1
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Lee RC, Corsano A, Tseng CY, Laohakunakorn N, Chou LYT. Rewireable Building Blocks for Enzyme-Powered DNA Computing Networks. J Am Chem Soc 2024. [PMID: 39255470 DOI: 10.1021/jacs.4c07221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Neural networks enable the processing of large, complex data sets with applications in disease diagnosis, cell profiling, and drug discovery. Beyond electronic computers, neural networks have been implemented using programmable biomolecules such as DNA; this confers unique advantages, such as greater portability, electricity-free operation, and direct analysis of patterns of biomolecules in solution. Analogous to bottlenecks in electronic computers, the computing power of DNA-based neural networks is limited by the ability to add more computing units, i.e., neurons. This limitation exists because current architectures require many nucleic acids to model a single neuron. Each additional neuron compounds existing problems such as long assembly times, high background signal, and cross-talk between components. Here, we test three strategies to solve this limitation and improve the scalability of DNA-based neural networks: (i) enzymatic synthesis for high-purity neurons, (ii) spatial patterning of neuron clusters based on their network position, and (iii) encoding neuron connectivity on a universal single-stranded DNA backbone. We show that neurons implemented via these strategies activate quickly, with a high signal-to-background ratio and process-weighted inputs. We rewired our modular neurons to demonstrate basic neural network motifs such as cascading, fan-in, and fan-out circuits. Finally, we designed a prototype two-layer microfluidic device to automate the operation of our circuits. We envision that our proposed design will help scale DNA-based neural networks due to its modularity, simplicity of synthesis, and compatibility with various neural network architectures. This will enable portable computing power for applications in portable diagnostics, compact data storage, and autonomous decision making for lab-on-a-chips.
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Affiliation(s)
- Ryan C Lee
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Room 420 Rosebrugh Building, Toronto, Ontario M5S 3E2, Canada
| | - Ariel Corsano
- Department of Bioengineering, McGill University, 3480 University Street Room, 350 McConnell Engineering Building, Montreal, Quebec H3A 0E9, Canada
| | - Chung Yi Tseng
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Room 420 Rosebrugh Building, Toronto, Ontario M5S 3E2, Canada
| | - Nadanai Laohakunakorn
- School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, The King's Buildings, Edinburgh, Scotland EH9 3FF, U.K
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Room 420 Rosebrugh Building, Toronto, Ontario M5S 3E2, Canada
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2
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Huster D, Maiti S, Herrmann A. Phospholipid Membranes as Chemically and Functionally Tunable Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312898. [PMID: 38456771 DOI: 10.1002/adma.202312898] [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: 11/29/2023] [Revised: 02/12/2024] [Indexed: 03/09/2024]
Abstract
The sheet-like lipid bilayer is the fundamental structural component of all cell membranes. Its building blocks are phospholipids and cholesterol. Their amphiphilic structure spontaneously leads to the formation of a bilayer in aqueous environment. Lipids are not just structural elements. Individual lipid species, the lipid membrane structure, and lipid dynamics influence and regulate membrane protein function. An exciting field is emerging where the membrane-associated material properties of different bilayer systems are used in designing innovative solutions for widespread applications across various fields, such as the food industry, cosmetics, nano- and biomedicine, drug storage and delivery, biotechnology, nano- and biosensors, and computing. Here, the authors summarize what is known about how lipids determine the properties and functions of biological membranes and how this has been or can be translated into innovative applications. Based on recent progress in the understanding of membrane structure, dynamics, and physical properties, a perspective is provided on how membrane-controlled regulation of protein functions can extend current applications and even offer new applications.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107, Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400 005, India
| | - Andreas Herrmann
- Freie Universität Berlin, Department Chemistry and Biochemistry, SupraFAB, Altensteinstr. 23a, D-14195, Berlin, Germany
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3
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Yang S, Bögels BWA, Wang F, Xu C, Dou H, Mann S, Fan C, de Greef TFA. DNA as a universal chemical substrate for computing and data storage. Nat Rev Chem 2024; 8:179-194. [PMID: 38337008 DOI: 10.1038/s41570-024-00576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
DNA computing and DNA data storage are emerging fields that are unlocking new possibilities in information technology and diagnostics. These approaches use DNA molecules as a computing substrate or a storage medium, offering nanoscale compactness and operation in unconventional media (including aqueous solutions, water-in-oil microemulsions and self-assembled membranized compartments) for applications beyond traditional silicon-based computing systems. To build a functional DNA computer that can process and store molecular information necessitates the continued development of strategies for computing and data storage, as well as bridging the gap between these fields. In this Review, we explore how DNA can be leveraged in the context of DNA computing with a focus on neural networks and compartmentalized DNA circuits. We also discuss emerging approaches to the storage of data in DNA and associated topics such as the writing, reading, retrieval and post-synthesis editing of DNA-encoded data. Finally, we provide insights into how DNA computing can be integrated with DNA data storage and explore the use of DNA for near-memory computing for future information technology and health analysis applications.
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Affiliation(s)
- Shuo Yang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Bas W A Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Can Xu
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Hongjing Dou
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Stephen Mann
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China.
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, UK.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
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4
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Sun C, Li M, Wang F. Programming and monitoring surface-confined DNA computing. Bioorg Chem 2024; 143:107080. [PMID: 38183684 DOI: 10.1016/j.bioorg.2023.107080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
DNA-based molecular computing has evolved to encompass a diverse range of functions, demonstrating substantial promise for both highly parallel computing and various biomedical applications. Recent advances in DNA computing systems based on surface reactions have demonstrated improved levels of specificity and computational speed compared to their solution-based counterparts that depend on three-dimensional molecular collisions. Herein, computational biomolecular interactions confined by various surfaces such as DNA origamis, nanoparticles, lipid membranes and chips are systematically reviewed, along with their manipulation methodologies. Monitoring techniques and applications for these surface-based computing systems are also described. The advantages and challenges of surface-confined DNA computing are discussed.
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Affiliation(s)
- Chenyun Sun
- 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
| | - Mingqiang Li
- 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.
| | - Fei Wang
- 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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5
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Wang Z, Zhang X, Wang Y, Fang Z, Jiang H, Yang Q, Zhu X, Liu M, Fan X, Kong J. Untethered Soft Microrobots with Adaptive Logic Gates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206662. [PMID: 36809583 PMCID: PMC10161047 DOI: 10.1002/advs.202206662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/16/2023] [Indexed: 05/06/2023]
Abstract
Integrating adaptative logic computation directly into soft microrobots is imperative for the next generation of intelligent soft microrobots as well as for the smart materials to move beyond stimulus-response relationships and toward the intelligent behaviors seen in biological systems. Acquiring adaptivity is coveted for soft microrobots that can adapt to implement different works and respond to different environments either passively or actively through human intervention like biological systems. Here, a novel and simple strategy for constructing untethered soft microrobots based on stimuli-responsive hydrogels that can switch logic gates according to the surrounding stimuli of environment is introduced. Different basic logic gates and combinational logic gates are integrated into a microrobot via a straightforward method. Importantly, two kinds of soft microrobots with adaptive logic gates are designed and fabricated, which can smartly switch logic operation between AND gate and OR gate under different surrounding environmental stimuli. Furthermore, a same magnetic microrobot with adaptive logic gate is used to capture and release the specified objects through the change of the surrounding environmental stimuli based on AND or OR logic gate. This work contributes an innovative strategy to integrate computation into small-scale untethered soft robots with adaptive logic gates.
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Affiliation(s)
- Zichao Wang
- MOE Key Laboratory of Materials Physics and Chemistry in Extraordinary Conditions, Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Xuan Zhang
- MOE Key Laboratory of Materials Physics and Chemistry in Extraordinary Conditions, Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Yang Wang
- MOE Key Laboratory of Materials Physics and Chemistry in Extraordinary Conditions, Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Ziyi Fang
- MOE Key Laboratory of Materials Physics and Chemistry in Extraordinary Conditions, Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - He Jiang
- MOE Key Laboratory of Materials Physics and Chemistry in Extraordinary Conditions, Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Qinglin Yang
- MOE Key Laboratory of Materials Physics and Chemistry in Extraordinary Conditions, Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Xuefeng Zhu
- MOE Key Laboratory of Materials Physics and Chemistry in Extraordinary Conditions, Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Mingze Liu
- MOE Key Laboratory of Materials Physics and Chemistry in Extraordinary Conditions, Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Xiaodong Fan
- MOE Key Laboratory of Materials Physics and Chemistry in Extraordinary Conditions, Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Jie Kong
- MOE Key Laboratory of Materials Physics and Chemistry in Extraordinary Conditions, Shaanxi Key Laboratory of Macromolecular Science and Technology, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
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6
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Zhao T, Chen L, Liu M, Lin R, Cai W, Hung CT, Wang S, Duan L, Zhang F, Elzatahry A, Li X, Zhao D. Emulsion-oriented assembly for Janus double-spherical mesoporous nanoparticles as biological logic gates. Nat Chem 2023:10.1038/s41557-023-01183-4. [PMID: 37055572 DOI: 10.1038/s41557-023-01183-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/13/2023] [Indexed: 04/15/2023]
Abstract
The ability of Janus nanoparticles to establish biological logic systems has been widely exploited, yet conventional non/uni-porous Janus nanoparticles are unable to fully mimic biological communications. Here we demonstrate an emulsion-oriented assembly approach for the fabrication of highly uniform Janus double-spherical MSN&mPDA (MSN, mesoporous silica nanoparticle; mPDA, mesoporous polydopamine) nanoparticles. The delicate Janus nanoparticle possesses a spherical MSN with a diameter of ~150 nm and an mPDA hemisphere with a diameter of ~120 nm. In addition, the mesopore size in the MSN compartment is tunable from ~3 to ~25 nm, while those in the mPDA compartments range from ~5 to ~50 nm. Due to the different chemical properties and mesopore sizes in the two compartments, we achieve selective loading of guests in different compartments, and successfully establish single-particle-level biological logic gates. The dual-mesoporous structure enables consecutive valve-opening and matter-releasing reactions within one single nanoparticle, facilitating the design of single-particle-level logic systems.
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Affiliation(s)
- Tiancong Zhao
- Department of Chemistry and Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), College of Chemistry and Materials, Fudan University, Shanghai, P. R. China
| | - Liang Chen
- Department of Chemistry and Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), College of Chemistry and Materials, Fudan University, Shanghai, P. R. China
| | - Minchao Liu
- Department of Chemistry and Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), College of Chemistry and Materials, Fudan University, Shanghai, P. R. China
| | - Runfeng Lin
- Department of Chemistry and Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), College of Chemistry and Materials, Fudan University, Shanghai, P. R. China
| | - Weiluo Cai
- Department of Musculoskeletal Tumor, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, P. R. China
| | - Chin-Te Hung
- Department of Chemistry and Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), College of Chemistry and Materials, Fudan University, Shanghai, P. R. China
| | - Shangfeng Wang
- Department of Chemistry and Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), College of Chemistry and Materials, Fudan University, Shanghai, P. R. China
| | - Linlin Duan
- Department of Chemistry and Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), College of Chemistry and Materials, Fudan University, Shanghai, P. R. China
| | - Fan Zhang
- Department of Chemistry and Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), College of Chemistry and Materials, Fudan University, Shanghai, P. R. China
| | - Ahmed Elzatahry
- Materials Science and Technology Program, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Xiaomin Li
- Department of Chemistry and Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), College of Chemistry and Materials, Fudan University, Shanghai, P. R. China.
| | - Dongyuan Zhao
- Department of Chemistry and Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, State Key Laboratory of Molecular Engineering of Polymers, Collaborative Innovation Center of Chemistry for Energy Materials (2011-iChEM), College of Chemistry and Materials, Fudan University, Shanghai, P. R. China.
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7
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Maingi V, Zhang Z, Thachuk C, Sarraf N, Chapman ER, Rothemund PWK. Digital nanoreactors to control absolute stoichiometry and spatiotemporal behavior of DNA receptors within lipid bilayers. Nat Commun 2023; 14:1532. [PMID: 36941256 PMCID: PMC10027858 DOI: 10.1038/s41467-023-36996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
Interactions between membrane proteins are essential for cell survival but are often poorly understood. Even the biologically functional ratio of components within a multi-subunit membrane complex-the native stoichiometry-is difficult to establish. Here we demonstrate digital nanoreactors that can control interactions between lipid-bound molecular receptors along three key dimensions: stoichiometric, spatial, and temporal. Each nanoreactor is based on a DNA origami ring, which both templates the synthesis of a liposome and provides tethering sites for DNA-based receptors (modelling membrane proteins). Receptors are released into the liposomal membrane using strand displacement and a DNA logic gate measures receptor heterodimer formation. High-efficiency tethering of receptors enables the kinetics of receptors in 1:1 and 2:2 absolute stoichiometries to be observed by bulk fluorescence, which in principle is generalizable to any ratio. Similar single-molecule-in-bulk experiments using DNA-linked membrane proteins could determine native stoichiometry and the kinetics of membrane protein interactions for applications ranging from signalling research to drug discovery.
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Affiliation(s)
- Vishal Maingi
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
| | - Zhao Zhang
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA
| | - Chris Thachuk
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
| | - Namita Sarraf
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Edwin R Chapman
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA.
| | - Paul W K Rothemund
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Computation & Neural Systems, California Institute of Technology, Pasadena, CA, USA.
- Department of Computation + Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
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8
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Jakšić Z, Obradov M, Jakšić O. Bio-Inspired Nanomembranes as Building Blocks for Nanophotonics, Plasmonics and Metamaterials. Biomimetics (Basel) 2022; 7:222. [PMID: 36546922 PMCID: PMC9775387 DOI: 10.3390/biomimetics7040222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
Nanomembranes are the most widespread building block of life, as they encompass cell and organelle walls. Their synthetic counterparts can be described as freestanding or free-floating structures thinner than 100 nm, down to monatomic/monomolecular thickness and with giant lateral aspect ratios. The structural confinement to quasi-2D sheets causes a multitude of unexpected and often counterintuitive properties. This has resulted in synthetic nanomembranes transiting from a mere scientific curiosity to a position where novel applications are emerging at an ever-accelerating pace. Among wide fields where their use has proven itself most fruitful are nano-optics and nanophotonics. However, the authors are unaware of a review covering the nanomembrane use in these important fields. Here, we present an attempt to survey the state of the art of nanomembranes in nanophotonics, including photonic crystals, plasmonics, metasurfaces, and nanoantennas, with an accent on some advancements that appeared within the last few years. Unlimited by the Nature toolbox, we can utilize a practically infinite number of available materials and methods and reach numerous properties not met in biological membranes. Thus, nanomembranes in nano-optics can be described as real metastructures, exceeding the known materials and opening pathways to a wide variety of novel functionalities.
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Affiliation(s)
- Zoran Jakšić
- Center of Microelectronic Technologies, Institute of Chemistry, Technology and Metallurgy, National Institute of the Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
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9
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Kim JM, Lee C, Lee Y, Lee J, Park SJ, Park S, Nam JM. Synthesis, Assembly, Optical Properties, and Sensing Applications of Plasmonic Gap Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2006966. [PMID: 34013617 DOI: 10.1002/adma.202006966] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Plasmonic gap nanostructures (PGNs) have been extensively investigated mainly because of their strongly enhanced optical responses, which stem from the high intensity of the localized field in the nanogap. The recently developed methods for the preparation of versatile nanogap structures open new avenues for the exploration of unprecedented optical properties and development of sensing applications relying on the amplification of various optical signals. However, the reproducible and controlled preparation of highly uniform plasmonic nanogaps and the prediction, understanding, and control of their optical properties, especially for nanogaps in the nanometer or sub-nanometer range, remain challenging. This is because subtle changes in the nanogap significantly affect the plasmonic response and are of paramount importance to the desired optical performance and further applications. Here, recent advances in the synthesis, assembly, and fabrication strategies, prediction and control of optical properties, and sensing applications of PGNs are discussed, and perspectives toward addressing these challenging issues and the future research directions are presented.
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Affiliation(s)
- Jae-Myoung Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Chungyeon Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Yeonhee Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Jinhaeng Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, 16419, South Korea
| | - So-Jung Park
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, South Korea
| | - Sungho Park
- Department of Chemistry, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
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10
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Piao J, Yuan W, Dong Y. Recent Progress of DNA Nanostructures on Amphiphilic Membranes. Macromol Biosci 2021; 21:e2000440. [PMID: 33759366 DOI: 10.1002/mabi.202000440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/24/2021] [Indexed: 11/11/2022]
Abstract
Employing DNA nanostructures mimicking membrane proteins on artificial amphiphilic membranes have been widely developed to understand the structures and functions of the natural membrane systems. In this review, the recent developments in artificial systems constructed by amphiphilic membranes and DNA nanostructures are summarized. First, the preparations and properties of the amphipathic bilayer models are introduced. Second, the interactions are discussed between the membrane and the DNA nanostructures, as well as their coassembly behaviors. Next, the alternative systems related to membrane protein-mediated signal transmission, selective distribution, transmembrane channels, and membrane fusion are also introduced. Moreover, the constructions of membrane skeleton protein-mimicking DNA nanostructures are also highlighted.
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Affiliation(s)
- Jiafang Piao
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
| | - Wei Yuan
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
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11
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Chen W, Cheng CA, Xiang D, Zink JI. Expanding nanoparticle multifunctionality: size-selected cargo release and multiple logic operations. NANOSCALE 2021; 13:5497-5506. [PMID: 33687426 DOI: 10.1039/d1nr00642h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Physically stimulated nanoparticles that deliver size-selected cargo and function as logic gates are reported. To achieve this goal the particle requires multiple components, and we recognized early on that the components, not just the released cargo, could be used to demonstrate logic operations (OR and AND logic). For stimuli, we chose two non-invasive types, red light and alternating magnetic fields (AMF), because they both have potential biological relevance. To realize cargo delivery with size selection and logic operations, we mechanized the surface of core@shell nanoparticles with a superparamagnetic core that generates localized heating when exposed to an AMF, and a mesoporous silica shell into which cargo molecules with different sizes were loaded. We demonstrate the core@shell nanoparticles can load the dual cargos with different sizes and subsequently release the smaller (∼0.5 nm) and bigger (∼2 nm) cargos in succession when stimulated by a red light followed by an AMF. Finally, we demonstrate that the multi-component nanoparticles could function as nanoparticle-based Boolean logic gates where AMF and red light served as the two inputs and the release of small cargo, and free cyclodextrin served as the outputs. The construction of two Boolean logic gates (OR, and AND) was realized.
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Affiliation(s)
- Wei Chen
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, 90095, USA. and California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, 90095, USA
| | - Chi-An Cheng
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, 90095, USA and Department of Bioengineering, University of California Los Angeles, Los Angeles, California, 90095, USA
| | - Danlei Xiang
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, 90095, USA.
| | - Jeffrey I Zink
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, 90095, USA. and California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, 90095, USA
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12
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Hassanzadeh P. The capabilities of nanoelectronic 2-D materials for bio-inspired computing and drug delivery indicate their significance in modern drug design. Life Sci 2021; 279:119272. [PMID: 33631171 DOI: 10.1016/j.lfs.2021.119272] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 12/13/2022]
Abstract
Remarkable advancements in the computational techniques and nanoelectronics have attracted considerable interests for development of highly-sophisticated materials (Ms) including the theranostics with optimal characteristics and innovative delivery systems. Analyzing the huge amounts of multivariate data and solving the newly-emerged complicated problems including the healthcare-related ones have created increasing demands for improving the computational speed and minimizing the consumption of energy. Shifting towards the non-von Neumann approaches enables performing specific computational tasks and optimizing the processing of signals. Besides usefulness for neuromorphic computing and increasing the efficiency of computation energy, 2-D electronic Ms are capable of optical sensing with ultra-fast and ultra-sensitive responses, mimicking the neurons, detection of pathogens or biomolecules, and prediction of the progression of diseases, assessment of the pharmacokinetics/pharmacodynamics of therapeutic candidates, mimicking the dynamics of the release of neurotransmitters or fluxes of ions that might provide a deeper knowledge about the computations and information flow in the brain, and development of more effective treatment protocols with improved outcomes. 2-D Ms appear as the major components of the next-generation electronically-enabled devices for highly-advanced computations, bio-imaging, diagnostics, tissue engineering, and designing smart systems for site-specific delivery of therapeutics that might result in the reduced adverse effects of drugs and improved patient compliance. This manuscript highlights the significance of 2-D Ms in the neuromorphic computing, optimizing the energy efficiency of the multi-step computations, providing novel architectures or multi-functional systems, improved performance of a variety of devices and bio-inspired functionalities, and delivery of theranostics.
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Affiliation(s)
- Parichehr Hassanzadeh
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 13169-43551, Iran.
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13
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Min S, Jeon YS, Choi H, Khatua C, Li N, Bae G, Jung HJ, Kim Y, Hong H, Shin J, Ko MJ, Ko HS, Kim T, Moon JH, Song JJ, Dravid VP, Kim YK, Kang H. Large and Externally Positioned Ligand-Coated Nanopatches Facilitate the Adhesion-Dependent Regenerative Polarization of Host Macrophages. NANO LETTERS 2020; 20:7272-7280. [PMID: 32910662 DOI: 10.1021/acs.nanolett.0c02655] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Macrophages can associate with extracellular matrix (ECM) demonstrating nanosequenced cell-adhesive RGD ligand. In this study, we devised barcoded materials composed of RGD-coated gold and RGD-absent iron nanopatches to show various frequencies and position of RGD-coated nanopatches with similar areas of iron and RGD-gold nanopatches that maintain macroscale and nanoscale RGD density invariant. Iron patches were used for substrate coupling. Both large (low frequency) and externally positioned RGD-coated nanopatches stimulated robust attachment in macrophages, compared with small (high frequency) and internally positioned RGD-coated nanopatches, respectively, which mediate their regenerative/anti-inflammatory M2 polarization. The nanobarcodes exhibited stability in vivo. We shed light into designing ligand-engineered nanostructures in an external position to facilitate host cell attachment, thereby eliciting regenerative host responses.
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Affiliation(s)
- Sunhong Min
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Yoo Sang Jeon
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
- Research Institute of Engineering and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Hyojun Choi
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Chandra Khatua
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Na Li
- Department of Otorhinolaryngology-Head and Neck Surgery, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Gunhyu Bae
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Hee Joon Jung
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- NUANCE Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Yuri Kim
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Hyunsik Hong
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jeongeun Shin
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Min Jun Ko
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Han Seok Ko
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Taesoon Kim
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jun Hwan Moon
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Jae-Jun Song
- Department of Otorhinolaryngology-Head and Neck Surgery, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- NUANCE Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Young Keun Kim
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
- Department of Biomicrosystem Technology, Korea University, Seoul 02841, Republic of Korea
| | - Heemin Kang
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
- Department of Biomicrosystem Technology, Korea University, Seoul 02841, Republic of Korea
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14
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Kim S, Kim N, Seo J, Park JE, Song EH, Choi SY, Kim JE, Cha S, Park HH, Nam JM. Nanoparticle-based computing architecture for nanoparticle neural networks. SCIENCE ADVANCES 2020; 6:eabb3348. [PMID: 32923638 PMCID: PMC7449691 DOI: 10.1126/sciadv.abb3348] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/14/2020] [Indexed: 05/02/2023]
Abstract
The lack of a scalable nanoparticle-based computing architecture severely limits the potential and use of nanoparticles for manipulating and processing information with molecular computing schemes. Inspired by the von Neumann architecture (VNA), in which multiple programs can be operated without restructuring the computer, we realized the nanoparticle-based VNA (NVNA) on a lipid chip for multiple executions of arbitrary molecular logic operations in the single chip without refabrication. In this system, nanoparticles on a lipid chip function as the hardware that features memory, processors, and output units, and DNA strands are used as the software to provide molecular instructions for the facile programming of logic circuits. NVNA enables a group of nanoparticles to form a feed-forward neural network, a perceptron, which implements functionally complete Boolean logic operations, and provides a programmable, resettable, scalable computing architecture and circuit board to form nanoparticle neural networks and make logical decisions.
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15
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Khatua C, Min S, Jung HJ, Shin JE, Li N, Jun I, Liu HW, Bae G, Choi H, Ko MJ, Jeon YS, Kim YJ, Lee J, Ko M, Shim G, Shin H, Lee S, Chung S, Kim YK, Song JJ, Dravid VP, Kang H. In Situ Magnetic Control of Macroscale Nanoligand Density Regulates the Adhesion and Differentiation of Stem Cells. NANO LETTERS 2020; 20:4188-4196. [PMID: 32406688 DOI: 10.1021/acs.nanolett.0c00559] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Developing materials with remote controllability of macroscale ligand presentation can mimic extracellular matrix (ECM) remodeling to regulate cellular adhesion in vivo. Herein, we designed charged mobile nanoligands with superparamagnetic nanomaterials amine-functionalized and conjugated with polyethylene glycol linker and negatively charged RGD ligand. We coupled negatively a charged nanoligand to a positively charged substrate by optimizing electrostatic interactions to allow reversible planar movement. We demonstrate the imaging of both macroscale and in situ nanoscale nanoligand movement by magnetically attracting charged nanoligand to manipulate macroscale ligand density. We show that in situ magnetic control of attracting charged nanoligand facilitates stem cell adhesion, both in vitro and in vivo, with reversible control. Furthermore, we unravel that in situ magnetic attraction of charged nanoligand stimulates mechanosensing-mediated differentiation of stem cells. This remote controllability of ECM-mimicking reversible ligand variations is promising for regulating diverse reparative cellular processes in vivo.
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Affiliation(s)
- Chandra Khatua
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Sunhong Min
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Hee Joon Jung
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Evanston, Illinois 60208, United States
- NUANCE Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Jeong Eun Shin
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Na Li
- Department of Otorhinolaryngology-Head and Neck Surgery, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Indong Jun
- Department of Otorhinolaryngology-Head and Neck Surgery, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Hui-Wen Liu
- School of Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Gunhyu Bae
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Hyojun Choi
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Min Jun Ko
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Yoo Sang Jeon
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Yu Jin Kim
- Institute for High Technology Materials and Devices, Korea University, Seoul 02841, Republic of Korea
| | - Joonbum Lee
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Minji Ko
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Gyubo Shim
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Hongchul Shin
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sangbum Lee
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Seok Chung
- Department of Biomicrosystem Technology, Korea University, Seoul 02841, Republic of Korea
- School of Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Young Keun Kim
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
- Department of Biomicrosystem Technology, Korea University, Seoul 02841, Republic of Korea
| | - Jae-Jun Song
- Department of Otorhinolaryngology-Head and Neck Surgery, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Evanston, Illinois 60208, United States
- NUANCE Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Heemin Kang
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea
- Department of Biomicrosystem Technology, Korea University, Seoul 02841, Republic of Korea
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16
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Gao J, Wu P, Fernandez A, Zhuang J, Thayumanavan S. Cellular AND Gates: Synergistic Recognition to Boost Selective Uptake of Polymeric Nanoassemblies. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jingjing Gao
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - Peidong Wu
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - Ann Fernandez
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - Jiaming Zhuang
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - S. Thayumanavan
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
- Molecular and Cellular Biology Program University of Massachusetts Amherst Amherst USA
- Center for Bioactive Delivery University of Massachusetts Amherst Amherst USA
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17
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Gao J, Wu P, Fernandez A, Zhuang J, Thayumanavan S. Cellular AND Gates: Synergistic Recognition to Boost Selective Uptake of Polymeric Nanoassemblies. Angew Chem Int Ed Engl 2020; 59:10456-10460. [DOI: 10.1002/anie.202002748] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Indexed: 12/30/2022]
Affiliation(s)
- Jingjing Gao
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - Peidong Wu
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - Ann Fernandez
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - Jiaming Zhuang
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - S. Thayumanavan
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
- Molecular and Cellular Biology Program University of Massachusetts Amherst Amherst USA
- Center for Bioactive Delivery University of Massachusetts Amherst Amherst USA
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18
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Darley E, Singh JKD, Surace NA, Wickham SFJ, Baker MAB. The Fusion of Lipid and DNA Nanotechnology. Genes (Basel) 2019; 10:E1001. [PMID: 31816934 PMCID: PMC6947036 DOI: 10.3390/genes10121001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/18/2019] [Accepted: 11/26/2019] [Indexed: 01/06/2023] Open
Abstract
Lipid membranes form the boundary of many biological compartments, including organelles and cells. Consisting of two leaflets of amphipathic molecules, the bilayer membrane forms an impermeable barrier to ions and small molecules. Controlled transport of molecules across lipid membranes is a fundamental biological process that is facilitated by a diverse range of membrane proteins, including ion-channels and pores. However, biological membranes and their associated proteins are challenging to experimentally characterize. These challenges have motivated recent advances in nanotechnology towards building and manipulating synthetic lipid systems. Liposomes-aqueous droplets enclosed by a bilayer membrane-can be synthesised in vitro and used as a synthetic model for the cell membrane. In DNA nanotechnology, DNA is used as programmable building material for self-assembling biocompatible nanostructures. DNA nanostructures can be functionalised with hydrophobic chemical modifications, which bind to or bridge lipid membranes. Here, we review approaches that combine techniques from lipid and DNA nanotechnology to engineer the topography, permeability, and surface interactions of membranes, and to direct the fusion and formation of liposomes. These approaches have been used to study the properties of membrane proteins, to build biosensors, and as a pathway towards assembling synthetic multicellular systems.
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Affiliation(s)
- Es Darley
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington 2052, Australia;
| | - Jasleen Kaur Daljit Singh
- School of Chemistry, University of Sydney, Camperdown 2006, Australia; (J.K.D.S.); (N.A.S.)
- School of Chemical and Biomolecular Engineering, University of Sydney, Camperdown 2006, Australia
- Sydney Nanoscience Institute, University of Sydney, Camperdown 2006, Australia
| | - Natalie A. Surace
- School of Chemistry, University of Sydney, Camperdown 2006, Australia; (J.K.D.S.); (N.A.S.)
| | - Shelley F. J. Wickham
- School of Chemistry, University of Sydney, Camperdown 2006, Australia; (J.K.D.S.); (N.A.S.)
- Sydney Nanoscience Institute, University of Sydney, Camperdown 2006, Australia
- School of Physics, University of Sydney, Camperdown 2006, Australia
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington 2052, Australia;
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
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19
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Kim S, Seo J, Park HH, Kim N, Oh JW, Nam JM. Plasmonic Nanoparticle-Interfaced Lipid Bilayer Membranes. Acc Chem Res 2019; 52:2793-2805. [PMID: 31553568 DOI: 10.1021/acs.accounts.9b00327] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Plasmonic nanoparticles are widely exploited in diverse bioapplications ranging from therapeutics to biosensing and biocomputing because of their strong and tunable light-matter interactions, facile and versatile chemical/biological ligand modifications, and biocompatibility. With the rapid growth of nanobiotechnology, understanding dynamic interactions between nanoparticles and biological systems at the molecular or single-particle level is becoming increasingly important for interrogating biological systems with functional nanostructures and for developing nanoparticle-based biosensors and therapeutic agents. Therefore, significant efforts have been devoted to precisely design and create nano-bio interfaces by manipulating the nanoparticles' size, shape, and surface ligand interactions with complex biological systems to maximize their performance and avoid unwanted responses, such as their agglomeration and cytotoxicity. However, investigating physicochemical interactions at the nano-bio interfaces in a quantitative and controllable manner remains challenging, as the interfaces involve highly complex networks between nanoparticles, biomolecules, and cells across multiple scales, each with a myriad of different chemical and biological interactions. A lipid bilayer is a membrane made of two layers of lipid molecules that forms a barrier around cells and plays structural and functional roles in diverse biological processes because they incorporate and present functional molecules (such as membrane proteins) with lateral fluidity. Plasmonic nanoparticles conjugated on lipid membranes provide reliable analytical labels and functional moieties that allow for studying and manipulating interactions between nanoparticles and molecules with single-particle resolution; they also serve as efficient tools for applying optical, mechanical, and thermal stimuli to biological systems, which stem from plasmonic properties. Recently, new opportunities have emerged by interfacing nanoparticle-modified lipid bilayers (NLBs) with complex systems such as molecular circuits and living systems. In this Account, we briefly review how plasmonic properties can be beneficially harnessed on lipid bilayer membranes to investigate the structures and functions of cellular membranes and to develop new platforms for biomedical applications. In particular, we discuss the versatility of supported lipid bilayers (SLBs), which are planar lipid bilayers on hydrophilic substrates, as dynamic biomaterials that provide lateral fluidity and cell membrane-like environments. We then summarize our efforts to create a quantitative analytical platform utilizing nanoparticles as active building blocks and SLBs as integrative substrates. Through this bottom-up approach, various functionalized nanoparticles have been introduced onto lipid bilayers to render nanoparticle-nanoparticle, nanoparticle-lipid bilayer, and biomolecule-lipid bilayer interfaces programmable. Our system provides a new class of tools for studying thermodynamics and kinetics in complex networks of nanostructures and for realizing unique applications in biosensing and biocomputing.
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Affiliation(s)
- Sungi Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jinyoung Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Ha H. Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Namjun Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jeong-Wook Oh
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
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20
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Seo J, Kim S, Park HH, Nam JM. Biocomputing with Nanostructures on Lipid Bilayers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900998. [PMID: 31026121 DOI: 10.1002/smll.201900998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Biocomputation is the algorithmic manipulation of biomolecules. Nanostructures, most notably DNA nanostructures and nanoparticles, become active substrates for biocomputation when modified with stimuli-responsive, programmable biomolecular ligands. This approach-biocomputing with nanostructures ("nano-bio computing")-allows autonomous control of matter and information at the nanoscale; their dynamic assemblies and beneficial properties can be directed without human intervention. Recently, lipid bilayers interfaced with nanostructures have emerged as a new biocomputing platform. This new nano-bio interface, which exploits lipid bilayers as a chemical circuit board for information processing, offers a unique reaction space for realizing nanostructure-based computation at a previously unexplored dimension. In this Concept, recent advances in nano-bio computing are briefly reviewed and the newly emerging concept of biocomputing with nanostructures on lipid bilayers is introduced.
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Affiliation(s)
- Jinyoung Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Sungi Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Ha H Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
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21
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Shah S, Song T, Song X, Yang M, Reif J. Implementing Arbitrary CRNs Using Strand Displacing Polymerase. LECTURE NOTES IN COMPUTER SCIENCE 2019. [DOI: 10.1007/978-3-030-26807-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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