1
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Mukherjee R, Sengar A, Cabello-García J, Ouldridge TE. Kinetic Proofreading Can Enhance Specificity in a Nonenzymatic DNA Strand Displacement Network. J Am Chem Soc 2024. [PMID: 38951503 DOI: 10.1021/jacs.3c14673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Kinetic proofreading is used throughout natural systems to enhance the specificity of molecular recognition. At its most basic level, kinetic proofreading uses a supply of chemical fuel to drive a recognition interaction out of equilibrium, allowing a single free-energy difference between correct and incorrect targets to be exploited two or more times. Despite its importance in biology, there has been little effort to incorporate kinetic proofreading into synthetic systems in which molecular recognition is important, such as nucleic acid nanotechnology. In this article, we introduce a DNA strand displacement-based kinetic proofreading motif, showing that the consumption of a DNA-based fuel can be used to enhance molecular recognition during a templated dimerization reaction. We then show that kinetic proofreading can enhance the specificity with which a probe discriminates single nucleotide mutations, both in terms of the initial rate with which the probe reacts and the long-time behavior.
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Affiliation(s)
- Rakesh Mukherjee
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Aditya Sengar
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | | | - Thomas E Ouldridge
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
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2
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Han X, Yu H, Zhang L, Weng Z, Dai L, Wang L, Song L, Wang Z, Zhao R, Wang L, Wang W, Bai D, Guo Y, Lv K, Xie G. Movable toehold for leakless self-assembly circuits. Biosens Bioelectron 2024; 245:115823. [PMID: 37979548 DOI: 10.1016/j.bios.2023.115823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/20/2023]
Abstract
Nonenzymatic self-assembly circuit utilizing hairpin substrates has been developed to be a powerful tool for information transduction, amplification and computation. However, the sensitivity, stability and application of this circuit are impeded by the presence of leakage which refers to undesired triggering in the absence of input. Herein, we proposed a movable toehold principle to suppress leakage and accelerate the catalytic reaction through removing partial hairpin toehold responsible for the leakage and transferring it to the catalyst. With movable toehold, catalytic hairpin assembly (called mtCHA) exhibited an excellent signal-to-background ratio of over 100, high robustness and improved specificity. In more complex circuit, including proximity recognition, signal amplification of small molecules (such as ATP), logic network, autocatalysis circuit and two-layer cascade circuit, mtCHA also demonstrated satisfactory performance. Our findings suggest that mtCHA holds great potential for broader applications, and the approach of repurposing harmful fragments into beneficial candidates can provide valuable insights for other chemical systems.
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Affiliation(s)
- Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhi Weng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Ling Dai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Li Wang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
| | - Lin Song
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Rong Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Luojia Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Weitao Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Dan Bai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yongcan Guo
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, LuZhou Key Laboratory of Nanobiosensing and Microfluidic Point-of-Care Testing, Luzhou 646000, PR China.
| | - Ke Lv
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China.
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3
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Hu M, Li X, Wu JN, Yang M, Wu T. DNAzyme-Based Dissipative DNA Strand Displacement for Constructing Temporal Logic Gates. ACS NANO 2024; 18:2184-2194. [PMID: 38193385 DOI: 10.1021/acsnano.3c09506] [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: 01/10/2024]
Abstract
Toehold-mediated DNA strand displacement is the foundation of dynamic DNA nanotechnology, encompassing a wide range of tools with diverse functions, dynamics, and thermodynamic properties. However, a majority of these tools are limited to unidirectional reactions driven by thermodynamics. In response to the growing field of dissipative DNA nanotechnology, we present an approach: DNAzyme-based dissipative DNA strand displacement (D-DSD), which combines the principles of dynamic DNA nanotechnology and dissipative DNA nanotechnology. D-DSD introduces circular and dissipative characteristics, distinguishing it from the unidirectional reactions observed in conventional strand displacement. We investigated the reaction mechanism of D-DSD and devised temporal control elements. By substituting temporal components, we designed two distinct temporal AND gates using fewer than 10 strands, eliminating the need for complex network designs. In contrast to previous temporal logic gates, our temporal storage is not through dynamics control or cross-inhibition but through autoregressive storage, a more modular and scalable approach to memory storage. D-DSD preserves the fundamental structure of toehold-mediated strand displacement, while offering enhanced simplicity and versatility.
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Affiliation(s)
- Minghao Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Xiaolong Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Jia-Ni Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Mengyao Yang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
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4
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Wang H, Zhang X, Liu Y, Zhou S. A nicking enzyme-assisted allosteric strategy for self-resetting DNA switching circuits. Analyst 2023; 149:169-179. [PMID: 37999719 DOI: 10.1039/d3an01677c] [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: 11/25/2023]
Abstract
The self-regulation of biochemical reaction networks is crucial for maintaining balance, stability, and adaptability within biological systems. DNA switching circuits, serving as basic units, play essential roles in regulating pathways, facilitating signal transduction, and processing biochemical reaction networks. However, the non-reusability of DNA switching circuits hinders its application in current complex information processing. Herein, we proposed a nicking enzyme-assisted allosteric strategy for constructing self-resetting DNA switching circuits to realize complex information processing. This strategy utilizes the unique cleavage ability of the nicking enzyme to achieve the automatic restoration of states. Based on this strategy, we implemented a self-resetting DNA switch. By leveraging the reusability of the DNA switch, we constructed a DNA switching circuit with selective activation characteristics and further extended its functionality to include fan-out and fan-in processes by expanding the number of functional modules and connection modes. Furthermore, we demonstrated the complex information processing capabilities of these switching circuits by integrating recognition, translation, and decision functional modules, which could analyze and transmit multiple input signals and realize parallel logic operations. This strategy simplifies the design of switching circuits and promotes the future development of biosensing, molecular computing, and nanomachines.
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Affiliation(s)
- Haoliang Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China.
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China.
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5
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Bai S, Xu B, Wu J, Xie G. Series or parallel toehold-mediated strand displacement and its application in circular RNA detection and logic gates. Biosens Bioelectron 2023; 241:115677. [PMID: 37696219 DOI: 10.1016/j.bios.2023.115677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/27/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023]
Abstract
Toehold-mediated strand displacement (TMSD) is widely employed in constructing a wide range of chemical reaction networks. In TMSD, single-stranded DNA or RNA can fold back upon itself to form a local short double-strand structure often hindering bimolecular hybridization. Here, based on series and parallel circuits, we introduce two mechanisms: series toehold-mediated strand displacement (STMSD) and parallel toehold-mediated strand displacement (PTMSD). These mechanisms can be highly effective when the target area is blocked by a secondary structure. In addition, these systems allow regulating the reaction rates spanning three to five orders of magnitude by adjusting the length of the two toeholds with the added advantage of multifunctional regulation and selectivity. To demonstrate the impressive function of this approach, a logic operation system based on STMSD was constructed to simulate the signal processing of a half-adder. We believe that the introduction of series and parallel toeholds will provide design flexibility contributing to the development of molecular computers, molecular robotics, and DNA-based biosensors.
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Affiliation(s)
- Shulian Bai
- Department of Clinical Laboratory, Medical Sciences Research Center, University-Town Hospital of Chongqing Medical University, Chongqing, 401331, China
| | - Bangtian Xu
- Department of Clinical Laboratory, Medical Sciences Research Center, University-Town Hospital of Chongqing Medical University, Chongqing, 401331, China
| | - Jiangling Wu
- Department of Clinical Laboratory, Medical Sciences Research Center, University-Town Hospital of Chongqing Medical University, Chongqing, 401331, China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, China.
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6
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Qureshi B, Juritz J, Poulton JM, Beersing-Vasquez A, Ouldridge TE. A universal method for analyzing copolymer growth. J Chem Phys 2023; 158:104906. [PMID: 36922142 DOI: 10.1063/5.0133489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Polymers consisting of more than one type of monomer, known as copolymers, are vital to both living and synthetic systems. Copolymerization has been studied theoretically in a number of contexts, often by considering a Markov process in which monomers are added or removed from the growing tip of a long copolymer. To date, the analysis of the most general models of this class has necessitated simulation. We present a general method for analyzing such processes without resorting to simulation. Our method can be applied to models with an arbitrary network of sub-steps prior to addition or removal of a monomer, including non-equilibrium kinetic proofreading cycles. Moreover, the approach allows for a dependency of addition and removal reactions on the neighboring site in the copolymer and thermodynamically self-consistent models in which all steps are assumed to be microscopically reversible. Using our approach, thermodynamic quantities such as chemical work; kinetic quantities such as time taken to grow; and statistical quantities such as the distribution of monomer types in the growing copolymer can be directly derived either analytically or numerically from the model definition.
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Affiliation(s)
- Benjamin Qureshi
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jordan Juritz
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jenny M Poulton
- Foundation for Fundamental Research on Matter (FOM), Institute for Atomic and Molecular Physics (AMOLF), 1098 XE Amsterdam, The Netherlands
| | | | - Thomas E Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
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7
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Hu M, Chu Z, Wang H, Zhao W, Wu T. Transformation of remote toehold-mediated strand displacement for expanding the regulatory toolbox. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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8
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Zhou W, Liao L, Fan X, Yao J, Jiang B. Programmable bidirectional dynamic DNA nano-device for accurate and ultrasensitive fluorescent detection of trace MUC1 biomarker in serums. Anal Chim Acta 2022; 1238:340643. [DOI: 10.1016/j.aca.2022.340643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/01/2022] [Accepted: 11/17/2022] [Indexed: 11/19/2022]
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9
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Mirzaiebadizi A, Ravan H, Dabiri S, Mohammadi P, Shahba A, Ziasistani M, Khatami M. An intelligent DNA nanorobot for detection of MiRNAs cancer biomarkers using molecular programming to fabricate a logic-responsive hybrid nanostructure. Bioprocess Biosyst Eng 2022; 45:1781-1797. [PMID: 36125526 DOI: 10.1007/s00449-022-02785-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022]
Abstract
Herein, we designed a DNA framework-based intelligent nanorobot using toehold-mediated strand displacement reaction-based molecular programming and logic gate operation for the selective and synchronous detection of miR21 and miR125b, which are known as significant cancer biomarkers. Moreover, to investigate the applicability of our design, DNA nanorobots were implemented as capping agents onto the pores of MSNs. These agents can develop a logic-responsive hybrid nanostructure capable of specific drug release in the presence of both targets. The prosperous synthesis steps were verified by FTIR, XRD, BET, UV-visible, FESEM-EDX mapping, and HRTEM analyses. Finally, the proper release of the drug in the presence of both target microRNAs was studied. This Hybrid DNA Nanostructure was designed with the possibility to respond to any target oligonucleotides with 22 nucleotides length.
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Affiliation(s)
- Amin Mirzaiebadizi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran.,Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Hadi Ravan
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Shahriar Dabiri
- Department of Pathology and Stem Cell Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| | - Pourya Mohammadi
- Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Arezoo Shahba
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahsa Ziasistani
- Department of Pathology and Stem Cell Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehrdad Khatami
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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10
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Liu WW, Zhang XL, Zhu L, Xu S, Chai YQ, Li ZH, Yuan R. Mismatch-fueled catalytic hairpin assembly mediated ultrasensitive biosensor for rapid detection of MicroRNA. Anal Chim Acta 2022; 1204:339663. [PMID: 35397899 DOI: 10.1016/j.aca.2022.339663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/04/2022] [Accepted: 02/25/2022] [Indexed: 11/18/2022]
Abstract
Herein, a mismatch-fueled catalytic hairpin assembly (MCHA) was rationally engineered, which possessed higher amplification efficiency and faster rate than catalytic hairpin assembly (CHA). Once input target microRNA-21(miRNA-21) triggers the MCHA, the hairpin DNA H1 will be opened to form the duplex H1-miRNA-21, then the mismatched hairpin DNA H2 could easily hybridize with H1-miRNA-21 to generate duplex H1-H2 and the miRNA-21 could be released to enter next cycle, thus generating amounts of output products. Impressively, the MCHA realizes a pretty shorter complete reaction time of 40 min and quite higher amplification efficiency of 9.56 × 106, which dramatically transcended the barrier: low amplification times and long reaction time in traditional CHA. As a proof of the concept, the elaborated MCHA as a hyper-efficiency and high-speed DNA signal-magnifier was successfully applied in ultrasensitive and rapid detection of miRNA-21 with the detection limit of 0.17 fM, which exploited an ingenious nucleic acid signal amplification technique for sensitive and fast detection of biomarkers in biosensing assay and clinic diagnose.
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Affiliation(s)
- Wei-Wei Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing Southwest University, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing Southwest University, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Liang Zhu
- Key Laboratory of Luminescence Analysis and Molecular Sensing Southwest University, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Sai Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing Southwest University, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing Southwest University, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Zhao-Hui Li
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing Southwest University, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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11
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Weng Z, Yu H, Luo W, Guo Y, Liu Q, Zhang L, Zhang Z, Wang T, Dai L, Zhou X, Han X, Wang L, Li J, Yang Y, Xie G. Cooperative Branch Migration: A Mechanism for Flexible Control of DNA Strand Displacement. ACS NANO 2022; 16:3135-3144. [PMID: 35113525 DOI: 10.1021/acsnano.1c10797] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
DNA strand displacement plays an essential role in the field of dynamic DNA nanotechnology. However, flexible regulation of strand displacement remains a significant challenge. Most previous regulatory tools focused on controllable activation of toehold and thus limited the design flexibility. Here, we introduce a regulatory tool termed cooperative branch migration (CBM), through which DNA strand displacement can be controlled by regulating the complementarity of branch migration domains. CBM shows perfect compatibility with the majority of existing regulatory tools, and when combined with forked toehold, it permits continuous fine-tuning of the strand displacement rate spanning 5 orders of magnitude. CBM manifests multifunctional regulation ability, including rate fine-tuning, continuous dynamic regulation, reaction resetting, and selective activation. To exemplify the powerful function, we also constructed a nested if-function signal processing system on the basis of cascading CBM reactions. We believe that the proposed regulatory strategy would effectively enrich the DNA strand displacement toolbox and ultimately promote the construction of DNA machines of higher complexity in nucleic acid research and biomedical applications.
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Affiliation(s)
- Zhi Weng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yongcan Guo
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, Luzhou, 646000, PR China
| | - Qian Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhang Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Ting Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Ling Dai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xi Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Luojia Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Junjie Li
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yujun Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
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12
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Juritz J, Poulton JM, Ouldridge TE. Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions. J Chem Phys 2022; 156:074103. [DOI: 10.1063/5.0077865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jordan Juritz
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jenny M. Poulton
- Foundation for Fundamental Research on Matter (FOM), Institute for Atomic and Molecular Physics (AMOLF), 1098 XE Amsterdam, The Netherlands
| | - Thomas E. Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
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13
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Fontana PW. Hidden Dissipation and Irreversibility in Maxwell's Demon. ENTROPY (BASEL, SWITZERLAND) 2022; 24:93. [PMID: 35052118 PMCID: PMC8774989 DOI: 10.3390/e24010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023]
Abstract
Maxwell's demon is an entity in a 150-year-old thought experiment that paradoxically appears to violate the second law of thermodynamics by reducing entropy without doing work. It has increasingly practical implications as advances in nanomachinery produce devices that push the thermodynamic limits imposed by the second law. A well-known explanation claiming that information erasure restores second law compliance fails to resolve the paradox because it assumes the second law a priori, and does not predict irreversibility. Instead, a purely mechanical resolution that does not require information theory is presented. The transport fluxes of mass, momentum, and energy involved in the demon's operation are analyzed and show that they imply "hidden" external work and dissipation. Computing the dissipation leads to a new lower bound on entropy production by the demon. It is strictly positive in all nontrivial cases, providing a more stringent limit than the second law and implying intrinsic thermodynamic irreversibility. The thermodynamic irreversibility is linked with mechanical irreversibility resulting from the spatial asymmetry of the demon's speed selection criteria, indicating one mechanism by which macroscopic irreversibility may emerge from microscopic dynamics.
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Affiliation(s)
- Paul W Fontana
- Physics Department, Seattle University, 901 12th Ave., Seattle, WA 98122, USA
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14
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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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15
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Mou L, Hong H, Xu X, Xia Y, Jiang X. Digital Hybridization Human Papillomavirus Assay with Attomolar Sensitivity without Amplification. ACS NANO 2021; 15:13077-13084. [PMID: 34324808 DOI: 10.1021/acsnano.1c02311] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Detection of nucleic acid without amplification can avoid problems associated with thermal cycling such as labor-intensiveness and aerosol pollution. Here we develop a droplet-based digital microfluidic hybridization assay for nucleic acid detection with attomolar sensitivity. This assay provides a clinically useful sensitivity for detecting human papillomavirus (HPV) without amplification. The sensitivity is accomplished using femtoliter-sized droplet microfluidics for concentrating enzyme-catalyzed fluorescent products into a detectable signal and magnetic beads for accelerating reaction time. Meanwhile, using magnetic beads and droplet microfluidic chips, we can improve the sampling efficiency over conventional methods. We characterized the sensitivity, selectivity, detection range, stability, and accuracy of our assay. Our assay is 50-fold more sensitive than the traditional hybrid capture assay. The assay without amplification avoids problems of complex handling procedures and aerosol pollution. The direct and sensitive detection of nucleic acid using a droplet microfluidic system provides an early disease diagnosis tool.
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Affiliation(s)
- Lei Mou
- Department of Clinical Laboratory, Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong 510150, P. R. China
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Honghai Hong
- Department of Clinical Laboratory, Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong 510150, P. R. China
| | - Xiaojian Xu
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Yong Xia
- Department of Clinical Laboratory, Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong 510150, P. R. China
| | - Xingyu Jiang
- Department of Clinical Laboratory, Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, Guangdong 510150, P. R. China
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
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16
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Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021; 8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.
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Affiliation(s)
- A. Sengar
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - T. E. Ouldridge
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - O. Henrich
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
| | - L. Rovigatti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- CNR Institute of Complex Systems, Sapienza University of Rome, Rome, Italy
| | - P. Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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17
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Jia Y, Hu Y. Cofactor-assisted three-way DNA junction-driven strand displacement. RSC Adv 2021; 11:30377-30382. [PMID: 35480263 PMCID: PMC9041134 DOI: 10.1039/d1ra05242j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/27/2021] [Indexed: 11/21/2022] Open
Abstract
Toehold-mediated strand displacement is widely used to construct and operate DNA nanodevices. Cooperative regulation of strand displacement with diverse factors is pivotal in the design and construction of functional and dynamic devices. Herein, a cofactor-assisted three-way DNA junction-driven strand displacement strategy was reported, which could tune the reaction kinetics by the collaboration of DNA and other types of stimulus. This strategy is responsive to various inputs by incorporation of the specific sequence into the three-way junction structure. Specifically, the cooperation of multiple factors changes the conformation of the specific domain and promotes the reaction. To demonstrate the strategy, adenosine triphosphate (ATP), HG2+, and pH were used as cofactors to modulate the displacement reaction. The electrophoresis and fluorescence experiments showed that the cooperative regulation of the strand displacement reaction could be achieved by diverse factors using this strategy. The proposed strategy provides design flexibility for dynamic DNA devices and may have potential in biosensing and biocomputing. Cooperative regulation of strand displacement with diverse factors was achieved by a cofactor-assisted three-way DNA junction-driven strategy. Using this strategy nanodevices reacted to various inputs by incorporating a specific sequence into the three-way junction structure.![]()
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Affiliation(s)
- Yufeng Jia
- School of Economics and Management, Shijiazhuang Tiedao University, Shijiazhuang 050043, P. R. China
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang 050043, P. R. China
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