401
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Yang Y, Tashiro R, Suzuki Y, Emura T, Hidaka K, Sugiyama H, Endo M. A Photoregulated DNA-Based Rotary System and Direct Observation of Its Rotational Movement. Chemistry 2017; 23:3979-3985. [PMID: 28199775 DOI: 10.1002/chem.201605616] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Indexed: 12/15/2022]
Abstract
Various DNA-based nanodevices have been developed on the nanometer scale using light as regulation input. However, the programmed controllability is still a major challenge for these artificial nanodevices. Herein, we demonstrate a rotary DNA nanostructure in which the rotations are controlled by light. A bar-shaped DNA rotor, fabricated as a stiff double-crossover molecule, was placed on the top of a rectangular DNA tile. The photoresponsive oligonucleotides modified with azobenzenes were employed as switching motifs to release/trap the rotor at specific angular position on DNA tile by switching photoirradiations between ultraviolet and visible light. As a result, two reconfigurable states (perpendicular and parallel) of rotor were obtained, in which the angular changes were characterized by AFM and fluorescence quenching assays. Moreover, the reversible rotary motions during the photoirradiation were directly visualized on the DNA tile surface in a nanometer-scale precision using a second-scale scanning of the high-speed AFM.
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Affiliation(s)
- Yangyang Yang
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Present address: Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ryu Tashiro
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minanitamagakicho, Suzuka-shi, Mie, 513-8670, Japan
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Present address: Frontier Research Institute, for Interdisciplinary Sciences, Tohoku University, Aramaki aza Aoba 6-3, Aoba-ku, Sendai, 980-8578, Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
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402
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Exploiting molecular motors as nanomachines: the mechanisms of de novo and re-engineered cytoskeletal motors. Curr Opin Biotechnol 2017; 46:20-26. [PMID: 28088100 DOI: 10.1016/j.copbio.2016.10.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 10/28/2016] [Indexed: 11/30/2022]
Abstract
Cytoskeletal molecular motors provide exciting proof that nanoscale transporters can be highly efficient, moving for microns along filamentous tracks by hydrolyzing ATP to fuel nanometer-size steps. For nanotechnology, such conversion of chemical energy into productive work serves as an enticing platform for re-purposing and re-engineering. It also provides a roadmap for successful molecular mechanisms that can be mimicked to create de novo molecular motors for nanotechnology applications. Here we focus specifically on how the mechanisms of molecular motors are being re-engineered for greater control over their transport parameters. We then discuss mechanistic work to create fully synthetic motors de novo and conclude with future directions in creating novel motor systems.
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403
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Tigges T, Heuser T, Tiwari R, Walther A. 3D DNA Origami Cuboids as Monodisperse Patchy Nanoparticles for Switchable Hierarchical Self-Assembly. NANO LETTERS 2016; 16:7870-7874. [PMID: 27802042 DOI: 10.1021/acs.nanolett.6b04146] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The rational design of anisotropic interaction patterns is a key step for programming colloid and nanoparticle self-assembly and emergent functions. Herein, we demonstrate a concept for harnessing the capabilities of 3D DNA origami for extensive supracolloidal self-assembly and showcase its use for making truly monodisperse, patchy, divalent nanocuboids that can self-assemble into supracolloidal fibrils via programmable DNA hybridization. A change in the number of connector duplexes at the patches reveals that multivalency and cooperativity play crucial roles to enhance superstructure formation. We further show thermal and chemical switching of the superstructures as the first steps toward reconfigurable self-assemblies. This concept lays the groundwork for merging monodisperse 3D DNA origami, featuring programmable patchiness and interactions, with nanoparticle self-assembly.
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Affiliation(s)
- Thomas Tigges
- DWI-Leibniz-Institute for Interactive Materials , Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Thomas Heuser
- DWI-Leibniz-Institute for Interactive Materials , Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Rahul Tiwari
- DWI-Leibniz-Institute for Interactive Materials , Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Andreas Walther
- Institute of Macromolecular Chemistry, Albert-Ludwigs-University of Freiburg , Stefan-Meier-Str. 31, 79104 Freiburg, Germany
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404
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Wang M, Huang H, Zhang Z, Xiao SJ. 2D DNA lattices constructed from two-tile DAE-O systems possessing circular central strands. NANOSCALE 2016; 8:18870-18875. [PMID: 27812582 DOI: 10.1039/c6nr06745j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We reported a classical two-tile system of DAE-O (doublecrossover, antiparallel, and even half-turns tiles with odd half-turns connection) to construct regular single crystalline 2D (two dimensional) DNA lattices, using pre-circularised oligonucleotides of 42-, 64-, and 84-nt (nucleotides) as the central looped strands in DAE tiles respectively. DAE tiles with 42- and 64-nt as central strands, either in circular form or in linear form, grew regular single crystalline lattices well. However DAE tiles including a circular 84-nt as the central strand grew single crystalline lattices, those including a linear 84-nt as the central strand grew polycrystalline 2D lattices. A subtle difference in the lateral rigidity of DAE tiles with regard to the duplex axis was suggested to be the cause of the morphological difference.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China.
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405
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Oligonucleotide-based recognition in colloidal systems - opportunities and challenges. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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406
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Martin TG, Bharat TAM, Joerger AC, Bai XC, Praetorius F, Fersht AR, Dietz H, Scheres SHW. Design of a molecular support for cryo-EM structure determination. Proc Natl Acad Sci U S A 2016; 113:E7456-E7463. [PMID: 27821763 PMCID: PMC5127339 DOI: 10.1073/pnas.1612720113] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there still exist ample opportunities for improvement in sample preparation. Macromolecular complexes may disassociate or adopt nonrandom orientations against the extended air-water interface that exists for a short time before the sample is frozen. We designed a hollow support structure using 3D DNA origami to protect complexes from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle, we concentrated on the transcription factor p53, which binds to specific DNA sequences on double-stranded DNA. The support structures spontaneously form monolayers of preoriented particles in a thin film of water, and offer advantages in particle picking and sorting. By controlling the position of the binding sequence on a single helix that spans the hollow support structure, we also sought to control the orientation of individual p53 complexes. Although the latter did not yet yield the desired results, the support structures did provide partial information about the relative orientations of individual p53 complexes. We used this information to calculate a tomographic 3D reconstruction, and refined this structure to a final resolution of ∼15 Å. This structure settles an ongoing debate about the symmetry of the p53 tetramer bound to DNA.
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Affiliation(s)
- Thomas G Martin
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Tanmay A M Bharat
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Andreas C Joerger
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
- German Cancer Consortium (DKTK), Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany
| | - Xiao-Chen Bai
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Florian Praetorius
- Physik Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany
| | - Alan R Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Hendrik Dietz
- Physik Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany
| | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom;
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407
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Kim J, Jones MR, Ou Z, Chen Q. In Situ Electron Microscopy Imaging and Quantitative Structural Modulation of Nanoparticle Superlattices. ACS NANO 2016; 10:9801-9808. [PMID: 27723304 DOI: 10.1021/acsnano.6b05270] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We use liquid-phase transmission electron microscopy (LP-TEM) to characterize the structure and dynamics of a solution-phase superlattice assembled from gold nanoprisms at the single particle level. The lamellar structure of the superlattice, determined by a balance of interprism interactions, is maintained and resolved under low-dose imaging conditions typically reserved for biomolecular imaging. In this dose range, we capture dynamic structural changes in the superlattice in real time, where contraction and smaller steady-state lattice constants are observed at higher electron dose rates. Quantitative analysis of the contraction mechanism based on a combination of direct LP-TEM imaging, ensemble small-angle X-ray scattering, and theoretical modeling allows us to elucidate: (1) the superlattice contraction in LP-TEM results from the screening of electrostatic repulsion due to as much as a 6-fold increase in the effective ionic strength in the solution upon electron beam illumination; and (2) the lattice constant serves as a means to understand the mechanism of the in situ interaction modulation and precisely calibrate electron dose rates with the effective ionic strength of the system. These results demonstrate that low-dose LP-TEM is a powerful tool for obtaining structural and kinetic properties of nanoassemblies in liquid conditions that closely resemble real experiments. We anticipate that this technique will be especially advantageous for those structures with heterogeneity or disorder that cannot be easily probed by ensemble methods and will provide important insight that will aid in the rational design of sophisticated reconfigurable nanomaterials.
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Affiliation(s)
| | - Matthew R Jones
- Department of Chemistry, University of California , Berkeley, California 94720, United States
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408
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Stahl E, Praetorius F, de Oliveira Mann CC, Hopfner KP, Dietz H. Impact of Heterogeneity and Lattice Bond Strength on DNA Triangle Crystal Growth. ACS NANO 2016; 10:9156-9164. [PMID: 27583560 DOI: 10.1021/acsnano.6b04787] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One key goal of DNA nanotechnology is the bottom-up construction of macroscopic crystalline materials. Beyond applications in fields such as photonics or plasmonics, DNA-based crystal matrices could possibly facilitate the diffraction-based structural analysis of guest molecules. Seeman and co-workers reported in 2009 the first designed crystal matrices based on a 38 kDa DNA triangle that was composed of seven chains. The crystal lattice was stabilized, unprecedentedly, by Watson-Crick base pairing. However, 3D crystallization of larger designed DNA objects that include more chains such as DNA origami remains an unsolved problem. Larger objects would offer more degrees of freedom and design options with respect to tailoring lattice geometry and for positioning other objects within a crystal lattice. The greater rigidity of multilayer DNA origami could also positively influence the diffractive properties of crystals composed of such particles. Here, we rationally explore the role of heterogeneity and Watson-Crick interaction strengths in crystal growth using 40 variants of the original DNA triangle as model multichain objects. Crystal growth of the triangle was remarkably robust despite massive chemical, geometrical, and thermodynamical sample heterogeneity that we introduced, but the crystal growth sensitively depended on the sequences of base pairs next to the Watson-Crick sticky ends of the triangle. Our results point to weak lattice interactions and high concentrations as decisive factors for achieving productive crystallization, while sample heterogeneity and impurities played a minor role.
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Affiliation(s)
- Evi Stahl
- Physik Department and Institute for Advanced Study, Technische Universität München , Am Coulombwall 4a, 85748 Garching near Munich, Germany
| | - Florian Praetorius
- Physik Department and Institute for Advanced Study, Technische Universität München , Am Coulombwall 4a, 85748 Garching near Munich, Germany
| | - Carina C de Oliveira Mann
- Department of Biochemistry and Gene Center, Ludwig-Maximilians-Universität , Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Karl-Peter Hopfner
- Department of Biochemistry and Gene Center, Ludwig-Maximilians-Universität , Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Hendrik Dietz
- Physik Department and Institute for Advanced Study, Technische Universität München , Am Coulombwall 4a, 85748 Garching near Munich, Germany
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409
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Amodio A, Adedeji AF, Castronovo M, Franco E, Ricci F. pH-Controlled Assembly of DNA Tiles. J Am Chem Soc 2016; 138:12735-12738. [PMID: 27631465 PMCID: PMC5054458 DOI: 10.1021/jacs.6b07676] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We demonstrate a strategy to trigger and finely control the assembly of supramolecular DNA nanostructures with pH. Control is achieved via a rationally designed strand displacement circuit that responds to pH and activates a downstream DNA tile self-assembly process. We observe that the DNA structures form under neutral/basic conditions, while the self-assembly process is suppressed under acidic conditions. The strategy presented here demonstrates a modular approach toward building systems capable of processing biochemical inputs and finely controlling the assembly of DNA-based nanostructures under isothermal conditions. In particular, the presented architecture is relevant for the development of complex DNA devices able to sense and respond to molecular markers associated with abnormal metabolism.
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Affiliation(s)
- Alessia Amodio
- Department of Chemistry, University of Rome , Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Abimbola Feyisara Adedeji
- PhD School of Nanotechnology, Department of Physics, University of Trieste , Via Valerio 2, 34127 Trieste, Italy.,Department of Medical and Biological Sciences, University of Udine , Piazzale Kolbe 4, 33100 Udine, Italy
| | - Matteo Castronovo
- PhD School of Nanotechnology, Department of Physics, University of Trieste , Via Valerio 2, 34127 Trieste, Italy.,Department of Medical and Biological Sciences, University of Udine , Piazzale Kolbe 4, 33100 Udine, Italy.,School of Food Science and Nutrition, University of Leeds , Leeds LS2 9JT, U.K
| | - Elisa Franco
- Department of Mechanical Engineering, University of California , Riverside, California 92521, United States
| | - Francesco Ricci
- Department of Chemistry, University of Rome , Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
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410
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Powell JT, Akhuetie-Oni BO, Zhang Z, Lin C. DNA Origami Rotaxanes: Tailored Synthesis and Controlled Structure Switching. Angew Chem Int Ed Engl 2016; 55:11412-6. [PMID: 27527591 PMCID: PMC5019031 DOI: 10.1002/anie.201604621] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/08/2016] [Indexed: 11/09/2022]
Abstract
Mechanically interlocked supramolecular assemblies are appealing building blocks for creating functional nanodevices. Herein, we describe the multistep assembly of large DNA origami rotaxanes that are capable of programmable structural switching. We validated the topology and structural integrity of these rotaxanes by analyzing the intermediate and final products of various assembly routes by electrophoresis and electron microscopy. We further analyzed two structure-switching behaviors of our rotaxanes, which are both mediated by DNA hybridization. In the first mechanism, the translational motion of the macrocycle can be triggered or halted at either terminus. In the second mechanism, the macrocycle can be elongated after completion of the rotaxane assembly, giving rise to a unique structure that is otherwise difficult to access.
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Affiliation(s)
- John T Powell
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA
| | - Benjamin O Akhuetie-Oni
- Department of Molecular, Cellular, and Developmental Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA.
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411
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Kye M, Lim YB. Reciprocal Self-Assembly of Peptide-DNA Conjugates into a Programmable Sub-10-nm Supramolecular Deoxyribonucleoprotein. Angew Chem Int Ed Engl 2016; 55:12003-7. [DOI: 10.1002/anie.201605696] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/22/2016] [Indexed: 02/03/2023]
Affiliation(s)
- Mahnseok Kye
- Department of Materials Science and Engineering; Yonsei University; 50 Yonsei-ro Seoul 03722 Korea
| | - Yong-beom Lim
- Department of Materials Science and Engineering; Yonsei University; 50 Yonsei-ro Seoul 03722 Korea
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412
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Kye M, Lim YB. Reciprocal Self-Assembly of Peptide-DNA Conjugates into a Programmable Sub-10-nm Supramolecular Deoxyribonucleoprotein. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mahnseok Kye
- Department of Materials Science and Engineering; Yonsei University; 50 Yonsei-ro Seoul 03722 Korea
| | - Yong-beom Lim
- Department of Materials Science and Engineering; Yonsei University; 50 Yonsei-ro Seoul 03722 Korea
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413
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Powell JT, Akhuetie-Oni BO, Zhang Z, Lin C. DNA Origami Rotaxanes: Tailored Synthesis and Controlled Structure Switching. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- John T. Powell
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Benjamin O. Akhuetie-Oni
- Department of Molecular, Cellular, and Developmental Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
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414
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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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415
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Linko V, Nummelin S, Aarnos L, Tapio K, Toppari JJ, Kostiainen MA. DNA-Based Enzyme Reactors and Systems. NANOMATERIALS 2016; 6:nano6080139. [PMID: 28335267 PMCID: PMC5224616 DOI: 10.3390/nano6080139] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/11/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
During recent years, the possibility to create custom biocompatible nanoshapes using DNA as a building material has rapidly emerged. Further, these rationally designed DNA structures could be exploited in positioning pivotal molecules, such as enzymes, with nanometer-level precision. This feature could be used in the fabrication of artificial biochemical machinery that is able to mimic the complex reactions found in living cells. Currently, DNA-enzyme hybrids can be used to control (multi-enzyme) cascade reactions and to regulate the enzyme functions and the reaction pathways. Moreover, sophisticated DNA structures can be utilized in encapsulating active enzymes and delivering the molecular cargo into cells. In this review, we focus on the latest enzyme systems based on novel DNA nanostructures: enzyme reactors, regulatory devices and carriers that can find uses in various biotechnological and nanomedical applications.
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Affiliation(s)
- Veikko Linko
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, Aalto 00076, Finland.
| | - Sami Nummelin
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, Aalto 00076, Finland.
| | - Laura Aarnos
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, Aalto 00076, Finland.
| | - Kosti Tapio
- Department of Physics, University of Jyvaskyla, Nanoscience Center, P.O. Box 35, Jyväskylä 40014, Finland.
| | - J Jussi Toppari
- Department of Physics, University of Jyvaskyla, Nanoscience Center, P.O. Box 35, Jyväskylä 40014, Finland.
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P.O. Box 16100, Aalto 00076, Finland.
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416
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Le JV, Luo Y, Darcy MA, Lucas CR, Goodwin MF, Poirier MG, Castro CE. Probing Nucleosome Stability with a DNA Origami Nanocaliper. ACS NANO 2016; 10:7073-84. [PMID: 27362329 PMCID: PMC5460529 DOI: 10.1021/acsnano.6b03218] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The organization of eukaryotic DNA into nucleosomes and chromatin undergoes dynamic structural changes to regulate genome processing, including transcription and DNA repair. Critical chromatin rearrangements occur over a wide range of distances, including the mesoscopic length scale of tens of nanometers. However, there is a lack of methodologies that probe changes over this mesoscopic length scale within chromatin. We have designed, constructed, and implemented a DNA-based nanocaliper that probes this mesoscopic length scale. We developed an approach of integrating nucleosomes into our nanocaliper at two attachment points with over 50% efficiency. Here, we focused on attaching the two DNA ends of the nucleosome to the ends of the two nanocaliper arms, so the hinge angle is a readout of the nucleosome end-to-end distance. We demonstrate that nucleosomes integrated with 6, 26, and 51 bp linker DNA are partially unwrapped by the nanocaliper by an amount consistent with previously observed structural transitions. In contrast, the nucleosomes integrated with the longer 75 bp linker DNA remain fully wrapped. We found that the nanocaliper angle is a sensitive measure of nucleosome disassembly and can read out transcription factor (TF) binding to its target site within the nucleosome. Interestingly, the nanocaliper not only detects TF binding but also significantly increases the probability of TF occupancy at its site by partially unwrapping the nucleosome. These studies demonstrate the feasibility of using DNA nanotechnology to both detect and manipulate nucleosome structure, which provides a foundation of future mesoscale studies of nucleosome and chromatin structural dynamics.
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Affiliation(s)
- Jenny V. Le
- Biophysics Graduate Program, The Ohio State University, Columbus OH 43214
| | - Yi Luo
- Biophysics Graduate Program, The Ohio State University, Columbus OH 43214
| | - Michael A. Darcy
- Department of Physics, The Ohio State University, Columbus OH 43214
| | | | | | - Michael G. Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus OH 43214
- Department of Physics, The Ohio State University, Columbus OH 43214
- Corresponding authors: ,
| | - Carlos E. Castro
- Biophysics Graduate Program, The Ohio State University, Columbus OH 43214
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus OH 43214
- Corresponding authors: ,
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417
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Kricka LJ, Fortina P, Park JY. Nanostructured luminescently labeled nucleic acids. LUMINESCENCE 2016; 32:132-141. [DOI: 10.1002/bio.3170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Larry J. Kricka
- Department of Pathology and Laboratory Medicine; University of Pennsylvania Medical Center; 3400 Spruce Street Philadelphia Pennsylvania 19104 USA
| | - Paolo Fortina
- Department of Cancer Biology, Cancer Genomics Laboratory, Sidney Kimmel Cancer Center; Thomas Jefferson University Jefferson Medical College; Philadelphia PA USA
- Department of Molecular Medicine; Universita’ La Sapienza; Rome Italy
| | - Jason Y. Park
- Department of Pathology and the Eugene McDermott Center for Human Growth and Development; University of Texas Southwestern Medical Center; Dallas Texas 75229 USA
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418
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Shrestha P, Emura T, Koirala D, Cui Y, Hidaka K, Maximuck WJ, Endo M, Sugiyama H, Mao H. Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores. Nucleic Acids Res 2016; 44:6574-82. [PMID: 27387283 PMCID: PMC5001620 DOI: 10.1093/nar/gkw610] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 06/24/2016] [Indexed: 01/13/2023] Open
Abstract
DNA nanoassemblies have demonstrated wide applications in various fields including nanomaterials, drug delivery and biosensing. In DNA origami, single-stranded DNA template is shaped into desired nanostructure by DNA staples that form Holliday junctions with the template. Limited by current methodologies, however, mechanical properties of DNA origami structures have not been adequately characterized, which hinders further applications of these materials. Using laser tweezers, here, we have described two mechanical properties of DNA nanoassemblies represented by DNA nanotubes, DNA nanopyramids and DNA nanotiles. First, mechanical stability of DNA origami structures is determined by the effective density of Holliday junctions along a particular stress direction. Second, mechanical isomerization observed between two conformations of DNA nanotubes at 10–35 pN has been ascribed to the collective actions of individual Holliday junctions, which are only possible in DNA origami with rotational symmetric arrangements of Holliday junctions, such as those in DNA nanotubes. Our results indicate that Holliday junctions control mechanical behaviors of DNA nanoassemblies. Therefore, they can be considered as ‘mechanophores’ that sustain mechanical properties of origami nanoassemblies. The mechanical properties observed here provide insights for designing better DNA nanostructures. In addition, the unprecedented mechanical isomerization process brings new strategies for the development of nano-sensors and actuators.
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Affiliation(s)
- Prakash Shrestha
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Yunxi Cui
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - William J Maximuck
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
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419
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Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers. J Struct Biol 2016; 197:26-36. [PMID: 27368129 DOI: 10.1016/j.jsb.2016.06.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/06/2016] [Accepted: 06/28/2016] [Indexed: 11/21/2022]
Abstract
Nucleic acids are central to the storage and transmission of genetic information. Mechanical properties, along with their sequence, both enable and fundamentally constrain the biological functions of DNA and RNA. For small deformations from the equilibrium conformations, nucleic acids are well described by an isotropic elastic rod model. However, external forces and torsional strains can induce conformational changes, giving rise to a complex force-torque phase diagram. This review focuses on magnetic tweezers as a powerful tool to precisely determine both the elastic parameters and conformational transitions of nucleic acids under external forces and torques at the single-molecule level. We review several variations of magnetic tweezers, in particular conventional magnetic tweezers, freely orbiting magnetic tweezers and magnetic torque tweezers, and discuss their characteristic capabilities. We then describe the elastic rod model for DNA and RNA and discuss conformational changes induced by mechanical stress. The focus lies on the responses to torque and twist, which are crucial in the mechanics and interactions of nucleic acids and can directly be measured using magnetic tweezers. We conclude by highlighting several recent studies of nucleic acid-protein and nucleic acid-small-molecule interactions as further applications of magnetic tweezers and give an outlook of some exciting developments to come.
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420
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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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421
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Programmable DNA Nanosystem for Molecular Interrogation. Sci Rep 2016; 6:27413. [PMID: 27270162 PMCID: PMC4895238 DOI: 10.1038/srep27413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 05/18/2016] [Indexed: 12/17/2022] Open
Abstract
We describe a self-assembling DNA-based nanosystem for interrogating molecular interactions. The nanosystem contains a rigid supporting dumbbell-shaped frame, a cylindrical central core, and a mobile ring that is coaxial with the core. Motion of the ring is influenced by several control elements whose force-generating capability is based on the transition of single-stranded DNA to double-stranded DNA. These forces can be directed to act in opposition to adhesive forces between the ring and the frame thereby providing a mechanism for molecular detection and interrogation at the ring-frame interface. As proof of principle we use this system to evaluate base stacking adhesion and demonstrate detection of a soluble nucleic acid viral genome mimic.
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422
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Kalinowski M, Haug R, Said H, Piasecka S, Kramer M, Richert C. Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures. Chembiochem 2016; 17:1150-5. [PMID: 27225865 DOI: 10.1002/cbic.201600061] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 01/25/2023]
Abstract
The folding of long DNA strands into designed nanostructures has evolved into an art. Being based on linear chains only, the resulting nanostructures cannot readily be transformed into covalently linked frameworks. Covalently linking strands in the context of folded DNA structures requires a robust method that avoids sterically demanding reagents or enzymes. Here we report chemical ligation of the 3'-amino termini of oligonucleotides and 5'-phosphorylated partner strands in templated reactions that produce phosphoramidate linkages. These reactions produce inter-nucleotide linkages that are isoelectronic and largely isosteric to phosphodiesters. Ligations were performed at three levels of complexity, including the extension of branched DNA hybrids and the ligation of six scaffold strands in a small origami.
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Affiliation(s)
- Matthäus Kalinowski
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Rüdiger Haug
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Hassan Said
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Sylwia Piasecka
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Markus Kramer
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany.
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423
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Chen H, Zhang H, Pan J, Cha TG, Li S, Andréasson J, Choi JH. Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts. ACS NANO 2016; 10:4989-96. [PMID: 27057775 DOI: 10.1021/acsnano.6b01339] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA origami has received enormous attention for its ability to program complex nanostructures with a few nanometer precision. Dynamic origami structures that change conformation in response to environmental cues or external signals hold great promises in sensing and actuation at the nanoscale. The reconfiguration mechanism of existing dynamic origami structures is mostly limited to single-stranded hinges and relies almost exclusively on DNA hybridization or strand displacement. Here, we show an alternative approach by demonstrating on-demand conformation changes with DNA-binding molecules, which intercalate between base pairs and unwind DNA double helices. The unwinding effect modulates the helicity mismatch in DNA origami, which significantly influences the internal stress and the global conformation of the origami structure. We demonstrate the switching of a polymerized origami nanoribbon between different twisting states and a well-constrained torsional deformation in a monomeric origami shaft. The structural transformation is shown to be reversible, and binding isotherms confirm the reconfiguration mechanism. This approach provides a rapid and reversible means to change DNA origami conformation, which can be used for dynamic and progressive control at the nanoscale.
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Affiliation(s)
- Haorong Chen
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Hanyu Zhang
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Jing Pan
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Tae-Gon Cha
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
| | - Shiming Li
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Joakim Andréasson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University , West Lafayette, Indiana 47907, United States
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424
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Ramakrishnan S, Krainer G, Grundmeier G, Schlierf M, Keller A. Structural stability of DNA origami nanostructures in the presence of chaotropic agents. NANOSCALE 2016; 8:10398-10405. [PMID: 27142120 DOI: 10.1039/c6nr00835f] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA origami represent powerful platforms for single-molecule investigations of biomolecular processes. The required structural integrity of the DNA origami may, however, pose significant limitations regarding their applicability, for instance in protein folding studies that require strongly denaturing conditions. Here, we therefore report a detailed study on the stability of 2D DNA origami triangles in the presence of the strong chaotropic denaturing agents urea and guanidinium chloride (GdmCl) and its dependence on concentration and temperature. At room temperature, the DNA origami triangles are stable up to at least 24 h in both denaturants at concentrations as high as 6 M. At elevated temperatures, however, structural stability is governed by variations in the melting temperature of the individual staple strands. Therefore, the global melting temperature of the DNA origami does not represent an accurate measure of their structural stability. Although GdmCl has a stronger effect on the global melting temperature, its attack results in less structural damage than observed for urea under equivalent conditions. This enhanced structural stability most likely originates from the ionic nature of GdmCl. By rational design of the arrangement and lengths of the individual staple strands used for the folding of a particular shape, however, the structural stability of DNA origami may be enhanced even further to meet individual experimental requirements. Overall, their high stability renders DNA origami promising platforms for biomolecular studies in the presence of chaotropic agents, including single-molecule protein folding or structural switching.
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Affiliation(s)
- Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, 33098 Paderborn, Germany.
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425
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In-Phase Assembly of Slim DNA Lattices with Small Circular DNA Motifs via Short Connections of 11 and 16 Base Pairs. Chembiochem 2016; 17:1132-7. [DOI: 10.1002/cbic.201600054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 12/14/2022]
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426
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Pfeifer W, Saccà B. From Nano to Macro through Hierarchical Self-Assembly: The DNA Paradigm. Chembiochem 2016; 17:1063-80. [DOI: 10.1002/cbic.201600034] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Wolfgang Pfeifer
- Centre for Medical Biotechnology (ZMB); University of Duisburg-Essen; Universitätstrasse 2 45117 Essen Germany
| | - Barbara Saccà
- Centre for Medical Biotechnology (ZMB); University of Duisburg-Essen; Universitätstrasse 2 45117 Essen Germany
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427
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Ke G, Liu M, Jiang S, Qi X, Yang YR, Wootten S, Zhang F, Zhu Z, Liu Y, Yang CJ, Yan H. Directional Regulation of Enzyme Pathways through the Control of Substrate Channeling on a DNA Origami Scaffold. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603183] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guoliang Ke
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation State Key Laboratory of Physical Chemistry of Solid Surfaces Collaborative Innovation Center of Chemistry for Energy Materials Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Minghui Liu
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Xiaodong Qi
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Yuhe Renee Yang
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Shaun Wootten
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Fei Zhang
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation State Key Laboratory of Physical Chemistry of Solid Surfaces Collaborative Innovation Center of Chemistry for Energy Materials Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Yan Liu
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
| | - Chaoyong James Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation State Key Laboratory of Physical Chemistry of Solid Surfaces Collaborative Innovation Center of Chemistry for Energy Materials Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Hao Yan
- Center for Molecular Design and Biomimetics Biodesign Institute School of Molecular Sciences at Arizona State University Tempe Arizona 85287 USA
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428
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Ke G, Liu M, Jiang S, Qi X, Yang YR, Wootten S, Zhang F, Zhu Z, Liu Y, Yang CJ, Yan H. Directional Regulation of Enzyme Pathways through the Control of Substrate Channeling on a DNA Origami Scaffold. Angew Chem Int Ed Engl 2016; 55:7483-6. [PMID: 27159899 DOI: 10.1002/anie.201603183] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/11/2022]
Abstract
Artificial multi-enzyme systems with precise and dynamic control over the enzyme pathway activity are of great significance in bionanotechnology and synthetic biology. Herein, we exploit a spatially addressable DNA nanoplatform for the directional regulation of two enzyme pathways (G6pDH-MDH and G6pDH-LDH) through the control of NAD(+) substrate channeling by specifically shifting NAD(+) between the two enzyme pairs. We believe that this concept will be useful for the design of regulatory biological circuits for synthetic biology and biomedicine.
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Affiliation(s)
- Guoliang Ke
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA.,The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Xiaodong Qi
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Yuhe Renee Yang
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Shaun Wootten
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Fei Zhang
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yan Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA.
| | - Chaoyong James Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Hao Yan
- Center for Molecular Design and Biomimetics, Biodesign Institute, School of Molecular Sciences at, Arizona State University, Tempe, Arizona, 85287, USA.
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429
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Schreck JS, Romano F, Zimmer MH, Louis AA, Doye JPK. Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model. ACS NANO 2016; 10:4236-47. [PMID: 27010928 DOI: 10.1021/acsnano.5b07664] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We use oxDNA, a coarse-grained model of DNA at the nucleotide level, to simulate large nanoprisms that are composed of multi-arm star tiles, in which the size of bulge loops that have been incorporated into the tile design is used to control the flexibility of the tiles. The oxDNA model predicts equilibrium structures for several different nanoprism designs that are in excellent agreement with the experimental structures as measured by cryoTEM. In particular we reproduce the chiral twisting of the top and bottom faces of the nanoprisms, as the bulge sizes in these structures are varied due to the greater flexibility of larger bulges. We are also able to follow how the properties of the star tiles evolve as the prisms are assembled. Individual star tiles are very flexible, but their structures become increasingly well-defined and rigid as they are incorporated into larger assemblies. oxDNA also finds that the experimentally observed prisms are more stable than their inverted counterparts, but interestingly this preference for the arms of the tiles to bend in a given direction only emerges after they are part of larger assemblies. These results show the potential for oxDNA to provide detailed structural insight as well as to predict the properties of DNA nanostructures and hence to aid rational design in DNA nanotechnology.
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Affiliation(s)
- John S Schreck
- 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
- Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca' Foscari Venezia , I-30123 Venezia, Italy
| | - Matthew H Zimmer
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, 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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430
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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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431
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Chandrasekaran AR, Anderson N, Kizer M, Halvorsen K, Wang X. Beyond the Fold: Emerging Biological Applications of DNA Origami. Chembiochem 2016; 17:1081-9. [PMID: 26928725 DOI: 10.1002/cbic.201600038] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/22/2023]
Abstract
The use of DNA as a material for nanoscale construction has blossomed in the past decade. This is largely attributable to the DNA origami technique, which has enabled construction of nanostructures ranging from simple two-dimensional sheets to complex three-dimensional objects with defined curves and edges. These structures are amenable to site-specific functionalization with nanometer precision, and have been shown to exhibit cellular biocompatibility and permeability. The DNA origami technique has already found widespread use in a variety of emerging biological applications such as biosensing, enzyme cascades, biomolecular analysis, biomimetics, and drug delivery. We highlight a few of these applications and comments on the prospects for this rapidly expanding field of research.
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Affiliation(s)
| | - Nate Anderson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. , .,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. ,
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432
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Niekamp S, Blumer K, Nafisi PM, Tsui K, Garbutt J, Douglas SM. Folding complex DNA nanostructures from limited sets of reusable sequences. Nucleic Acids Res 2016; 44:e102. [PMID: 27036861 PMCID: PMC4914096 DOI: 10.1093/nar/gkw208] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/18/2016] [Indexed: 02/06/2023] Open
Abstract
Scalable production of DNA nanostructures remains a substantial obstacle to realizing new applications of DNA nanotechnology. Typical DNA nanostructures comprise hundreds of DNA oligonucleotide strands, where each unique strand requires a separate synthesis step. New design methods that reduce the strand count for a given shape while maintaining overall size and complexity would be highly beneficial for efficiently producing DNA nanostructures. Here, we report a method for folding a custom template strand by binding individual staple sequences to multiple locations on the template. We built several nanostructures for well-controlled testing of various design rules, and demonstrate folding of a 6-kb template by as few as 10 unique strand sequences binding to 10 ± 2 locations on the template strand.
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Affiliation(s)
- Stefan Niekamp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Katy Blumer
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Parsa M Nafisi
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Kathy Tsui
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - John Garbutt
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Shawn M Douglas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
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433
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Weigandt J, Chung CL, Jester SS, Famulok M. Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures. Angew Chem Int Ed Engl 2016; 55:5512-6. [PMID: 27010370 PMCID: PMC4850751 DOI: 10.1002/anie.201601042] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/03/2016] [Indexed: 11/08/2022]
Abstract
We report the stepwise assembly of supramolecular daisy chain rotaxanes (DCR) made of double-stranded DNA: Small dsDNA macrocycles bearing an axle assemble into a pseudo-DCR precursor that was connected to rigid DNA stoppers to form DCR with the macrocycles hybridized to the axles. In presence of release oligodeoxynucleotides (rODNs), the macrocycles are released from their respective hybridization sites on the axles, leading to stable mechanically interlocked DCRs. Besides the expected threaded DCRs, certain amounts of externally hybridized structures were observed, which dissociate into dumbbell structures in presence of rODNs. We show that the genuine DCRs have significantly higher degrees of freedom in their movement along the thread axle than the hybridized DCR precursors. Interlocking of DNA in DCRs might serve as a versatile principle for constructing functional DNA nanostructures where the movement of the subunits is restricted within precisely confined tolerance ranges.
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Affiliation(s)
- Johannes Weigandt
- LIMES Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Chia-Ling Chung
- LIMES Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Stefan-S Jester
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Michael Famulok
- LIMES Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany. .,Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.
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434
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Weigandt J, Chung C, Jester S, Famulok M. Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Johannes Weigandt
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Chia‐Ling Chung
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Stefan‐S. Jester
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Michael Famulok
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
- Center of Advanced European Studies and Research Ludwig-Erhard-Allee 2 53175 Bonn Germany
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435
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Self-assembly of size-controlled liposomes on DNA nanotemplates. Nat Chem 2016; 8:476-83. [PMID: 27102682 PMCID: PMC5021307 DOI: 10.1038/nchem.2472] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 02/03/2016] [Indexed: 12/22/2022]
Abstract
Artificial lipid-bilayer membranes are valuable tools for the study of membrane structure and dynamics. For applications such as the study of vesicular transport and drug delivery, there is a pressing need for artificial vesicles with controlled size. However, controlling vesicle size and shape with nanometre precision is challenging, and approaches to achieve this can be heavily affected by lipid composition. Here, we present a bio-inspired templating method to generate highly monodispersed sub-100-nm unilamellar vesicles, where liposome self-assembly was nucleated and confined inside rigid DNA nanotemplates. Using this method, we produce homogeneous liposomes with four distinct predefined sizes. We also show that the method can be used with a variety of lipid compositions and probe the mechanism of templated liposome formation by capturing key intermediates during membrane self-assembly. The DNA nanotemplating strategy represents a conceptually novel way to guide lipid bilayer formation and could be generalized to engineer complex membrane/protein structures with nanoscale precision.
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436
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Regulation at a distance of biomolecular interactions using a DNA origami nanoactuator. Nat Commun 2016; 7:10935. [PMID: 26988942 PMCID: PMC4802031 DOI: 10.1038/ncomms10935] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 02/03/2016] [Indexed: 12/31/2022] Open
Abstract
The creation of nanometre-sized structures that exhibit controllable motions and functions is a critical step towards building nanomachines. Recent developments in the field of DNA nanotechnology have begun to address these goals, demonstrating complex static or dynamic nanostructures made of DNA. Here we have designed and constructed a rhombus-shaped DNA origami ‘nanoactuator' that uses mechanical linkages to copy distance changes induced on one half (‘the driver') to be propagated to the other half (‘the mirror'). By combining this nanoactuator with split enhanced green fluorescent protein (eGFP), we have constructed a DNA–protein hybrid nanostructure that demonstrates tunable fluorescent behaviours via long-range allosteric regulation. In addition, the nanoactuator can be used as a sensor that responds to specific stimuli, including changes in buffer composition and the presence of restriction enzymes or specific nucleic acids. The construction of nano-machines requires building nano-scale structures with controllable functions. Here the authors use DNA origami to construct an allosteric actuator which can act as signal propagator and an environmental sensor.
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437
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Prinz J, Heck C, Ellerik L, Merk V, Bald I. DNA origami based Au-Ag-core-shell nanoparticle dimers with single-molecule SERS sensitivity. NANOSCALE 2016; 8:5612-20. [PMID: 26892770 PMCID: PMC4778414 DOI: 10.1039/c5nr08674d] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 02/11/2016] [Indexed: 05/17/2023]
Abstract
DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 10(10), which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled.
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Affiliation(s)
- J Prinz
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany.
| | - C Heck
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany. and BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489 Berlin, Germany and Department of Chemistry + SALSA, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - L Ellerik
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany.
| | - V Merk
- Department of Chemistry + SALSA, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - I Bald
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany. and BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489 Berlin, Germany
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438
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Zenk J, Tuntivate C, Schulman R. Kinetics and Thermodynamics of Watson–Crick Base Pairing Driven DNA Origami Dimerization. J Am Chem Soc 2016; 138:3346-54. [DOI: 10.1021/jacs.5b10502] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- John Zenk
- Chemical
and Biomolecular Engineering and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chanon Tuntivate
- Chemical
and Biomolecular Engineering and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Chemical
and Biomolecular Engineering and ‡Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
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439
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Fern J, Lu J, Schulman R. The Energy Landscape for the Self-Assembly of a Two-Dimensional DNA Origami Complex. ACS NANO 2016; 10:1836-1844. [PMID: 26820483 DOI: 10.1021/acsnano.5b05309] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
While the self-assembly of different types of DNA origami into well-defined complexes could produce nanostructures on which thousands of locations can be independently functionalized with nanometer-scale precision, current assembly processes have low yields. Biomolecular complex formation requires relatively strong interactions and reversible assembly pathways that prevent kinetic trapping. To characterize how these issues control origami complex yields, the equilibrium constants for each possible reaction for the assembly of a heterotetrameric ring, the unit cell of a rectangular lattice, were measured using fluorescence colocalization microscopy. We found that origami interface structure controlled reaction free energies. Cooperativity, measured for the first time for a DNA nanostructure assembly reaction, was weak. Simulations of assembly kinetics suggest assembly occurs via parallel pathways with the primary mechanism of assembly being hierarchical: two dimers form that then bind to one another to complete the ring.
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Affiliation(s)
- Joshua Fern
- Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Jennifer Lu
- Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
- Computer Science, Johns Hopkins University , Baltimore, Maryland 21218, United States
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440
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Krissanaprasit A, Madsen M, Knudsen JB, Gudnason D, Surareungchai W, Birkedal V, Gothelf KV. Programmed Switching of Single Polymer Conformation on DNA Origami. ACS NANO 2016; 10:2243-2250. [PMID: 26766635 DOI: 10.1021/acsnano.5b06894] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA nanotechnology offers precise geometrical control of the positioning of materials, and it is increasingly also being used in the development of nanomechanical devices. Here we describe the development of a nanomechanical device that allows switching of the position of a single-molecule conjugated polymer. The polymer is functionalized with short single-stranded (ss) DNA strands that extend from the backbone of the polymer and serve as handles. The DNA polymer conjugate can be aligned on DNA origami in three well-defined geometries (straight line, left-turned, and right-turned pattern) by DNA hybridization directed by single-stranded guiding strands and ssDNA tracks extending from the origami surface and polymer handle. We demonstrate switching of a conjugated organic polymer conformation between left- and right-turned conformations of the polymer on DNA origami based on toehold-mediated strand displacement. The switching is observed by atomic force microscopy and by Förster resonance energy transfer between the polymer and two different organic dyes positioned in close proximity to the respective patterns. Using this method, the polymer conformation can be switched six times successively. This controlled nanomechanical switching of conjugated organic polymer conformation demonstrates unique control of the shape of a single polymer molecule, and it may constitute a new component for the development of reconfigurable nanophotonic and nanoelectronic devices.
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Affiliation(s)
- Abhichart Krissanaprasit
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi , Bangkhuntien Campus, Bangkok 10150, Thailand
| | | | | | | | - Werasak Surareungchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi , Bangkhuntien Campus, Bangkok 10150, Thailand
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441
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Jacobs WM, Frenkel D. Self-Assembly of Structures with Addressable Complexity. J Am Chem Soc 2016; 138:2457-67. [DOI: 10.1021/jacs.5b11918] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- William M. Jacobs
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Daan Frenkel
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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442
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A light-driven three-dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function. Nat Commun 2016; 7:10591. [PMID: 26830310 PMCID: PMC4740900 DOI: 10.1038/ncomms10591] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/02/2016] [Indexed: 12/23/2022] Open
Abstract
Nature has developed striking light-powered proteins such as bacteriorhodopsin, which can convert light energy into conformational changes for biological functions. Such natural machines are a great source of inspiration for creation of their synthetic analogues. However, synthetic molecular machines typically operate at the nanometre scale or below. Translating controlled operation of individual molecular machines to a larger dimension, for example, to 10-100 nm, which features many practical applications, is highly important but remains challenging. Here we demonstrate a light-driven plasmonic nanosystem that can amplify the molecular motion of azobenzene through the host nanostructure and consequently translate it into reversible chiroptical function with large amplitude modulation. Light is exploited as both energy source and information probe. Our plasmonic nanosystem bears unique features of optical addressability, reversibility and modulability, which are crucial for developing all-optical molecular devices with desired functionalities.
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443
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Ketterer P, Willner EM, Dietz H. Nanoscale rotary apparatus formed from tight-fitting 3D DNA components. SCIENCE ADVANCES 2016; 2:e1501209. [PMID: 26989778 PMCID: PMC4788491 DOI: 10.1126/sciadv.1501209] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/07/2015] [Indexed: 05/19/2023]
Abstract
We report a nanoscale rotary mechanism that reproduces some of the dynamic properties of biological rotary motors in the absence of an energy source, such as random walks on a circle with dwells at docking sites. Our mechanism is built modularly from tight-fitting components that were self-assembled using multilayer DNA origami. The apparatus has greater structural complexity than previous mechanically interlocked objects and features a well-defined angular degree of freedom without restricting the range of rotation. We studied the dynamics of our mechanism using single-particle experiments analogous to those performed previously with actin-labeled adenosine triphosphate synthases. In our mechanism, rotor mobility, the number of docking sites, and the dwell times at these sites may be controlled through rational design. Our prototype thus realizes a working platform toward creating synthetic nanoscale rotary motors. Our methods will support creating other complex nanoscale mechanisms based on tightly fitting, sterically constrained, but mobile, DNA components.
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444
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Krieg E, Bastings MMC, Besenius P, Rybtchinski B. Supramolecular Polymers in Aqueous Media. Chem Rev 2016; 116:2414-77. [DOI: 10.1021/acs.chemrev.5b00369] [Citation(s) in RCA: 527] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - Pol Besenius
- Institute
of Organic Chemistry, Johannes Gutenberg-Universität Mainz, Mainz 55128, Germany
| | - Boris Rybtchinski
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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445
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Li M, Yu J, Li J, Wang EB, Wang G, Mao C. Self-assembly of DNA double multi-arm junctions (DMaJs). RSC Adv 2016. [DOI: 10.1039/c6ra15145k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Expanding the legendary DNA double crossover (DX) motif: pairs of multiple-arm DNA junctions have been coupled into well-behaved DX-like nanomotifs for nanoconstruction.
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Affiliation(s)
- Mo Li
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Jinwen Yu
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Jingtong Li
- The Institute of Respiratory Diseases
- Xinqiao Hospital
- Chongqing 400037
- China
| | - Eric Ben Wang
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Guansong Wang
- The Institute of Respiratory Diseases
- Xinqiao Hospital
- Chongqing 400037
- China
| | - Chengde Mao
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
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446
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Surin M. From nucleobase to DNA templates for precision supramolecular assemblies and synthetic polymers. Polym Chem 2016. [DOI: 10.1039/c6py00480f] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this minireview, we report on the recent advances of utilization of nucleobases and DNA as templates to achieve well-defined supramolecular polymers, synthetic polymers, and sequence-controlled polymers.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel Materials
- Center for Innovation and Research in Materials and Polymers
- University of Mons – UMONS
- B-7000 Mons
- Belgium
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447
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Funke JJ, Dietz H. Placing molecules with Bohr radius resolution using DNA origami. NATURE NANOTECHNOLOGY 2016; 11:47-52. [PMID: 26479026 DOI: 10.1038/nnano.2015.240] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/09/2015] [Indexed: 05/17/2023]
Abstract
Molecular self-assembly with nucleic acids can be used to fabricate discrete objects with defined sizes and arbitrary shapes. It relies on building blocks that are commensurate to those of biological macromolecular machines and should therefore be capable of delivering the atomic-scale placement accuracy known today only from natural and designed proteins. However, research in the field has predominantly focused on producing increasingly large and complex, but more coarsely defined, objects and placing them in an orderly manner on solid substrates. So far, few objects afford a design accuracy better than 5 nm, and the subnanometre scale has been reached only within the unit cells of designed DNA crystals. Here, we report a molecular positioning device made from a hinged DNA origami object in which the angle between the two structural units can be controlled with adjuster helices. To test the positioning capabilities of the device, we used photophysical and crosslinking assays that report the coordinate of interest directly with atomic resolution. Using this combination of placement and analysis, we rationally adjusted the average distance between fluorescent molecules and reactive groups from 1.5 to 9 nm in 123 discrete displacement steps. The smallest displacement step possible was 0.04 nm, which is slightly less than the Bohr radius. The fluctuation amplitudes in the distance coordinate were also small (±0.5 nm), and within a factor of two to three of the amplitudes found in protein structures.
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Affiliation(s)
- Jonas J Funke
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748 Garching near Munich, Germany
| | - Hendrik Dietz
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748 Garching near Munich, Germany
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448
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Lee DS, Qian H, Tay CY, Leong DT. Cellular processing and destinies of artificial DNA nanostructures. Chem Soc Rev 2016; 45:4199-225. [DOI: 10.1039/c5cs00700c] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review gives a panoramic view of the many DNA nanotechnology applications in cells, mechanistic understanding of how and where their interactions occur and their subsequent outcomes.
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Affiliation(s)
- Di Sheng Lee
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
- Department of Materials Science and Engineering
| | - Hang Qian
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
| | - Chor Yong Tay
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
- School of Materials Science and Engineering
| | - David Tai Leong
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
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449
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Ma X, Zhang Y, Zhang Y, Peng C, Che Y, Zhao J. Stepwise Formation of Photoconductive Nanotubes through a New Top-Down Method. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:7746-7751. [PMID: 26485110 DOI: 10.1002/adma.201503771] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 08/31/2015] [Indexed: 06/05/2023]
Abstract
In contrast to the widely used bottom-up strategy for preparing various complex nanostructures, the top-down strategy is rarely applied to generate complex nanostructures. This study reports the use of a unique combination of bottom-up and top-down processes for the time-resolved stepwise fabrication of novel photoconductive nanotubes from elaborately designed asymmetric perylene diimide molecules.
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Affiliation(s)
- Xiaojie Ma
- Beijing National Laboratory of Molecular Sciences, Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yibin Zhang
- Beijing National Laboratory of Molecular Sciences, Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yifan Zhang
- Beijing National Laboratory of Molecular Sciences, Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Cheng Peng
- Beijing National Laboratory of Molecular Sciences, Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yanke Che
- Beijing National Laboratory of Molecular Sciences, Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jincai Zhao
- Beijing National Laboratory of Molecular Sciences, Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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450
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Wang R, Gorday K, Nuckolls C, Wind SJ. Control of DNA origami inter-tile connection with vertical linkers. Chem Commun (Camb) 2015; 52:1610-3. [PMID: 26662034 DOI: 10.1039/c5cc08185h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This communication describes a new method that enables high yield assembly along both of the two-dimensional edges of DNA origami tiles by controlling the Mg(2+) concentration; high Mg(2+) concentrations promote linkage connections between the vertical edges of the tiles. As a demonstration, DNA origami dimers assembled from two rectangular origami along the vertical edges are used as scaffolds for the double sided assembly of gold nanoparticles with different inter-particle spacings.
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Affiliation(s)
- Risheng Wang
- Department of Applied Physics & Applied Mathematics, Columbia University, New York, NY 10027, USA.
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