The analyses are carried out for two types of loading: uniform tensile displacement applied on all the DNA strands and asymmetric tensile displacement applied to strands at diagonal corners of the nanoplate.
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Affiliation(s)
- Bowen Liang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210
| | - Anand Nagarajan
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210
| | - Michael W. Hudoba
- Department of Engineering, Otterbein University, Westerville, OH 43081
| | - Ricardo Alvarez
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210
| | - Carlos E. Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210
| | - Soheil Soghrati
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210 e-mail:
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11
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Chatzieleftheriou S, Adendorff MR, Lagaros ND. Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures. J Chem Inf Model 2016; 56:1963-1978. [DOI: 10.1021/acs.jcim.6b00356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Stavros Chatzieleftheriou
- Institute of Structural Analysis & Antiseismic Research, Department of Structural Engineering, School of Civil Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, GR-15780 Athens, Greece
| | - Matthew R. Adendorff
- Laboratory of Computational Biology & Biophysics, Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States
| | - Nikos D. Lagaros
- Institute of Structural Analysis & Antiseismic Research, Department of Structural Engineering, School of Civil Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Zografou Campus, GR-15780 Athens, Greece
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12
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Bruetzel LK, Gerling T, Sedlak SM, Walker PU, Zheng W, Dietz H, Lipfert J. Conformational Changes and Flexibility of DNA Devices Observed by Small-Angle X-ray Scattering. NANO LETTERS 2016; 16:4871-4879. [PMID: 27356232 DOI: 10.1021/acs.nanolett.6b01338] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Self-assembled DNA origami nanostructures enable the creation of precisely defined shapes at the molecular scale. Dynamic DNA devices that are capable of switching between defined conformations could afford completely novel functionalities for diagnostic, therapeutic, or engineering applications. Developing such objects benefits strongly from experimental feedback about conformational changes and 3D structures, ideally in solution, free of potential biases from surface attachment or labeling. Here, we demonstrate that small-angle X-ray scattering (SAXS) can quantitatively resolve the conformational changes of a DNA origami two-state switch device as a function of the ionic strength of the solution. In addition, we show how SAXS data allow for refinement of the predicted idealized three-dimensional structure of the DNA object using a normal mode approach based on an elastic network model. The results reveal deviations from the idealized design geometries that are otherwise difficult to resolve. Our results establish SAXS as a powerful tool to investigate conformational changes and solution structures of DNA origami and we anticipate our methodology to be broadly applicable to increasingly complex DNA and RNA devices.
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Affiliation(s)
- Linda K Bruetzel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany
| | - Thomas Gerling
- Physik Department, Walter Schottky Institute, Technische Universität München , Am Coulombwall 4a, 85748 Garching near Munich, Germany
| | - Steffen M Sedlak
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany
| | - Philipp U Walker
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany
| | - Wenjun Zheng
- Physics Department, State University of New York at Buffalo , Buffalo, New York 14260, United States
| | - Hendrik Dietz
- Physik Department, Walter Schottky Institute, Technische Universität München , Am Coulombwall 4a, 85748 Garching near Munich, Germany
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany
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13
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Dhakal S, Adendorff MR, Liu M, Yan H, Bathe M, Walter NG. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis. NANOSCALE 2016; 8:3125-3137. [PMID: 26788713 DOI: 10.1039/c5nr07263h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The control of enzymatic reactions using nanoscale DNA devices offers a powerful application of DNA nanotechnology uniquely derived from actuation. However, previous characterization of enzymatic reaction rates using bulk biochemical assays reported suboptimal function of DNA devices such as tweezers. To gain mechanistic insight into this deficiency and to identify design rules to improve their function, here we exploit the synergy of single molecule imaging and computational modeling to characterize the three-dimensional structures and catalytic functions of DNA tweezer-actuated nanoreactors. Our analysis revealed two important deficiencies--incomplete closure upon actuation and conformational heterogeneity. Upon rational redesign of the Holliday junctions located at their hinge and arms, we found that the DNA tweezers could be more completely and uniformly closed. A novel single molecule enzyme assay was developed to demonstrate that our design improvements yield significant, independent enhancements in the fraction of active enzyme nanoreactors and their individual substrate turnover frequencies. The sequence-level design strategies explored here may aid more broadly in improving the performance of DNA-based nanodevices including biological and chemical sensors.
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Affiliation(s)
- Soma Dhakal
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Matthew R Adendorff
- Department of Biological Engineering, Laboratory for Computational Biology & Biophysics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Mark Bathe
- Department of Biological Engineering, Laboratory for Computational Biology & Biophysics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Nils G Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA.
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