1
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Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
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Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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2
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Liu Y, Dai Z, Xie X, Li B, Jia S, Li Q, Li M, Fan C, Liu X. Spacer-Programmed Two-Dimensional DNA Origami Assembly. J Am Chem Soc 2024; 146:5461-5469. [PMID: 38355136 DOI: 10.1021/jacs.3c13180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Two-dimensional (2D) DNA origami assembly represents a powerful approach to the programmable design and construction of advanced 2D materials. Within the context of hybridization-mediated 2D DNA origami assembly, DNA spacers play a pivotal role as essential connectors between sticky-end regions and DNA origami units. Here, we demonstrated that programming the spacer length, which determines the binding radius of DNA origami units, could effectively tune sticky-end hybridization reactions to produce distinct 2D DNA origami arrays. Using DNA-PAINT super-resolution imaging, we unveiled the significant impact of spacer length on the hybridization efficiency of sticky ends for assembling square DNA origami (SDO) units. We also found that the assembly efficiency and pattern diversity of 2D DNA origami assemblies were critically dependent on the spacer length. Remarkably, we realized a near-unity yield of ∼98% for the assembly of SDO trimers and tetramers via this spacer-programmed strategy. At last, we revealed that spacer lengths and thermodynamic fluctuations of SDO are positively correlated, using molecular dynamics simulations. Our study thus paves the way for the precision assembly of DNA nanostructures toward higher complexity.
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Affiliation(s)
- Yongjun Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zheze Dai
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaodong Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bochen Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sisi Jia
- Zhangjiang Laboratory, Shanghai 201210, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Schmid SY, Lachowski K, Chiang HT, Pozzo L, De Yoreo J, Zhang S. Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics. Angew Chem Int Ed Engl 2023; 62:e202309725. [PMID: 37702227 DOI: 10.1002/anie.202309725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.
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Affiliation(s)
- Sakshi Yadav Schmid
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kacper Lachowski
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
| | - Huat Thart Chiang
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
| | - Lilo Pozzo
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Jim De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
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4
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Chen C, Luo X, Kaplan AE, Bawendi MG, Macfarlane RJ, Bathe M. Ultrafast dense DNA functionalization of quantum dots and rods for scalable 2D array fabrication with nanoscale precision. SCIENCE ADVANCES 2023; 9:eadh8508. [PMID: 37566651 PMCID: PMC10421044 DOI: 10.1126/sciadv.adh8508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/14/2023] [Indexed: 08/13/2023]
Abstract
Scalable fabrication of two-dimensional (2D) arrays of quantum dots (QDs) and quantum rods (QRs) with nanoscale precision is required for numerous device applications. However, self-assembly-based fabrication of such arrays using DNA origami typically suffers from low yield due to inefficient QD and QR DNA functionalization. In addition, it is challenging to organize solution-assembled DNA origami arrays on 2D device substrates while maintaining their structural fidelity. Here, we reduced manufacturing time from a few days to a few minutes by preparing high-density DNA-conjugated QDs/QRs from organic solution using a dehydration and rehydration process. We used a surface-assisted large-scale assembly (SALSA) method to construct 2D origami lattices directly on solid substrates to template QD and QR 2D arrays with orientational control, with overall loading yields exceeding 90%. Our fabrication approach enables the scalable, high fidelity manufacturing of 2D addressable QDs and QRs with nanoscale orientational and spacing control for functional 2D photonic devices.
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Affiliation(s)
- Chi Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xin Luo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexander E. K. Kaplan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Moungi G. Bawendi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert J. Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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5
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Tang Y, Liu H, Wang Q, Qi X, Yu L, Šulc P, Zhang F, Yan H, Jiang S. DNA Origami Tessellations. J Am Chem Soc 2023. [PMID: 37329284 DOI: 10.1021/jacs.3c03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Molecular tessellation research aims to elucidate the underlying principles that govern intricate patterns in nature and to leverage these principles to create precise and ordered structures across multiple scales, thereby facilitating the emergence of novel functionalities. DNA origami nanostructures are excellent building blocks for constructing tessellation patterns. However, the size and complexity of DNA origami tessellation systems are currently limited by several unexplored factors relevant to the accuracy of essential design parameters, the applicability of design strategies, and the compatibility between different tiles. Here, we present a general method for creating DNA origami tiles that grow into tessellation patterns with micrometer-scale order and nanometer-scale precision. Interhelical distance (D) was identified as a critical design parameter determining tile conformation and tessellation outcome. Finely tuned D facilitated the accurate geometric design of monomer tiles with minimized curvature and improved tessellation capability, enabling the formation of single-crystalline lattices ranging from tens to hundreds of square micrometers. The general applicability of the design method was demonstrated by 9 tile geometries, 15 unique tile designs, and 12 tessellation patterns covering Platonic, Laves, and Archimedean tilings. Particularly, we took two strategies to increase the complexity of DNA origami tessellation, including reducing the symmetry of monomer tiles and coassembling tiles of different geometries. Both yielded various tiling patterns that rivaled Platonic tilings in size and quality, indicating the robustness of the optimized tessellation system. This study will promote DNA-templated, programmable molecular and material patterning and open up new opportunities for applications in metamaterial engineering, nanoelectronics, and nanolithography.
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Affiliation(s)
- Yue Tang
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Hao Liu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Qi Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaodong Qi
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Lu Yu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Fei Zhang
- Department of Chemistry, School of Arts & Sciences-Newark, Rutgers University, Newark, New Jersey 07102, United States
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Shuoxing Jiang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
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6
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He Z, Shi K, Li J, Chao J. Self-assembly of DNA origami for nanofabrication, biosensing, drug delivery, and computational storage. iScience 2023; 26:106638. [PMID: 37187699 PMCID: PMC10176269 DOI: 10.1016/j.isci.2023.106638] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Since the pioneering work of immobile DNA Holliday junction by Ned Seeman in the early 1980s, the past few decades have witnessed the development of DNA nanotechnology. In particular, DNA origami has pushed the field of DNA nanotechnology to a new level. It obeys the strict Watson-Crick base pairing principle to create intricate structures with nanoscale accuracy, which greatly enriches the complexity, dimension, and functionality of DNA nanostructures. Benefiting from its high programmability and addressability, DNA origami has emerged as versatile nanomachines for transportation, sensing, and computing. This review will briefly summarize the recent progress of DNA origami, two-dimensional pattern, and three-dimensional assembly based on DNA origami, followed by introduction of its application in nanofabrication, biosensing, drug delivery, and computational storage. The prospects and challenges of assembly and application of DNA origami are also discussed.
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Affiliation(s)
- Zhimei He
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Kejun Shi
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Jinggang Li
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Corresponding author
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7
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Suzuki Y, Sugiyama H, Endo M. Two-Dimensional DNA Origami Lattices Assembled on Lipid Bilayer Membranes. Methods Mol Biol 2023; 2639:83-90. [PMID: 37166712 DOI: 10.1007/978-1-0716-3028-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Molecular self-assembly has attracted much attention as a method to create novel supramolecular architectures. The scaffolded DNA origami method has enabled the construction of almost arbitrarily shaped DNA nanostructures, which can be further used as components of higher-order architectures. Here, we describe a method to construct and visualize two-dimensional (2D) lattices self-assembled from DNA origami tiles on lipid bilayer membranes. The weak adsorption of DNA origami tiles onto the mica-supported lipid bilayer allows their lateral diffusion along the surface, facilitating interactions among the tiles to assemble and form large 2D lattices. Depending on the design (i.e., shape, size, and interactions with each other) of DNA origami tiles, a variety of 2D lattices made of DNA are constructed.
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Affiliation(s)
- Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aoba-ku, Sendai, Japan
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu, Mie, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan.
- Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Osaka, Japan.
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8
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Abstract
Hierarchical assembly of programmable DNA frameworks─such as DNA origami─paves the way for versatile nanometer-precise parallel nanopatterning up to macroscopic scales. As of now, the rapid evolution of the DNA nanostructure design techniques and the accessibility of these methods provide a feasible platform for building highly ordered DNA-based assemblies for various purposes. So far, a plethora of different building blocks based on DNA tiles and DNA origami have been introduced, but the dynamics of the large-scale lattice assembly of such modules is still poorly understood. Here, we focus on the dynamics of two-dimensional surface-assisted DNA origami lattice assembly at mica and lipid substrates and the techniques for prospective three-dimensional assemblies, and finally, we summarize the potential applications of such systems.
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Affiliation(s)
- Sofia Julin
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Adrian Keller
- Paderborn
University, Technical and Macromolecular
Chemistry, Warburger
Str. 100, 33098 Paderborn, Germany,
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland,LIBER
Center of Excellence, Aalto University, 00076 Aalto, Finland,
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9
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Yang N, Wang Y, Wang X, Zhang F, Xiao Y, Yan B, Zhang T, Liu X, Li Y. Label-Free Detection of DNA Supramolecular Structure Formation by Surface-Enhanced Raman Spectroscopy. J Phys Chem Lett 2022; 13:6208-6214. [PMID: 35770782 DOI: 10.1021/acs.jpclett.2c01461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The precise self-assembly of DNA molecules can be used to create nanoprecision supramolecular materials. However, the lack of methods to characterize such supramolecular materials limits their development. Surface-enhanced Raman spectroscopy (SERS) is widely used to detect the secondary structure of simple DNA molecules, but its application in the revealing of complex DNA supramolecular information remains challenging. Herein, we proposed a modified SERS-based platform able to provide structural information on DNA supramolecular materials. The silver nanoparticle-enhanced substrate uses acetonitrile as an internal standard and modifier, and calcium ions are used as an aggregating agent to induce the formation of stable "hotspots" of silver nanoparticles, where the base planes in DNA supramolecules are perpendicular to the surface of the substrate, obtaining enhanced Raman signals of base ring in both single-stranded DNA and DNA supramolecules for the first time. The structure of DNA supramolecules was efficiently characterized using this technique, showing the great application potential of this technique in the structural analysis of nucleic acids and their ligands.
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Affiliation(s)
- Ni Yang
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
| | - Yunpeng Wang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Xiaotong Wang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Fenghai Zhang
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
| | - Yanlong Xiao
- The Second Hospital of Jilin University, Jilin University, Changchun 130041, P. R. China
| | - Bingdi Yan
- The Second Hospital of Jilin University, Jilin University, Changchun 130041, P. R. China
| | - Ting Zhang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Xin Liu
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Yang Li
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
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Surface Assembly of DNA Origami on a Lipid Bilayer Observed Using High-Speed Atomic Force Microscopy. Molecules 2022; 27:molecules27134224. [PMID: 35807467 PMCID: PMC9268156 DOI: 10.3390/molecules27134224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022] Open
Abstract
The micrometer-scale assembly of various DNA nanostructures is one of the major challenges for further progress in DNA nanotechnology. Programmed patterns of 1D and 2D DNA origami assembly using specific DNA strands and micrometer-sized lattice assembly using cross-shaped DNA origami were performed on a lipid bilayer surface. During the diffusion of DNA origami on the membrane surface, the formation of lattices and their rearrangement in real-time were observed using high-speed atomic force microscopy (HS-AFM). The formed lattices were used to further assemble DNA origami tiles into their cavities. Various patterns of lattice–tile complexes were created by changing the interactions between the lattice and tiles. For the control of the nanostructure formation, the photo-controlled assembly and disassembly of DNA origami were performed reversibly, and dynamic assembly and disassembly were observed on a lipid bilayer surface using HS-AFM. Using a lipid bilayer for DNA origami assembly, it is possible to perform a hierarchical assembly of multiple DNA origami nanostructures, such as the integration of functional components into a frame architecture.
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11
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Xu Z, Huang Y, Yin H, Zhu X, Tian Y, Min Q. DNA origami-based protein manipulation systems: From function regulation to biological application. Chembiochem 2021; 23:e202100597. [PMID: 34958167 DOI: 10.1002/cbic.202100597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/18/2021] [Indexed: 11/07/2022]
Abstract
Proteins directly participate in tremendous physiological processes and mediate a variety of cellular functions. However, precise manipulation of proteins with predefined relative position and stoichiometry for understanding protein-protein interactions and guiding cellular behaviors are still challenging. With superior programmability of DNA molecules, DNA origami technology is able to construct arbitrary nanostructures that can accurately control the arrangement of proteins with various functionalities to solve these problems. Herein, starting from the classification of DNA origami nanostructures and the category of assembled proteins, we summarize the existing DNA origami-based protein manipulation systems (PMSs), review the advances on the regulation of their functions, and discuss their applications in cellular behavior modulation and disease therapy. Moreover, the limitations and potential directions of DNA origami-based PMSs are also presented, which may offer guidance for rational construction and ingenious application.
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Affiliation(s)
- Ziqi Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Yide Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Hao Yin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Xurong Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
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12
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Guo R, Li M, Zuo X. DNA Framework-Mediated Geometric Renormalization of Gold Nanoparticles on a Two-Dimensional Fluidic Membrane Interface. Chempluschem 2021; 86:1472-1475. [PMID: 34520133 DOI: 10.1002/cplu.202100344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/02/2021] [Indexed: 01/03/2023]
Abstract
The precise arrangement of single entity is a crucial objective of nanoscience and holds great promise in various fields such as biology and material science. In this work, we develop a "DNA framework-mediated geometric renormalization" (DFMGR) strategy to reassemble gold nanoparticles into specific geometric shapes on a 2-dimensional (2D) fluidic membrane interface. Cholesterol-modified AuNPs are randomly anchored on the supported lipid bilayer (SLB) via the cholesterol-lipid interaction. We demonstrate that AuNPs are laterally mobile on SLB and could be further rearranged into a specific geometric shape by DNA framework containing algebraically topological DNA arms. Using scanning electron microscope (SEM) imaging approach, simple geometric shapes, such as points assembled by monomers, line segments assembled by dimers, triangles assembled by trimers are visually presented. Interestingly, we found that the statistic angle (58.77°) and side length (12.21 nm) of triangles obtained from SEM images were both agreed well with the theoretical angle of 60° and side length of 12.58 nm. And the relative error of the angle calculated was as low as 0.33 %. These results indicated that the DFMGR strategy showed precise regulation ability for the AuNPs renormalization. We believe that DNA framework-mediated geometric renormalization strategy would be a powerful means for regulating ligand-receptor interactions in biosystems and for nanoparticle assembling in material science.
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Affiliation(s)
- Ruiyan Guo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University
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13
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Xin Y, Shen B, Kostiainen MA, Grundmeier G, Castro M, Linko V, Keller A. Scaling Up DNA Origami Lattice Assembly. Chemistry 2021; 27:8564-8571. [PMID: 33780583 PMCID: PMC8252642 DOI: 10.1002/chem.202100784] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 12/31/2022]
Abstract
The surface-assisted hierarchical assembly of DNA origami nanostructures is a promising route to fabricate regular nanoscale lattices. In this work, the scalability of this approach is explored and the formation of a homogeneous polycrystalline DNA origami lattice at the mica-electrolyte interface over a total surface area of 18.75 cm2 is demonstrated. The topological analysis of more than 50 individual AFM images recorded at random locations over the sample surface showed only minuscule and random variations in the quality and order of the assembled lattice. The analysis of more than 450 fluorescence microscopy images of a quantum dot-decorated DNA origami lattice further revealed a very homogeneous surface coverage over cm2 areas with only minor boundary effects at the substrate edges. At total DNA costs of € 0.12 per cm2 , this large-scale nanopatterning technique holds great promise for the fabrication of functional surfaces.
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Affiliation(s)
- Yang Xin
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| | - Boxuan Shen
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Mauri A. Kostiainen
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Guido Grundmeier
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| | - Mario Castro
- Grupo Interdisciplinar de Sistemas Complejos and Instituto de Investigación TecnológicaUniversidad Pontificia Comillas de MadridMadrid28015Spain
| | - Veikko Linko
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
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14
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Constructing Large 2D Lattices Out of DNA-Tiles. Molecules 2021; 26:molecules26061502. [PMID: 33801952 PMCID: PMC8000633 DOI: 10.3390/molecules26061502] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.
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15
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Li F, Li J, Dong B, Wang F, Fan C, Zuo X. DNA nanotechnology-empowered nanoscopic imaging of biomolecules. Chem Soc Rev 2021; 50:5650-5667. [DOI: 10.1039/d0cs01281e] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA nanotechnology has led to the rise of DNA nanostructures, which possess programmable shapes and are capable of organizing different functional molecules and materials. A variety of DNA nanostructure-based imaging probes have been developed.
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Affiliation(s)
- Fan Li
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Jiang Li
- Bioimaging Center
- Shanghai Synchrotron Radiation Facility
- Zhangjiang Laboratory
- Shanghai Advanced Research Institute
- Chinese Academy of Sciences
| | - Baijun Dong
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Fei Wang
- Frontiers Science Center for Transformative Molecules
- School of Chemistry and Chemical Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- China
| | - Chunhai Fan
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Xiaolei Zuo
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
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16
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Liu S, Murata S, Kawamata I. DNA Ring Motif with Flexible Joints. MICROMACHINES 2020; 11:mi11110987. [PMID: 33142895 PMCID: PMC7693582 DOI: 10.3390/mi11110987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/17/2022]
Abstract
The invention of DNA origami has expanded the geometric complexity and functionality of DNA nanostructures. Using DNA origami technology, we develop a flexible multi-joint ring motif as a novel self-assembling module. The motif can connect with each other through self-complementary sequences on its segments. The flexible joints can be fixed in a straightened position as desired, thereby allowing the motif to take various shapes. We can adjust the number of flexible joints and the number of connectable segments, thereby enabling programmable self-assembly of the motif. We successfully produced the motif and evaluated several self-assembly patterns. The proposed multi-joint ring motif can provide a novel method for creating functional molecular devices.
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Affiliation(s)
- Shiyun Liu
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (S.L.); (S.M.)
| | - Satoshi Murata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (S.L.); (S.M.)
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (S.L.); (S.M.)
- Natural Science Division, Faculty of Core Research, Ochanomizu University, Tokyo 112-8610, Japan
- Correspondence:
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17
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Kielar C, Zhu S, Grundmeier G, Keller A. Quantitative Assessment of Tip Effects in Single-Molecule High-Speed Atomic Force Microscopy Using DNA Origami Substrates. Angew Chem Int Ed Engl 2020; 59:14336-14341. [PMID: 32485088 PMCID: PMC7496922 DOI: 10.1002/anie.202005884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Indexed: 01/19/2023]
Abstract
High-speed atomic force microscopy (HS-AFM) is widely employed in the investigation of dynamic biomolecular processes at a single-molecule level. However, it remains an open and somewhat controversial question, how these processes are affected by the rapidly scanned AFM tip. While tip effects are commonly believed to be of minor importance in strongly binding systems, weaker interactions may significantly be disturbed. Herein, we quantitatively assess the role of tip effects in a strongly binding system using a DNA origami-based single-molecule assay. Despite its femtomolar dissociation constant, we find that HS-AFM imaging can disrupt monodentate binding of streptavidin (SAv) to biotin (Bt) even under gentle scanning conditions. To a lesser extent, this is also observed for the much stronger bidentate SAv-Bt complex. The presented DNA origami-based assay can be universally employed to quantify tip effects in strongly and weakly binding systems and to optimize the experimental settings for their reliable HS-AFM imaging.
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Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
- Present address: Institute of Resource EcologyHelmholtz-Zentrum Dresden-RossendorfBautzner Landstraße 40001328DresdenGermany
| | - Siqi Zhu
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| | - Guido Grundmeier
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| | - Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
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18
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Kielar C, Zhu S, Grundmeier G, Keller A. Quantitative Assessment of Tip Effects in Single‐Molecule High‐Speed Atomic Force Microscopy Using DNA Origami Substrates. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular Chemistry Paderborn University Warburger Str. 100 33098 Paderborn Germany
- Present address: Institute of Resource Ecology Helmholtz-Zentrum Dresden-Rossendorf Bautzner Landstraße 400 01328 Dresden Germany
| | - Siqi Zhu
- Technical and Macromolecular Chemistry Paderborn University Warburger Str. 100 33098 Paderborn Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry Paderborn University Warburger Str. 100 33098 Paderborn Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry Paderborn University Warburger Str. 100 33098 Paderborn Germany
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19
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Fan S, Cheng J, Liu Y, Wang D, Luo T, Dai B, Zhang C, Cui D, Ke Y, Song J. Proximity-Induced Pattern Operations in Reconfigurable DNA Origami Domino Array. J Am Chem Soc 2020; 142:14566-14573. [DOI: 10.1021/jacs.0c06061] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Sisi Fan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongfang Wang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tao Luo
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bin Dai
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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20
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Cao HH, Abel GR, Gu Q, Gueorguieva GAV, Zhang Y, Nanney WA, Provencio ET, Ye T. Seeding the Self-Assembly of DNA Origamis at Surfaces. ACS NANO 2020; 14:5203-5212. [PMID: 32053349 DOI: 10.1021/acsnano.9b09348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Unlike supramolecular self-assembly methods that can organize many distinct components into designer shapes in a homogeneous solution (e.g., DNA origami), only relatively simple, symmetric structures consisting of a few distinct components have been self-assembled at solid surfaces. As the self-assembly process is confined to the surface/interface by mostly nonspecific attractive interactions, an open question is how these interfacial interactions affect multicomponent self-assembly. To gain a mechanistic understanding of the roles of the surface environment in DNA origami self-assembly, here we studied the oligonucleotide-assisted folding of a long single-stranded DNA (ssDNA scaffold) that was end-tethered to a dynamic surface, which could actively regulate the DNA-surface interactions. The results showed that even weak surface attractions can lead to defective structures by inhibiting the merging of multiple domains into complete structures. A combination of surface anchoring and deliberate regulation of DNA-surface interactions allowed us to depart from the existing paradigm of surface confinement via nonspecific interactions and enabled DNA origami folding to proceed in a solution-like environment. Importantly, our strategy retains the key advantages of surface-mediated self-assembly. For example, surface-anchored oligonucleotides could sequence-specifically initiate the growth of DNA origamis of specific sizes and shapes. Our work enables information to be encoded into a surface and expressed into complex DNA surface architectures for potential nanoelectronic and nanophotonic applications. In addition, our approach to surface confinement may facilitate the 2D self-assembly of other molecular components, such as proteins, as maintaining conformational freedom may be a general challenge in the self-assembly of complex structures at surfaces.
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Affiliation(s)
- Huan H Cao
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Gary R Abel
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Qufei Gu
- Materials and Biomaterials Science and Engineering, University of California, Merced, California 95343, United States
| | | | - Yehan Zhang
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Warren A Nanney
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Eric T Provencio
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Tao Ye
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
- Materials and Biomaterials Science and Engineering, University of California, Merced, California 95343, United States
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21
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Fan S, Wang D, Cheng J, Liu Y, Luo T, Cui D, Ke Y, Song J. Information Coding in a Reconfigurable DNA Origami Domino Array. Angew Chem Int Ed Engl 2020; 59:12991-12997. [PMID: 32304157 DOI: 10.1002/anie.202003823] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Indexed: 01/26/2023]
Abstract
DNA nanostructures with programmable nanoscale patterns has been achieved in the past decades, and molecular information coding (MIC) on those designed nanostructures has gained increasing attention for information security. However, achieving steganography and cryptography synchronously on DNA nanostructures remains a challenge. Herein, we demonstrated MIC in a reconfigurable DNA origami domino array (DODA), which can reconfigure intrinsic patterns but keep the DODA outline the same for steganography. When a set of keys (DNA strands) are added, the cryptographic data can be translated into visible patterns within DODA. More complex cryptography with the ASCII code within a programmable 6×6 lattice is demonstrated to demosntrate the versatility of MIC in the DODA. Furthermore, an anti-counterfeiting approach based on conformational transformation-mediated toehold strand displacement reaction is designed to protect MIC from decoding and falsification.
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Affiliation(s)
- Sisi Fan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dongfang Wang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tao Luo
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
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22
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Fan S, Wang D, Cheng J, Liu Y, Luo T, Cui D, Ke Y, Song J. Information Coding in a Reconfigurable DNA Origami Domino Array. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sisi Fan
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Dongfang Wang
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Tao Luo
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
| | - Jie Song
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
- Institute of Cancer and Basic Medicine (IBMC) Chinese Academy of Sciences The Cancer Hospital of the University of Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
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23
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Xin Y, Ji X, Grundmeier G, Keller A. Dynamics of lattice defects in mixed DNA origami monolayers. NANOSCALE 2020; 12:9733-9743. [PMID: 32324191 DOI: 10.1039/d0nr01252a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The surface-assisted hierarchical assembly of DNA nanostructures into regular lattices is not only a promising route toward the fabrication of molecular lithography masks over macroscopic surface areas, but also represents an intriguing model system that enables the direct real-time observation of interface-related dynamic phenomena such as adsorption, desorption, and diffusion that are hardly accessible in other lattice-forming systems. In this work, we employ in situ high-speed atomic force microscopy to investigate the development of mixed DNA origami monolayers consisting of DNA origami triangles with threefold symmetry in the presence of rectangular DNA origami impurities with fourfold symmetry. The dynamic formation and annealing of the resulting defects is monitored in dependence of the triangle-to-rectangle ratio and correlated with the achieved lattice order. We find that the overall order of the formed DNA origami monolayer is rather resilient with regard to the presence of impurities. We even find indications that the deliberate addition of impurities at low concentrations may lead to slightly improved lattice order, presumable because they facilitate the dynamic rearrangement of neighboring lattice triangles and thus aid the annealing of non-impurity defects. Deliberate doping of DNA origami lattices with differently shaped impurities during assembly may thus provide a route toward further enhancing lattice quality via impurity-assisted annealing of lattice defects.
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Affiliation(s)
- Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Xueyin Ji
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany.
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24
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Sato Y, Morita M, Suzuki Y. Session 1SCA-Utilizing soft compartments/interfaces for the creation of artificial biosystems. Biophys Rev 2020; 12:257-259. [PMID: 32067194 DOI: 10.1007/s12551-020-00647-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/11/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
- Yusuke Sato
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8502, Japan.
| | - Masamune Morita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, 305-8566, Japan.
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-Aza Aoba, Aoba-ku, Sendai, 980-8578, Japan.
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25
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Carloni LE, Bezzu CG, Bonifazi D. Patterning Porous Networks through Self-Assembly of Programmed Biomacromolecules. Chemistry 2019; 25:16179-16200. [PMID: 31491049 DOI: 10.1002/chem.201902576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/11/2019] [Indexed: 11/08/2022]
Abstract
Two-dimensional (2D) porous networks are of great interest for the fabrication of complex organized functional materials for potential applications in nanotechnologies and nanoelectronics. This review aims at providing an overview of bottom-up approaches towards the engineering of 2D porous networks by using biomacromolecules, with a particular focus on nucleic acids and proteins. The first part illustrates how the advancements in DNA nanotechnology allowed for the attainment of complex ordered porous two-dimensional DNA nanostructures, thanks to a biomimetic approach based on DNA molecules self-assembly through specific hydrogen-bond base pairing. The second part focuses the attention on how polypeptides and proteins structural properties could be used to engineer organized networks templating the formation of multifunctional materials. The structural organization of all examples is discussed as revealed by scanning probe microscopy or transmission electron microscopy imaging techniques.
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Affiliation(s)
- Laure-Elie Carloni
- Department of Chemistry and Namur Research College (NARC), University of Namur, Rue de Bruxelles 61, Namur, 5000, Belgium
| | - C Grazia Bezzu
- Cardiff University, School of Chemistry, Park Place, Main Building, CF10 3AT, Cardiff, Wales, UK
| | - Davide Bonifazi
- Cardiff University, School of Chemistry, Park Place, Main Building, CF10 3AT, Cardiff, Wales, UK
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26
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Yu Y, Zhou Y, Zhu M, Liu M, Zhu H, Chen Y, Su G, Chen W, Peng H. Programming a split G-quadruplex in a DNA nanocage and its microRNA imaging in live cells. Chem Commun (Camb) 2019; 55:5131-5134. [PMID: 30973555 DOI: 10.1039/c9cc02096a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A novel approach to program target-responsive devices by incorporating the split G4 motifs in a DNA nanocage has been developed. The rigid prism outcompetes the flexible one in reaction kinetics and signal/background ratios, which can be easily internalized by cells and successfully applied in microRNA imaging in live cells.
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Affiliation(s)
- Yanyan Yu
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China.
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27
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Fan S, Wang D, Kenaan A, Cheng J, Cui D, Song J. Create Nanoscale Patterns with DNA Origami. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805554. [PMID: 31018040 DOI: 10.1002/smll.201805554] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/16/2019] [Indexed: 05/21/2023]
Abstract
Structural deoxyribonucleic acid (DNA) nanotechnology offers a robust platform for diverse nanoscale shapes that can be used in various applications. Among a wide variety of DNA assembly strategies, DNA origami is the most robust one in constructing custom nanoshapes and exquisite patterns. In this account, the static structural and functional patterns assembled on DNA origami are reviewed, as well as the reconfigurable assembled architectures regulated through dynamic DNA nanotechnology. The fast progress of dynamic DNA origami nanotechnology facilitates the construction of reconfigurable patterns, which can further be used in many applications such as optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.
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Affiliation(s)
- Sisi Fan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dongfang Wang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ahmad Kenaan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200011, China
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28
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Endo M. AFM-based single-molecule observation of the conformational changes of DNA structures. Methods 2019; 169:3-10. [PMID: 30978504 DOI: 10.1016/j.ymeth.2019.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/01/2019] [Accepted: 04/05/2019] [Indexed: 01/26/2023] Open
Abstract
Direct visualization of the biomolecules of interest is a straightforward way to elucidate the physical properties of individual molecules and their reaction processes. Atomic force microscopy (AFM) enables direct imaging of biomolecules in suitable solution conditions. As AFM visualizes the molecules at a nanometer-scale spatial resolution, a versatile observation platform is required for precise imaging of the molecules in action. The DNA origami technology allows precise placement of target molecules in a designed nanostructure, enabling their detection at the single-molecule level. We used DNA origami technology for visualizing the detailed movement of target molecules in reactions using high-speed AFM (HS-AFM), which enables the analysis of dynamic movement of biomolecules with a subsecond time resolution. By combining the DNA origami system and HS-AFM, DNA conformational changes, including G-quadruplex formation and disruption and B-Z transition, were visualized. In addition, enzyme-based reactions such as DNA recombination were also visualized at the single-molecule level using this combined observation system. Moreover, the enzyme-based reaction could be directly regulated in the DNA origami frame by imposing structural stress on the substrate DNAs to elucidate the reaction mechanism. These target-orientated observation systems should contribute to a detailed analysis of biomolecular motions in real time at molecular resolution.
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Affiliation(s)
- Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan.
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29
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Kielar C, Ramakrishnan S, Fricke S, Grundmeier G, Keller A. Dynamics of DNA Origami Lattice Formation at Solid-Liquid Interfaces. ACS APPLIED MATERIALS & INTERFACES 2018; 10:44844-44853. [PMID: 30501167 DOI: 10.1021/acsami.8b16047] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The self-organized formation of regular patterns is not only a fascinating topic encountered in a multitude of natural and artificial systems, but also presents a versatile and powerful route toward large-scale nanostructure assembly and materials synthesis. The hierarchical, interface-assisted assembly of DNA origami nanostructures into regular, 2D lattices represents a particularly promising example, as the resulting lattices may exhibit an astonishing degree of order and can be further utilized as masks in molecular lithography. Here, we thus investigate the development of order in such 2D DNA origami lattices assembled on mica surfaces by employing in situ high-speed atomic force microscopy imaging. DNA origami lattice formation is found to resemble thin-film growth in several aspects. In particular, the Na+/Mg2+ ratio controls DNA origami adsorption, surface diffusion, and desorption, and is thus equivalent in its effects to substrate temperature which controls adatom dynamics in thin-film deposition. Consequently, we observe a pronounced dependence of lattice order on Na+ concentration. At low Na+ concentrations, lattice formation resembles random deposition and results in unordered monolayers, whereas very high Na+ concentrations are accompanied by rapid diffusion and especially DNA origami desorption, which prevent lattice formation. At intermediate Na+ concentrations, highly ordered DNA origami lattices are obtained that display an intricate symmetry, stemming from the complex shape of the employed Rothemund triangle. Nevertheless, even under such optimized conditions, the lattices display a considerable number of defects, including grain boundaries, point and line defects, and screw-like dislocations. By monitoring the dynamics of selected lattice defects, we identify mechanisms that limit the obtainable degree of lattice order. Possible routes toward further increasing lattice order by postassembly annealing are discussed.
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Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Sebastian Fricke
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
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30
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Petersen P, Tikhomirov G, Qian L. Information-based autonomous reconfiguration in systems of interacting DNA nanostructures. Nat Commun 2018; 9:5362. [PMID: 30560865 PMCID: PMC6299139 DOI: 10.1038/s41467-018-07805-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/28/2018] [Indexed: 12/31/2022] Open
Abstract
The dynamic interactions between complex molecular structures underlie a wide range of sophisticated behaviors in biological systems. In building artificial molecular machines out of DNA, an outstanding challenge is to develop mechanisms that can control the kinetics of interacting DNA nanostructures and that can compose the interactions together to carry out system-level functions. Here we show a mechanism of DNA tile displacement that follows the principles of toehold binding and branch migration similar to DNA strand displacement, but occurs at a larger scale between interacting DNA origami structures. Utilizing this mechanism, we show controlled reaction kinetics over five orders of magnitude and programmed cascades of reactions in multi-structure systems. Furthermore, we demonstrate the generality of tile displacement for occurring at any location in an array in any order, illustrated as a tic-tac-toe game. Our results suggest that tile displacement is a simple-yet-powerful mechanism that opens up the possibility for complex structural components in artificial molecular machines to undergo information-based reconfiguration in response to their environments.
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Affiliation(s)
- Philip Petersen
- Biology, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Grigory Tikhomirov
- Bioengineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Lulu Qian
- Bioengineering, California Institute of Technology, Pasadena, CA, 91125, USA. .,Computer Science, California Institute of Technology, Pasadena, CA, 91125, USA.
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