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Choi Y, Choi H, Lee AC, Lee H, Kwon S. A Reconfigurable DNA Accordion Rack. Angew Chem Int Ed Engl 2018; 57:2811-2815. [DOI: 10.1002/anie.201709362] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Yeongjae Choi
- Department of Electrical and Computer Engineering; Seoul National University; 1, Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Hansol Choi
- Department of Electrical and Computer Engineering; Seoul National University; 1, Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Amos C. Lee
- Interdisciplinary Program for Bioengineering; Seoul National University; 1, Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Hyunung Lee
- Department of Electrical and Computer Engineering; Seoul National University; 1, Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering; Seoul National University; 1, Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
- Interdisciplinary Program for Bioengineering; Seoul National University; 1, Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
- Institute of Entrepreneurial Bio Convergence; Seoul National University; 1, Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
- Seoul National University Hospital Biomedical Research Institute; Seoul National University Hospital; 101, Daehak-ro Jongno-gu Seoul 03080 Republic of Korea
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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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Ora A, Järvihaavisto E, Zhang H, Auvinen H, Santos HA, Kostiainen MA, Linko V. Cellular delivery of enzyme-loaded DNA origami. Chem Commun (Camb) 2018; 52:14161-14164. [PMID: 27869278 DOI: 10.1039/c6cc08197e] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In this communication, we show that active enzymes can be delivered into HEK293 cells in vitro when they are attached to tubular DNA origami nanostructures. We use bioluminescent enzymes as a cargo and monitor their activity from a cell lysate. The results show that the enzymes stay intact and retain their activity in the transfection process. The method is highly modular, which makes it a compelling candidate for a great variety of delivery applications.
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Affiliation(s)
- Ari Ora
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Erika Järvihaavisto
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Hongbo Zhang
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00790 Helsinki, Finland
| | - Henni Auvinen
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Hélder A Santos
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00790 Helsinki, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
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Boulais É, Sawaya NPD, Veneziano R, Andreoni A, Banal JL, Kondo T, Mandal S, Lin S, Schlau-Cohen GS, Woodbury NW, Yan H, Aspuru-Guzik A, Bathe M. Programmed coherent coupling in a synthetic DNA-based excitonic circuit. NATURE MATERIALS 2018; 17:159-166. [PMID: 29180771 DOI: 10.1038/nmat5033] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 10/18/2017] [Indexed: 06/07/2023]
Abstract
Natural light-harvesting systems spatially organize densely packed chromophore aggregates using rigid protein scaffolds to achieve highly efficient, directed energy transfer. Here, we report a synthetic strategy using rigid DNA scaffolds to similarly program the spatial organization of densely packed, discrete clusters of cyanine dye aggregates with tunable absorption spectra and strongly coupled exciton dynamics present in natural light-harvesting systems. We first characterize the range of dye-aggregate sizes that can be templated spatially by A-tracts of B-form DNA while retaining coherent energy transfer. We then use structure-based modelling and quantum dynamics to guide the rational design of higher-order synthetic circuits consisting of multiple discrete dye aggregates within a DX-tile. These programmed circuits exhibit excitonic transport properties with prominent circular dichroism, superradiance, and fast delocalized exciton transfer, consistent with our quantum dynamics predictions. This bottom-up strategy offers a versatile approach to the rational design of strongly coupled excitonic circuits using spatially organized dye aggregates for use in coherent nanoscale energy transport, artificial light-harvesting, and nanophotonics.
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Affiliation(s)
- Étienne Boulais
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- MIT-Harvard Center for Excitonics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nicolas P D Sawaya
- MIT-Harvard Center for Excitonics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Rémi Veneziano
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Alessio Andreoni
- Center for Innovation in Medicine, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- MIT-Harvard Center for Excitonics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Toru Kondo
- MIT-Harvard Center for Excitonics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sarthak Mandal
- Center for Innovation in Medicine, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Su Lin
- Center for Innovation in Medicine, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Gabriela S Schlau-Cohen
- MIT-Harvard Center for Excitonics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Neal W Woodbury
- Center for Innovation in Medicine, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Hao Yan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Alán Aspuru-Guzik
- MIT-Harvard Center for Excitonics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- MIT-Harvard Center for Excitonics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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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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57
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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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Wagenbauer KF, Engelhardt FAS, Stahl E, Hechtl VK, Stömmer P, Seebacher F, Meregalli L, Ketterer P, Gerling T, Dietz H. How We Make DNA Origami. Chembiochem 2017; 18:1873-1885. [PMID: 28714559 DOI: 10.1002/cbic.201700377] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Indexed: 12/14/2022]
Abstract
DNA origami has attracted substantial attention since its invention ten years ago, due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. Although the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know-how for designing and producing the particles with sufficient quality and for preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know-how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge. To foster faster progress, we share in this article the experience in making and preparing DNA origami that we have accumulated over recent years. We discuss design solutions for creating advanced structural motifs including corners and various types of hinges that expand the design space for the more rigid multilayer DNA origami and provide guidelines for preventing undesired aggregation and on how to induce specific oligomerization of multiple DNA origami building blocks. In addition, we provide detailed protocols and discuss the expected results for five key methods that allow efficient and damage-free preparation of DNA origami. These methods are agarose-gel purification, filtration through molecular cut-off membranes, PEG precipitation, size-exclusion chromatography, and ultracentrifugation-based sedimentation. The guide for creating advanced design motifs and the detailed protocols with their experimental characterization that we describe here should lower the barrier for researchers to accomplish the full DNA origami production workflow.
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Affiliation(s)
- Klaus F Wagenbauer
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Floris A S Engelhardt
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Evi Stahl
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Vera K Hechtl
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Pierre Stömmer
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Fabian Seebacher
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Letizia Meregalli
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Philip Ketterer
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Thomas Gerling
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Hendrik Dietz
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
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Schiffels D, Szalai V, Liddle JA. Molecular Precision at Micrometer Length Scales: Hierarchical Assembly of DNA-Protein Nanostructures. ACS NANO 2017; 11:6623-6629. [PMID: 28651051 PMCID: PMC11314666 DOI: 10.1021/acsnano.7b00320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2024]
Abstract
Robust self-assembly across length scales is a ubiquitous feature of biological systems but remains challenging for synthetic structures. Taking a cue from biology-where disparate molecules work together to produce large, functional assemblies-we demonstrate how to engineer microscale structures with nanoscale features: Our self-assembly approach begins by using DNA polymerase to controllably create double-stranded DNA (dsDNA) sections on a single-stranded template. The single-stranded DNA (ssDNA) sections are then folded into a mechanically flexible skeleton by the origami method. This process simultaneously shapes the structure at the nanoscale and directs the large-scale geometry. The DNA skeleton guides the assembly of RecA protein filaments, which provides rigidity at the micrometer scale. We use our modular design strategy to assemble tetrahedral, rectangular, and linear shapes of defined dimensions. This method enables the robust construction of complex assemblies, greatly extending the range of DNA-based self-assembly methods.
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Affiliation(s)
- Daniel Schiffels
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899
- Maryland NanoCenter, University of Maryland, College Park, MD 20742
| | - Veronika Szalai
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - J. Alexander Liddle
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899
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Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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61
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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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Schöneweiß EC, Saccà B. The collective behavior of spring-like motifs tethered to a DNA origami nanostructure. NANOSCALE 2017; 9:4486-4496. [PMID: 28317958 DOI: 10.1039/c6nr08314e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Dynamic DNA nanotechnology relies on the integration of small switchable motifs at suitable positions of DNA nanostructures, thus enabling the manipulation of matter with nanometer spatial accuracy in a trigger-dependent fashion. Typical examples of such motifs are hairpins, whose elongation into duplexes can be used to perform long-range, translational movements. In this work, we used temperature-dependent FRET spectroscopy to determine the thermal stabilities of distinct sets of hairpins integrated into the central seam of a DNA origami structure. We then developed a hybrid spring model to describe the energy landscape of the tethered hairpins, combining the thermodynamic nearest-neighbor energy of duplex DNA with the entropic free energy of single-stranded DNA estimated using a worm-like chain approximation. We show that the organized scaffolding of multiple hairpins enhances the thermal stability of the device and that the coordinated action of the tethered motors can be used to mechanically unfold a G-quadruplex motif bound to the inner cavity of the origami structure, thus surpassing the operational capabilities of freely diffusing motors. Finally, we increased the complexity of device functionality through the insertion of two sets of parallel hairpins, resulting in four distinct states and in the reversible localization of desired molecules within the reconfigurable regions of the origami architecture.
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Affiliation(s)
- E-C Schöneweiß
- Centre for Medical Biotechnology (ZMB) and Centre for Nano Integration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätstr. 2, 45117 Essen, Germany.
| | - B Saccà
- Centre for Medical Biotechnology (ZMB) and Centre for Nano Integration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätstr. 2, 45117 Essen, Germany.
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63
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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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64
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Estrich NA, Hernandez-Garcia A, de Vries R, LaBean TH. Engineered Diblock Polypeptides Improve DNA and Gold Solubility during Molecular Assembly. ACS NANO 2017; 11:831-842. [PMID: 28048935 DOI: 10.1021/acsnano.6b07291] [Citation(s) in RCA: 22] [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
Programmed molecular recognition is being developed for the bionanofabrication of mixed organic/inorganic supramolecular assemblies for applications in electronics, photonics, and medicine. For example, DNA-based nanotechnology seeks to exploit the easily programmed complementary base-pairing of DNA to direct assembly of complex, designed nanostructures. Optimal solution conditions for bionanofabrication, mimicking those of biological systems, may involve high concentrations of biomacromolecules (proteins, nucleic acids, etc.) and significant concentrations of various ions (Mg2+, Na+, Cl-, etc.). Given a desire to assemble diverse inorganic components (metallic nanoparticles, quantum dots, carbon nanostructures, etc.), it will be increasingly difficult to find solution conditions simultaneously compatible with all components. Frequently, the use of chemical surfactants is undesirable, leaving a need for the development of alternative strategies. Herein, we discuss the use of artificial, diblock polypeptides in the role of solution compatibilizing agents for molecular assembly. We describe the use of two distinct diblock polypeptides with affinity for DNA in the stabilization of DNA origami and DNA-functionalized gold nanoparticles (spheres and rods) in solution, protection of DNA from enzymatic degradation, as well as two 3D tetrahedral DNA origamis. We present initial data showing that the diblock polypeptides promote the formation in the solution of desired organic/inorganic assemblies.
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Affiliation(s)
- Nicole A Estrich
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
| | - Armando Hernandez-Garcia
- Simpson Querrey Institute for Bionanotechnology, Northwestern University , Evanston, Illinois 60208, United States
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research Centre , Wageningen 6708 PB, The Netherlands
| | - Renko de Vries
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research Centre , Wageningen 6708 PB, The Netherlands
| | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University , Raleigh, North Carolina 27606, United States
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Bhatia D, Arumugam S, Nasilowski M, Joshi H, Wunder C, Chambon V, Prakash V, Grazon C, Nadal B, Maiti PK, Johannes L, Dubertret B, Krishnan Y. Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. NATURE NANOTECHNOLOGY 2016; 11:1112-1119. [PMID: 27548358 PMCID: PMC5122452 DOI: 10.1038/nnano.2016.150] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/15/2016] [Indexed: 05/07/2023]
Abstract
Functionalization of quantum dots (QDs) with a single biomolecular tag using traditional approaches in bulk solution has met with limited success. DNA polyhedra consist of an internal void bounded by a well-defined three-dimensional structured surface. The void can house cargo and the surface can be functionalized with stoichiometric and spatial precision. Here, we show that monofunctionalized QDs can be realized by encapsulating QDs inside DNA icosahedra and functionalizing the DNA shell with an endocytic ligand. We deployed the DNA-encapsulated QDs for real-time imaging of three different endocytic ligands-folic acid, galectin-3 (Gal3) and the Shiga toxin B-subunit (STxB). Single-particle tracking of Gal3- or STxB-functionalized QD-loaded DNA icosahedra allows us to monitor compartmental dynamics along endocytic pathways. These DNA-encapsulated QDs, which bear a unique stoichiometry of endocytic ligands, represent a new class of molecular probes for quantitative imaging of endocytic receptor dynamics.
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Affiliation(s)
- Dhiraj Bhatia
- Chemical Biology of Membranes and Therapeutic Delivery unit, Institut Curie, PSL Research University, Institut national de la santé et de la recherche médicale, U 1143, Centre national de la recherche scientifique, Unité mixte de recherche 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra, Bellary Road, Bangalore 560065, India
| | - Senthil Arumugam
- Chemical Biology of Membranes and Therapeutic Delivery unit, Institut Curie, PSL Research University, Institut national de la santé et de la recherche médicale, U 1143, Centre national de la recherche scientifique, Unité mixte de recherche 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Michel Nasilowski
- Laboratoire Physique et Etude des Matériaux UMR8213 École Supérieure de Physique et de Chimie Industrielles ParisTech-CNRS - Université Pierre et Marie Curie Sorbonne Universités 10 rue Vauquelin, 75005 Paris, France
| | - Himanshu Joshi
- Department of Physics, Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
| | - Christian Wunder
- Chemical Biology of Membranes and Therapeutic Delivery unit, Institut Curie, PSL Research University, Institut national de la santé et de la recherche médicale, U 1143, Centre national de la recherche scientifique, Unité mixte de recherche 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Valérie Chambon
- Chemical Biology of Membranes and Therapeutic Delivery unit, Institut Curie, PSL Research University, Institut national de la santé et de la recherche médicale, U 1143, Centre national de la recherche scientifique, Unité mixte de recherche 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Ved Prakash
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra, Bellary Road, Bangalore 560065, India
- Department of Chemistry, The University of Chicago, 929 E, 57th Street, Chicago, Illinois 60637, USA
| | | | - Brice Nadal
- Nexdot, 10 rue Vauquelin, 75005 Paris, France
| | - Prabal K Maiti
- Department of Physics, Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
| | - Ludger Johannes
- Chemical Biology of Membranes and Therapeutic Delivery unit, Institut Curie, PSL Research University, Institut national de la santé et de la recherche médicale, U 1143, Centre national de la recherche scientifique, Unité mixte de recherche 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Benoit Dubertret
- Laboratoire Physique et Etude des Matériaux UMR8213 École Supérieure de Physique et de Chimie Industrielles ParisTech-CNRS - Université Pierre et Marie Curie Sorbonne Universités 10 rue Vauquelin, 75005 Paris, France
| | - Yamuna Krishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra, Bellary Road, Bangalore 560065, India
- Department of Chemistry, The University of Chicago, 929 E, 57th Street, Chicago, Illinois 60637, USA
- Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, 5812 South Ellis Avenue, Chicago, Illinois 60637, USA
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66
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Gao Y, Mi Y, Lakerveld R. An optimization‐based approach for structural design of self‐assembled DNA tiles. AIChE J 2016. [DOI: 10.1002/aic.15546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yu Gao
- Dept. of Chemical and Biomolecular EngineeringThe Hong Kong University of Science and TechnologyClear Water Bay Hong Kong S.A.R
| | - Yongli Mi
- Dept. of Chemical and Biomolecular EngineeringThe Hong Kong University of Science and TechnologyClear Water Bay Hong Kong S.A.R
| | - Richard Lakerveld
- Dept. of Chemical and Biomolecular EngineeringThe Hong Kong University of Science and TechnologyClear Water Bay Hong Kong S.A.R
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67
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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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68
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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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69
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Benson E, Mohammed A, Bosco A, Teixeira AI, Orponen P, Högberg B. Computer-Aided Production of Scaffolded DNA Nanostructures from Flat Sheet Meshes. Angew Chem Int Ed Engl 2016; 55:8869-72. [PMID: 27304204 PMCID: PMC6680348 DOI: 10.1002/anie.201602446] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Indexed: 01/19/2023]
Abstract
The use of DNA as a nanoscale construction material has been a rapidly developing field since the 1980s, in particular since the introduction of scaffolded DNA origami in 2006. Although software is available for DNA origami design, the user is generally limited to architectures where finding the scaffold path through the object is trivial. Herein, we demonstrate the automated conversion of arbitrary two-dimensional sheets in the form of digital meshes into scaffolded DNA nanostructures. We investigate the properties of DNA meshes based on three different internal frameworks in standard folding buffer and physiological salt buffers. We then employ the triangulated internal framework and produce four 2D structures with complex outlines and internal features. We demonstrate that this highly automated technique is capable of producing complex DNA nanostructures that fold with high yield to their programmed configurations, covering around 70 % more surface area than classic origami flat sheets.
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Affiliation(s)
- Erik Benson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | | | - Alessandro Bosco
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Ana I Teixeira
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Pekka Orponen
- Department of Computer Science, Aalto University, 00076, Aalto, Finland
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden.
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70
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Linko V, Ora A, Kostiainen MA. DNA Nanostructures as Smart Drug-Delivery Vehicles and Molecular Devices. Trends Biotechnol 2016; 33:586-594. [PMID: 26409777 DOI: 10.1016/j.tibtech.2015.08.001] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 11/28/2022]
Abstract
DNA molecules can be assembled into custom predesigned shapes via hybridization of sequence-complementary domains. The folded structures have high spatial addressability and a tremendous potential to serve as platforms and active components in a plethora of bionanotechnological applications. DNA is a truly programmable material, and its nanoscale engineering thus opens up numerous attractive possibilities to develop novel methods for therapeutics. The tailored molecular devices could be used in targeting cells and triggering the cellular actions in the biological environment. In this review we focus on the DNA-based assemblies - primarily DNA origami nanostructures - that could perform complex tasks in cells and serve as smart drug-delivery vehicles in, for example, cancer therapy, prodrug medication, and enzyme replacement therapy.
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Affiliation(s)
- Veikko Linko
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, PO Box 16100, 00076 Aalto, Finland
| | - Ari Ora
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, PO Box 16100, 00076 Aalto, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, PO Box 16100, 00076 Aalto, Finland.
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71
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Huang Y, Huang W, Chan L, Zhou B, Chen T. A multifunctional DNA origami as carrier of metal complexes to achieve enhanced tumoral delivery and nullified systemic toxicity. Biomaterials 2016; 103:183-196. [PMID: 27388944 DOI: 10.1016/j.biomaterials.2016.06.053] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/17/2016] [Accepted: 06/21/2016] [Indexed: 12/20/2022]
Abstract
The use of metal complexes in cancer treatment is hampered by the insufficient accumulation in tumor regions and observable systemic toxicity due to their nonspecificity in vivo. Herein we present a cancer-targeted DNA origami as biocompatible nanocarrier of metal complexes to achieve advanced antitumor effect. The formation of unique tetrahedral nanostructure of DNA cages effectively enhances the interaction between ruthenium polypyridyl complexes (RuPOP) and the cages, thus increasing the drug loading efficacy. Conjugation of biotin to the DNA-based nanosystem (Bio-cage@Ru) enhances its specific cellular uptake, drug retention and cytotoxicity against HepG2 cells. Different from free RuPOP and the cage itself, Bio-cage@Ru translocates to cell nucleus after internalization, where it undergoes self-immolative cleavage in response to DNases, leading to triggered drug release and induction of ROS-mediated cell apoptosis. Moreover, in the nude mice model, the nanosystem specifically accumulates in tumor sites, thus exhibits satisfactory in vivo antitumor efficacy, and alleviates the damage of liver, kidney, lung and heart function of nude mice induced by RuPOP and tumor xenografts. Collectively, this study demonstrates a strategy for construction of biocompatible and cancer-targeted DNA origami with enhanced anticancer efficacy and reduced toxicity for next-generation cancer therapy.
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Affiliation(s)
- Yanyu Huang
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Wei Huang
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Leung Chan
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Binwei Zhou
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Tianfeng Chen
- Department of Chemistry, Jinan University, Guangzhou 510632, China.
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72
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Benson E, Mohammed A, Bosco A, Teixeira AI, Orponen P, Högberg B. Computer-Aided Production of Scaffolded DNA Nanostructures from Flat Sheet Meshes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Erik Benson
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; 17177 Stockholm Sweden
| | | | - Alessandro Bosco
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; 17177 Stockholm Sweden
| | - Ana I. Teixeira
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; 17177 Stockholm Sweden
| | - Pekka Orponen
- Department of Computer Science; Aalto University; 00076 Aalto Finland
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics; Karolinska Institutet; 17177 Stockholm Sweden
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73
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Wang P, Gaitanaros S, Lee S, Bathe M, Shih WM, Ke Y. Programming Self-Assembly of DNA Origami Honeycomb Two-Dimensional Lattices and Plasmonic Metamaterials. J Am Chem Soc 2016; 138:7733-40. [DOI: 10.1021/jacs.6b03966] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pengfei Wang
- Wallance
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Stavros Gaitanaros
- Department
of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Seungwoo Lee
- SKKU
Advanced Institute of Nanotechnology & School of Chemical Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Mark Bathe
- Department
of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - William M. Shih
- Wyss
Institute for Biologically Inspired Engineering and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical
School, Harvard University, Boston, Massachusetts 02115, United States
| | - Yonggang Ke
- Wallance
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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74
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Veneziano R, Ratanalert S, Zhang K, Zhang F, Yan H, Chiu W, Bathe M. Designer nanoscale DNA assemblies programmed from the top down. Science 2016; 352:1534. [PMID: 27229143 DOI: 10.1126/science.aaf4388] [Citation(s) in RCA: 409] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/03/2016] [Indexed: 12/16/2022]
Abstract
Scaffolded DNA origami is a versatile means of synthesizing complex molecular architectures. However, the approach is limited by the need to forward-design specific Watson-Crick base pairing manually for any given target structure. Here, we report a general, top-down strategy to design nearly arbitrary DNA architectures autonomously based only on target shape. Objects are represented as closed surfaces rendered as polyhedral networks of parallel DNA duplexes, which enables complete DNA scaffold routing with a spanning tree algorithm. The asymmetric polymerase chain reaction is applied to produce stable, monodisperse assemblies with custom scaffold length and sequence that are verified structurally in three dimensions to be high fidelity by single-particle cryo-electron microscopy. Their long-term stability in serum and low-salt buffer confirms their utility for biological as well as nonbiological applications.
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Affiliation(s)
- Rémi Veneziano
- 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
| | - Kaiming Zhang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fei Zhang
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ 85287, USA
| | - Hao Yan
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ 85287, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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75
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Kohman RE, Cha SS, Man HY, Han X. Light-Triggered Release of Bioactive Molecules from DNA Nanostructures. NANO LETTERS 2016; 16:2781-5. [PMID: 26935839 PMCID: PMC4959465 DOI: 10.1021/acs.nanolett.6b00530] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recent innovations in DNA nanofabrication allow the creation of intricately shaped nanostructures ideally suited for many biological applications. To advance the use of DNA nanotechnology for the controlled release of bioactive molecules, we report a general strategy that uses light to liberate encapsulated cargoes from DNA nanostructures with high spatiotemporal precision. Through the incorporation of a custom, photolabile cross-linker, we encapsulated cargoes ranging in size from small molecules to full-sized proteins within DNA nanocages and then released such cargoes upon brief exposure to light. This novel molecular uncaging technique offers a general approach for precisely releasing a large variety of bioactive molecules, allowing investigation into their mechanism of action, or finely tuned delivery with high temporal precision for broad biomedical and materials applications.
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Affiliation(s)
- Richie E Kohman
- Biomedical Engineering Department, Boston University , Boston, Massachusetts 02215, United States
| | - Susie S Cha
- Biomedical Engineering Department, Boston University , Boston, Massachusetts 02215, United States
| | - Heng-Ye Man
- Biology Department, Boston University , Boston, Massachusetts 02215, United States
| | - Xue Han
- Biomedical Engineering Department, Boston University , Boston, Massachusetts 02215, United States
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76
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Kumar V, Palazzolo S, Bayda S, Corona G, Toffoli G, Rizzolio F. DNA Nanotechnology for Cancer Therapy. Am J Cancer Res 2016; 6:710-25. [PMID: 27022418 PMCID: PMC4805665 DOI: 10.7150/thno.14203] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/27/2016] [Indexed: 02/07/2023] Open
Abstract
DNA nanotechnology is an emerging and exciting field, and represents a forefront frontier for the biomedical field. The specificity of the interactions between complementary base pairs makes DNA an incredible building material for programmable and very versatile two- and three-dimensional nanostructures called DNA origami. Here, we analyze the DNA origami and DNA-based nanostructures as a drug delivery system. Besides their physical-chemical nature, we dissect the critical factors such as stability, loading capability, release and immunocompatibility, which mainly limit in vivo applications. Special attention was dedicated to highlighting the boundaries to be overcome to bring DNA nanostructures closer to the bedside of patients.
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77
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Snodin BEK, Romano F, Rovigatti L, Ouldridge TE, Louis AA, Doye JPK. Direct Simulation of the Self-Assembly of a Small DNA Origami. ACS NANO 2016; 10:1724-37. [PMID: 26766072 DOI: 10.1021/acsnano.5b05865] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in solution. In general, we see attachment of new staple strands occurring in parallel, but with cooperativity evident for the binding of the second domain of a staple if the adjacent junction is already partially formed. For a system with exactly one copy of each staple strand, we observe a complete assembly pathway in an intermediate temperature window; at low temperatures successful assembly is prevented by misbonding while at higher temperature the free-energy barriers to assembly become too large for assembly on our simulation time scales. For high-concentration systems involving a large staple strand excess, we never see complete assembly because there are invariably instances where two copies of the same staple both bind to the scaffold, creating a kinetic trap that prevents the complete binding of either staple. This mutual staple blocking could also lead to aggregates of partially formed origamis in real systems, and helps to rationalize certain successful origami design strategies.
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Affiliation(s)
- Benedict E K Snodin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Lorenzo Rovigatti
- Faculty of Physics, University of Vienna , Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Thomas E Ouldridge
- Department of Mathematics, Imperial College , 180 Queen's Gate, London SW7 2AZ, United Kingdom
| | - 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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78
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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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79
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Sedeh RS, Pan K, Adendorff MR, Hallatschek O, Bathe KJ, Bathe M. Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies. J Chem Theory Comput 2015; 12:261-73. [PMID: 26636351 DOI: 10.1021/acs.jctc.5b00965] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic nucleic acids can be programmed to form precise three-dimensional structures on the nanometer-scale. These thermodynamically stable complexes can serve as structural scaffolds to spatially organize functional molecules including multiple enzymes, chromophores, and force-sensing elements with internal dynamics that include substrate reaction-diffusion, excitonic energy transfer, and force-displacement response that often depend critically on both the local and global conformational dynamics of the nucleic acid assembly. However, high molecular weight assemblies exhibit long time-scale and large length-scale motions that cannot easily be sampled using all-atom computational procedures such as molecular dynamics. As an alternative, here we present a computational framework to compute the overdamped conformational dynamics of structured nucleic acid assemblies and apply it to a DNA-based tweezer, a nine-layer DNA origami ring, and a pointer-shaped DNA origami object, which consist of 204, 3,600, and over 7,000 basepairs, respectively. The framework employs a mechanical finite element model for the DNA nanostructure combined with an implicit solvent model to either simulate the Brownian dynamics of the assembly or alternatively compute its Brownian modes. Computational results are compared with an all-atom molecular dynamics simulation of the DNA-based tweezer. Several hundred microseconds of Brownian dynamics are simulated for the nine-layer ring origami object to reveal its long time-scale conformational dynamics, and the first ten Brownian modes of the pointer-shaped structure are predicted.
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Affiliation(s)
| | | | | | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley , Berkeley, California 94720, United States
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80
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Jabbari H, Aminpour M, Montemagno C. Computational Approaches to Nucleic Acid Origami. ACS COMBINATORIAL SCIENCE 2015; 17:535-47. [PMID: 26348196 DOI: 10.1021/acscombsci.5b00079] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recent advances in experimental DNA origami have dramatically expanded the horizon of DNA nanotechnology. Complex 3D suprastructures have been designed and developed using DNA origami with applications in biomaterial science, nanomedicine, nanorobotics, and molecular computation. Ribonucleic acid (RNA) origami has recently been realized as a new approach. Similar to DNA, RNA molecules can be designed to form complex 3D structures through complementary base pairings. RNA origami structures are, however, more compact and more thermodynamically stable due to RNA's non-canonical base pairing and tertiary interactions. With all these advantages, the development of RNA origami lags behind DNA origami by a large gap. Furthermore, although computational methods have proven to be effective in designing DNA and RNA origami structures and in their evaluation, advances in computational nucleic acid origami is even more limited. In this paper, we review major milestones in experimental and computational DNA and RNA origami and present current challenges in these fields. We believe collaboration between experimental nanotechnologists and computer scientists are critical for advancing these new research paradigms.
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Affiliation(s)
- Hosna Jabbari
- Ingenuity Lab, 11421 Saskatchewan
Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemical and Materials Engineering, University of Alberta, Edmonton T6G 2V4, Canada
| | - Maral Aminpour
- Ingenuity Lab, 11421 Saskatchewan
Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemical and Materials Engineering, University of Alberta, Edmonton T6G 2V4, Canada
| | - Carlo Montemagno
- Ingenuity Lab, 11421 Saskatchewan
Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemical and Materials Engineering, University of Alberta, Edmonton T6G 2V4, Canada
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81
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Zakeri B, Lu TK. DNA nanotechnology: new adventures for an old warhorse. Curr Opin Chem Biol 2015; 28:9-14. [PMID: 26056949 PMCID: PMC4818966 DOI: 10.1016/j.cbpa.2015.05.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/11/2015] [Accepted: 05/14/2015] [Indexed: 10/23/2022]
Abstract
As the blueprint of life, the natural exploits of DNA are admirable. However, DNA should not only be viewed within a biological context. It is an elegantly simple yet functionally complex chemical polymer with properties that make it an ideal platform for engineering new nanotechnologies. Rapidly advancing synthesis and sequencing technologies are enabling novel unnatural applications for DNA beyond the realm of genetics. Here we explore the chemical biology of DNA nanotechnology for emerging applications in communication and digital data storage. Early studies of DNA as an alternative to magnetic and optical storage mediums have not only been promising, but have demonstrated the potential of DNA to revolutionize the way we interact with digital data in the future.
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Affiliation(s)
- Bijan Zakeri
- Department of Electrical Engineering and Computer Science, Department of Biological Engineering, Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA.
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science, Department of Biological Engineering, Research Laboratory of Electronics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA.
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82
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Surana S, Shenoy AR, Krishnan Y. Designing DNA nanodevices for compatibility with the immune system of higher organisms. NATURE NANOTECHNOLOGY 2015; 10:741-7. [PMID: 26329110 PMCID: PMC4862568 DOI: 10.1038/nnano.2015.180] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 07/17/2015] [Indexed: 05/05/2023]
Abstract
DNA is proving to be a powerful scaffold to construct molecularly precise designer DNA devices. Recent trends reveal their ever-increasing deployment within living systems as delivery devices that not only probe but also program and re-program a cell, or even whole organisms. Given that DNA is highly immunogenic, we outline the molecular, cellular and organismal response pathways that designer nucleic acid nanodevices are likely to elicit in living systems. We address safety issues applicable when such designer DNA nanodevices interact with the immune system. In light of this, we discuss possible molecular programming strategies that could be integrated with such designer nucleic acid scaffolds to either evade or stimulate the host response with a view to optimizing and widening their applications in higher organisms.
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Affiliation(s)
- Sunaina Surana
- Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, 60637 Illinois, USA
| | - Avinash R. Shenoy
- Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK
- ;
| | - Yamuna Krishnan
- Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, 60637 Illinois, USA
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK-UAS, Bellary Road, Bangalore 560065, India
- ;
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83
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Shen B, Linko V, Tapio K, Kostiainen MA, Toppari JJ. Custom-shaped metal nanostructures based on DNA origami silhouettes. NANOSCALE 2015; 7:11267-72. [PMID: 26066528 DOI: 10.1039/c5nr02300a] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The DNA origami technique provides an intriguing possibility to develop customized nanostructures for various bionanotechnological purposes. One target is to create tailored bottom-up-based plasmonic devices and metamaterials based on DNA metallization or controlled attachment of nanoparticles to the DNA designs. In this article, we demonstrate an alternative approach: DNA origami nanoshapes can be utilized in creating accurate, uniform and entirely metallic (e.g. gold, silver and copper) nanostructures on silicon substrates. The technique is based on developing silhouettes of the origamis in the grown silicon dioxide layer, and subsequently using this layer as a mask for further patterning. The proposed method has a high spatial resolution, and the fabrication yields can approach 90%. The approach allows a cost-effective, parallel, large-scale patterning on a chip with fully tailored metallic nanostructures; the DNA origami shape and the applied metal can be specifically chosen for each conceivable implementation.
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Affiliation(s)
- Boxuan Shen
- University of Jyvaskyla, Department of Physics, Nanoscience Center, P.O. Box 35, FI-40014. and University of Jyväskylä, Finland.
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84
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Affiliation(s)
- Yuhe R. Yang
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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85
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Iacovelli F, Falconi M. Decoding the conformation-linked functional properties of nucleic acids by the use of computational tools. FEBS J 2015; 282:3298-310. [DOI: 10.1111/febs.13315] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/16/2015] [Accepted: 04/29/2015] [Indexed: 12/25/2022]
Affiliation(s)
| | - Mattia Falconi
- Department of Biology; University of Rome “Tor Vergata”; Italy
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86
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Castro CE, Su HJ, Marras AE, Zhou L, Johnson J. Mechanical design of DNA nanostructures. NANOSCALE 2015; 7:5913-21. [PMID: 25655237 DOI: 10.1039/c4nr07153k] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems.
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Affiliation(s)
- Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.
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