1
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Zhao F, Frandsen M, Capodaglio S, Sleiman HF. DNA-Mediated Peptide Assembly into Protein Mimics. J Am Chem Soc 2024; 146:1946-1956. [PMID: 38226787 DOI: 10.1021/jacs.3c08984] [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: 01/17/2024]
Abstract
The design of new protein structures is challenging due to their vast sequence space and the complexity of protein folding. Here, we report a new modular DNA-templated strategy to construct protein mimics. We achieve the spatial control of multiple peptide units by conjugation with DNA and hybridization to a branched DNA trimer template followed by covalent stapling of the preorganized peptides into a single unit. A library of protein mimics with different lengths, sequences, and heptad registers has been efficiently constructed. DNA-templated protein mimics show an α-helix or coiled-coil motif formation even when they are constructed from weakly interacting peptide units. Their attached DNA handles can be used to exert dynamic control over the protein mimics' secondary and tertiary structures. This modular strategy will facilitate the development of DNA-encoded protein libraries for the rapid discovery of new therapeutics, enzymes, and antibody mimics.
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Affiliation(s)
- Fangzhou Zhao
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Martin Frandsen
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, Aarhus 8000, Denmark
| | - Sabrina Capodaglio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma I-43124, Italy
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
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2
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Yin H, Cheng Q, Bardelang D, Wang R. Challenges and Opportunities of Functionalized Cucurbiturils for Biomedical Applications. JACS AU 2023; 3:2356-2377. [PMID: 37772183 PMCID: PMC10523374 DOI: 10.1021/jacsau.3c00273] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 09/30/2023]
Abstract
Cucurbit[n]uril (CB[n]) macrocycles (especially CB[5] to CB[8]) have shown exceptional attributes since their discovery in 2000. Their stability, water solubility, responsiveness to several stimuli, and remarkable binding properties have enabled a growing number of biological applications. Yet, soon after their discovery, the challenge of their functionalization was set. Nevertheless, after more than two decades, a myriad of CB[n] derivatives has been described, many of them used in cells or in vivo for advanced applications. This perspective summarizes key advances of this burgeoning field and points to the next opportunities and remaining challenges to fully express the potential of these fascinating macrocycles in biology and biomedical sciences.
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Affiliation(s)
- Hang Yin
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University
of Macau, Taipa, Macau 999078, China
| | - Qian Cheng
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University
of Macau, Taipa, Macau 999078, China
| | | | - Ruibing Wang
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University
of Macau, Taipa, Macau 999078, China
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3
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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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4
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Wang T, Bai T, Tan Z, Ohayon YP, Sha R, Vecchioni S, Seeman NC, Wei B. Mesojunction-Based Design Paradigm of Structural DNA Nanotechnology. J Am Chem Soc 2023; 145:2455-2460. [PMID: 36657115 DOI: 10.1021/jacs.2c11731] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mesojunctions were introduced as a basic type of crossover configuration in the early development of structural DNA nanotechnology. However, the investigations of self-assembly from multiple mesojunction complexes have been overlooked in comparison to their counterparts based on regular junctions. In this work, we designed standardized component strands for the construction of complex mesojunction lattices. Three typical mesojunction configurations with three and four arms were showcased in the self-assembly of 1-, 2-, and 3-dimensional lattices constructed from both a scaffold-free tiling approach and a scaffolded origami approach.
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Affiliation(s)
- Tianqi Wang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Tanxi Bai
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Zhenyu Tan
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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5
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Li S, Wang Y, Ge W, Zhang W, Lu B, Feng F, Ni C, Xiao SJ. Tuning the Roundabout of Four-Point-Star Tiles with the Core Arm Length of Three Half-Turns for 2D DNA Arrays. Chemistry 2023; 29:e202202863. [PMID: 36251733 DOI: 10.1002/chem.202202863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Indexed: 11/05/2022]
Abstract
By rationally adjusting the weaving modes of point-star tiles, the curvature inherent in the tiles can be changed, and various DNA nanostructures can be assembled, such as planar wireframe meshes, perforated wireframe tubes, and curved wireframe polyhedra. Based on the weaving and tiling architectures for traditional point-star tiles with the core arm length at two DNA half-turns, we improved the weaving modes of our newly reported four-point-star tiles with the core arm length at three half-turns to adjust their curvature and rigidity for assembling 2D arrays of DNA grids and tubes. Following our previous terms and methods to analyze the structural details of E-tiling tubes, we used the chiral indices (n,m) to describe the most abundant tube of typical assemblies; especially, we applied both one-locus and/or dual-locus biotin/streptavidin (SA) labelling strategies to define the configurations of two specific tubes, along with the absolute conformations of their component tiles. Such structural details of the DNA tubes composed of tiles with addressable concave and convex faces and packing directions should help us understand their physio-chemical and biological properties, and therefore promote their applications in drug delivery, biocatalysis, biomedicine, etc.
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Affiliation(s)
- Shijie Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Yantong Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Wei Ge
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Wei Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Biao Lu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Feiyang Feng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Caihong Ni
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
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6
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John J, Joseph A, Kadavan LJ, Prabhu PS, Prabhu DJ, John F, George J. DNA Nanostructures in Pharmaceutical Applications. ChemistrySelect 2022. [DOI: 10.1002/slct.202203004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jinju John
- Bioorganic Laboratory Department of Chemistry Sacred Heart College (Autonomous), Thevara Kochi Kerala India 682013
| | - Ajinsh Joseph
- Bioorganic Laboratory Department of Chemistry Sacred Heart College (Autonomous), Thevara Kochi Kerala India 682013
| | - Liya J. Kadavan
- Bioorganic Laboratory Department of Chemistry Sacred Heart College (Autonomous), Thevara Kochi Kerala India 682013
| | - Prathibha S. Prabhu
- Bioorganic Laboratory Department of Chemistry Sacred Heart College (Autonomous), Thevara Kochi Kerala India 682013
| | - Deepak J. Prabhu
- Maharajas College (Government Autonomous) Park Avenue Road, Opposite Subash Bose Park Ernakulam Kochi Kerala India 682011
| | - Franklin John
- Bioorganic Laboratory Department of Chemistry Sacred Heart College (Autonomous), Thevara Kochi Kerala India 682013
| | - Jinu George
- Bioorganic Laboratory Department of Chemistry Sacred Heart College (Autonomous), Thevara Kochi Kerala India 682013
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7
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Mao D, Lu C, Zhang R, Zhu L, Song Y, Feng C, Zhang Q, Chen T, Yang Y, Chen G, Zhu X, Tan W. Computer-Aided Design of DNA Self-Limited Assembly for Relative Quantification of Membrane Proteins. Anal Chem 2022; 94:10263-10270. [PMID: 35726775 DOI: 10.1021/acs.analchem.2c01909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Immunofluorescence imaging of cells plays a vital role in biomedical research and clinical diagnosis. However, when it is applied to relative quantification of proteins, it suffers from insufficient fluorescence intensity or partial overexposure, resulting in inaccurate relative quantification. Herein, we report a computer-aided design of DNA self-limited assembly (CAD-SLA) technology and apply it for relative quantification of membrane proteins, a concept proposed for the first time. CAD-SLA can achieve exponential cascade signal amplification in one pot and terminate at any desired level. By conjugating CAD-SLA with immunofluorescence, in situ imaging of cell membrane proteins is achieved with a controllable amplification level. Besides, comprehensive fluorescence intensity information from fluorescent images can be obtained, accurately showing relative quantitative information. Slight protein expression differences previously indistinguishable by immunofluorescence or Western blotting can now be discriminated, making fluorescence imaging-based relative quantification a promising tool for membrane protein analysis. From the perspectives of both DNA self-assembly technology and immunofluorescence technology, this work has solved difficult problems and provided important reference for future development.
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Affiliation(s)
- Dongsheng Mao
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, P. R. China.,Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Cuicui Lu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Runchi Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Liucun Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Yuchen Song
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Qianqian Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Tianshu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Yu Yang
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.,Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022, P. R. China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, P. R. China
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8
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Zhou K, Mei Z, Lei Y, Guan Z, Mao C, Li Y. Boosted Productivity in Single-Tile-Based DNA Polyhedra Assembly by Simple Cation Replacement. Chembiochem 2022; 23:e202200138. [PMID: 35676202 DOI: 10.1002/cbic.202200138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/08/2022] [Indexed: 11/11/2022]
Abstract
Cations such as divalent magnesium ion (Mg2+ ) play an essential role in DNA self-assembly. However, the strong electrostatic shielding effect of Mg2+ would be disadvantageous in some situations that require relatively weak interactions to allow a highly reversible error-correcting mechanism in the process of assembly. Herein, by substituting the conventional divalent Mg2+ with monovalent sodium ion (Na+ ), we have achieved one-pot high-yield assembly of tile-based DNA polyhedra at micromolar concentration of tiles, at least 10 times higher than the DNA concentrations reported previously. This strategy takes advantage of coexisting counterions and is expected to surmount the major obstacle to potential applications of such DNA nanostructures: large-scale production.
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Affiliation(s)
- Kaixuan Zhou
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Zhichao Mei
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Yunxiang Lei
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Zhen Guan
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Yulin Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction Engineering, School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, P. R. China
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9
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Zhang W, Jiang C, Guo X, Muhammad Faran Ashraf Baig M, Ni C, Xiao SJ. 2D DNA lattices assembled from DX-coupled tiles. J Colloid Interface Sci 2022; 616:499-508. [DOI: 10.1016/j.jcis.2022.02.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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10
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Rothenbühler S, Iacovache I, Langenegger SM, Zuber B, Häner R. Complex DNA Architectonics─Self-Assembly of Amphiphilic Oligonucleotides into Ribbons, Vesicles, and Asterosomes. Bioconjug Chem 2022; 34:70-77. [PMID: 35357155 PMCID: PMC9854621 DOI: 10.1021/acs.bioconjchem.2c00077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The precise arrangement of structural subunits is a key factor for the proper shape and function of natural and artificial supramolecular assemblies. In DNA nanotechnology, the geometrically well-defined double-stranded DNA scaffold serves as an element of spatial control for the precise arrangement of functional groups. Here, we describe the supramolecular assembly of chemically modified DNA hybrids into diverse types of architectures. An amphiphilic DNA duplex serves as the sole structural building element of the nanosized supramolecular structures. The morphology of the assemblies is governed by a single subunit of the building block. The chemical nature of this subunit, i.e., polyethylene glycols of different chain length or a carbohydrate moiety, exerts a dramatic influence on the architecture of the assemblies. Cryo-electron microscopy revealed the arrangement of the individual DNA duplexes within the different constructs. Thus, the morphology changes from vesicles to ribbons with increasing length of a linear polyethylene glycol. Astoundingly, attachment of a N-acetylgalactosamine carbohydrate to the DNA duplex moiety produces an unprecedented type of star-shaped architecture. The novel DNA architectures presented herein imply an extension of the current concept of DNA materials and shed new light on the fast-growing field of DNA nanotechnology.
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Affiliation(s)
- Simon Rothenbühler
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Ioan Iacovache
- Institute
of Anatomy, University of Bern, Baltzerstrasse 2, CH-3012 Bern, Switzerland
| | - Simon M. Langenegger
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Benoît Zuber
- Institute
of Anatomy, University of Bern, Baltzerstrasse 2, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland,
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11
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Gao D, Ma N, Yan X, Ji M, Zhu JJ, Min Q, Tian Y. Low-entropy lattices engineered through bridged DNA origami frames. Chem Sci 2021; 13:283-289. [PMID: 35059178 PMCID: PMC8694312 DOI: 10.1039/d1sc05060e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/30/2021] [Indexed: 11/21/2022] Open
Abstract
The transformation from disorder to order in self-assembly is an autonomous entropy-decreasing process. The spatial organization of nanoscale anisotropic building blocks involves the intrinsic heterogeneity in three dimensions and requires sufficiently precise control to coordinate intricate interactions. Only a few approaches have been shown to achieve the anisotropic extension from components to assemblies. Here, we demonstrate the ability to engineer three-dimensional low-entropy lattices at the nucleotide level from modular DNA origami frames. Through the programmable DNA bridging strategy, DNA domains of the same composition are periodically arranged in the crystal growth directions. We combine the site-specific positioning of guest nanoparticles to reflect the anisotropy control, which is validated by small-angle X-ray scattering and electron microscopy. We expect that our DNA origami-mediated crystallization method will facilitate both the exploration of refined self-assembly platforms and the creation of anisotropic metamaterials. Through the bridging principle, DNA origami building blocks are integrated into ordered self-assembled structures. Periodically arranged DNA domains can locate the nanoparticles in a uniform site to achieve precise control of the contents.![]()
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Affiliation(s)
- Di Gao
- 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
| | - Ningning Ma
- 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
| | - Xuehui Yan
- 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
| | - Min Ji
- 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
| | - Jun-Jie 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
| | - 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
| | - 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 .,Shenzhen Research Institute of Nanjing University Shenzhen 518000 China
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12
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Singh U, Morya V, Datta B, Ghoroi C, Bhatia D. Stimuli Responsive, Programmable DNA Nanodevices for Biomedical Applications. Front Chem 2021; 9:704234. [PMID: 34277571 PMCID: PMC8278982 DOI: 10.3389/fchem.2021.704234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
Of the multiple areas of applications of DNA nanotechnology, stimuli-responsive nanodevices have emerged as an elite branch of research owing to the advantages of molecular programmability of DNA structures and stimuli-responsiveness of motifs and DNA itself. These classes of devices present multiples areas to explore for basic and applied science using dynamic DNA nanotechnology. Herein, we take the stake in the recent progress of this fast-growing sub-area of DNA nanotechnology. We discuss different stimuli, motifs, scaffolds, and mechanisms of stimuli-responsive behaviours of DNA nanodevices with appropriate examples. Similarly, we present a multitude of biological applications that have been explored using DNA nanodevices, such as biosensing, in vivo pH-mapping, drug delivery, and therapy. We conclude by discussing the challenges and opportunities as well as future prospects of this emerging research area within DNA nanotechnology.
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Affiliation(s)
- Udisha Singh
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Vinod Morya
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Bhaskar Datta
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Chinmay Ghoroi
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, India
- Chemical Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, India
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13
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Cui Y, Yan J, Wei B. Hybrid Wireframe DNA Nanostructures with Scaffolded and Scaffold‐Free Modules. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Yan Cui
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
- Beijing No. 2 Middle School—Chaoyang Beijing 100025 China
| | - Jun Yan
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Bryan Wei
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
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14
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Hybrid Wireframe DNA Nanostructures with Scaffolded and Scaffold‐Free Modules. Angew Chem Int Ed Engl 2021; 60:9345-9350. [DOI: 10.1002/anie.202015564] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/21/2020] [Indexed: 01/04/2023]
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15
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Zhang T. DNA origami-based microtubule analogue. NANOTECHNOLOGY 2020; 31:50LT01. [PMID: 33034304 DOI: 10.1088/1361-6528/abb395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A microtubule hollow structure is one type of cytoskeletons which directs a number of important cellular functions. When recapitulating biological events in a cell-free system, artificial frames are often required to execute similar cytoskeletal functions in synthetic systems. Here, I report a prototypical microtubular assembly using a DNA origami nanostructuring method. Through structural design at the molecular level, 32HB (helices bundle)-based DNA origami objects can form micrometers long tubular structures via shape-complementary side patterns engagement and head-to-tail blunt-end stacking. Multiple parameters have been investigated to gain optimized polymerization conditions. Conformational change with an open vs closed hinge is also included, rendering conformational changes for a dynamic assembly. When implementing further improved external regulation with DNA dynamics (DNA strand displacement reactions or using other switchable non-canonical DNA secondary structures) or chemical stimuli, the DNA origami-based microtubule analogue will have great potential to assemble and disassemble on purpose and conduct significantly complicated cytoskeletal tasks in vitro.
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Affiliation(s)
- Tao Zhang
- Department of Applied Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, Shandong Province 264005, People's Republic of China
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16
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Chandrasekaran AR, Mathivanan J, Ebrahimi P, Vilcapoma J, Chen AA, Halvorsen K, Sheng J. Hybrid DNA/RNA nanostructures with 2'-5' linkages. NANOSCALE 2020; 12:21583-21590. [PMID: 33089274 PMCID: PMC7644649 DOI: 10.1039/d0nr05846g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nucleic acid nanostructures with different chemical compositions have shown utility in biological applications as they provide additional assembly parameters and enhanced stability. The naturally occurring 2'-5' linkage in RNA is thought to be a prebiotic analogue and has potential use in antisense therapeutics. Here, we report the first instance of DNA/RNA motifs containing 2'-5' linkages. We synthesized and incorporated RNA strands with 2'-5' linkages into different DNA motifs with varying number of branch points (a duplex, four arm junction, double crossover motif and tensegrity triangle motif). Using experimental characterization and molecular dynamics simulations, we show that hybrid DNA/RNA nanostructures can accommodate interspersed 2'-5' linkages with relatively minor effect on the formation of these structures. Further, the modified nanostructures showed improved resistance to ribonuclease cleavage, indicating their potential use in the construction of robust drug delivery vehicles with prolonged stability in physiological conditions.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- To whom correspondence should be addressed: (ARC), (JS)
| | - Johnsi Mathivanan
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Parisa Ebrahimi
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Alan A. Chen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
- To whom correspondence should be addressed: (ARC), (JS)
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17
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Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chem Rev 2020; 120:9420-9481. [DOI: 10.1021/acs.chemrev.0c00294] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Lu Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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18
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Piskunen P, Nummelin S, Shen B, Kostiainen MA, Linko V. Increasing Complexity in Wireframe DNA Nanostructures. Molecules 2020; 25:E1823. [PMID: 32316126 PMCID: PMC7221932 DOI: 10.3390/molecules25081823] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 11/17/2022] Open
Abstract
Structural DNA nanotechnology has recently gained significant momentum, as diverse design tools for producing custom DNA shapes have become more and more accessible to numerous laboratories worldwide. Most commonly, researchers are employing a scaffolded DNA origami technique by "sculpting" a desired shape from a given lattice composed of packed adjacent DNA helices. Albeit relatively straightforward to implement, this approach contains its own apparent restrictions. First, the designs are limited to certain lattice types. Second, the long scaffold strand that runs through the entire structure has to be manually routed. Third, the technique does not support trouble-free fabrication of hollow single-layer structures that may have more favorable features and properties compared to objects with closely packed helices, especially in biological research such as drug delivery. In this focused review, we discuss the recent development of wireframe DNA nanostructures-methods relying on meshing and rendering DNA-that may overcome these obstacles. In addition, we describe each available technique and the possible shapes that can be generated. Overall, the remarkable evolution in wireframe DNA structure design methods has not only induced an increase in their complexity and thus expanded the prevalent shape space, but also already reached a state at which the whole design process of a chosen shape can be carried out automatically. We believe that by combining cost-effective biotechnological mass production of DNA strands with top-down processes that decrease human input in the design procedure to minimum, this progress will lead us to a new era of DNA nanotechnology with potential applications coming increasingly into view.
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Affiliation(s)
- Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, P.O. Box 15100, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, P.O. Box 15100, 00076 Aalto, Finland
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19
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Ge H, Wang D, Pan Y, Guo Y, Li H, Zhang F, Zhu X, Li Y, Zhang C, Huang L. Sequence‐Dependent DNA Functionalization of Upconversion Nanoparticles and Their Programmable Assemblies. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Huan Ge
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Dongya Wang
- Departments of Radiology and CardiologyShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghai Jiao Tong University School of Medicine 600 Yishan Road Shanghai 200233 China
| | - Yue Pan
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Yuanyuan Guo
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Hongyu Li
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Fan Zhang
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Xinyuan Zhu
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Yuehua Li
- Departments of Radiology and CardiologyShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghai Jiao Tong University School of Medicine 600 Yishan Road Shanghai 200233 China
| | - Chuan Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Ling Huang
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
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20
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Ge H, Wang D, Pan Y, Guo Y, Li H, Zhang F, Zhu X, Li Y, Zhang C, Huang L. Sequence‐Dependent DNA Functionalization of Upconversion Nanoparticles and Their Programmable Assemblies. Angew Chem Int Ed Engl 2020; 59:8133-8137. [DOI: 10.1002/anie.202000831] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/17/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Huan Ge
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Dongya Wang
- Departments of Radiology and CardiologyShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghai Jiao Tong University School of Medicine 600 Yishan Road Shanghai 200233 China
| | - Yue Pan
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Yuanyuan Guo
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Hongyu Li
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Fan Zhang
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Xinyuan Zhu
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Yuehua Li
- Departments of Radiology and CardiologyShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghai Jiao Tong University School of Medicine 600 Yishan Road Shanghai 200233 China
| | - Chuan Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Ling Huang
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
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21
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Zhang Y, Reinhardt A, Wang P, Song J, Ke Y. Programming the Nucleation of DNA Brick Self-Assembly with a Seeding Strand. Angew Chem Int Ed Engl 2020; 59:8594-8600. [PMID: 32043698 DOI: 10.1002/anie.201915063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/13/2020] [Indexed: 01/13/2023]
Abstract
Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a "seed" strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4-7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self-assembly of DNA nanostructures.
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Affiliation(s)
- Yingwei Zhang
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100082, China
| | - Aleks Reinhardt
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Pengfei Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jie Song
- Department of Instrument Science and Engineering, School of Electronic Information and electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA, 30322, USA
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22
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Zhang Y, Reinhardt A, Wang P, Song J, Ke Y. Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yingwei Zhang
- State Key Laboratory of Chemical Resource Engineering College of Materials Science and Engineering Beijing University of Chemical Technology Beijing 100082 China
| | - Aleks Reinhardt
- Department of Chemistry University of Cambridge Cambridge CB2 1EW UK
| | - Pengfei Wang
- Institute of Molecular Medicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Jie Song
- Department of Instrument Science and Engineering School of Electronic Information and electrical Engineering Shanghai Jiao Tong University Shanghai 200127 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Emory University School of Medicine Atlanta GA 30322 USA
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23
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Wang L, Cheng L, Li G, Liu K, Zhang Z, Li P, Dong S, Yu W, Huang F, Yan X. A Self-Cross-Linking Supramolecular Polymer Network Enabled by Crown-Ether-Based Molecular Recognition. J Am Chem Soc 2020; 142:2051-2058. [PMID: 31905287 DOI: 10.1021/jacs.9b12164] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Supramolecular polymers based on host-guest molecular recognition have emerged as promising platforms for the development of smart materials. However, the studies on them are primarily conducted in solution and/or in the gel state. In contrast, little is known about dynamic properties and applications of supramolecular polymers in bulk. Herein, we present a self-cross-linking supramolecular polymer network (SPN) as a model system to understand the bulk properties controlled by noncovalent interactions. Specifically, the SPN monomer is composed of two benzo-21-crown-7 (B21C7) host units and two dialkylammonium salt guest moieties on a four-arm core, wherein complementary host-guest complexation drives the formation of the SPN with [2]pseudorotaxane linkages between B21C7 and ammonium motifs. The dynamic and reversible behaviors of the linkages are evaluated by measurement of viscoelasticity. The results indicate that the host-guest molecular recognition becomes highly dynamic at elevated temperature. Moreover, the relatively high activation energy of the SPN manifests itself as a new type of thermoplastic material with network topology freezing glass transition. Finally, we demonstrate how these findings provide insights into the malleability and processability of the SPN by simple demos. The fundamental understanding gained from the research on this SPN in bulk will facilitate the advancement and application of supramolecular materials.
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Affiliation(s)
- Lei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules , Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China
| | - Lin Cheng
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules , Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China
| | - Guangfeng Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules , Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China
| | - Kai Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules , Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China
| | - Zhaoming Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules , Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China
| | - Peitong Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules , Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China
| | - Shengyi Dong
- College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , People's Republic of China
| | - Wei Yu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules , Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China
| | - Feihe Huang
- State Key Laboratory of Chemical Engineering, Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry , Zhejiang University , Hangzhou 310027 , People's Republic of China
| | - Xuzhou Yan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules , Shanghai Jiao Tong University , Shanghai 200240 , People's Republic of China
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24
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Sanchez-Rueda EG, Rodriguez-Cristobal E, Moctezuma González CL, Hernandez-Garcia A. Protein-coated dsDNA nanostars with high structural rigidity and high enzymatic and thermal stability. NANOSCALE 2019; 11:18604-18611. [PMID: 31578534 DOI: 10.1039/c9nr05225a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA nanotechnology creates precise shape-specific nanostructures through the self-assembly of short ssDNA oligonucleotides. One such shape, which has relevant biomedical applications due to its multivalency, is the star. However, building star-like nanostructures with a large size (>100 nm) using ssDNA is complex and challenging. This study presents a novel strategy to prepare stiff and large dsDNA nanostars by assembling duplex DNA fragments into star-shapes that are subsequently coated with a virus-inspired protein. The protein binds dsDNA and overcomes the high structural flexibility of naked dsDNA. The nanostar-like dsDNA templates with up to six arms were prepared by self-assembly of PCR-produced dsDNA fragments (211 to 722 bp) with a central DNA junction. Through gel electrophoresis and Atomic Force Microscopy it is demonstrated that single dsDNA nanostars are self-assembled and coated with the protein, and this has a large stiffening effect on the nanostar. Furthermore, the coating significantly enhances stability at high temperatures and protects nanostars against nuclease degradation for at least 10 hours. This study shows that DNA-binding proteins can be harnessed as structural "rigidifiers" of flexible branched dsDNA templates. This strategy opens a way to prepare structurally defined hybrid protein-dsDNA nanostructures that could be exploited as building blocks for novel DNA nanomaterials.
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Affiliation(s)
- Eddie G Sanchez-Rueda
- Laboratory of Biomolecular Engineering and Bionanotechnology, Chemistry of Biomacromolecules Department, Institute of Chemistry, National Autonomous University of Mexico, Ciudad Universitaria, Coyoacan, Mexico City 04310, Mexico.
| | - Estefani Rodriguez-Cristobal
- Laboratory of Biomolecular Engineering and Bionanotechnology, Chemistry of Biomacromolecules Department, Institute of Chemistry, National Autonomous University of Mexico, Ciudad Universitaria, Coyoacan, Mexico City 04310, Mexico.
| | - Claudia L Moctezuma González
- Laboratory of Biomolecular Engineering and Bionanotechnology, Chemistry of Biomacromolecules Department, Institute of Chemistry, National Autonomous University of Mexico, Ciudad Universitaria, Coyoacan, Mexico City 04310, Mexico.
| | - Armando Hernandez-Garcia
- Laboratory of Biomolecular Engineering and Bionanotechnology, Chemistry of Biomacromolecules Department, Institute of Chemistry, National Autonomous University of Mexico, Ciudad Universitaria, Coyoacan, Mexico City 04310, Mexico.
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