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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; 146:26148-26160. [PMID: 39255470 DOI: 10.1021/jacs.4c07221] [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: 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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He Y, Liu M, Wang Y, Liu Y. Self-Regulated Assembly and Disassembly of Gold Nanoparticles for Low-Temperature Time Indication. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2403216. [PMID: 39171494 DOI: 10.1002/smll.202403216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/02/2024] [Indexed: 08/23/2024]
Abstract
The color-changing self-assembly and autonomous disassembly of colloidal gold nanoparticles (AuNPs) is reported by simply mixing negatively charged phosphine ligand-capped AuNPs with partially oxidized polyethylene glycol (PEG). The assembly of AuNPs is initiated by PEG adsorption, which disrupts the hydration layer of AuNPs, leading to depletion attraction and reduction of hydration repulsion among the AuNPs. The oxidative species in PEG subsequently oxidize and remove the charged ligands from the AuNP surface, resulting in a decrease and reversal of the negative surface charge. This causes the PEG to adsorb on AuNPs in a tighter and more direct manner, providing strong steric shielding to the AuNPs, thereby triggering the disassembly of the AuNP assemblies. The self-regulated assembly-disassembly process can be tuned widely by controlling chemical conditions of PEG, nanoparticle concentration, and the environmental conditions, suggesting potential applications as colorimetric time-temperature indicators for food and medicine storage conditions. As a proof of concept, it is demonstrated that the lifetime of the color-changing assembly-disassembly process can be extended from tens of minutes to weeks when subjected to a refrigerated environment, with tunability achievable through varying polymer conditions and storage atmospheres.
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Affiliation(s)
- Yi He
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, Sichuan, 610500, P. R. China
| | - Mingqin Liu
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, Sichuan, 610500, P. R. China
| | - Yuan Wang
- School of Manufacture Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, 621010, P. R. China
| | - Yiding Liu
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, Sichuan, 610500, P. R. China
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3
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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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4
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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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5
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Zhang Y, Chen Y, Liu X, Ling Q, Wu R, Yang J, Zhang C. Programmable Primer Switching for Regulating Enzymatic DNA Circuits. ACS NANO 2024; 18:5089-5100. [PMID: 38286819 DOI: 10.1021/acsnano.3c12000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Developing DNA strand displacement reactions (SDRs) offers crucial technical support for regulating artificial nucleic acid circuits and networks. More recently, enzymatic SDR-based DNA circuits have gained significant attention because of their modular design, high orthogonality signaling, and extremely fast reaction rates. Typical enzymatic SDRs are regulated by relatively long primers (20-30 nucleotides) that hybridize to form stable double-stranded structures, facilitating enzyme-initiated events. Implementing more flexible primer-based enzymatic SDR regulations remains challenging due to the lack of convenient and simple primer control mechanism, which consequently limits the development of enzymatic DNA circuits. In this study, we propose an approach, termed primer switching regulation, that implements programmable and flexible regulations of enzymatic circuits by introducing switchable wires into the enzymatic circuits. We applied this method to generate diverse enzymatic DNA circuits, including cascading, fan-in/fan-out, dual-rail, feed-forward, and feedback functions. Through this method, complex circuit functions can be implemented by just introducing additional switching wires without reconstructing the basic circuit frameworks. The method is experimentally demonstrated to provide flexible and programmable regulations to control enzymatic DNA circuits and has future applications in DNA computing, biosensing, and DNA storage.
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Affiliation(s)
- Yongpeng Zhang
- 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
| | - Xuan Liu
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Qian Ling
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| | - Ranfeng Wu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
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6
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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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7
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Darwish AS, Lemaoui T, AlYammahi J, Taher H, Benguerba Y, Banat F, AlNashef IM. Molecular Insights into Potential Hydrophobic Deep Eutectic Solvents for Furfural Extraction Guided by COSMO-RS and Machine Learning. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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9
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Wei X, Chen C, Zhao Y, Harazinska E, Bathe M, Hernandez R. Molecular Structure of Single-Stranded DNA on the ZnS Surface of Quantum Dots. ACS NANO 2022; 16:6666-6675. [PMID: 35405067 PMCID: PMC9048700 DOI: 10.1021/acsnano.2c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
DNA-based nanoparticle assemblies have emerged as leading candidates in the development of bioimaging materials, photonic devices, and computing materials. Here, we combine atomistic simulations and experiments to characterize the wrapping mechanism of chimeric single-stranded DNA (ssDNA) on CdSe-ZnS (core-shell) quantum dots (QDs) at different ratios of the phosphorothioate (PS) modification of the bases. We use an implicit solvent, all-atom ssDNA model to match the experimentally calculated ssDNA conformation at low salt concentrations. Through simulation, we find that 3-mercaptopropionic acid (MPA) induces electrostatic repulsion and O-(2-mercaptoethyl)-Ó-methyl-hexa (ethylene glycol) (mPEG) induces steric exclusion, and both reduce the binding affinity of ssDNA. In both simulation and experiment, we find that ssDNA is closer to the QD surface when the QD size is larger. The effect of the PS-base ratio on the conformation of ssDNA is also elaborated in this work. We found through MD simulations, and confirmed by transmission electron microscopy, that the maximum valence numbers are 1, 2, and 3 on QDs of 6, 9, and 14 nm in diameter, respectively. We conclude that the maximum ssDNA valence number is linearly related to the QD size, n ∝ R, and justify this finding through an electrostatic repulsion mechanism.
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Affiliation(s)
- Xingfei Wei
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chi Chen
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yinong Zhao
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ewa Harazinska
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mark Bathe
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rigoberto Hernandez
- Department
of Chemistry, Chemical & Biomolecular Engineering and Materials Science
& Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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10
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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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Lee W, Yu M, Lim D, Kang T, Song Y. Programmable DNA-Based Boolean Logic Microfluidic Processing Unit. ACS NANO 2021; 15:11644-11654. [PMID: 34232017 DOI: 10.1021/acsnano.1c02153] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As molecular computing materials, information-encoded deoxyribonucleic acid (DNA) strands provide a logical computing process by cascaded and parallel chain reactions. However, the reactions in DNA-based combinational logic computing are mostly achieved through a manual process by adding desired DNA molecules in a single microtube or a substrate. For DNA-based Boolean logic, using microfluidic chips can afford automated operation, programmable control, and seamless combinational logic operation, similar to electronic microprocessors. In this paper, we present a programmable DNA-based microfluidic processing unit (MPU) chip that can be controlled via a personal computer for performing DNA calculations. To fabricate this DNA-based MPU, polydimethylsiloxane was cast using double-sided molding techniques for alignment between the microfluidics and valve switch. For a uniform surface, molds fabricated using a three-dimensional printer were spin-coated by a polymer. For programming control, the valve switch arms were operated by servo motors. In the MPU controlled via a personal computer or smartphone application, the molecules with two input DNAs and a logic template DNA were reacted for the basic AND and OR operations. Furthermore, the DNA molecules reacted in a cascading manner for combinational AND and OR operations. Finally, we demonstrated a 2-to-1 multiplexer and the XOR operation with a three-step cascade reaction using the simple DNA-based MPU, which can perform Boolean logic operations (AND, OR, and NOT). Through logic combination, this DNA-based Boolean logic MPU, which can be operated using programming language, is expected to facilitate the development of complex functional circuits such as arithmetic logical units and neuromorphic circuits.
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Affiliation(s)
- Wonjin Lee
- Department of Nano-bioengineering, Incheon National University, Academy-to 119, Incheon, Korea, 22012
| | - Minsang Yu
- Department of Nano-bioengineering, Incheon National University, Academy-to 119, Incheon, Korea, 22012
| | - Doyeon Lim
- Department of Nano-bioengineering, Incheon National University, Academy-to 119, Incheon, Korea, 22012
| | - Taeseok Kang
- Department of Nano-bioengineering, Incheon National University, Academy-to 119, Incheon, Korea, 22012
| | - Youngjun Song
- Department of Nano-bioengineering, Incheon National University, Academy-to 119, Incheon, Korea, 22012
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