1
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Peng Z, Kanno S, Shimba K, Miyamoto Y, Yagi T. Synthetic DNA nanopores for direct molecular transmission between lipid vesicles. NANOSCALE 2024; 16:12174-12183. [PMID: 38842009 DOI: 10.1039/d4nr01344a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Lipid vesicles hold potential as artificial cells in bottom-up synthetic biology, and as tools in drug delivery and biosensing. Transmitting molecular signals is a key function for vesicle-based systems. One strategy to achieve this function is by releasing molecular signals from vesicles through nanopores. Nevertheless, in this strategy, an excess of molecular signals may be required to reach the targets, due to the dispersion of the signals during diffusion. The key to achieving the efficient utilization of signals is to shorten the distance between the sender vesicle and the target. Here, we present a pair of DNA nanopores that can connect and form a direct molecular pathway between vesicles. The nanopores are self-assembled from nine single DNA strands, including six 14-nucleotide single-stranded overhangs as sticky-end segments, enabling them to bind with each other. Incorporating nanopores shortens the distance between different populations of vesicles, allowing less diffusion of molecules into bulk solution. To further reduce the loss of molecules, a DNA nanocap is added to one of the nanopore's openings. The nanocap can be removed through the toehold-mediated DNA strand displacement when the nanopore meets its counterpart. Our DNA nanopores provide a novel molecular transmission tool to lipid vesicles-based systems.
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Affiliation(s)
- Zugui Peng
- School of Engineering, Tokyo Institute of Technology, 403, Ishikawadai Bldg. 3, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| | - Shoichiro Kanno
- School of Engineering, Tokyo Institute of Technology, 403, Ishikawadai Bldg. 3, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| | - Kenta Shimba
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8563, Japan
| | - Yoshitaka Miyamoto
- School of Engineering, Tokyo Institute of Technology, 403, Ishikawadai Bldg. 3, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
- Department of Maternal-Fetal Biology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Tohru Yagi
- School of Engineering, Tokyo Institute of Technology, 403, Ishikawadai Bldg. 3, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
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2
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Fan G, Corbin N, Chung M, Gill TM, Moore EB, Karbelkar AA, Furst AL. Highly Efficient Carbon Dioxide Electroreduction via DNA-Directed Catalyst Immobilization. JACS AU 2024; 4:1413-1421. [PMID: 38665653 PMCID: PMC11040669 DOI: 10.1021/jacsau.3c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/28/2024]
Abstract
Electrochemical reduction of carbon dioxide (CO2) is a promising route to up-convert this industrial byproduct. However, to perform this reaction with a small-molecule catalyst, the catalyst must be proximal to an electrode surface. Efforts to immobilize molecular catalysts on electrodes have been stymied by the need to optimize the immobilization chemistries on a case-by-case basis. Taking inspiration from nature, we applied DNA as a molecular-scale "Velcro" to investigate the tethering of three porphyrin-based catalysts to electrodes. This tethering strategy improved both the stability of the catalysts and their Faradaic efficiencies (FEs). DNA-catalyst conjugates were immobilized on screen-printed carbon and carbon paper electrodes via DNA hybridization with nearly 100% efficiency. Following immobilization, a higher catalyst stability at relevant potentials is observed. Additionally, lower overpotentials are required for the generation of carbon monoxide (CO). Finally, high FE for CO generation was observed with the DNA-immobilized catalysts as compared to the unmodified small-molecule systems, as high as 79.1% FE for CO at -0.95 V vs SHE using a DNA-tethered catalyst. This work demonstrates the potential of DNA "Velcro" as a powerful strategy for catalyst immobilization. Here, we demonstrated improved catalytic characteristics of molecular catalysts for CO2 valorization, but this strategy is anticipated to be generalizable to any reaction that proceeds in aqueous solutions.
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Affiliation(s)
- Gang Fan
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Nathan Corbin
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Minju Chung
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas M. Gill
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Evan B. Moore
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Amruta A. Karbelkar
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Ariel L. Furst
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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Zhu S, Peng H, Kong H, Yan Q, Xia K, Wang L, Zhu Y, Luo S. Visualization of the hepatic and renal cell uptake and trafficking of tetrahedral DNA origami in tumour. Cell Prolif 2024:e13643. [PMID: 38572799 DOI: 10.1111/cpr.13643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
DNA nanostructures, known for their programmability, ease of modification, and favourable biocompatibility, have gained widespread application in the biomedical field. Among them, Tetrahedral DNA Origami (TDOs), as a novel DNA nanostructure, possesses well-defined structures, multiple modification sites, and large cavities, making it a promising drug carrier. However, current understanding of TDOs' interactions with biological systems, particularly with target cells and organs, remains unexplored, limiting its further applications in biomedicine. In this work, we prepared TDOs with an average particle size of 40 nm and labelled them with Cy5 fluorescent molecules. Following intravenous injection in mice, the uptake of TDOs by different types of liver and kidney cells was observed. Results indicated that TDOs accumulate in renal tubules and are metabolized by Kupffer cells, epithelial cells, and hepatocytes in the liver. Additionally, in a tumour-bearing mouse model, TDOs passively targeted tumour tissues and exhibited excellent tumour penetration and retention after rapid metabolism in hepatocytes. Our findings provide crucial insights for the development of TDO-based drug delivery systems.
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Affiliation(s)
- Shitai Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongzhen Peng
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, China
| | - Huating Kong
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Qinglong Yan
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, China
- Xiangfu Laboratory, Jiashan, China
| | - Kai Xia
- Xiangfu Laboratory, Jiashan, China
- Shanghai Frontier Innovation Research Institute, Shanghai, China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, China
| | - Ying Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai, China
| | - Shihua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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4
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Zhao F, Frandsen M, Capodaglio S, Sleiman HF. DNA-Mediated Peptide Assembly into Protein Mimics. J Am Chem Soc 2024; 146:1946-1956. [PMID: 38226787 DOI: 10.1021/jacs.3c08984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The design of new protein structures is challenging due to their vast sequence space and the complexity of protein folding. Here, we report a new modular DNA-templated strategy to construct protein mimics. We achieve the spatial control of multiple peptide units by conjugation with DNA and hybridization to a branched DNA trimer template followed by covalent stapling of the preorganized peptides into a single unit. A library of protein mimics with different lengths, sequences, and heptad registers has been efficiently constructed. DNA-templated protein mimics show an α-helix or coiled-coil motif formation even when they are constructed from weakly interacting peptide units. Their attached DNA handles can be used to exert dynamic control over the protein mimics' secondary and tertiary structures. This modular strategy will facilitate the development of DNA-encoded protein libraries for the rapid discovery of new therapeutics, enzymes, and antibody mimics.
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Affiliation(s)
- Fangzhou Zhao
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Martin Frandsen
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, Aarhus 8000, Denmark
| | - Sabrina Capodaglio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma I-43124, Italy
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
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5
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Yang J, Wang J, Liu X, Chen Y, Liang Y, Wang Q, Jiang S, Zhang C. Translocation of Proteins through Solid-State Nanopores Using DNA Polyhedral Carriers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303715. [PMID: 37496044 DOI: 10.1002/smll.202303715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/11/2023] [Indexed: 07/28/2023]
Abstract
The detection of biomolecules at the single molecule level has important applications in the fields of biosensing and biomedical diagnosis. The solid-state nanopore (SS nanopore) is a sensitive tool for detecting single molecules because of its unique label-free and low sample consumption properties. SS nanopore translocation of small biomolecules is typically driven by an electronic field force and is thus influenced by the charge, shape, and size of the target molecules. Therefore, it remains challenging to control the translocation of biomolecules through SS nanopores, particularly for different proteins with complex conformations and unique charges. Toward this problem, a DNA polyhedral carrier coating strategy to assist protein translocation through SS nanopores is developed, which facilitates target protein detection. The current signal-to-noise ratios are improved significantly using this DNA carrier loading strategy. The proposed method should aid the detection of proteins, which are difficult to translocate through nanopores. This coating-assisted method offers a wide range of applications for SS nanopore detection and promotes the development of single-molecule detection.
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Affiliation(s)
- Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Juan Wang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Xuan Liu
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yiming Chen
- School of Electronics Engineering and Computer Science, Peking University, Beijing, 100871, China
| | - Yuan Liang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Qi Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Shuoxing Jiang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Beijing, 100871, China
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6
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Kaviani S, Fakih HH, Asohan J, Katolik A, Damha MJ, Sleiman HF. Sequence-Controlled Spherical Nucleic Acids: Gene Silencing, Encapsulation, and Cellular Uptake. Nucleic Acid Ther 2023; 33:265-276. [PMID: 37196168 DOI: 10.1089/nat.2022.0062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
Antisense oligonucleotides (ASOs) can predictably alter RNA processing and control protein expression; however, challenges in the delivery of these therapeutics to specific tissues, poor cellular uptake, and endosomal escape have impeded progress in translating these agents into the clinic. Spherical nucleic acids (SNAs) are nanoparticles with a DNA external shell and a hydrophobic core that arise from the self-assembly of ASO strands conjugated to hydrophobic polymers. SNAs have recently shown significant promise as vehicles for improving the efficacy of ASO cellular uptake and gene silencing. However, to date, no studies have investigated the effect of the hydrophobic polymer sequence on the biological properties of SNAs. In this study, we created a library of ASO conjugates by covalently attaching polymers with linear or branched [dodecanediol phosphate] units and systematically varying polymer sequence and composition. We show that these parameters can significantly impact encapsulation efficiency, gene silencing activity, SNA stability, and cellular uptake, thus outlining optimized polymer architectures for gene silencing.
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Affiliation(s)
- Sepideh Kaviani
- Department of Chemistry, McGill University, Montreal, Canada
| | - Hassan H Fakih
- Department of Chemistry, McGill University, Montreal, Canada
| | - Jathavan Asohan
- Department of Chemistry, McGill University, Montreal, Canada
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Canada
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Canada
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7
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Cao S, Lin L, Zhao Y, Guo L, Zhu Y, Wang L, Li J. Programming Aggregate States of DNA Nanorods with Sub-10 nm Hydrophobic Patterns for Tunable Cell Entry. JACS AU 2023; 3:1004-1009. [PMID: 37124296 PMCID: PMC10131207 DOI: 10.1021/jacsau.3c00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 05/03/2023]
Abstract
The intracellular application of DNA nanodevices is challenged by their inadequate cellular entry efficiency, which may be addressed by the development of amphiphilic DNA nanostructures. However, the impact of the spatial distribution of hydrophobicity in cell entry has not been fully explored. Here, we program a spectrum of amphiphilic DNA nanostructures displaying diverse sub-10 nm patterns of cholesterol, which result in distinct aggregate states in the aqueous solution and thus varied cell entry efficiencies. We find that the hydrophobic patterns can lead to discrete aggregate states, from monomers to low-number oligomers (n = 1-6). We demonstrate that the monomers or oligomers with moderate hydrophobic density are preferred for cell entry, with up to ∼174-fold improvement relative to unmodified ones. Our study provides a new clue for the rational design of amphiphilic DNA nanostructures for intracellular applications.
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Affiliation(s)
- Shuting Cao
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- The
Interdisciplinary Research Center, Shanghai Synchrotron Radiation
Facility, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, Shanghai 201210, China
| | - Lixuan Lin
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- The
Interdisciplinary Research Center, Shanghai Synchrotron Radiation
Facility, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, Shanghai 201210, China
| | - Yan Zhao
- Institute
of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Linjie Guo
- The
Interdisciplinary Research Center, Shanghai Synchrotron Radiation
Facility, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, Shanghai 201210, China
- Institute
of Materials Biology, Shanghai University, Shanghai 200444, China
| | - Ying Zhu
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- The
Interdisciplinary Research Center, Shanghai Synchrotron Radiation
Facility, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, Shanghai 201210, China
- Institute
of Materials Biology, Shanghai University, Shanghai 200444, China
| | - Lihua Wang
- Division
of Physical Biology, CAS Key Laboratory of Interfacial Physics and
Technology, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- The
Interdisciplinary Research Center, Shanghai Synchrotron Radiation
Facility, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, Shanghai 201210, China
- Institute
of Materials Biology, Shanghai University, Shanghai 200444, China
| | - Jiang 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
- University
of Chinese Academy of Sciences, Beijing 100049, China
- The
Interdisciplinary Research Center, Shanghai Synchrotron Radiation
Facility, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, Shanghai 201210, China
- Institute
of Materials Biology, Shanghai University, Shanghai 200444, China
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8
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Li X, Dai X, Pan Y, Sun Y, Yang B, Chen K, Wang Y, Xu JF, Dong Y, Yang YR, Yan LT, Liu D. Studies on the Synergistic Effect of Tandem Semi-Stable Complementary Domains on Sequence-Defined DNA Block Copolymers. J Am Chem Soc 2022; 144:21267-21277. [DOI: 10.1021/jacs.2c08930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Xin Li
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaobin Dai
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yufan Pan
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yawei Sun
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (Huadong), Qingdao 258000, China
| | - Bo Yang
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Kun Chen
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - You Wang
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jiang-Fei Xu
- Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yuhe Renee Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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9
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Mathew SS, Ahamed AAS, Abraham I, Prabhu DD, John F, George J. Self‐Assemblies of DNA ‐ Amphiphiles Nanostructures for New Design Strategies of Varied Morphologies. ChemistrySelect 2022. [DOI: 10.1002/slct.202202146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - A A Subuhan Ahamed
- School of Chemistry University of Hyderabad Hyderabad 500046 Telangana India
| | - Ignatious Abraham
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Deepak D Prabhu
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Franklin John
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Jinu George
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
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10
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Rizzuto FJ, Dore MD, Rafique MG, Luo X, Sleiman HF. DNA Sequence and Length Dictate the Assembly of Nucleic Acid Block Copolymers. J Am Chem Soc 2022; 144:12272-12279. [PMID: 35762655 DOI: 10.1021/jacs.2c03506] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The self-assembly of block copolymers is often rationalized by structure and microphase separation; pathways that diverge from this parameter space may provide new mechanisms of polymer assembly. Here, we show that the sequence and length of single-stranded DNA directly influence the self-assembly of sequence-defined DNA block copolymers. While increasing the length of DNA led to predictable changes in self-assembly, changing only the sequence of DNA produced three distinct structures: spherical micelles (spherical nucleic acids, SNAs) from flexible poly(thymine) DNA, fibers from semirigid mixed-sequence DNA, and networked superstructures from rigid poly(adenine) DNA. The secondary structure of poly(adenine) DNA strands drives a temperature-dependent polymerization and assembly mechanism: copolymers stored in an SNA reservoir form fibers after thermal activation, which then aggregate upon cooling to form interwoven networks. DNA is often used as a programming code that aids in nanostructure addressability and function. Here, we show that the inherent physical and chemical properties of single-stranded DNA sequences also make them an ideal material to direct self-assembled morphologies and select for new methods of supramolecular polymerization.
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Affiliation(s)
- Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC H3A 08B, Canada
| | - Michael D Dore
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC H3A 08B, Canada
| | | | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC H3A 08B, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC H3A 08B, Canada
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11
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Integrated DNA triangular prism nanomachines for two-stage dynamic recognizing and bio-imaging from surface to the inside of living cells. Biosens Bioelectron 2022; 213:114478. [PMID: 35732084 DOI: 10.1016/j.bios.2022.114478] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/19/2022] [Accepted: 06/08/2022] [Indexed: 11/22/2022]
Abstract
The identification and detection of biomarkers in cancer cells play an essential role in the early detection of diseases, especially the detection of dual-biomarker. However, one of the most important limiting factors is how to realize the identification and labeling of biomarkers dynamically from the plasma membrane to the cytoplasm in living cells. In this study, integrated DNA triangular prism nanomachines (IDTPNs), a two-stage identification and dynamic bio-imaging strategy, recognize biomarkers from the plasma membrane to the cytoplasm have been designed. DNA triangular prism (DTP) was selected to act as a delivery platform with the aptamer Sgc8c and P53 modified on the side as the recognition molecules. Through the specific recognition of aptamers and the superior internalization of DTP, the IDTPNs realize the dynamic responses to PTK7 and p53 from the membrane to the cytoplasm in living cells. It is proved that the IDTPNs can be used for dynamic dual-biomarker recognition and bio-image from the surface to the inside of tumor cells automatically. Therefore, the strategy we developed provides a reliable platform for tumor diagnosis and biomarker research.
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12
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Winterwerber P, Whitfield CJ, Ng DYW, Weil T. Multi‐Wellenlängen‐Photopolymerisation von stabilen Poly(katecholamin)‐DNA‐Origami‐Nanostrukturen**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Pia Winterwerber
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Colette J. Whitfield
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - David Y. W. Ng
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Tanja Weil
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
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13
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Rubio-Sánchez R, Fabrini G, Cicuta P, Di Michele L. Amphiphilic DNA nanostructures for bottom-up synthetic biology. Chem Commun (Camb) 2021; 57:12725-12740. [PMID: 34750602 PMCID: PMC8631003 DOI: 10.1039/d1cc04311k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/28/2021] [Indexed: 12/28/2022]
Abstract
DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.
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Affiliation(s)
- Roger Rubio-Sánchez
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Giacomo Fabrini
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
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14
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Winterwerber P, Whitfield CJ, Ng DYW, Weil T. Multi-Wavelength Photopolymerization of Stable Poly(Catecholamines)-DNA Origami Nanostructures. Angew Chem Int Ed Engl 2021; 61:e202111226. [PMID: 34813135 PMCID: PMC9303804 DOI: 10.1002/anie.202111226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Indexed: 11/23/2022]
Abstract
The synthesis of multicomponent polymer hybrids with nanometer precision is chemically challenging in the bottom‐up synthesis of complex nanostructures. Here, we leverage the fidelity of the DNA origami technique to install a multiple wavelength responsive photopolymerization system with nanometer resolution. By precisely immobilizing various photosensitizers on the origami template, which are only activated at their respective maximum wavelength, we can control sequential polymerization processes. In particular, the triggered photosensitizers generate reactive oxygen species that in turn initiate the polymerization of the catecholamines dopamine and norepinephrine. We imprint polymeric layers at designated positions on DNA origami, which modifies the polyanionic nature of the DNA objects, thus promoting their uptake into living cells while preserving their integrity. Our herein proposed method provides a rapid platform to access complex 3D nanostructures by customizing material and biological interfaces.
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Affiliation(s)
- Pia Winterwerber
- Max Planck Institute for Polymer Research: Max-Planck-Institut fur Polymerforschung, Synthesis of Macromolecules, GERMANY
| | - Colette J Whitfield
- Max Planck Institute for Polymer Research: Max-Planck-Institut fur Polymerforschung, Synthesis of Macromolecules, GERMANY
| | - David Y W Ng
- Max Planck Institute for Polymer Research: Max-Planck-Institut fur Polymerforschung, Synthesis of Macromolecules, GERMANY
| | - Tanja Weil
- Max-Planck-Institut fur Polymerforschung, Synthesis of Macromolecules, Ackermannweg 10, 55128, Mainz, GERMANY
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15
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Li F, Lv Z, Zhang X, Dong Y, Ding X, Li Z, Li S, Yao C, Yang D. Supramolecular Self‐Assembled DNA Nanosystem for Synergistic Chemical and Gene Regulations on Cancer Cells. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Feng Li
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Zhaoyue Lv
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Xue Zhang
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Yuhang Dong
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Xiaohui Ding
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Zhemian Li
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Shuai Li
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology Key Laboratory of Systems Bioengineering (MOE) Institute of Biomolecular and Biomedical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
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16
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Li F, Lv Z, Zhang X, Dong Y, Ding X, Li Z, Li S, Yao C, Yang D. Supramolecular Self-Assembled DNA Nanosystem for Synergistic Chemical and Gene Regulations on Cancer Cells. Angew Chem Int Ed Engl 2021; 60:25557-25566. [PMID: 34533880 DOI: 10.1002/anie.202111900] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Indexed: 12/20/2022]
Abstract
Incorporating multiple molecular interactions within a system to realize the metabolic reprogramming of cancer cells is prospected to be of great potential in cancer therapy. Herein, we report a supramolecular self-assembled DNA nanosystem, which reprogrammed the cellular antioxidant system via synergistic chemical and gene regulations. In the nanosystem, amphipathic telluroether was coordinated with MnII to self-assemble into micelle, on which a siNrf2 integrated DNA network was assembled. The great electron-donating capability of telluroether was revealed to greatly promote MnII -based Fenton-like reaction to generate subversive . OH in cancer cells. In response to adenosine triphosphoric acid, the siNrf2 was specially released in cytoplasm for down-regulating expression of detoxification enzymes, which enhanced chemocatalysis-mediated oxidative stress in cancer cells, thus significantly suppressing tumor progression.
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Affiliation(s)
- Feng Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Zhaoyue Lv
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Xue Zhang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Xiaohui Ding
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Zhemian Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), Institute of Biomolecular and Biomedical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, P. R. China
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17
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Whitfield C, Zhang M, Winterwerber P, Wu Y, Ng DYW, Weil T. Functional DNA-Polymer Conjugates. Chem Rev 2021; 121:11030-11084. [PMID: 33739829 PMCID: PMC8461608 DOI: 10.1021/acs.chemrev.0c01074] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Indexed: 02/07/2023]
Abstract
DNA nanotechnology has seen large developments over the last 30 years through the combination of solid phase synthesis and the discovery of DNA nanostructures. Solid phase synthesis has facilitated the availability of short DNA sequences and the expansion of the DNA toolbox to increase the chemical functionalities afforded on DNA, which in turn enabled the conception and synthesis of sophisticated and complex 2D and 3D nanostructures. In parallel, polymer science has developed several polymerization approaches to build di- and triblock copolymers bearing hydrophilic, hydrophobic, and amphiphilic properties. By bringing together these two emerging technologies, complementary properties of both materials have been explored; for example, the synthesis of amphiphilic DNA-polymer conjugates has enabled the production of several nanostructures, such as spherical and rod-like micelles. Through both the DNA and polymer parts, stimuli-responsiveness can be instilled. Nanostructures have consequently been developed with responsive structural changes to physical properties, such as pH and temperature, as well as short DNA through competitive complementary binding. These responsive changes have enabled the application of DNA-polymer conjugates in biomedical applications including drug delivery. This review discusses the progress of DNA-polymer conjugates, exploring the synthetic routes and state-of-the-art applications afforded through the combination of nucleic acids and synthetic polymers.
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Affiliation(s)
- Colette
J. Whitfield
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Meizhou Zhang
- Hubei
Key Laboratory of Bioinorganic Chemistry and Materia Medica, School
of Chemistry and Chemical Engineering, Huazhong
University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan 430074, People’s Republic of China
| | - Pia Winterwerber
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuzhou Wu
- Hubei
Key Laboratory of Bioinorganic Chemistry and Materia Medica, School
of Chemistry and Chemical Engineering, Huazhong
University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan 430074, People’s Republic of China
| | - David Y. W. Ng
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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18
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Dore MD, Trinh T, Zorman M, de Rochambeau D, Platnich CM, Xu P, Luo X, Remington JM, Toader V, Cosa G, Li J, Sleiman HF. Thermosetting supramolecular polymerization of compartmentalized DNA fibers with stereo sequence and length control. Chem 2021. [DOI: 10.1016/j.chempr.2021.05.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Diederichs T, Tampé R. Membrane-Suspended Nanopores in Microchip Arrays for Stochastic Transport Recording and Sensing. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.703673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The transport of nutrients, xenobiotics, and signaling molecules across biological membranes is essential for life. As gatekeepers of cells, membrane proteins and nanopores are key targets in pharmaceutical research and industry. Multiple techniques help in elucidating, utilizing, or mimicking the function of biological membrane-embedded nanodevices. In particular, the use of DNA origami to construct simple nanopores based on the predictable folding of nucleotides provides a promising direction for innovative sensing and sequencing approaches. Knowledge of translocation characteristics is crucial to link structural design with function. Here, we summarize recent developments and compare features of membrane-embedded nanopores with solid-state analogues. We also describe how their translocation properties are characterized by microchip systems. The recently developed silicon chips, comprising solid-state nanopores of 80 nm connecting femtoliter cavities in combination with vesicle spreading and formation of nanopore-suspended membranes, will pave the way to characterize translocation properties of nanopores and membrane proteins in high-throughput and at single-transporter resolution.
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20
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Multifunctional polymeric micellar nanomedicine in the diagnosis and treatment of cancer. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 126:112186. [PMID: 34082985 DOI: 10.1016/j.msec.2021.112186] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
Polymeric micelles are a prevalent topic of research for the past decade, especially concerning their fitting ability to deliver drug and diagnostic agents. This delivery system offers outstanding advantages, such as biocompatibility, high loading efficiency, water-solubility, and good stability in biological fluids, to name a few. The multifunctional polymeric micellar architect offers the added capability to adapt its surface to meet the looked-for clinical needs. This review cross-talks the recent reports, proof-of-concept studies, patents, and clinical trials that utilize polymeric micellar family architectures concerning cancer targeted delivery of anticancer drugs, gene therapeutics, and diagnostic agents. The manuscript also expounds on the underlying opportunities, allied challenges, and ways to resolve their bench-to-bedside translation for allied clinical applications.
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21
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Loth C, Charles L, Lutz JF, Nerantzaki M. Precisely Defined Aptamer- b-Poly(phosphodiester) Conjugates Prepared by Phosphoramidite Polymer Chemistry. ACS Macro Lett 2021; 10:481-485. [PMID: 35549221 DOI: 10.1021/acsmacrolett.1c00164] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Uniform conjugates combining a DNA aptamer (either anti-MUC1 or ATP aptamer) and a synthetic polymer segment were synthesized by automated phosphoramidite chemistry. This multistep growth polymer chemistry enables the use of both natural (i.e., nucleoside phosphoramidites) and non-natural monomers (e.g., alkyl- and oligo(ethylene glycol)-phosphoramidites). Thus, in the present work, six different aptamer-polymer conjugates were synthesized and characterized by ion-exchange HPLC, circular dichroism spectroscopy, and electrospray mass spectrometry. All these methods evidenced the formation of uniform molecules with precisely controlled chain-length and monomer sequences. Furthermore, aptamer folding was not affected by polymer bioconjugation. The method described herein is straightforward and allows covalent attachment of homopolymers and copolymers to biofunctional DNA aptamers.
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Affiliation(s)
- Capucine Loth
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Laurence Charles
- Aix Marseille Université, CNRS, UMR 7273, Institute of Radical Chemistry, 13397, Marseille Cedex 20, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Maria Nerantzaki
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
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22
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Hannewald N, Winterwerber P, Zechel S, Ng DYW, Hager MD, Weil T, Schubert US. DNA Origami Meets Polymers: A Powerful Tool for the Design of Defined Nanostructures. Angew Chem Int Ed Engl 2021; 60:6218-6229. [PMID: 32649033 PMCID: PMC7984297 DOI: 10.1002/anie.202005907] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Indexed: 12/19/2022]
Abstract
The combination of DNA origami nanostructures and polymers provides a new possibility to access defined structures in the 100 nm range. In general, DNA origami serves as a versatile template for the highly specific arrangement of polymer chains. Polymer-DNA hybrid nanostructures can either be created by growing the polymer from the DNA template or by attaching preformed polymers to the DNA scaffold. These conjugations can be of a covalent nature or be based on base-pair hybridization between respectively modified polymers and DNA origami. Furthermore, the negatively charged DNA backbone permits interaction with positively charged polyelectrolytes to form stable complexes. The combination of polymers with tuneable characteristics and DNA origami allows the creation of a new class of hybrid materials, which could offer exciting applications for controlled energy transfer, nanoscale organic circuits, or the templated synthesis of nanopatterned polymeric structures.
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Affiliation(s)
- Nadine Hannewald
- Laboratory of Organic and Macromolecular Chemistry (IOMC)Friedrich Schiller University JenaHumboldtstrasse 1007743JenaGermany
- Jena Center for Soft Matter (JCSM)Friedrich Schiller University JenaPhilosophenweg 707743JenaGermany
| | - Pia Winterwerber
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Stefan Zechel
- Laboratory of Organic and Macromolecular Chemistry (IOMC)Friedrich Schiller University JenaHumboldtstrasse 1007743JenaGermany
- Jena Center for Soft Matter (JCSM)Friedrich Schiller University JenaPhilosophenweg 707743JenaGermany
| | - David Y. W. Ng
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Martin D. Hager
- Laboratory of Organic and Macromolecular Chemistry (IOMC)Friedrich Schiller University JenaHumboldtstrasse 1007743JenaGermany
- Jena Center for Soft Matter (JCSM)Friedrich Schiller University JenaPhilosophenweg 707743JenaGermany
| | - Tanja Weil
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Ulrich S. Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC)Friedrich Schiller University JenaHumboldtstrasse 1007743JenaGermany
- Jena Center for Soft Matter (JCSM)Friedrich Schiller University JenaPhilosophenweg 707743JenaGermany
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23
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Feng L, Li J, Sun J, Wang L, Fan C, Shen J. Recent Advances of DNA Nanostructure-Based Cell Membrane Engineering. Adv Healthc Mater 2021; 10:e2001718. [PMID: 33458966 DOI: 10.1002/adhm.202001718] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/20/2020] [Indexed: 01/30/2023]
Abstract
Materials that can regulate the composition and structure of the cell membrane to fabricate engineered cells with defined functions are in high demand. Compared with other biomolecules, DNA has unique advantages in cell membrane engineering due to its excellent programmability and biocompatibility. Especially, the near-atomic scale precision of DNA nanostructures facilitates the investigation of structure-property relations on the cell membrane. In this review, first the state of the art of functional DNA nanostructures is summarized, and then the overview of the use of DNA nanostructures to engineer the cell membrane is presented. Subsequently, applications of DNA nanostructures in modifying cell membrane morphology, controlling ions transport, and synthesizing high precise liposomes are highlighted. Finally, the challenges and outlook on using DNA nanostructures for cell membrane engineering are discussed.
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Affiliation(s)
- Lingyu Feng
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jiang 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
- University of Chinese Academy of Sciences Beijing 100049 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Jielin Sun
- Key Laboratory of Systems Biomedicine (Ministry of Education) Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Lihua Wang
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
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24
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Li F, Yu W, Zhang J, Dong Y, Ding X, Ruan X, Gu Z, Yang D. Spatiotemporally programmable cascade hybridization of hairpin DNA in polymeric nanoframework for precise siRNA delivery. Nat Commun 2021; 12:1138. [PMID: 33602916 PMCID: PMC7893159 DOI: 10.1038/s41467-021-21442-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/20/2021] [Indexed: 01/27/2023] Open
Abstract
DNA nanostructures have been demonstrated as promising carriers for gene delivery. In the carrier design, spatiotemporally programmable assembly of DNA under nanoconfinement is important but has proven highly challenging due to the complexity-scalability-error of DNA. Herein, a DNA nanotechnology-based strategy via the cascade hybridization chain reaction (HCR) of DNA hairpins in polymeric nanoframework has been developed to achieve spatiotemporally programmable assembly of DNA under nanoconfinement for precise siRNA delivery. The nanoframework is prepared via precipitation polymerization with Acrydite-DNA as cross-linker. The potential energy stored in the loops of DNA hairpins can overcome the steric effect in the nanoframework, which can help initiate cascade HCR of DNA hairpins and achieve efficient siRNA loading. The designer tethering sequence between DNA and RNA guarantees a triphosadenine triggered siRNA release specifically in cellular cytoplasm. Nanoframework provides stability and ease of functionalization, which helps address the complexity-scalability-error of DNA. It is exemplified that the phenylboronate installation on nanoframework enhanced cellular uptake and smoothed the lysosomal escape. Cellular results show that the siRNA loaded nanoframework down-regulated the levels of relevant mRNA and protein. In vivo experiments show significant therapeutic efficacy of using siPLK1 loaded nanoframework to suppress tumor growth.
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Affiliation(s)
- Feng Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Wenting Yu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Jiaojiao Zhang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Xiaohui Ding
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Xinhua Ruan
- Department of Cardiac Surgery, Tianjin Union Medical Centre, Tianjin, P.R. China
| | - Zi Gu
- School of Chemical Engineering, Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, Australia
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China.
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25
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Fakih HH, Katolik A, Malek-Adamian E, Fakhoury JJ, Kaviani S, Damha MJ, Sleiman HF. Design and enhanced gene silencing activity of spherical 2'-fluoroarabinose nucleic acids (FANA-SNAs). Chem Sci 2021; 12:2993-3003. [PMID: 34164068 PMCID: PMC8179377 DOI: 10.1039/d0sc06645a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Drug delivery vectors for nucleic acid therapeutics (NATs) face significant barriers for translation into the clinic. Spherical nucleic acids (SNAs) – nanoparticles with an exterior shell made up of DNA strands and a hydrophobic interior – have recently shown great potential as vehicles to improve the biodistribution and efficacy of NATs. To date, SNA design has not taken advantage of the powerful chemical modifications available to NATs. Here, we modify SNAs with 2′-deoxy-2′-fluoro-d-arabinonucleic acid (FANA-SNA), and show increased stability, enhanced gene silencing potency and unaided uptake (gymnosis) as compared to free FANA. By varying the spacer region between the nucleic acid strand and the attached hydrophobic polymer, we show that a cleavable DNA based spacer is essential for maximum activity. This design feature will be important when implementing functionalized nucleic acids into nanostructures for gene silencing. The modularity of the FANA-SNA was demonstrated by silencing two different targets. Transfection-free delivery was superior for the modified SNA compared to the free FANA oligonucleotide. Optimizing FANA modified spherical nucleic acids (FANA-SNAs) for highly efficient delivery of nucleic acid therapeutics.![]()
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Affiliation(s)
- Hassan H Fakih
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Adam Katolik
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | | | - Johans J Fakhoury
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Sepideh Kaviani
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Masad J Damha
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
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26
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Sequence-Defined DNA Amphiphiles for Drug Delivery: Synthesis and Self-Assembly. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2020; 2063:87-100. [PMID: 31667765 DOI: 10.1007/978-1-0716-0138-9_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
DNA nanotechnology has been used to create DNA containing nanostructures with well-defined sizes and shapes-properties highly applicable to drug delivery. By appending sequence-defined hydrophobic segments to DNA, DNA amphiphiles are created whose structures and modes of self-assembly mimic specialized biomacromolecules such as proteins. Automated, solid-phase DNA synthesis is a scalable and robust technique that has been optimized for several decades to make DNA oligomers. Using the same method and with minimal additional cost, DNA amphiphiles are synthesized with total control of monomer sequence. A variety of synthetic monomers may be appended to DNA depending on the application, but of particular interest is a linear twelve-carbon alkyl chain (C12). This chapter describes the synthesis, purification, and characterization of a DNA amphiphile consisting of twelve C12 units covalently attached to a 19mer DNA sequence (C1212-DNA19). These DNA amphiphiles self-assemble into spherical nanoparticles with potential applications for nucleic acid delivery. Methods common to chemistry and molecular biology are employed, including high-performance liquid chromatography and gel electrophoresis, as well as the more specialized imaging technique of atomic force microscopy.
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27
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Hannewald N, Winterwerber P, Zechel S, Ng DYW, Hager MD, Weil T, Schubert US. Kombination von DNA‐Origami und Polymeren: Eine leistungsstarke Methode zum Aufbau definierter Nanostrukturen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Nadine Hannewald
- Lehrstuhl für Organische und Makromolekulare Chemie (IOMC) Friedrich-Schiller-Universität Jena Humboldtstraße 10 07743 Jena Deutschland
- Jena Center for Soft Matter (JCSM) Friedrich-Schiller-Universität Jena Philosophenweg 7 07743 Jena Deutschland
| | - Pia Winterwerber
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Stefan Zechel
- Lehrstuhl für Organische und Makromolekulare Chemie (IOMC) Friedrich-Schiller-Universität Jena Humboldtstraße 10 07743 Jena Deutschland
- Jena Center for Soft Matter (JCSM) Friedrich-Schiller-Universität Jena Philosophenweg 7 07743 Jena Deutschland
| | - David Y. W. Ng
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Martin D. Hager
- Lehrstuhl für Organische und Makromolekulare Chemie (IOMC) Friedrich-Schiller-Universität Jena Humboldtstraße 10 07743 Jena Deutschland
- Jena Center for Soft Matter (JCSM) Friedrich-Schiller-Universität Jena Philosophenweg 7 07743 Jena Deutschland
| | - Tanja Weil
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Ulrich S. Schubert
- Lehrstuhl für Organische und Makromolekulare Chemie (IOMC) Friedrich-Schiller-Universität Jena Humboldtstraße 10 07743 Jena Deutschland
- Jena Center for Soft Matter (JCSM) Friedrich-Schiller-Universität Jena Philosophenweg 7 07743 Jena Deutschland
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28
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Edwardson TGW, Tetter S, Hilvert D. Two-tier supramolecular encapsulation of small molecules in a protein cage. Nat Commun 2020; 11:5410. [PMID: 33106476 PMCID: PMC7588467 DOI: 10.1038/s41467-020-19112-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Expanding protein design to include other molecular building blocks has the potential to increase structural complexity and practical utility. Nature often employs hybrid systems, such as clathrin-coated vesicles, lipid droplets, and lipoproteins, which combine biopolymers and lipids to transport a broader range of cargo molecules. To recapitulate the structure and function of such composite compartments, we devised a supramolecular strategy that enables porous protein cages to encapsulate poorly water-soluble small molecule cargo through templated formation of a hydrophobic surfactant-based core. These lipoprotein-like complexes protect their cargo from sequestration by serum proteins and enhance the cellular uptake of fluorescent probes and cytotoxic drugs. This design concept could be applied to other protein cages, surfactant mixtures, and cargo molecules to generate unique hybrid architectures and functional capabilities.
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Affiliation(s)
| | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093, Zurich, Switzerland.
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29
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Peng X, Yang ZZ, Yang P, Chai YQ, Liang WB, Li ZH, Yuan R. Rapid self-disassembly of DNA diblock copolymer micelles via target induced hydrophilic-hydrophobic regulation for sensitive MiRNA detection. Chem Commun (Camb) 2020; 56:10215-10218. [PMID: 32748935 DOI: 10.1039/d0cc03858j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this work, a novel DNA nanostructure with a shorter assembly time and larger loading capacity was constructed using amphiphilic DNA-alkane group (Spacer C12)10 conjugates encapsulating plentiful fat-soluble fluorescent dyes into the hydrophobic core to form the DNA micelles, which could be rapidly self-disassembled via target induced hydrophilic-hydrophobic regulation to release fluorescent dyes from micelles to the organic phase, realizing the fast and sensitive detection of microRNA.
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Affiliation(s)
- Xin Peng
- Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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30
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Lückerath T, Koynov K, Loescher S, Whitfield CJ, Nuhn L, Walther A, Barner‐Kowollik C, Ng DYW, Weil T. DNA-Polymer Nanostructures by RAFT Polymerization and Polymerization-Induced Self-Assembly. Angew Chem Int Ed Engl 2020; 59:15474-15479. [PMID: 32301556 PMCID: PMC7496909 DOI: 10.1002/anie.201916177] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/01/2020] [Indexed: 01/06/2023]
Abstract
Nanostructures derived from amphiphilic DNA-polymer conjugates have emerged prominently due to their rich self-assembly behavior; however, their synthesis is traditionally challenging. Here, we report a novel platform technology towards DNA-polymer nanostructures of various shapes by leveraging polymerization-induced self-assembly (PISA) for polymerization from single-stranded DNA (ssDNA). A "grafting from" protocol for thermal RAFT polymerization from ssDNA under ambient conditions was developed and utilized for the synthesis of functional DNA-polymer conjugates and DNA-diblock conjugates derived from acrylates and acrylamides. Using this method, PISA was applied to manufacture isotropic and anisotropic DNA-polymer nanostructures by varying the chain length of the polymer block. The resulting nanostructures were further functionalized by hybridization with a dye-labelled complementary ssDNA, thus establishing PISA as a powerful route towards intrinsically functional DNA-polymer nanostructures.
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Affiliation(s)
- Thorsten Lückerath
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Kaloian Koynov
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Sebastian Loescher
- Institute for Macromolecular ChemistryFreiburg UniversityStefan Meier Str. 3179104FreiburgGermany
- Freiburg Institute for Interactive Materials and Bioinspired Technologies (FIT)Georges-Köhler-Allee 10579104FreiburgGermany
| | - Colette J. Whitfield
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Lutz Nuhn
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Andreas Walther
- Institute for Macromolecular ChemistryFreiburg UniversityStefan Meier Str. 3179104FreiburgGermany
- Freiburg Institute for Interactive Materials and Bioinspired Technologies (FIT)Georges-Köhler-Allee 10579104FreiburgGermany
| | - Christopher Barner‐Kowollik
- Centre for Materials Science, School of Chemistry and PhysicsQueensland University of Technology (QUT)2 George StreetQLD4000BrisbaneAustralia
- Macromolecular ArchitecturesInstitute for Chemical Technology and Polymer Chemistry (ITCP)Karlsruhe Institute of Technology (KIT)Engersserstraße 1876131KarlsruheGermany
| | - David Y. W. Ng
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Tanja Weil
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
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31
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Lückerath T, Koynov K, Loescher S, Whitfield CJ, Nuhn L, Walther A, Barner‐Kowollik C, Ng DYW, Weil T. DNA‐Polymer‐Nanostrukturen durch RAFT‐Polymerisation und polymerisationsinduzierte Selbstassemblierung. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Thorsten Lückerath
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Kaloian Koynov
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Sebastian Loescher
- Institut für Makromolekulare Chemie Universität Freiburg Stefan Meier Straße 31 79104 Freiburg Deutschland
- Freiburger Zentrum für Interaktive Werkstoffe und Bioinspirierte Technologien (FIT) Georges-Köhler-Allee 105 79104 Freiburg Deutschland
| | - Colette J. Whitfield
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Lutz Nuhn
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Andreas Walther
- Institut für Makromolekulare Chemie Universität Freiburg Stefan Meier Straße 31 79104 Freiburg Deutschland
- Freiburger Zentrum für Interaktive Werkstoffe und Bioinspirierte Technologien (FIT) Georges-Köhler-Allee 105 79104 Freiburg Deutschland
| | - Christopher Barner‐Kowollik
- Centre for Materials Science School of Chemistry and Physics Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
- Makromolekulare Architekturen Institut für Technische Chemie und Polymerchemie (ITCP) Karlsruher Institut für Technologie (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
| | - David Y. W. Ng
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Tanja Weil
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
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32
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Xiao F, Chen Z, Wei Z, Tian L. Hydrophobic Interaction: A Promising Driving Force for the Biomedical Applications of Nucleic Acids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001048. [PMID: 32832360 PMCID: PMC7435255 DOI: 10.1002/advs.202001048] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/28/2020] [Indexed: 05/13/2023]
Abstract
The comprehensive understanding and proper use of supramolecular interactions have become critical for the development of functional materials, and so is the biomedical application of nucleic acids (NAs). Relatively rare attention has been paid to hydrophobic interaction compared with hydrogen bonding and electrostatic interaction of NAs. However, hydrophobic interaction shows some unique properties, such as high tunability for application interest, minimal effect on NA functionality, and sensitivity to external stimuli. Therefore, the widespread use of hydrophobic interaction has promoted the evolution of NA-based biomaterials in higher-order self-assembly, drug/gene-delivery systems, and stimuli-responsive systems. Herein, the recent progress of NA-based biomaterials whose fabrications or properties are highly determined by hydrophobic interactions is summarized. 1) The hydrophobic interaction of NA itself comes from the accumulation of base-stacking forces, by which the NAs with certain base compositions and chain lengths show properties similar to thermal-responsive polymers. 2) In conjugation with hydrophobic molecules, NA amphiphiles show interesting self-assembly structures with unique properties in many new biosensing and therapeutic strategies. 3) The working-mechanisms of some NA-based complex materials are also dependent on hydrophobic interactions. Moreover, in recent attempts, NA amphiphiles have been applied in organizing macroscopic self-assembly of DNA origami and controlling the cell-cell interactions.
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Affiliation(s)
- Fan Xiao
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
- School of Materials Science and EngineeringHarbin Institute of TechnologyNangang DistrictHarbin150001P. R. China
| | - Zhe Chen
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
- Cancer Centre and Centre of ReproductionDevelopment and AgingFaculty of Health SciencesUniversity of MacauTaipaMacau999078P. R. China
| | - Zixiang Wei
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
- Cancer Centre and Centre of ReproductionDevelopment and AgingFaculty of Health SciencesUniversity of MacauTaipaMacau999078P. R. China
| | - Leilei Tian
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
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33
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Lu X, Fu H, Shih KC, Jia F, Sun Y, Wang D, Wang Y, Ekatan S, Nieh MP, Lin Y, Zhang K. DNA-Mediated Step-Growth Polymerization of Bottlebrush Macromonomers. J Am Chem Soc 2020; 142:10297-10301. [PMID: 32453555 DOI: 10.1021/jacs.0c03806] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein, we report the DNA-mediated self-assembly of bivalent bottlebrush polymers, a process akin to the step-growth polymerization of small molecule monomers. In these "condensation reactions", the polymer serves as a steric guide to limit DNA hybridization in a fixed direction, while the DNA serves as a functional group equivalent, connecting complementary brushes to form well-defined, one-dimensional nanostructures. The polymerization was studied using spectroscopy, microscopy, and scattering techniques and was modeled numerically. The model made predictions of the degree of polymerization and size distribution of the assembled products, and suggested the potential for branching at hybridization junctions, all of which were confirmed experimentally. This study serves as a theoretical basis for the polymer-assembly approach which has the potential to open up new possibilities for suprapolymers with controlled architecture, macromonomer sequence, and end-group functionalities.
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Affiliation(s)
- Xueguang Lu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Hailin Fu
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States.,Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States.,Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Kuo-Chih Shih
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Fei Jia
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Yehui Sun
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Dali Wang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Yuyan Wang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Stephen Ekatan
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States.,Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Mu-Ping Nieh
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States.,Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Yao Lin
- Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269, United States.,Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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34
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35
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Xie N, Wang H, Quan K, Feng F, Huang J, Wang K. Self-assembled DNA-Based geometric polyhedrons: Construction and applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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36
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Xiao F, Wei Z, Wang M, Hoff A, Bao Y, Tian L. Oligonucleotide-Polymer Conjugates: From Molecular Basics to Practical Application. Top Curr Chem (Cham) 2020; 378:24. [PMID: 32064539 DOI: 10.1007/s41061-020-0286-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/21/2020] [Indexed: 12/18/2022]
Abstract
DNA exhibits many attractive properties, such as programmability, precise self-assembly, sequence-coded biomedical functions, and good biocompatibility; therefore, DNA has been used extensively as a building block to construct novel nanomaterials. Recently, studies on oligonucleotide-polymer conjugates (OPCs) have attracted increasing attention. As hybrid molecules, OPCs exhibit novel properties, e.g., sophisticated self-assembly behaviors, which are distinct from the simple combination of the functions of DNA and polymer, making OPCs interesting and useful. The synthesis and applications of OPCs are highly dependent on the choice of the polymer block, but a systematic summary of OPCs based on their molecular structures is still lacking. In order to design OPCs for further applications, it is necessary to thoroughly understand the structure-function relationship of OPCs. In this review, we carefully categorize recently developed OPCs by the structures of the polymer blocks, and discuss the synthesis, purification, and applications for each category. Finally, we will comment on future prospects for OPCs.
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Affiliation(s)
- Fan Xiao
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, Guangdong, People's Republic of China.,School of Materials Science and Engineering, Harbin Institute of Technology, Nangang District, Harbin, 150001, People's Republic of China
| | - Zixiang Wei
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Maggie Wang
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225-9150, USA
| | - Alexandra Hoff
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225-9150, USA
| | - Ying Bao
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225-9150, USA.
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, Guangdong, People's Republic of China.
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37
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Kim F, Chen T, Burgess T, Rasie P, Selinger TL, Greschner A, Rizis G, Carneiro K. Functionalized DNA nanostructures as scaffolds for guided mineralization. Chem Sci 2019; 10:10537-10542. [PMID: 32055376 PMCID: PMC6988742 DOI: 10.1039/c9sc02811k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/26/2019] [Indexed: 11/21/2022] Open
Abstract
The field of DNA nanotechnology uses synthetic DNA strands as building blocks for designing complex shapes in one-, two- and three-dimensions. Here, we investigate whether DNA nanostructures are feasible platforms for the precise organization of polyaspartic acid (pAsp), a known mineral carrier, with a goal towards biomimetic mineralization for enamel regeneration. We describe the preparation of DNA-pAsp conjugates and their subsequent assembly into ordered nanostructures. Covalent attachment of pAsp to DNA was noted to hinder DNA nanostructure formation past a certain threshold (50% pAsp) when tested on a previously published DNA system. However, a simplified double stranded DNA system (3sDH system) was more robust and efficient in its pAsp incorporation. In addition, the 3sDH system was successful in organizing mineral inducing groups in one dimension at repeating intervals of 28.7 ± 4.0 nm, as determined by atomic force microscopy. Our results demonstrate that DNA nanostructures can be functionalized with pAsp and act as a platform to investigate guided mineralization.
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Affiliation(s)
- Francesca Kim
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Tong Chen
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Trevor Burgess
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Prakash Rasie
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Tim Luca Selinger
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Andrea Greschner
- Institut National de la Recherche Scientifique (INRS) , EMT Research Center , Varennes , QC J3X 1S2 , Canada
| | - Georgios Rizis
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Karina Carneiro
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
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Dobscha JR, Castillo HD, Li Y, Fadler RE, Taylor RD, Brown AA, Trainor CQ, Tait SL, Flood AH. Sequence-Defined Macrocycles for Understanding and Controlling the Build-up of Hierarchical Order in Self-Assembled 2D Arrays. J Am Chem Soc 2019; 141:17588-17600. [PMID: 31503483 PMCID: PMC7461245 DOI: 10.1021/jacs.9b06410] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Anfinsen's dogma that sequence dictates structure is fundamental to understanding the activity and assembly of proteins. This idea has been applied to all manner of oligomers but not to the behavior of cyclic oligomers, aka macrocycles. We do this here by providing the first proofs that sequence controls the hierarchical assembly of nonbiological macrocycles, in this case, at graphite surfaces. To design macrocycles with one (AAA), two (AAB), or three (ABC) different carbazole units, we needed to subvert the synthetic preferences for one-pot macrocyclizations. We developed a new stepwise synthesis with sequence-defined targets made in 11, 17, and 22 steps with 25, 10, and 5% yields, respectively. The linear build up of primary sequence (1°) also enabled a thermal Huisgen cycloaddition to proceed regioselectively for the first time using geometric control. The resulting macrocycles are planar (2° structure) and form H-bonded dimers (3°) at surfaces. Primary sequences encoded into the suite of tricarb macrocycles were shown by scanning-tunneling microscopy (STM) to impact the next levels of supramolecular ordering (4°) and 2D crystalline polymorphs (5°) at solution-graphite interfaces. STM imaging of an AAB macrocycle revealed the formation of a new gap phase that was inaccessible using only C3-symmetric macrocycles. STM imaging of two additional sequence-controlled macrocycles (AAD, ABE) allowed us to identify the factors driving the formation of this new polymorph. This demonstration of how sequence controls the hierarchical patterning of macrocycles raises the importance of stepwise syntheses relative to one-pot macrocyclizations to offer new approaches for greater understanding and control of hierarchical assembly.
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Affiliation(s)
- James R. Dobscha
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Henry D. Castillo
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Yan Li
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Rachel E. Fadler
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Rose D. Taylor
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Andrew A. Brown
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Colleen Q. Trainor
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Steven L. Tait
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Amar H. Flood
- Molecular Materials Design Laboratory, Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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39
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Magdalena Estirado E, Aleman Garcia MA, Schill J, Brunsveld L. Multivalent Ultrasensitive Interfacing of Supramolecular 1D Nanoplatforms. J Am Chem Soc 2019; 141:18030-18037. [PMID: 31622094 PMCID: PMC6856958 DOI: 10.1021/jacs.9b05629] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multivalent display on linear platforms is used by many biomolecular systems to effectively interact with their corresponding binding partners in a dose-responsive and ultrasensitive manner appropriate to the biological system at hand. Synthetic supramolecular multivalent displays offer a matching approach for the modular and bottom-up construction and systematic study of dynamic 1D materials. Fundamental studies into multivalent interactions between such linear, 1D materials have been lacking because of the absence of appropriate modular nanoplatforms. In this work we interfaced two synthetic multivalent linear nanoplatforms based on a dynamic supramolecular polymer, formed by hybrid discotic-oligonucleotide monomers, and a series of complementary DNA-duplex-based multivalent ligands, also with appended short oligonucleotides. The combination of these two multivalent nanoplatforms provides for the first time entry to study multivalent effects in dynamic 1D systems, of relevance for the conceptual understanding of multivalency in biology and for the generation of novel multivalent biomaterials. Together the two nanoscaffolds provide easy access to libraries of multivalent ligands with tunable affinities. The DNA scaffold allows for exact control over valency and spatial ligand distribution, and the discotic supramolecular polymer allows for dynamic adaptation and control over receptor density. The interaction between the two nanoplatforms was studied as a function of ligand interaction strength, valency, and density. Usage of the enhancement parameter β allowed quantification of the effects of ligand valency and affinity. The results reveal a generalized principle of additive binding increments. Receptor density is shown to be crucially and nonlinearly correlated to complex formation, leading to ultrasensitive responses. The results reveal that, not unlike biomolecular signaling, high density multivalent display of receptors is crucial for functionally increased affinities.
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Affiliation(s)
- Eva Magdalena Estirado
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands
| | - Miguel Angel Aleman Garcia
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands
| | - Jurgen Schill
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands
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40
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Zhang C, Wang Z, Liu Y, Yang J, Zhang X, Li Y, Pan L, Ke Y, Yan H. Nicking-Assisted Reactant Recycle To Implement Entropy-Driven DNA Circuit. J Am Chem Soc 2019; 141:17189-17197. [DOI: 10.1021/jacs.9b07521] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
- College of Medical Technology, Peking University Health Science Center, Beijing 100871, China
| | - Zhiyu Wang
- Huazhong University of Science and Technology, Wuhan 430074, Hubei China
| | | | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Xinxin Zhang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Yifan Li
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Linqiang Pan
- Huazhong University of Science and Technology, Wuhan 430074, Hubei China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, Georgia 30322, United States
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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41
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Hendrikse SIS, Gras SL, Ellis AV. Opportunities and Challenges in DNA-Hybrid Nanomaterials. ACS NANO 2019; 13:8512-8516. [PMID: 31415144 DOI: 10.1021/acsnano.9b06186] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nature has inspired the development of many life-like materials. Although still simplistic, key biological functionalities have been incorporated, enabling a wide variety of applications. DNA-based systems, in particular, show high promise due to their ability to merge specific Watson-Crick base pairing with unique properties that are also programmable, scalable, or dynamic. By combining the fields of DNA-based covalent polymers, DNA origami, and DNA-functionalized supramolecular polymers, new frontiers in next-generation DNA-based hybrid materials that can outperform current bioartificial systems will be realized. Many challenges must still be overcome before this emerging technology can be materialized.
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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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Xu Y, Jiang S, Simmons CR, Narayanan RP, Zhang F, Aziz AM, Yan H, Stephanopoulos N. Tunable Nanoscale Cages from Self-Assembling DNA and Protein Building Blocks. ACS NANO 2019; 13:3545-3554. [PMID: 30835439 DOI: 10.1021/acsnano.8b09798] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Three-dimensional (3D) cages are one of the most important targets for nanotechnology. Both proteins and DNA have been used as building blocks to create tunable nanoscale cages for a wide range of applications, but each molecular type has its own limitations. Here, we report a cage constructed from both protein and DNA building blocks through the use of covalent protein-DNA conjugates. We modified a homotrimeric protein (KDPG aldolase) with three identical single-stranded DNA handles by functionalizing a reactive cysteine residue introduced via site-directed mutagenesis. This protein-DNA building block was coassembled with a triangular DNA structure bearing three complementary arms to the handles, resulting in tetrahedral cages comprising six DNA sides capped by the protein trimer. The dimensions of the cage could be tuned through the number of turns per DNA arm (3 turns ∼ 10 nm, 4 turns ∼ 14 nm), and the hybrid structures were purified and characterized to confirm the three-dimensional structure. Cages were also modified with DNA using click chemistry and using aldolase trimers bearing the noncanonical amino acid 4-azidophenylalanine, demonstrating the generality of the method. Our approach will allow for the construction of nanomaterials that possess the advantages of both protein and DNA nanotechnology and find applications in fields such as targeted delivery, structural biology, biomedicine, and catalytic materials.
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Zhao B, Gao Z, Zheng Y, Gao C. Scalable Synthesis of Positively Charged Sequence-Defined Functional Polymers. J Am Chem Soc 2019; 141:4541-4546. [PMID: 30835105 DOI: 10.1021/jacs.9b00172] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Synthesizing and characterizing sequence-defined polymers with positively charged backbone are great challenges. By alternately processing Menschutkin reaction and Cu-catalyzed azide-alkyne cycloaddition reaction, we successfully synthesized series of scalable cationic sequence-defined polymers with quaternary ammonium backbone up to 12 repeating units and characterized their precise structures. Due to the dramatic polarity difference between weak polar feed molecules and strong polar target molecules, simple precipitation in weak polar solvents is enough to obtain pure sequence-defined polymers. Such a polar-inverse strategy (PIS), without protecting groups and solid support, offers extremely high yields up to 68% after 12 reaction steps (i.e., average yield >95% for each step), favoring cost-effective large-scale production. Because of the independent reactivity of selected functional groups, the cationic sequence-defined polymers are highly programmable, including backbone composition, sequence order, functional side groups, terminal groups and topological structure. Sequence information decoding is easily achieved according to Maldi-Tof mass spectrum without retrospecting its synthetic history, resulting in a great superiority in the field of information transmitting and reading. The resulting multifunctional sequence-defined polymers are water-soluble and positively charged, opening the avenue to bioapplications such as condensing DNA, gene transfection and drug delivery.
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Affiliation(s)
- Bo Zhao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , P. R. China
| | - Zhengguo Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , P. R. China.,Department of Polymer Science and Engineering, College of Chemistry and Chemical Engineering , Yantai University , 30 Qingquan Road , Yantai 264005 , P. R. China
| | - Yaochen Zheng
- Department of Polymer Science and Engineering, College of Chemistry and Chemical Engineering , Yantai University , 30 Qingquan Road , Yantai 264005 , P. R. China
| | - Chao Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering , Zhejiang University , Hangzhou 310027 , P. R. China
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Affiliation(s)
- Fei Jia
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Hui Li
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Runhua Chen
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410007, China
| | - Ke Zhang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha, 410007, China
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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Chidchob P, Offenbartl-Stiegert D, McCarthy D, Luo X, Li J, Howorka S, Sleiman HF. Spatial Presentation of Cholesterol Units on a DNA Cube as a Determinant of Membrane Protein-Mimicking Functions. J Am Chem Soc 2018; 141:1100-1108. [DOI: 10.1021/jacs.8b11898] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Pongphak Chidchob
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Daniel Offenbartl-Stiegert
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Dillon McCarthy
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Xin Luo
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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Taylor LLK, Riddell IA, Smulders MMJ. Selbstorganisation von funktionellen diskreten dreidimensionalen Architekturen in Wasser. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lauren L. K. Taylor
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen Niederlande
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Taylor LLK, Riddell IA, Smulders MMJ. Self-Assembly of Functional Discrete Three-Dimensional Architectures in Water. Angew Chem Int Ed Engl 2018; 58:1280-1307. [DOI: 10.1002/anie.201806297] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL UK
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen The Netherlands
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Lueckerath T, Strauch T, Koynov K, Barner-Kowollik C, Ng DYW, Weil T. DNA–Polymer Conjugates by Photoinduced RAFT Polymerization. Biomacromolecules 2018; 20:212-221. [DOI: 10.1021/acs.biomac.8b01328] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thorsten Lueckerath
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tina Strauch
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Christopher Barner-Kowollik
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), George Street, Brisbane, Queensland 4000, Australia
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstraße 18, 76131 Karlsruhe, Germany
| | - David Y. W. Ng
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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