1
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Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024; 13:1038-1058. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [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] [Indexed: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
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Affiliation(s)
- Xisen Cao
- 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
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, 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
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
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2
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Li Y, Zheng H, Lu H, Duan M, Li C, Li M, Li J, Wang L, Li Q, Chen J, Shen J. Noncanonical Condensation of Nucleic Acid Chains by Hydrophobic Gold Nanocrystals. JACS AU 2023; 3:2206-2215. [PMID: 37654586 PMCID: PMC10466341 DOI: 10.1021/jacsau.3c00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 09/02/2023]
Abstract
Nucleic acid condensates are essential for various biological processes and have numerous applications in nucleic acid nanotechnology, gene therapy, and mRNA vaccines. However, unlike the in vivo condensation that is dependent on motor proteins, the in vitro condensation efficiency remains to be improved. Here, we proposed a hydrophobic interaction-driven mechanism for condensing long nucleic acid chains using atomically precise hydrophobic gold nanoclusters (Au NCs). We found that hydrophobic Au NCs could condense long single-stranded DNA or RNA to form composites of spherical nanostructures, which further assembled into bead-shaped suprastructures in the presence of excessive Au NCs. Thus, suprastructures displayed gel-like behaviors, and Au NCs could diffuse freely inside the condensates, which resemble the collective motions of condensin complexes inside chromosomes. The dynamic hydrophobic interactions between Au NCs and bases allow for the reversible release of nucleic acids in the presence of mild triggering agents. Our method represents a significant advancement toward the development of more efficient and versatile nucleic acid condensation techniques.
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Affiliation(s)
- Yu Li
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai 201800, China
- Department
of Stem Cells and Regenerative Medicine, Translational Medicine Research
Center, Naval Medical University, 800, Xiangyin Road, Shanghai 200433 ,China
| | - Haoran Zheng
- 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
| | - Hui Lu
- Zhangjiang
Laboratory, 100 Haike
Road, Shanghai 201210, China
| | - Mulin Duan
- 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
| | - Cong 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
| | - Jiang Li
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Lihua Wang
- Zhangjiang
Laboratory, 100 Haike
Road, Shanghai 201210, China
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, 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
| | - Jing Chen
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Jianlei Shen
- 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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Shirt-Ediss B, Connolly J, Elezgaray J, Torelli E, Navarro SA, Bacardit J, Krasnogor N. Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists. Comput Struct Biotechnol J 2023; 21:3615-3626. [PMID: 37520280 PMCID: PMC10371787 DOI: 10.1016/j.csbj.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Designs for scaffolded DNA origami nanostructures are commonly and minimally published as the list of DNA staple and scaffold sequences required. In nearly all cases, high-level editable design files (e.g. caDNAno) which generated the low-level sequences are not made available. This de facto 'raw sequence' exchange format allows published origami designs to be re-attempted in the laboratory by other groups, but effectively stops designs from being significantly modified or re-purposed for new future applications. To make the raw sequence exchange format more accessible to further design and engineering, in this work we propose the first algorithmic solution to the inverse problem of converting staple/scaffold sequences back to a 'guide schematic' resembling the original origami schematic. The guide schematic can be used to aid the manual re-input of an origami into a CAD tool like caDNAno, hence recovering a high-level editable design file. Creation of a guide schematic can also be used to double check that a list of staple strand sequences does not have errors and indeed does assemble into a desired origami nanostructure prior to costly laboratory experimentation. We tested our reverse algorithm on 36 diverse origami designs from the literature and found that 29 origamis (81 %) had a good quality guide schematic recovered from raw sequences. Our software is made available at https://revnano.readthedocs.io.
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Affiliation(s)
- Ben Shirt-Ediss
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Jordan Connolly
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Juan Elezgaray
- Centre de Recherche Paul Pascal, CNRS, UMR503, Pessac 33600, France
| | - Emanuela Torelli
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Silvia Adriana Navarro
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Jaume Bacardit
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
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4
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Makino T, Nakane D, Tanaka M. Self-Assembled Micro-Sized Hexagons Built from Short DNA in a Crowded Environment. Chembiochem 2022; 23:e202200360. [PMID: 36200404 DOI: 10.1002/cbic.202200360] [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: 06/27/2022] [Revised: 10/05/2022] [Indexed: 02/03/2023]
Abstract
DNA programmable structures of various morphologies have attracted extensive attention due to their potential for materials science and biomedical applications. Here, we report the formation of micro-sized hexagons via assembly of only one pair of short double-stranded DNA in buffer-salt poly(ethylene glycol) solution. Each DNA strand had complementary bases with a two-base overhang. The procedure of heating and subsequent cooling of blunt-ended double-stranded DNA resulted in different assemblies. These results indicated that end-to-end adhesion at the terminals induced by complementary overhangs were required to construct the hexagonal DNA assemblies. The stable formation of the hexagons was highly dependent on heating temperature. In addition, concentration adjustments of DNA and poly(ethylene glycol) were essential. Circular dichroism spectral measurements and polarization microscopy observations indicated parallel alignment of double-stranded DNA in the hexagonal platelet. Self-assembled micro-sized hexagons composed of simple building blocks may have great potential for future biomedical device development.
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Affiliation(s)
- Tetsunao Makino
- Department of Engineering Science Graduate School of Informatics and Engineering, The University of Electro-Communications 1-5-1 Chofugaoka, Chofu, Tokyo, 182-8585, Japan
| | - Daisuke Nakane
- Department of Engineering Science Graduate School of Informatics and Engineering, The University of Electro-Communications 1-5-1 Chofugaoka, Chofu, Tokyo, 182-8585, Japan
| | - Makiko Tanaka
- Department of Engineering Science Graduate School of Informatics and Engineering, The University of Electro-Communications 1-5-1 Chofugaoka, Chofu, Tokyo, 182-8585, Japan
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5
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Cumberworth A, Frenkel D, Reinhardt A. Simulations of DNA-Origami Self-Assembly Reveal Design-Dependent Nucleation Barriers. NANO LETTERS 2022; 22:6916-6922. [PMID: 36037484 PMCID: PMC9479157 DOI: 10.1021/acs.nanolett.2c01372] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which involves both the binding of staple strands and the folding of the scaffold strand, is unclear. Here, using Monte Carlo simulations of a lattice model of DNA origami, we find that some, but not all, designs can have a nucleation barrier and that this barrier disappears at lower temperatures, rationalizing the success of isothermal assembly. We show that the height of the nucleation barrier depends primarily on the coaxial stacking of staples that are adjacent on the same helix, a parameter that can be modified with staple design. Creating a nucleation barrier to DNA-origami assembly could be useful in optimizing assembly times and yields, while eliminating the barrier may allow for fast molecular sensors that can assemble/disassemble without hysteresis in response to changes in the environment.
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Affiliation(s)
| | - Daan Frenkel
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Aleks Reinhardt
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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6
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Masukawa M, Sato Y, Yu F, Tsumoto K, Yoshikawa K, Takinoue M. Water-in-water droplets selectively uptake self-assembled DNA nano/microstructures: a versatile method for purification in DNA nanotechnology. Chembiochem 2022; 23:e202200240. [PMID: 35686962 PMCID: PMC9544409 DOI: 10.1002/cbic.202200240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/08/2022] [Indexed: 11/10/2022]
Abstract
DNA is an excellent material for constructing self-assembled nano/microstructures. Owing to the widespread use of DNA as a building block in laboratories and industry, it is desirable to increase the efficiency of all steps involved in producing self-assembled DNA structures. One of the bottlenecks is the purification required to separate the excess components from the target structures. This paper describes a purification method based on the fractionation by water-in-water (W/W) droplets composed of phase-separated dextran-rich droplets in a polyethylene glycol (PEG)-rich continuous phase. The dextran-rich droplets facilitate the selective uptake of self-assembled DNA nano/microstructures and allow the separation of the target structure. This study investigates the ability to purify DNA origami, DNA hydrogels, and DNA microtubes. The W/W-droplet fractionation allows the purification of structures of a broad size spectrum without changes to the protocol. By quantifying the activity of deoxyribozyme-modified DNA origami after W/W-droplet purification, this study demonstrates that this method sufficiently preserves the accessibility to the surface of a functional DNA nanostructure. It is considered that the W/W-droplet fractionation could become one of the standard methods for the purification of self-assembled DNA nano/microstructures for biomedical and nanotechnology applications owing to its low cost and simplicity.
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Affiliation(s)
- Marcos Masukawa
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku, Computer Science, JAPAN
| | - Yusuke Sato
- Kyushu Institute of Technology - Iizuka Campus: Kyushu Kogyo Daigaku - Iizuka Campus, Intelligent and Control Systems, JAPAN
| | - Fujio Yu
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku, Computer Science, JAPAN
| | - Kanta Tsumoto
- Mie University: Mie Daigaku, Chemistry for Materials, JAPAN
| | - Kenichi Yoshikawa
- Kyoto University: Kyoto Daigaku, Center for Integrative Medicine and Physics, Institute for Advanced Study, JAPAN
| | - Masahiro Takinoue
- Tokyo Institute of Technology, Department of Computer Science, 4259-J2-36 Nagatsuta-cho, Midori-ku, 226-8502, Yokohama, JAPAN
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7
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Sakai Y, Wilkens GD, Wolski K, Zapotoczny S, Heddle JG. Topogami: Topologically Linked DNA Origami. ACS NANOSCIENCE AU 2022; 2:57-63. [PMID: 35211697 PMCID: PMC8861903 DOI: 10.1021/acsnanoscienceau.1c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
DNA origami is a widely used DNA nanotechnology that allows construction of two-dimensional and three-dimensional nanometric shapes. The designability and rigidity of DNA origami make it an ideal material for construction of topologically linked molecules such as catenanes, which are attractive for their potential as motors and molecular machines. However, a general method for production of topologically linked DNA origami has been lacking. Here, we show that catenated single-stranded DNA circles can be produced and used as a universal scaffold for the production of topologically linked (catenated) DNA origami structures where the individual linked structures can be of any arbitrary design. Assembly of these topologically linked DNA origami structures is achieved via a simple one-pot annealing protocol.
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Affiliation(s)
- Yusuke Sakai
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Gerrit D Wilkens
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.,Postgraduate School of Molecular Medicine, Żwirki I Wigury 61, 02-091 Warsaw, Poland
| | - Karol Wolski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Szczepan Zapotoczny
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Jonathan G Heddle
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
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8
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Gangrade A, Stephanopoulos N, Bhatia D. Programmable, self-assembled DNA nanodevices for cellular programming and tissue engineering. NANOSCALE 2021; 13:16834-16846. [PMID: 34622910 DOI: 10.1039/d1nr04475c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
DNA-based nanotechnology has evolved into an autonomous, highly innovative, and dynamic field of research at the nexus of supramolecular chemistry, nanotechnology, materials science, and biotechnology. DNA-based materials, including origami nanodevices, have started to emerge as an ideal scaffold for use in cellular programming, tissue engineering, and drug delivery applications. We cover herein the applications for DNA as a scaffold for interfacing with, and guiding, the activity of biological systems like cells and tissues. Although DNA is a highly programmable molecular building block, it suffers from a lack of functional capacity for guiding and modulating cells. Coupling DNA to biologically active molecules can bestow bioactivity to these nanodevices. The main goal of such nanodevices is to synthesize systems that can bind to cells and mimic the extracellular environment, and serve as a highly promising toolbox for multiple applications in cellular programming and tissue engineering. DNA-based programmable devices offer a highly promising approach for programming collections of cells, tissue engineering, and regenerative medicine applications.
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Affiliation(s)
- Ankit Gangrade
- Biological Engineering, Indian Institute of Technology Gandhinagar, India.
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, India.
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, India
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9
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The biological applications of DNA nanomaterials: current challenges and future directions. Signal Transduct Target Ther 2021; 6:351. [PMID: 34620843 PMCID: PMC8497566 DOI: 10.1038/s41392-021-00727-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 02/08/2023] Open
Abstract
DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.
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10
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Noteborn WEM, Abendstein L, Sharp TH. One-Pot Synthesis of Defined-Length ssDNA for Multiscaffold DNA Origami. Bioconjug Chem 2020; 32:94-98. [PMID: 33307668 PMCID: PMC7830112 DOI: 10.1021/acs.bioconjchem.0c00644] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA origami nanostructures generally require a single scaffold strand of specific length, combined with many small staple strands. Ideally, the length of the scaffold strand should be dictated by the size of the designed nanostructure. However, synthesizing arbitrary-length single-stranded DNA in sufficient quantities is difficult. Here, we describe a straightforward and accessible method to produce defined-length ssDNA scaffolds using PCR and subsequent selective enzymatic digestion with T7 exonuclease. This approach produced ssDNA with higher yields than other methods and without the need for purification, which significantly decreased the time from PCR to obtaining pure DNA origami. Furthermore, this enabled us to perform true one-pot synthesis of defined-size DNA origami nanostructures. Additionally, we show that multiple smaller ssDNA scaffolds can efficiently substitute longer scaffolds in the formation of DNA origami.
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Affiliation(s)
- Willem E M Noteborn
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Leoni Abendstein
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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11
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Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies. Molecules 2020; 25:molecules25153386. [PMID: 32722650 PMCID: PMC7435391 DOI: 10.3390/molecules25153386] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022] Open
Abstract
DNA origami nanocarriers have emerged as a promising tool for many biomedical applications, such as biosensing, targeted drug delivery, and cancer immunotherapy. These highly programmable nanoarchitectures are assembled into any shape or size with nanoscale precision by folding a single-stranded DNA scaffold with short complementary oligonucleotides. The standard scaffold strand used to fold DNA origami nanocarriers is usually the M13mp18 bacteriophage’s circular single-stranded DNA genome with limited design flexibility in terms of the sequence and size of the final objects. However, with the recent progress in automated DNA origami design—allowing for increasing structural complexity—and the growing number of applications, the need for scalable methods to produce custom scaffolds has become crucial to overcome the limitations of traditional methods for scaffold production. Improved scaffold synthesis strategies will help to broaden the use of DNA origami for more biomedical applications. To this end, several techniques have been developed in recent years for the scalable synthesis of single stranded DNA scaffolds with custom lengths and sequences. This review focuses on these methods and the progress that has been made to address the challenges confronting custom scaffold production for large-scale DNA origami assembly.
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12
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DNA Nanotechnology for Building Sensors, Nanopores and Ion-Channels. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:331-370. [PMID: 31713205 DOI: 10.1007/978-981-13-9791-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology has revolutionised the capabilities to shape and control three-dimensional structures at the nanometre scale. Designer sensors, nanopores and ion-channels built from DNA have great potential for both cross-disciplinary research and applications. Here, we introduce the concept of structural DNA nanotechnology, including DNA origami, and give an overview of the work flow from design to assembly, characterisation and application of DNA-based functional systems. Chemical functionalisation of DNA has opened up pathways to transform static DNA structures into dynamic nanomechanical sensors. We further introduce nanopore sensing as a powerful label-free single-molecule technique and discuss how it can benefit from DNA nanotechnology. Especially exciting is the possibility to create membrane-inserted DNA nanochannels that mimic their protein-based natural counterparts in form and function. In this chapter we review the status quo of DNA sensors, nanopores and ion channels, highlighting opportunities and challenges for their future development.
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13
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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14
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Lam MH, Briggs K, Kastritis K, Magill M, Madejski GR, McGrath JL, de Haan HW, Tabard-Cossa V. Entropic Trapping of DNA with a Nanofiltered Nanopore. ACS APPLIED NANO MATERIALS 2019; 2:4773-4781. [PMID: 32577609 PMCID: PMC7310961 DOI: 10.1021/acsanm.9b00606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Elucidating the kinetics of DNA passage through a solid-state nanopore is a fertile field of research, and mechanisms for controlling capture, passage, and trapping of biopolymers are likely to find numerous technological applications. Here we present a nanofiltered nanopore device, which forms an entropic cage for DNA following first passage through the nanopore, trapping the translocated DNA and permitting recapture for subsequent reanalysis and investigation of kinetics of passage under confinement. We characterize the trapping properties of this nanodevice by driving individual DNA polymers into the nanoscale gap separating the nanofilter and the pore, forming an entropic cage similar to a "two pores in series" device, leaving polymers to diffuse in the cage for various time lengths, and attempting to recapture the same molecule. We show that the cage results in effectively permanent trapping when the radius of gyration of the target polymer is significantly larger than the radii of the pores in the nanofilter. We also compare translocation dynamics as a function of translocation direction in order to study the effects of confinement on DNA just prior to translocation, providing further insight into the nanopore translocation process. This nanofiltered nanopore device realizes simple fabrication of a femtoliter nanoreactor in which to study fundamental biophysics and biomolecular reactions on the single-molecule level. The device provides an electrically-permeable single-molecule trap with a higher entropic barrier to escape than previous attempts to fabricate similar structures.
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Affiliation(s)
- Michelle H. Lam
- Department of Physics, University of Ottawa, Ottawa, ON, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, ON, Canada
| | | | - Martin Magill
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
| | - Gregory R. Madejski
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - James L. McGrath
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - Hendrick W. de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
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15
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Wolfrum M, Schwarz RJ, Schwarz M, Kramer M, Richert C. Stabilizing DNA nanostructures through reversible disulfide crosslinking. NANOSCALE 2019; 11:14921-14928. [PMID: 31360975 DOI: 10.1039/c9nr05143k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Designed DNA nanostructures can be generated in a wide range of sizes and shapes and have the potential to become exciting tools in material sciences, catalysis and medicine. However, DNA nanostructures are thermally labile assemblies of delicate biomacromolecules, and the lability hampers the use in many applications. Disulfide crosslinking is nature's successful approach to stabilize folded proteins against denaturation. It is therefore interesting to ask whether similar approaches can be used to stabilize DNA nanostructures. Here we report the synthesis of two 2'-deoxynucleoside phosphoramidites and two nucleosides linked to controlled pore glass that can be used to prepare oligodeoxynucleotides with protected thiol groups via automated DNA synthesis. Strands with one, two, three or four thiol-bearing nucleotides were prepared. One nicked duplex and three different nanostructures were assembled, the protected thiols were liberated under non-denaturing conditions, and disulfide crosslinking was induced with oxygen. Up to 19 crosslinks were thus placed in folded DNA structures up to 1456 nucleotides in size. The crosslinked structures had increased thermal stability, with UV-melting points 9-50 °C above that of the control structure. Disulfides were converted back to free thiols under reducing conditions. The redox-dependent increase in stability makes crosslinked DNA nanostructures attractive for the construction of responsive materials and biomedical applications.
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Affiliation(s)
- Manpreet Wolfrum
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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16
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Hu Y, Niemeyer CM. From DNA Nanotechnology to Material Systems Engineering. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806294. [PMID: 30767279 DOI: 10.1002/adma.201806294] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/29/2018] [Indexed: 05/25/2023]
Abstract
In the past 35 years, DNA nanotechnology has grown to a highly innovative and vibrant field of research at the interface of chemistry, materials science, biotechnology, and nanotechnology. Herein, a short summary of the state of research in various subdisciplines of DNA nanotechnology, ranging from pure "structural DNA nanotechnology" over protein-DNA assemblies, nanoparticle-based DNA materials, and DNA polymers to DNA surface technology is given. The survey shows that these subdisciplines are growing ever closer together and suggests that this integration is essential in order to initiate the next phase of development. With the increasing implementation of machine-based approaches in microfluidics, robotics, and data-driven science, DNA-material systems will emerge that could be suitable for applications in sensor technology, photonics, as interfaces between technical systems and living organisms, or for biomimetic fabrication processes.
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Affiliation(s)
- Yong Hu
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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17
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Engelhardt FS, Praetorius F, Wachauf CH, Brüggenthies G, Kohler F, Kick B, Kadletz KL, Pham PN, Behler KL, Gerling T, Dietz H. Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds. ACS NANO 2019; 13:5015-5027. [PMID: 30990672 PMCID: PMC6992424 DOI: 10.1021/acsnano.9b01025] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
DNA origami nano-objects are usually designed around generic single-stranded "scaffolds". Many properties of the target object are determined by details of those generic scaffold sequences. Here, we enable designers to fully specify the target structure not only in terms of desired 3D shape but also in terms of the sequences used. To this end, we built design tools to construct scaffold sequences de novo based on strand diagrams, and we developed scalable production methods for creating design-specific scaffold strands with fully user-defined sequences. We used 17 custom scaffolds having different lengths and sequence properties to study the influence of sequence redundancy and sequence composition on multilayer DNA origami assembly and to realize efficient one-pot assembly of multiscaffold DNA origami objects. Furthermore, as examples for functionalized scaffolds, we created a scaffold that enables direct, covalent cross-linking of DNA origami via UV irradiation, and we built DNAzyme-containing scaffolds that allow postfolding DNA origami domain separation.
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Affiliation(s)
- Floris
A. S. Engelhardt
- Physics
Department and Lehrstuhl für Bioverfahrenstechnik, Technical University of Munich, Am Coulombwall 4a, 85748 Garching bei München, Germany
| | - Florian Praetorius
- Physics
Department and Lehrstuhl für Bioverfahrenstechnik, Technical University of Munich, Am Coulombwall 4a, 85748 Garching bei München, Germany
| | - Christian H. Wachauf
- Physics
Department and Lehrstuhl für Bioverfahrenstechnik, Technical University of Munich, Am Coulombwall 4a, 85748 Garching bei München, Germany
| | - Gereon Brüggenthies
- Physics
Department and Lehrstuhl für Bioverfahrenstechnik, Technical University of Munich, Am Coulombwall 4a, 85748 Garching bei München, Germany
| | - Fabian Kohler
- Physics
Department and Lehrstuhl für Bioverfahrenstechnik, Technical University of Munich, Am Coulombwall 4a, 85748 Garching bei München, Germany
| | - Benjamin Kick
- Physics
Department and Lehrstuhl für Bioverfahrenstechnik, Technical University of Munich, Am Coulombwall 4a, 85748 Garching bei München, Germany
| | - Karoline L. Kadletz
- Physics
Department and Lehrstuhl für Bioverfahrenstechnik, Technical University of Munich, Am Coulombwall 4a, 85748 Garching bei München, Germany
| | - Phuong Nhi Pham
- Physics
Department and Lehrstuhl für Bioverfahrenstechnik, Technical University of Munich, Am Coulombwall 4a, 85748 Garching bei München, Germany
| | - Karl L. Behler
- Physics
Department and Lehrstuhl für Bioverfahrenstechnik, Technical University of Munich, Am Coulombwall 4a, 85748 Garching bei München, Germany
| | - Thomas Gerling
- Physics
Department and Lehrstuhl für Bioverfahrenstechnik, Technical University of Munich, Am Coulombwall 4a, 85748 Garching bei München, Germany
| | - Hendrik Dietz
- Physics
Department and Lehrstuhl für Bioverfahrenstechnik, Technical University of Munich, Am Coulombwall 4a, 85748 Garching bei München, Germany
- E-mail:
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18
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Roth E, Glick Azaria A, Girshevitz O, Bitler A, Garini Y. Measuring the Conformation and Persistence Length of Single-Stranded DNA Using a DNA Origami Structure. NANO LETTERS 2018; 18:6703-6709. [PMID: 30352164 DOI: 10.1021/acs.nanolett.8b02093] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Measuring the mechanical properties of single-stranded DNA (ssDNA) is a challenge that has been addressed by different methods lately. The short persistence length, fragile structure, and the appearance of stem loops complicate the measurement, and this leads to a large variability in the measured values. Here we describe an innovative method based on DNA origami for studying the biophysical properties of ssDNA. By synthesizing a DNA origami structure that consists of two rigid rods with an ssDNA segment between them, we developed a method to characterize the effective persistence length of a random-sequence ssDNA while allowing the formation of stem loops. We imaged the structure with an atomic force microscope (AFM); the rigid rods provide a means for the exact identification of the ssDNA ends. This leads to an accurate determination of the end-to-end distance of each ssDNA segment, and by fitting the measured distribution to the ideal chain polymer model we measured an effective persistence length of 1.98 ± 0.72 nm. This method enables one to measure short or long strands of ssDNA, and it can cope with the formation of stem loops that are often formed along ssDNA. We envision that this method can be used for measuring stem loops for determining the effect of repetitive nucleotide sequences and environmental conditions on the mechanical properties of ssDNA and the effect of interacting proteins with ssDNA. We further noted that the method can be extended to nanoprobes for measuring the interactions of specific DNA sequences, because the DNA origami rods (or similar structures) can hold multiple fluorescent probes that can be easily detected.
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Affiliation(s)
- Efrat Roth
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Alex Glick Azaria
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Olga Girshevitz
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Arkady Bitler
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
| | - Yuval Garini
- Physics Department and Institute for Nanotechnology , Bar Ilan University , Ramat Gan 5290002 , Israel
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19
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Nafisi PM, Aksel T, Douglas SM. Construction of a novel phagemid to produce custom DNA origami scaffolds. Synth Biol (Oxf) 2018; 3. [PMID: 30984875 PMCID: PMC6461039 DOI: 10.1093/synbio/ysy015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA origami, a method for constructing nanoscale objects, relies on a long single strand of DNA to act as the 'scaffold' to template assembly of numerous short DNA oligonucleotide 'staples'. The ability to generate custom scaffold sequences can greatly benefit DNA origami design processes. Custom scaffold sequences can provide better control of the overall size of the final object and better control of low-level structural details, such as locations of specific base pairs within an object. Filamentous bacteriophages and related phagemids can work well as sources of custom scaffold DNA. However, scaffolds derived from phages require inclusion of multi-kilobase DNA sequences in order to grow in host bacteria, and those sequences cannot be altered or removed. These fixed-sequence regions constrain the design possibilities of DNA origami. Here, we report the construction of a novel phagemid, pScaf, to produce scaffolds that have a custom sequence with a much smaller fixed region of 393 bases. We used pScaf to generate new scaffolds ranging in size from 1512 to 10 080 bases and demonstrated their use in various DNA origami shapes and assemblies. We anticipate our pScaf phagemid will enhance development of the DNA origami method and its future applications.
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Affiliation(s)
- Parsa M Nafisi
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Tural Aksel
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Shawn M Douglas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
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20
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Nummelin S, Kommeri J, Kostiainen MA, Linko V. Evolution of Structural DNA Nanotechnology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703721. [PMID: 29363798 DOI: 10.1002/adma.201703721] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/17/2017] [Indexed: 05/24/2023]
Abstract
The research field entitled structural DNA nanotechnology emerged in the beginning of the 1980s as the first immobile synthetic nucleic acid junctions were postulated and demonstrated. Since then, the field has taken huge leaps toward advanced applications, especially during the past decade. This Progress Report summarizes how the controllable, custom, and accurate nanostructures have recently evolved together with powerful design and simulation software. Simultaneously they have provided a significant expansion of the shape space of the nanostructures. Today, researchers can select the most suitable fabrication methods, and design paradigms and software from a variety of options when creating unique DNA nanoobjects and shapes for a plethora of implementations in materials science, optics, plasmonics, molecular patterning, and nanomedicine.
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Affiliation(s)
- Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Juhana Kommeri
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
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21
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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22
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Kroener F, Heerwig A, Kaiser W, Mertig M, Rant U. Electrical Actuation of a DNA Origami Nanolever on an Electrode. J Am Chem Soc 2017; 139:16510-16513. [PMID: 29111693 DOI: 10.1021/jacs.7b10862] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Development of electrically powered DNA origami nanomachines requires effective means to actuate moving origami parts by externally applied electric fields. We demonstrate how origami nanolevers on an electrode can be manipulated (switched) at high frequency by alternating voltages. Orientation switching is long-time stable and can be induced by applying low voltages of 200 mV. The mechanical response time of a 100 nm long origami lever to an applied voltage step is less than 100 μs, allowing dynamic control of the induced motion. Moreover, through voltage assisted capture, origamis can be immobilized from folding solution without purification, even in the presence of excess staple strands. The results establish a way for interfacing and controlling DNA origamis with standard electronics, and enable their use as moving parts in electro-mechanical nanodevices.
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Affiliation(s)
- Felix Kroener
- Technische Universitaet Dresden , 01069 Dresden, Germany.,Dynamic Biosensors GmbH , 82152 Planegg, Germany
| | - Andreas Heerwig
- Kurt-Schwabe-Institut fuer Mess- und Sensortechnik Meinsberg e.V. , 04736 Waldheim, Germany
| | | | - Michael Mertig
- Technische Universitaet Dresden , 01069 Dresden, Germany.,Kurt-Schwabe-Institut fuer Mess- und Sensortechnik Meinsberg e.V. , 04736 Waldheim, Germany
| | - Ulrich Rant
- Dynamic Biosensors GmbH , 82152 Planegg, Germany
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23
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Wan N, Hong Z, Wang H, Fu X, Zhang Z, Li C, Xia H, Fang Y, Li M, Zhan Y, Yang X. A DNA Origami Mechanical Device for the Regulation of Microcosmic Structural Rigidity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700866. [PMID: 28902974 DOI: 10.1002/smll.201700866] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/28/2017] [Indexed: 06/07/2023]
Abstract
DNA origami makes it feasible to fabricate a tremendous number of DNA nanostructures with various geometries, dimensions, and functionalities. Moreover, an increasing amount of research on DNA nanostructures is focused on biological and biomedical applications. Here, the reversible regulation of microcosmic structural rigidity is accomplished using a DNA origami device in vitro. The designed DNA origami monomer is composed of an internal central axis and an external sliding tube. Due to the external tube sliding, the device transforms between flexible and rigid states. By transporting the device into the liposome, the conformational change of the origami device induces a structural change in the liposome. The results obtained demonstrate that the programmed DNA origami device can be applied to regulate the microcosmic structural rigidity of liposomes. Because microcosmic structural rigidity is important to cell proliferation and function, the results obtained potentially provide a foundation for the regulation of cell microcosmic structural rigidity using DNA nanostructures.
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Affiliation(s)
- Neng Wan
- National Education Base of Biological Science, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Zhouping Hong
- National Education Base of Biological Science, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Bei Shizhang Advanced Class of Life Science Research, co-founded by Huazhong University of Science and Technology & Institute of Biophysics, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Wuhan, 430074, P. R. China
| | - Huading Wang
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Xin Fu
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Ziyue Zhang
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Chao Li
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Bioinformatics, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Han Xia
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Yan Fang
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Department of Nanomedicine and Biopharmaceutics, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Yi Zhan
- Innovation Base of Life Science and Technology, Qiming College, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Bei Shizhang Advanced Class of Life Science Research, co-founded by Huazhong University of Science and Technology & Institute of Biophysics, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Wuhan, 430074, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Student Affairs Office, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Xiangliang Yang
- Department of Nanomedicine and Biopharmaceutics, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
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24
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Kramer M, Richert C. Enzyme-Free Ligation of 5'-Phosphorylated Oligodeoxynucleotides in a DNA Nanostructure. Chem Biodivers 2017; 14. [PMID: 28710838 DOI: 10.1002/cbdv.201700315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/12/2017] [Indexed: 01/05/2023]
Abstract
Multicomponent reactions are difficult synthetic transformations. For DNA, there is a special opportunity to align multiple strands in a folded nanostructure, so that they are preorganized to give a specific sequence. Multistrand reactions in DNA origami structures have previously been performed using photochemical crosslinking, 1,3-diploar cycloadditions or phosphoramidate-forming reactions. Here we report carbodiimide-driven phosphodiester formation in a small origami sheet that produces DNA strands up to 600 nucleotides in length in a single step. The method uses otherwise unmodified oligodeoxynucleotides with a 5'-terminal phosphate as starting materials. Compared to an enzymatic multistrand ligation involving linear duplexes, the carbodiimide-driven ligation gave fewer side products, as detected by gel electrophoresis. The full-length 600mer product was successfully amplified by polymerase chain reaction.
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Affiliation(s)
- Markus Kramer
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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25
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Wagenbauer KF, Engelhardt FAS, Stahl E, Hechtl VK, Stömmer P, Seebacher F, Meregalli L, Ketterer P, Gerling T, Dietz H. How We Make DNA Origami. Chembiochem 2017; 18:1873-1885. [PMID: 28714559 DOI: 10.1002/cbic.201700377] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Indexed: 12/14/2022]
Abstract
DNA origami has attracted substantial attention since its invention ten years ago, due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. Although the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know-how for designing and producing the particles with sufficient quality and for preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know-how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge. To foster faster progress, we share in this article the experience in making and preparing DNA origami that we have accumulated over recent years. We discuss design solutions for creating advanced structural motifs including corners and various types of hinges that expand the design space for the more rigid multilayer DNA origami and provide guidelines for preventing undesired aggregation and on how to induce specific oligomerization of multiple DNA origami building blocks. In addition, we provide detailed protocols and discuss the expected results for five key methods that allow efficient and damage-free preparation of DNA origami. These methods are agarose-gel purification, filtration through molecular cut-off membranes, PEG precipitation, size-exclusion chromatography, and ultracentrifugation-based sedimentation. The guide for creating advanced design motifs and the detailed protocols with their experimental characterization that we describe here should lower the barrier for researchers to accomplish the full DNA origami production workflow.
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Affiliation(s)
- Klaus F Wagenbauer
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Floris A S Engelhardt
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Evi Stahl
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Vera K Hechtl
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Pierre Stömmer
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Fabian Seebacher
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Letizia Meregalli
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Philip Ketterer
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Thomas Gerling
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Hendrik Dietz
- Physics Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
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26
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Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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27
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Schwarz RJ, Richert C. A four-helix bundle DNA nanostructure with binding pockets for pyrimidine nucleotides. NANOSCALE 2017; 9:7047-7054. [PMID: 28327725 DOI: 10.1039/c7nr00094d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Designed DNA nanostructures of impressive size have been described, but designed structures of the size of protein enzymes that bind organic ligands with high specificity are rare. Here we report a four-helix motif consisting of three synthetic strands with 65 base pairs and 165 nucleotides in total that folds well. Furthermore, we show that in the interior of this small folded DNA nanostructure, cavities can be set up that bind pyrimidine nucleotides with micromolar affinity. Base-specific binding for both thymidine and cytidine derivatives is demonstrated. The binding affinity depends on the position in the structure, as expected for recognition beyond simple base pairing. The folding motif reported here can help to expand DNA nanotechnology into the realm of selective molecular recognition that is currently dominated by protein-based enzymes and receptors.
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Affiliation(s)
- Rainer Joachim Schwarz
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany.
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28
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A Quick-responsive DNA Nanotechnology Device for Bio-molecular Homeostasis Regulation. Sci Rep 2016; 6:31379. [PMID: 27506964 PMCID: PMC4979213 DOI: 10.1038/srep31379] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/12/2016] [Indexed: 01/01/2023] Open
Abstract
Physiological processes such as metabolism, cell apoptosis and immune responses, must be strictly regulated to maintain their homeostasis and achieve their normal physiological functions. The speed with which bio-molecular homeostatic regulation occurs directly determines the ability of an organism to adapt to conditional changes. To produce a quick-responsive regulatory system that can be easily utilized for various types of homeostasis, a device called nano-fingers that facilitates the regulation of physiological processes was constructed using DNA origami nanotechnology. This nano-fingers device functioned in linked open and closed phases using two types of DNA tweezers, which were covalently coupled with aptamers that captured specific molecules when the tweezer arms were sufficiently close. Via this specific interaction mechanism, certain physiological processes could be simultaneously regulated from two directions by capturing one biofactor and releasing the other to enhance the regulatory capacity of the device. To validate the universal application of this device, regulation of the homeostasis of the blood coagulant thrombin was attempted using the nano-fingers device. It was successfully demonstrated that this nano-fingers device achieved coagulation buffering upon the input of fuel DNA. This nano-device could also be utilized to regulate the homeostasis of other types of bio-molecules.
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29
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Veneziano R, Ratanalert S, Zhang K, Zhang F, Yan H, Chiu W, Bathe M. Designer nanoscale DNA assemblies programmed from the top down. Science 2016; 352:1534. [PMID: 27229143 DOI: 10.1126/science.aaf4388] [Citation(s) in RCA: 405] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/03/2016] [Indexed: 12/16/2022]
Abstract
Scaffolded DNA origami is a versatile means of synthesizing complex molecular architectures. However, the approach is limited by the need to forward-design specific Watson-Crick base pairing manually for any given target structure. Here, we report a general, top-down strategy to design nearly arbitrary DNA architectures autonomously based only on target shape. Objects are represented as closed surfaces rendered as polyhedral networks of parallel DNA duplexes, which enables complete DNA scaffold routing with a spanning tree algorithm. The asymmetric polymerase chain reaction is applied to produce stable, monodisperse assemblies with custom scaffold length and sequence that are verified structurally in three dimensions to be high fidelity by single-particle cryo-electron microscopy. Their long-term stability in serum and low-salt buffer confirms their utility for biological as well as nonbiological applications.
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Affiliation(s)
- Rémi Veneziano
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kaiming Zhang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fei Zhang
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ 85287, USA
| | - Hao Yan
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ 85287, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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30
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Kalinowski M, Haug R, Said H, Piasecka S, Kramer M, Richert C. Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures. Chembiochem 2016; 17:1150-5. [PMID: 27225865 DOI: 10.1002/cbic.201600061] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 01/25/2023]
Abstract
The folding of long DNA strands into designed nanostructures has evolved into an art. Being based on linear chains only, the resulting nanostructures cannot readily be transformed into covalently linked frameworks. Covalently linking strands in the context of folded DNA structures requires a robust method that avoids sterically demanding reagents or enzymes. Here we report chemical ligation of the 3'-amino termini of oligonucleotides and 5'-phosphorylated partner strands in templated reactions that produce phosphoramidate linkages. These reactions produce inter-nucleotide linkages that are isoelectronic and largely isosteric to phosphodiesters. Ligations were performed at three levels of complexity, including the extension of branched DNA hybrids and the ligation of six scaffold strands in a small origami.
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Affiliation(s)
- Matthäus Kalinowski
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Rüdiger Haug
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Hassan Said
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Sylwia Piasecka
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Markus Kramer
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany.
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31
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Chandrasekaran AR, Anderson N, Kizer M, Halvorsen K, Wang X. Beyond the Fold: Emerging Biological Applications of DNA Origami. Chembiochem 2016; 17:1081-9. [PMID: 26928725 DOI: 10.1002/cbic.201600038] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/22/2023]
Abstract
The use of DNA as a material for nanoscale construction has blossomed in the past decade. This is largely attributable to the DNA origami technique, which has enabled construction of nanostructures ranging from simple two-dimensional sheets to complex three-dimensional objects with defined curves and edges. These structures are amenable to site-specific functionalization with nanometer precision, and have been shown to exhibit cellular biocompatibility and permeability. The DNA origami technique has already found widespread use in a variety of emerging biological applications such as biosensing, enzyme cascades, biomolecular analysis, biomimetics, and drug delivery. We highlight a few of these applications and comments on the prospects for this rapidly expanding field of research.
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Affiliation(s)
| | - Nate Anderson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. , .,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. ,
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32
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Niekamp S, Blumer K, Nafisi PM, Tsui K, Garbutt J, Douglas SM. Folding complex DNA nanostructures from limited sets of reusable sequences. Nucleic Acids Res 2016; 44:e102. [PMID: 27036861 PMCID: PMC4914096 DOI: 10.1093/nar/gkw208] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/18/2016] [Indexed: 02/06/2023] Open
Abstract
Scalable production of DNA nanostructures remains a substantial obstacle to realizing new applications of DNA nanotechnology. Typical DNA nanostructures comprise hundreds of DNA oligonucleotide strands, where each unique strand requires a separate synthesis step. New design methods that reduce the strand count for a given shape while maintaining overall size and complexity would be highly beneficial for efficiently producing DNA nanostructures. Here, we report a method for folding a custom template strand by binding individual staple sequences to multiple locations on the template. We built several nanostructures for well-controlled testing of various design rules, and demonstrate folding of a 6-kb template by as few as 10 unique strand sequences binding to 10 ± 2 locations on the template strand.
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Affiliation(s)
- Stefan Niekamp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Katy Blumer
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Parsa M Nafisi
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Kathy Tsui
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - John Garbutt
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Shawn M Douglas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
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33
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Chandrasekaran AR. Programmable DNA scaffolds for spatially-ordered protein assembly. NANOSCALE 2016; 8:4436-4446. [PMID: 26852879 DOI: 10.1039/c5nr08685j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed.
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34
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Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
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35
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Koch C, Wabbel K, Eber FJ, Krolla-Sidenstein P, Azucena C, Gliemann H, Eiben S, Geiger F, Wege C. Modified TMV Particles as Beneficial Scaffolds to Present Sensor Enzymes. FRONTIERS IN PLANT SCIENCE 2015; 6:1137. [PMID: 26734040 PMCID: PMC4689848 DOI: 10.3389/fpls.2015.01137] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/30/2015] [Indexed: 05/22/2023]
Abstract
Tobacco mosaic virus (TMV) is a robust nanotubular nucleoprotein scaffold increasingly employed for the high density presentation of functional molecules such as peptides, fluorescent dyes, and antibodies. We report on its use as advantageous carrier for sensor enzymes. A TMV mutant with a cysteine residue exposed on every coat protein (CP) subunit (TMVCys) enabled the coupling of bifunctional maleimide-polyethylene glycol (PEG)-biotin linkers (TMVCys/Bio). Its surface was equipped with two streptavidin [SA]-conjugated enzymes: glucose oxidase ([SA]-GOx) and horseradish peroxidase ([SA]-HRP). At least 50% of the CPs were decorated with a linker molecule, and all thereof with active enzymes. Upon use as adapter scaffolds in conventional "high-binding" microtiter plates, TMV sticks allowed the immobilization of up to 45-fold higher catalytic activities than control samples with the same input of enzymes. Moreover, they increased storage stability and reusability in relation to enzymes applied directly to microtiter plate wells. The functionalized TMV adsorbed to solid supports showed a homogeneous distribution of the conjugated enzymes and structural integrity of the nanorods upon transmission electron and atomic force microscopy. The high surface-increase and steric accessibility of the viral scaffolds in combination with the biochemical environment provided by the plant viral coat may explain the beneficial effects. TMV can, thus, serve as a favorable multivalent nanoscale platform for the ordered presentation of bioactive proteins.
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Affiliation(s)
- Claudia Koch
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Katrin Wabbel
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Fabian J. Eber
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Peter Krolla-Sidenstein
- Chemistry of Oxydic and Organic Interfaces, Karlsruhe Institute of Technology, Institute of Functional InterfacesKarlsruhe, Germany
| | - Carlos Azucena
- Chemistry of Oxydic and Organic Interfaces, Karlsruhe Institute of Technology, Institute of Functional InterfacesKarlsruhe, Germany
| | - Hartmut Gliemann
- Chemistry of Oxydic and Organic Interfaces, Karlsruhe Institute of Technology, Institute of Functional InterfacesKarlsruhe, Germany
| | - Sabine Eiben
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
| | - Fania Geiger
- Department of New Materials and Biosystems, Max-Planck-Institute for Intelligent SystemsStuttgart, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of StuttgartStuttgart, Germany
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36
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Brown S, Majikes J, Martínez A, Girón TM, Fennell H, Samano EC, LaBean TH. An easy-to-prepare mini-scaffold for DNA origami. NANOSCALE 2015; 7:16621-4. [PMID: 26413973 DOI: 10.1039/c5nr04921k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The DNA origami strategy for assembling designed supramolecular complexes requires ssDNA as a scaffold strand. A system is described that was designed approximately one third the length of the M13 bacteriophage genome for ease of ssDNA production. Folding of the 2404-base ssDNA scaffold into a variety of origami shapes with high assembly yields is demonstrated.
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Affiliation(s)
- S Brown
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen 2100, Denmark.
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37
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Scheible MB, Ong LL, Woehrstein JB, Jungmann R, Yin P, Simmel FC. A Compact DNA Cube with Side Length 10 nm. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:5200-5. [PMID: 26294348 PMCID: PMC4707664 DOI: 10.1002/smll.201501370] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/09/2015] [Indexed: 05/09/2023]
Abstract
A small and compact DNA cube with zeptoliter volume is constructed by means of a generalized DNA brick concept using short synthetic oligonucleotides with varying lengths. By mimicking design principles from the DNA origami technique, the DNA cube offers higher stability and assembly yields compared to other approaches. Its potential application as nanoscale fluorescent probe is demonstrated using super-resolution imaging.
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Affiliation(s)
- Max B. Scheible
- Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
- Nanosystems Initiative Munich, Schellingstr. 4, 80799 München, Germany
| | - Luvena L. Ong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Cir, Boston, MA 02115, USA
| | - Johannes B. Woehrstein
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Cir, Boston, MA 02115, USA
- Max Planck Institute of Biochemistry and LMU, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry and LMU, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Cir, Boston, MA 02115, USA
| | - Friedrich C. Simmel
- Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
- Nanosystems Initiative Munich, Schellingstr. 4, 80799 München, Germany
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38
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Schwenger A, Gerlach C, Griesser H, Richert C. Synthesis of eight-arm, branched oligonucleotide hybrids and studies on the limits of DNA-driven assembly. J Org Chem 2014; 79:11558-66. [PMID: 25407332 DOI: 10.1021/jo5022053] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Oligonucleotide hybrids with organic cores as rigid branching elements and four or six CG dimer strands have been shown to form porous materials from dilute aqueous solution. In order to explore the limits of this form of DNA-driven assembly, we prepared hybrids with three or eight DNA arms via solution-phase syntheses, using H-phosphonates of protected dinucleoside phosphates. This included the synthesis of (CG)8TREA, where TREA stands for the tetrakis[4-(resorcin-5-ylethynyl)phenyl]adamantane core. The ability of the new compounds to assemble in a DNA-driven fashion was studied by UV-melting analysis and NMR, using hybrids with self-complementary CG zipper arms or non-self-complementary TC dimer arms. The three-arm hybrid failed to form a material under conditions where four-arm hybrids did so. Further, the assembly of TREA hybrids appears to be dominated by hydrophobic interactions, not base pairing of the DNA arms. These results help in the design of materials forming by multivalent DNA-DNA interactions.
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Affiliation(s)
- Alexander Schwenger
- Institute for Organic Chemistry, University of Stuttgart , 70569 Stuttgart, Germany
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39
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DNA from natural sources in design of functional devices. Methods 2014; 67:105-15. [DOI: 10.1016/j.ymeth.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 02/20/2014] [Accepted: 03/02/2014] [Indexed: 01/01/2023] Open
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40
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Erkelenz M, Bauer DM, Meyer R, Gatsogiannis C, Raunser S, Saccà B, Niemeyer CM. A facile method for preparation of tailored scaffolds for DNA-origami. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:73-77. [PMID: 23861344 DOI: 10.1002/smll.201300701] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/30/2013] [Indexed: 06/02/2023]
Abstract
A convenient PCR cloning strategy allows one to prepare hundreds of picomoles of circular single-stranded DNA molecules, which are suitable as scaffolds for the assembly of DNA origami structures. The method is based on a combination of site-directed mutagenesis and site- and ligation-independent cloning protocols, with simultaneous insertion of a nicking endonuclease restriction site on a double-stranded plasmid of desired length and sequence.
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Affiliation(s)
- Michael Erkelenz
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto Hahn Str. 6, 44227 Dortmund, Germany
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41
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The enabled state of DNA nanotechnology. Curr Opin Biotechnol 2013; 24:555-61. [DOI: 10.1016/j.copbio.2013.02.001] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 01/22/2013] [Accepted: 02/01/2013] [Indexed: 11/18/2022]
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42
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Wang P, Ko SH, Tian C, Hao C, Mao C. RNA-DNA hybrid origami: folding of a long RNA single strand into complex nanostructures using short DNA helper strands. Chem Commun (Camb) 2013; 49:5462-4. [PMID: 23660602 DOI: 10.1039/c3cc41707g] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quick folding of a long RNA strand using short DNA staple strands (at a 1 : 1 ratio) into various pre-designed nanostructures in high yields has been demonstrated.
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Affiliation(s)
- Pengfei Wang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
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