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Yan C, Fang C, Gan J, Wang J, Zhao X, Wang X, Li J, Zhang Y, Liu H, Li X, Bai J, Liu J, Hong W. From Molecular Electronics to Molecular Intelligence. ACS NANO 2024. [PMID: 39395180 DOI: 10.1021/acsnano.4c10389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2024]
Abstract
Molecular electronics is a field that explores the ultimate limits of electronic device dimensions by using individual molecules as operable electronic devices. Over the past five decades since the proposal of a molecular rectifier by Aviram and Ratner in 1974 ( Chem. Phys. Lett.1974,29, 277-283), researchers have developed various fabrication and characterization techniques to explore the electrical properties of molecules. With the push of electrical characterizations and data analysis methodologies, the reproducibility issues of the single-molecule conductance measurement have been chiefly resolved, and the origins of conductance variation among different devices have been investigated. Numerous prototypical molecular electronic devices with external physical and chemical stimuli have been demonstrated based on the advances of instrumental and methodological developments. These devices enable functions such as switching, logic computing, and synaptic-like computing. However, as the goal of molecular electronics, how can molecular-based intelligence be achieved through single-molecule electronic devices? At the fiftieth anniversary of molecular electronics, we try to answer this question by summarizing recent progress and providing an outlook on single-molecule electronics. First, we review the fabrication methodologies for molecular junctions, which provide the foundation of molecular electronics. Second, the preliminary efforts of molecular logic devices toward integration circuits are discussed for future potential intelligent applications. Third, some molecular devices with sensing applications through physical and chemical stimuli are introduced, demonstrating phenomena at a single-molecule scale beyond conventional macroscopic devices. From this perspective, we summarize the current challenges and outlook prospects by describing the concepts of "AI for single-molecule electronics" and "single-molecule electronics for AI".
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Affiliation(s)
- Chenshuai Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Chao Fang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Jinyu Gan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Jia Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Xin Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Xiaojing Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Jing Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Yanxi Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Haojie Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Xiaohui Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Jie Bai
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Junyang Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & Institute of Artificial Intelligence & Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, China
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2
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Yin D, Xiong R, Yang Z, Feng J, Liu W, Li S, Li M, Ruan H, Li J, Li L, Lai L, Guo X. Mapping Full Conformational Transition Dynamics of Intrinsically Disordered Proteins Using a Single-Molecule Nanocircuit. ACS NANO 2024. [PMID: 39276130 DOI: 10.1021/acsnano.4c04064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/16/2024]
Abstract
Intrinsically disordered proteins (IDPs) are emerging therapeutic targets for human diseases. However, probing their transient conformations remains challenging because of conformational heterogeneity. To address this problem, we developed a biosensor using a point-functionalized silicon nanowire (SiNW) that allows for real-time sampling of single-molecule dynamics. A single IDP, N-terminal transactivation domain of tumor suppressor protein p53 (p53TAD1), was covalently conjugated to the SiNW through chemical engineering, and its conformational transition dynamics was characterized as current fluctuations. Furthermore, when a globular protein ligand in solution bound to the targeted p53TAD1, protein-protein interactions could be unambiguously distinguished from large-amplitude current signals. These proof-of-concept experiments enable semiquantitative, realistic characterization of the structural properties of IDPs and constitute the basis for developing a valuable tool for protein profiling and drug discovery in the future.
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Affiliation(s)
- Dongbao Yin
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Ruoyao Xiong
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
| | - Zhiheng Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Jianfei Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
| | - Wenzhe Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
| | - Shiyun Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
| | - Mingyao Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
| | - Hao Ruan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
| | - Jie Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
| | - Lidong Li
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, P. R. China
| | - Luhua Lai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, P. R. China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
- Center of Single-Molecule Sciences, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin 300350, P. R. China
- National Biomedical Imaging Center, Peking University, Beijing 100871, P. R. China
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Gao C, Gao Q, Zhao C, Huo Y, Zhang Z, Yang J, Jia C, Guo X. Technologies for investigating single-molecule chemical reactions. Natl Sci Rev 2024; 11:nwae236. [PMID: 39224448 PMCID: PMC11367963 DOI: 10.1093/nsr/nwae236] [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: 01/11/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 09/04/2024] Open
Abstract
Single molecules, the smallest independently stable units in the material world, serve as the fundamental building blocks of matter. Among different branches of single-molecule sciences, single-molecule chemical reactions, by revealing the behavior and properties of individual molecules at the molecular scale, are particularly attractive because they can advance the understanding of chemical reaction mechanisms and help to address key scientific problems in broad fields such as physics, chemistry, biology and materials science. This review provides a timely, comprehensive overview of single-molecule chemical reactions based on various technical platforms such as scanning probe microscopy, single-molecule junction, single-molecule nanostructure, single-molecule fluorescence detection and crossed molecular beam. We present multidimensional analyses of single-molecule chemical reactions, offering new perspectives for research in different areas, such as photocatalysis/electrocatalysis, organic reactions, surface reactions and biological reactions. Finally, we discuss the opportunities and challenges in this thriving field of single-molecule chemical reactions.
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Affiliation(s)
- Chunyan Gao
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Qinghua Gao
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Cong Zhao
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Yani Huo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Zhizhuo Zhang
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Jinlong Yang
- Hefei National Research Center for Physical Sciences at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300350, China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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Liu Y, Zhai Y, Hu H, Liao Y, Liu H, Liu X, He J, Wang L, Wang H, Li L, Zhou X, Xiao X. Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400011. [PMID: 38698560 PMCID: PMC11234411 DOI: 10.1002/advs.202400011] [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: 01/01/2024] [Revised: 04/09/2024] [Indexed: 05/05/2024]
Abstract
DNA is commonly employed as a substrate for the building of artificial logic networks due to its excellent biocompatibility and programmability. Till now, DNA logic circuits are rapidly evolving to accomplish advanced operations. Nonetheless, nowadays, most DNA circuits remain to be disposable and lack of field programmability and thereby limits their practicability. Herein, inspired by the Configurable Logic Block (CLB), the CLB-based erasable field-programmable DNA circuit that uses clip strands as its operation-controlling signals is presented. It enables users to realize diverse functions with limited hardware. CLB-based basic logic gates (OR and AND) are first constructed and demonstrated their erasability and field programmability. Furthermore, by adding the appropriate operation-controlling strands, multiple rounds of programming are achieved among five different logic operations on a two-layer circuit. Subsequently, a circuit is successfully built to implement two fundamental binary calculators: half-adder and half-subtractor, proving that the design can imitate silicon-based binary circuits. Finally, a comprehensive CLB-based circuit is built that enables multiple rounds of switch among seven different logic operations including half-adding and half-subtracting. Overall, the CLB-based erasable field-programmable circuit immensely enhances their practicability. It is believed that design can be widely used in DNA logic networks due to its efficiency and convenience.
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Affiliation(s)
- Yizhou Liu
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Yuxuan Zhai
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Hao Hu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Yuheng Liao
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Huan Liu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Xiao Liu
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Jiachen He
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Limei Wang
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Hongxun Wang
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
| | - Longjie Li
- School of Life Science and TechnologyWuhan Polytechnic UniversityWuhan430023China
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
| | - Xiaoyu Zhou
- Department of Precision Diagnostic and Therapeutic TechnologyCity University of Hong Kong Shenzhen Futian Research InstituteShenzhenGuangdong518000China
| | - Xianjin Xiao
- Institute of Reproductive HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
- Department of Laboratory MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China
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5
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Voorspoels A, Gevers J, Santermans S, Akkan N, Martens K, Willems K, Van Dorpe P, Verhulst AS. Design Principles of DNA-Barcodes for Nanopore-FET Readout, Based on Molecular Dynamics and TCAD Simulations. J Phys Chem A 2024. [PMID: 38712508 DOI: 10.1021/acs.jpca.4c01772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Nanopore field-effect transistor (NP-FET) devices hold great promise as sensitive single-molecule sensors, which provide CMOS-based on-chip readout and are also highly amenable to parallelization. A plethora of applications will therefore benefit from NP-FET technology, such as large-scale molecular analysis (e.g., proteomics). Due to its potential for parallelization, the NP-FET looks particularly well-suited for the high-throughput readout of DNA-based barcodes. However, to date, no study exists that unravels the bit-rate capabilities of NP-FET devices. In this paper, we design DNA-based barcodes by labeling a piece of double-stranded DNA with dumbbell-like DNA structures. We explore the impact of both the size of the dumbbells and their spacing on achievable bit-rates. The conformational fluctuations of this DNA-origami, as observed by molecular dynamics (MD) simulation, are accounted for when selecting label sizes. An experimentally informed 3D continuum nanofluidic-nanoelectronic device model subsequently predicts both the ionic current and FET signals. We present a barcode design for a conceptually generic NP-FET, with a 14 nm diameter pore, operating in conditions corresponding to experiments. By adjusting the spacing between the labels to half the length of the pore, we show that a bit-rate of 78 kbit·s-1 is achievable. This lies well beyond the state-of-the-art of ≈40 kbit·s-1, with significant headroom for further optimizations. We also highlight the advantages of NP-FET readout based on the larger signal size and sinusoidal signal shape.
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Affiliation(s)
- Aderik Voorspoels
- Imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | - Juliette Gevers
- Imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | | | - Nihat Akkan
- Imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | - Koen Martens
- Imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | | | - Pol Van Dorpe
- Imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | - Anne S Verhulst
- Imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department of Electrical Engineering (ESAT), KU Leuven, Kasteelpark Arenberg 10, B-3001 Leuven, Belgium
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6
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Liu W, Chen L, Yin D, Yang Z, Feng J, Sun Q, Lai L, Guo X. Visualizing single-molecule conformational transition and binding dynamics of intrinsically disordered proteins. Nat Commun 2023; 14:5203. [PMID: 37626077 PMCID: PMC10457384 DOI: 10.1038/s41467-023-41018-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) play crucial roles in cellular processes and hold promise as drug targets. However, the dynamic nature of IDPs remains poorly understood. Here, we construct a single-molecule electrical nanocircuit based on silicon nanowire field-effect transistors (SiNW-FETs) and functionalize it with an individual disordered c-Myc bHLH-LZ domain to enable label-free, in situ, and long-term measurements at the single-molecule level. We use the device to study c-Myc interaction with Max and/or small molecule inhibitors. We observe the self-folding/unfolding process of c-Myc and reveal its interaction mechanism with Max and inhibitors through ultrasensitive real-time monitoring. We capture a relatively stable encounter intermediate ensemble of c-Myc during its transition from the unbound state to the fully folded state. The c-Myc/Max and c-Myc/inhibitor dissociation constants derived are consistent with other ensemble experiments. These proof-of-concept results provide an understanding of the IDP-binding/folding mechanism and represent a promising nanotechnology for IDP conformation/interaction studies and drug discovery.
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Affiliation(s)
- Wenzhe Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China
| | - Limin Chen
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, P. R. China
| | - Dongbao Yin
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China
| | - Zhiheng Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China
| | - Jianfei Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China
| | - Qi Sun
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China.
| | - Luhua Lai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China.
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, P. R. China.
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, P. R. China.
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China.
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350, Tianjin, P. R. China.
- National Biomedical Imaging Center, Peking University, Beijing, 100871, P. R. China.
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7
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Sun R, Lv J, Xue X, Yu S, Tan Z. Chemical Sensors using Single-Molecule Electrical Measurements. Chem Asian J 2023; 18:e202300181. [PMID: 37080926 DOI: 10.1002/asia.202300181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/15/2023] [Accepted: 04/16/2023] [Indexed: 04/22/2023]
Abstract
Driven by the digitization and informatization of contemporary society, electrical sensors are developing toward minimal structure, intelligent function, and high detection resolution. Single-molecule electrical measurement techniques have been proven to be capable of label-free molecular recognition and detection, which opens a new strategy for the design of efficient single-molecule detection sensors. In this review, we outline the main advances and potentials of single-molecule electronics for qualitative identification and recognition assays at the single-molecule level. Strategies for single-molecule electro-sensing and its main applications are reviewed, mainly in the detection of ions, small molecules, oligomers, genetic materials, and proteins. This review summarizes the remaining challenges in the current development of single-molecule electrical sensing and presents some potential perspectives for this field.
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Affiliation(s)
- Ruiqin Sun
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Jieyao Lv
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Xinyi Xue
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Shiyong Yu
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
| | - Zhibing Tan
- College of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010021, P. R. China
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Yang Z, Wang J, Yin B, Liu W, Yin D, Shen J, Wang W, Li L, Guo X. Stimuli-Induced Subconformation Transformation of the PSI-LHCI Protein at Single-Molecule Resolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205945. [PMID: 37114832 PMCID: PMC10323662 DOI: 10.1002/advs.202205945] [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: 10/12/2022] [Revised: 04/11/2023] [Indexed: 06/19/2023]
Abstract
Photosynthesis is a very important process for the current biosphere which can maintain such a subtle and stable circulatory ecosystem on earth through the transformation of energy and substance. Even though been widely studied in various aspects, the physiological activities, such as intrinsic structural vibration and self-regulation process to stress of photosynthetic proteins, are still not in-depth resolved in real-time. Herein, utilizing silicon nanowire biosensors with ultrasensitive temporal and spatial resolution, real-time responses of a single photosystem I-light harvesting complex I (PSI-LHCI) supercomplex of Pisum sativum to various conditions, including gradient variations in temperature, illumination, and electric field, are recorded. Under different temperatures, there is a bi-state switch process associated with the intrinsic thermal vibration behavior. When the variations of illumination and the bias voltage are applied, two additional shoulder states, probably derived from the self-conformational adjustment, are observed. Based on real-time monitoring of the dynamic processes of the PSI-LHCI supercomplex under various conditions, it is successively testified to promising nanotechnology for protein profiling and biological functional integration in photosynthesis studies.
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Affiliation(s)
- Zhiheng Yang
- State Key Laboratory for Advanced Metals and MaterialsSchool of Materials Science and EngineeringUniversity of Science and Technology BeijingBeijing100083P. R. China
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking University292 Chengfu Road, Haidian DistrictBeijing100871P. R. China
| | - Jie Wang
- Photosynthesis Research CenterKey Laboratory of PhotobiologyInstitute of BotanyChinese Academy of SciencesBeijing100093P. R. China
| | - Bing Yin
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking University292 Chengfu Road, Haidian DistrictBeijing100871P. R. China
| | - Wenzhe Liu
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking University292 Chengfu Road, Haidian DistrictBeijing100871P. R. China
| | - Dongbao Yin
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking University292 Chengfu Road, Haidian DistrictBeijing100871P. R. China
| | - Jianren Shen
- Photosynthesis Research CenterKey Laboratory of PhotobiologyInstitute of BotanyChinese Academy of SciencesBeijing100093P. R. China
| | - Wenda Wang
- Photosynthesis Research CenterKey Laboratory of PhotobiologyInstitute of BotanyChinese Academy of SciencesBeijing100093P. R. China
| | - Lidong Li
- State Key Laboratory for Advanced Metals and MaterialsSchool of Materials Science and EngineeringUniversity of Science and Technology BeijingBeijing100083P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking University292 Chengfu Road, Haidian DistrictBeijing100871P. R. China
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterCollege of Electronic Information and Optical EngineeringNankai University38 Tongyan Road, Jinnan DistrictTianjin300350P. R. China
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9
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Li X, Ge W, Guo S, Bai J, Hong W. Characterization and Application of Supramolecular Junctions. Angew Chem Int Ed Engl 2023; 62:e202216819. [PMID: 36585932 DOI: 10.1002/anie.202216819] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
The convergence of supramolecular chemistry and single-molecule electronics offers a new perspective on supramolecular electronics, and provides a new avenue toward understanding and application of intermolecular charge transport at the molecular level. In this review, we will provide an overview of the advances in the characterization technique for the investigation of intermolecular charge transport, and summarize the experimental investigation of several non-covalent interactions, including π-π stacking interactions, hydrogen bonding, host-guest interactions and σ-σ interactions at the single-molecule level. We will also provide a perspective on supramolecular electronics and discuss the potential applications and future challenges.
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Affiliation(s)
- Xiaohui Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Wenhui Ge
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Shuhan Guo
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Jie Bai
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
| | - Wenjing Hong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering & College of Materials & IKKEM, Xiamen University, Xiamen, 361005, China
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10
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Santermans S, Hellings G, Heyns M, Van Roy W, Martens K. Unraveling the impact of nano-scaling on silicon field-effect transistors for the detection of single-molecules. NANOSCALE 2023; 15:2354-2368. [PMID: 36644797 DOI: 10.1039/d2nr05267a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Electrolyte-gated silicon field-effect transistors (FETs) capable of detecting single molecules could enable high-throughput molecular sensing chips to advance, for example, genomics or proteomics. For solid-gated silicon FETs it is well-known that nano-scaled devices become sensitive to single elementary charges near the silicon-oxide interface. However, in electrolyte-gated FETs, electrolyte screening strongly reduces sensitivity to charges near the gate oxide. The question arises whether nano-scaling electrolyte-gated FETs can entail a sufficiently large signal-to-noise ratio (SNR) for the detection of single molecules. We enhanced a technology computer-aided design tool with electrolyte screening models to calculate the impact of the FET geometry on the single-molecule signal and FET noise. Our continuum FET model shows that a sufficiently large single-molecule SNR is only obtained when nano-scaling all FET channel dimensions. Moreover, we show that the expected scaling trend of the single-molecule SNR breaks down and no longer results in improvements for geometries approaching the decananometer size. This is the characteristic size of the FET channel region modulated by a typical molecule. For gate lengths below 50 nm, the overlap of the modulated region with the highly conductive junctions leads to saturation of the SNR. For cross-sections below 10-30 nm, SNR degrades due to the overlap of the modulated region with the convex FET corners where a larger local gate capacitance reduces charge sensitivity. In our study, assuming a commercial solid-state FET noise amplitude, we find that a suspended nanowire FET architecture with 35 nm length and 5 × 10 nm2 cross-section results in the highest SNR of about 10 for a 15-base DNA oligo in a 15 mM electrolyte. In contrast with typical silicon nanowire FET sensors which possess micron-scale gate lengths, we find it to be key that all channel dimensions are scaled down to the decananometer range.
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Affiliation(s)
- Sybren Santermans
- imec, Kapeldreef 75, 3001 Leuven, Belgium.
- Department of Materials Engineering, University of Leuven, Kasteelpark Arenberg 44, 3001 Leuven, Belgium
| | | | - Marc Heyns
- imec, Kapeldreef 75, 3001 Leuven, Belgium.
- Department of Materials Engineering, University of Leuven, Kasteelpark Arenberg 44, 3001 Leuven, Belgium
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11
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Single-exonuclease nanocircuits reveal the RNA degradation dynamics of PNPase and demonstrate potential for RNA sequencing. Nat Commun 2023; 14:552. [PMID: 36725855 PMCID: PMC9892577 DOI: 10.1038/s41467-023-36278-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
The degradation process of RNA is decisive in guaranteeing high-fidelity translation of genetic information in living organisms. However, visualizing the single-base degradation process in real time and deciphering the degradation mechanism at the single-enzyme level remain formidable challenges. Here, we present a reliable in-situ single-PNPase-molecule dynamic electrical detector based on silicon nanowire field-effect transistors with ultra-high temporal resolution. These devices are capable of realizing real-time and label-free monitoring of RNA analog degradation with single-base resolution, including RNA analog binding, single-nucleotide hydrolysis, and single-base movement. We discover a binding event of the enzyme (near the active site) with the nucleoside, offering a further understanding of the RNA degradation mechanism. Relying on systematic analyses of independent reads, approximately 80% accuracy in RNA nucleoside sequencing is achieved in a single testing process. This proof-of-concept sets up a Complementary Metal Oxide Semiconductor (CMOS)-compatible playground for the development of high-throughput detection technologies toward mechanistic exploration and single-molecule sequencing.
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12
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Liu W, Li J, Xu Y, Yin D, Zhu X, Fu H, Su X, Guo X. Complete Mapping of DNA‐Protein Interactions at the Single‐Molecule Level. ADVANCED SCIENCE 2021; 8:2101383. [PMCID: PMC8655176 DOI: 10.1002/advs.202101383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
DNA–protein interaction plays an essential role in the storage, expression, and regulation of genetic information. A 1D/3D facilitated diffusion mechanism has been proposed to explain the extraordinarily rapid rate of DNA‐binding protein (DBP) searching for cognate sequence along DNA and further studied by single‐molecule experiments. However, direct observation of the detailed chronological protein searching image is still a formidable challenge. Here, for the first time, a single‐molecule electrical monitoring technique is utilized to realize label‐free detection of the DBP–DNA interaction process based on high‐gain silicon nanowire field‐effect transistors (SiNW FETs). The whole binding process of WRKY domain and DNA has been visualized with high sensitivity and single‐base resolution. Impressively, the swinging of hydrogen bonds between amino acid residues and bases in DNA induce the dynamic collective motion of DBP–DNA. This in situ, label‐free electrical detection platform provides a practical experimental methodology for dynamic studies of various biomolecules.
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Affiliation(s)
- Wenzhe Liu
- State Key Laboratory for Structural Chemistry of Unstable and Stable SpeciesBeijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
| | - Jie Li
- State Key Laboratory for Structural Chemistry of Unstable and Stable SpeciesBeijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
- Shenzhen Bay LaboratoryShenzhen518132P. R. China
| | - Yongping Xu
- State Key Laboratory of Protein and Plant Gene ResearchBiomedical Pioneering Innovation Center (BIOPIC)Peking UniversityBeijing100871P. R. China
| | - Dongbao Yin
- State Key Laboratory for Structural Chemistry of Unstable and Stable SpeciesBeijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
| | - Xin Zhu
- Center of Single‐Molecule SciencesFrontiers Science Center for New Organic MatterInstitute of Modern OpticsCollege of Electronic Information and Optical EngineeringNankai University38 Tongyan Road, Jinnan DistrictTianjin300350P. R. China
| | - Huanyan Fu
- Center of Single‐Molecule SciencesFrontiers Science Center for New Organic MatterInstitute of Modern OpticsCollege of Electronic Information and Optical EngineeringNankai University38 Tongyan Road, Jinnan DistrictTianjin300350P. R. China
| | - Xiaodong Su
- State Key Laboratory of Protein and Plant Gene ResearchBiomedical Pioneering Innovation Center (BIOPIC)Peking UniversityBeijing100871P. R. China
| | - Xuefeng Guo
- State Key Laboratory for Structural Chemistry of Unstable and Stable SpeciesBeijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
- Center of Single‐Molecule SciencesFrontiers Science Center for New Organic MatterInstitute of Modern OpticsCollege of Electronic Information and Optical EngineeringNankai University38 Tongyan Road, Jinnan DistrictTianjin300350P. R. China
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13
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Nicholson DA, Jia B, Nesbitt DJ. Measuring Excess Heat Capacities of Deoxyribonucleic Acid (DNA) Folding at the Single-Molecule Level. J Phys Chem B 2021; 125:9719-9726. [PMID: 34415161 DOI: 10.1021/acs.jpcb.1c05555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Measurements of the thermodynamic properties of biomolecular folding (ΔG°, ΔH°, ΔS°, etc.) provide a wealth of information on the folding process and have long played a central role in biophysical investigation. In particular, the excess heat capacity of folding (ΔCP) is crucial, as typically measured in bulk ensemble studies by differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). Here, we report the first measurements of ΔCP at the single-molecule level using the single-molecule fluorescence resonance energy transfer (smFRET) as well as the very first measurements of the heat capacity change associated with achieving the transition state (ΔC‡P) for nucleic acid folding. The deoxyribonucleic acid (DNA) hairpin used in these studies exhibits an excess heat capacity for hybridization (ΔCP = -340 ± 60 J/mol/K per base pair) consistent with the range of literature expectations (ΔCP = -100 to -420 J/mol/K per base pair). Furthermore, the measured activation heat capacities (ΔC‡P) for such hairpin unfolding are consistent with a folding transition state containing few fully formed base pairs, in agreement with prevailing models of DNA hybridization.
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Affiliation(s)
- David A Nicholson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Bin Jia
- Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado, Boulder, Colorado 80309, United States
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14
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Wong KL, Liu J. Factors and methods to modulate DNA hybridization kinetics. Biotechnol J 2021; 16:e2000338. [PMID: 34411451 DOI: 10.1002/biot.202000338] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/09/2022]
Abstract
DNA oligonucleotides are widely used in a diverse range of research fields from analytical chemistry, molecular biology, nanotechnology to drug delivery. In these applications, DNA hybridization is often the most important enabling reaction. Achieving control over hybridization kinetics and a high yield of hybridized products is needed to ensure high-quality and reproducible results. Since DNA strands are highly negatively charged and can also fold upon itself to form various intramolecular structures, DNA hybridization needs to overcome these barriers. Nucleation and diffusion are two main kinetic limiting steps although their relative importance differs in different conditions. The effects of length and sequence, temperature, pH, salt concentration, cationic polymers, organic solvents, freezing and crowding agents are summarized in the context of overcoming these barriers. This article will help researchers in the biotechnology-related fields to better understand and control DNA hybridization, as well as provide a landscape for future work in simulation and experiment to optimize DNA hybridization systems.
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Affiliation(s)
- Kingsley L Wong
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
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15
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Yang Z, Qi C, Liu W, Yin D, Yu L, Li L, Guo X. Revealing Conformational Transition Dynamics of Photosynthetic Proteins in Single-Molecule Electrical Circuits. J Phys Chem Lett 2021; 12:3853-3859. [PMID: 33856226 DOI: 10.1021/acs.jpclett.1c00884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The function of proteins depends on their structural flexibility and conformational change. By utilizing silicon-nanowire-based single-molecule electrical circuits, here we present a label-free real-time measurement method that can directly monitor conformational changes of a photosynthetic LH1-RC complex, reaching the ultimate goal of analytic chemistry. These results manifest that the conformation of the LH1-RC complex vibrates among four conformations with strong temperature dependence. At the optimal temperature, States 2 and 3 occupy the main conformations of the LH1-RC complex, and its conformational variation mostly emerges as anharmonic vibration modes, which contributes to photon acquisition and heat transmission. The influence of light activation on occurrence percentage is observed, resulting from light-driven quivering of pigments. Therefore, this avenue proves to be an efficient platform for revealing the fundamental mechanisms of various biological processes in vitro.
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Affiliation(s)
- Zhiheng Yang
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Chenhui Qi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Wenzhe Liu
- Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Dongbao Yin
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Longjiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Lidong Li
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
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16
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Li P, Jia C, Guo X. Structural Transition Dynamics in Carbon
Electrode‐Based Single‐Molecule
Junctions. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000529] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Peihui Li
- Center of Single‐Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University 38 Tongyan Road, Jinnan District Tianjin 300350 China
| | - Chuancheng Jia
- Center of Single‐Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University 38 Tongyan Road, Jinnan District Tianjin 300350 China
| | - Xuefeng Guo
- Center of Single‐Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University 38 Tongyan Road, Jinnan District Tianjin 300350 China
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University Beijing 100871 China
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17
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Ke G, Su D, Li Y, Zhao Y, Wang H, Liu W, Li M, Yang Z, Xiao F, Yuan Y, Huang F, Mo F, Wang P, Guo X. An accurate, high-speed, portable bifunctional electrical detector for COVID-19. SCIENCE CHINA MATERIALS 2021; 64:739-747. [PMID: 33552629 PMCID: PMC7852050 DOI: 10.1007/s40843-020-1577-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/25/2020] [Indexed: 05/17/2023]
Abstract
UNLABELLED Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has rapidly spread and caused a severe global pandemic. Because no specific drugs are available for COVID-19 and few vaccines are available for SARS-CoV-2, accurate and rapid diagnosis of COVID-19 has been the most crucial measure to control this pandemic. Here, we developed a portable bifunctional electrical detector based on graphene fieldeffect transistors for SARS-CoV-2 through either nucleic acid hybridization or antigen-antibody protein interaction, with ultra-low limits of detection of ~0.1 and ~1 fg mL-1 in phosphate buffer saline, respectively. We validated our method by assessment of RNA extracts from the oropharyngeal swabs of ten COVID-19 patients and eight healthy subjects, and the IgM/IgG antibodies from serum specimens of six COVID-19 patients and three healthy subjects. Here we show that the diagnostic results are in excellent agreement with the findings of polymerase chain reaction-based optical methods; they also exhibit rapid detection speed (~10 min for nucleic acid detection and ~5 min for immunoassay). Therefore, our assay provides an efficient, accurate tool for high-throughput point-of-care testing. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material is available in the online version of this article at 10.1007/s40843-020-1577-y.
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Affiliation(s)
- Guojun Ke
- Institute of Polymer Optoelectronic Materials and Devices, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou, 510640 China
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Dingkai Su
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Yu Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Yu Zhao
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, 100871 China
| | - Honggang Wang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, 100871 China
| | - Wanjian Liu
- Qingdao Shuojing Biological Technology Co., Ltd., Qingdao, 266112 China
| | - Man Li
- Department of Pathology, Beijing Ditan Hospital Capital Medical University, Beijing, 100015 China
| | - Zhiting Yang
- Qingdao Shuojing Biological Technology Co., Ltd., Qingdao, 266112 China
| | - Fang Xiao
- Institute of Digital Economy Industry, Hangzhou, 310015 China
| | - Yao Yuan
- Beijing Sylincom Technology Co., Ltd., Beijing, 100081 China
| | - Fei Huang
- Institute of Polymer Optoelectronic Materials and Devices, State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou, 510640 China
| | - Fanyang Mo
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing, 100871 China
| | - Peng Wang
- Department of Pathology, Beijing Ditan Hospital Capital Medical University, Beijing, 100015 China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
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18
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Li P, Jia C, Guo X. Molecule-Based Transistors: From Macroscale to Single Molecule. CHEM REC 2020; 21:1284-1299. [PMID: 33140918 DOI: 10.1002/tcr.202000114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/22/2022]
Abstract
Molecule-based field-effect transistors (FETs) are of great significance as they have a wide range of application prospects, such as logic operations, information storage and sensor monitoring. This account mainly introduces and reviews our recent work in molecular FETs. Specifically, through molecular and device design, we have systematically investigated the construction and performance of FETs from macroscale to nanoscale and even single molecule. In particular, we have proposed the broad concept of molecular FETs, whose functions can be achieved through various external controls, such as light stimulation, and other physical, chemical or biological interactions. In the end, we tend to focus the discussion on the development challenges of single-molecule FETs, and propose prospects for further breakthroughs in this field.
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Affiliation(s)
- Peihui Li
- Center of Single-Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, 300350, Tianjin, China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, 300350, Tianjin, China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, 300350, Tianjin, China.,Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China
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19
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Mensah K, Cissé I, Pierret A, Rosticher M, Palomo J, Morfin P, Plaçais B, Bockelmann U. DNA Hybridization Measured with Graphene Transistor Arrays. Adv Healthc Mater 2020; 9:e2000260. [PMID: 32602657 DOI: 10.1002/adhm.202000260] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/04/2020] [Indexed: 12/20/2022]
Abstract
Arrays of field-effect transistors are fabricated from chemical vapor deposition grown graphene (GFETs) and label-free detection of DNA hybridization performed down to femtomolar concentrations. A process is developed for large-area graphene sheets, which includes a thin Al2 O3 layer, protecting the graphene from contamination during photolithographic patterning and a SiOx capping for biocompatibility. It enables fabrication of high-quality transistor arrays, exhibiting stable close-to-zero Dirac point voltages under ambient conditions. Passivation of the as-fabricated chip with a layer composed of two different oxides avoids direct electrochemical contact between the DNA solutions and the graphene layer during hybridization detection. DNA probe molecules are electrostatically immobilized via poly-l-lysine coating of the chip surface. Adsorption of this positively charged polymer induces a positive shift of the Dirac point and subsequent immobilization of negatively charged DNA probes induces a negative shift. Spatially resolved hybridization of DNA sequences is performed on the GFET arrays. End-point as well as real-time in situ measurements of hybridization are achieved. A detection limit of 10 fm is observed for hybridization of 20-nucleotide DNA targets. Typical voltage signals are around 100 mV and spurious drifts below 1 mV per hour.
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Affiliation(s)
- Kokoura Mensah
- Laboratoire NanobiophysiqueESPCI ParisUniversité PSLCNRS Paris 75005 France
| | - Ismaïl Cissé
- Laboratoire NanobiophysiqueESPCI ParisUniversité PSLCNRS Paris 75005 France
| | - Aurélie Pierret
- Laboratoire de Physique de l'Ecole Normale SupérieureENSUniversité PSLCNRSSorbonne UniversitéUniversité Paris‐Diderot Paris 75005 France
| | - Michael Rosticher
- Laboratoire de Physique de l'Ecole Normale SupérieureENSUniversité PSLCNRSSorbonne UniversitéUniversité Paris‐Diderot Paris 75005 France
| | - José Palomo
- Laboratoire de Physique de l'Ecole Normale SupérieureENSUniversité PSLCNRSSorbonne UniversitéUniversité Paris‐Diderot Paris 75005 France
| | - Pascal Morfin
- Laboratoire de Physique de l'Ecole Normale SupérieureENSUniversité PSLCNRSSorbonne UniversitéUniversité Paris‐Diderot Paris 75005 France
| | - Bernard Plaçais
- Laboratoire de Physique de l'Ecole Normale SupérieureENSUniversité PSLCNRSSorbonne UniversitéUniversité Paris‐Diderot Paris 75005 France
| | - Ulrich Bockelmann
- Laboratoire NanobiophysiqueESPCI ParisUniversité PSLCNRS Paris 75005 France
- Institut Cochin 22 rue Méchain Paris 75014 France
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20
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Bochtler M. Arrhenius-law-governed homo- and heteroduplex dissociation. Phys Rev E 2020; 101:032405. [PMID: 32289932 DOI: 10.1103/physreve.101.032405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/14/2020] [Indexed: 06/11/2023]
Abstract
A simple model of temperature-increase-driven homo- or heteroduplex dissociation is analyzed. It features a temperature-independent association constant, and a dissociation constant that increases with temperature according to an Arrhenius law. The model is analytically tractable for quasiequilibrium conditions, for two special cases in the intermediate regime, and in the strongly irreversible regime. In the latter, the fraction of isolated components depends on temperature according to a Gumbel minimal value distribution. The model suggests a logarithmic dependence of the dissociation temperature on the rate of temperature increase. It further predicts that the dissociation occurs in a twice broader temperature interval for slow than fast temperature increase. Finally, the model points to a previously overlooked source of discrepancy between apparent van't Hoff and calorimetric enthalpies. Applied to short double stranded DNA, the model explains the dependence of the melting temperature on the rate of temperature increase, and the twice lower width of the melting transition in low salt compared to high salt conditions.
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Affiliation(s)
- Matthias Bochtler
- IIMCB, Trojdena 4, 02-109 Warsaw, Poland and Polish Academy of Sciences, IBB, Pawinskiego 5a, 02-106 Warsaw, Poland
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21
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Shi H, Liu B, Nussbaumer F, Rangadurai A, Kreutz C, Al-Hashimi HM. NMR Chemical Exchange Measurements Reveal That N6-Methyladenosine Slows RNA Annealing. J Am Chem Soc 2019; 141:19988-19993. [PMID: 31826614 DOI: 10.1021/jacs.9b10939] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N6-Methyladenosine (m6A) is an abundant epitranscriptomic modification that plays important roles in many aspects of RNA metabolism. While m6A is thought to mainly function by recruiting reader proteins to specific RNA sites, the modification can also reshape RNA-protein and RNA-RNA interactions by altering RNA structure mainly by destabilizing base pairing. Little is known about how m6A and other epitranscriptomic modifications might affect the kinetic rates of RNA folding and other conformational transitions that are also important for cellular activity. Here, we used NMR R1ρ relaxation dispersion and chemical exchange saturation transfer to noninvasively and site-specifically measure nucleic acid hybridization kinetics. The methodology was validated on two DNA duplexes and then applied to examine how a single m6A alters the hybridization kinetics in two RNA duplexes. The results show that m6A minimally impacts the rate constant for duplex dissociation, changing koff by ∼1-fold but significantly slows the rate of duplex annealing, decreasing kon by ∼7-fold. A reduction in the annealing rate was observed robustly for two different sequence contexts at different temperatures, both in the presence and absence of Mg2+. We propose that rotation of the N6-methyl group from the preferred syn conformation in the unpaired nucleotide to the energetically disfavored anti conformation required for Watson-Crick pairing is responsible for the reduced annealing rate. The results help explain why in mRNA m6A slows down tRNA selection and more generally suggest that m6A may exert cellular functions by reshaping the kinetics of RNA conformational transitions.
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Affiliation(s)
- Honglue Shi
- Department of Chemistry , Duke University , Durham , North Carolina 27710 , United States
| | - Bei Liu
- Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States
| | - Felix Nussbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , 6020 Innsbruck , Austria
| | - Atul Rangadurai
- Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) , University of Innsbruck , 6020 Innsbruck , Austria
| | - Hashim M Al-Hashimi
- Department of Chemistry , Duke University , Durham , North Carolina 27710 , United States.,Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States
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22
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Schueder F, Stein J, Stehr F, Auer A, Sperl B, Strauss MT, Schwille P, Jungmann R. An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions. Nat Methods 2019; 16:1101-1104. [DOI: 10.1038/s41592-019-0584-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/26/2019] [Indexed: 11/09/2022]
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23
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Chen X, Zhou C, Guo X. Ultrasensitive Detection and Binding Mechanism of Cocaine in an Aptamer‐based Single‐molecule Device. CHINESE J CHEM 2019. [DOI: 10.1002/cjoc.201900225] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xinjiani Chen
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Academy for Advanced Interdisciplinary Studies, Center for Life SciencesPeking University Beijing 100871 China
| | - Chenguang Zhou
- Beijing National Laboratory for Molecular Science, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular EngineeringPeking University Beijing 100871 China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Science, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular EngineeringPeking University Beijing 100871 China
- Department of Materials Science and Engineering, College of EngineeringPeking University Beijing 100871 China
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24
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Chen H, Hu H, Tao C, Clauson RM, Moncion I, Luan X, Hwang S, Sough A, Sansanaphongpricha K, Liao J, Paholak HJ, Stevers NO, Wang G, Liu B, Sun D. Self-Assembled Au@Fe Core/Satellite Magnetic Nanoparticles for Versatile Biomolecule Functionalization. ACS APPLIED MATERIALS & INTERFACES 2019; 11:23858-23869. [PMID: 31245984 DOI: 10.1021/acsami.9b05544] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Although the functionalization of magnetic nanoparticles (MNPs) with biomolecules has been widely explored for various biological applications, achieving efficient bioconjugations with a wide range of biomolecules through a single, universal, and versatile platform remains a challenge, which may significantly impact their applications' outcomes. Here, we report a novel MNP platform composed of Au@Fe core/satellite nanoparticles (CSNPs) for versatile and efficient bioconjugations. The engineering of the CSNPs is facilely formed through the self-assembly of ultrasmall gold nanoparticles (AuNPs, 2-3 nm in diameter) around MNPs with a polysiloxane-containing polymer coating. The formation of the hybrid magnetic nanostructure is revealed by absorption spectroscopy, dynamic light scattering (DLS), transmission electron microscopy (TEM), element analysis using atomic absorption spectroscopy, and vibrating sample magnetometer. The versatility of biomolecule loading to the CSNP is revealed through the bioconjugation of a wide range of relevant biomolecules, including streptavidin, antibodies, peptides, and oligonucleotides. Characterizations including DLS, TEM, lateral flow strip assay, fluorescence assay, giant magnetoresistive nanosensor array, high-performance liquid chromatography, and absorption spectrum are performed to further confirm the efficiency of various bioconjugations to the CSNP. In conclusion, this study demonstrates that the CSNP is a novel MNP-based platform that offers versatile and efficient surface functionalization with various biomolecules.
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Affiliation(s)
- Hongwei Chen
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Hongxiang Hu
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Chun Tao
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Ryan M Clauson
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Ila Moncion
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Xin Luan
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Sangyeul Hwang
- IMRA America, Inc. , 1044 Woodridge Avenue , Ann Arbor , Michigan 48105 , United States
| | - Ashley Sough
- IMRA America, Inc. , 1044 Woodridge Avenue , Ann Arbor , Michigan 48105 , United States
| | - Kanokwan Sansanaphongpricha
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Jinhui Liao
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Hayley J Paholak
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Nicholas O Stevers
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Guoping Wang
- IMRA America, Inc. , 1044 Woodridge Avenue , Ann Arbor , Michigan 48105 , United States
| | - Bing Liu
- IMRA America, Inc. , 1044 Woodridge Avenue , Ann Arbor , Michigan 48105 , United States
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Michigan , Ann Arbor , Michigan 48109 , United States
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25
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Hon J, Gonzalez RL. Bayesian-Estimated Hierarchical HMMs Enable Robust Analysis of Single-Molecule Kinetic Heterogeneity. Biophys J 2019; 116:1790-1802. [PMID: 31010664 DOI: 10.1016/j.bpj.2019.02.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/27/2019] [Accepted: 02/13/2019] [Indexed: 10/27/2022] Open
Abstract
Single-molecule kinetic experiments allow the reaction trajectories of individual biomolecules to be directly observed, eliminating the effects of population averaging and providing a powerful approach for elucidating the kinetic mechanisms of biomolecular processes. A major challenge to the analysis and interpretation of these experiments, however, is the kinetic heterogeneity that almost universally complicates the recorded single-molecule signal versus time trajectories (i.e., signal trajectories). Such heterogeneity manifests as changes and/or differences in the transition rates that are observed within individual signal trajectories or across a population of signal trajectories. Because characterizing kinetic heterogeneity can provide critical mechanistic information, we have developed a computational method that effectively and comprehensively enables such analysis. To this end, we have developed a computational algorithm and software program, hFRET, that uses the variational approximation for Bayesian inference to estimate the parameters of a hierarchical hidden Markov model, thereby enabling robust identification and characterization of kinetic heterogeneity. Using simulated signal trajectories, we demonstrate the ability of hFRET to accurately and precisely characterize kinetic heterogeneity. In addition, we use hFRET to analyze experimentally recorded signal trajectories reporting on the conformational dynamics of ribosomal pre-translocation (PRE) complexes. The results of our analyses demonstrate that PRE complexes exhibit kinetic heterogeneity, reveal the physical origins of this heterogeneity, and allow us to expand the current model of PRE complex dynamics. The methods described here can be applied to signal trajectories generated using any type of signal and can be easily extended to the analysis of signal trajectories exhibiting more complex kinetic behaviors. Moreover, variations of our approach can be easily developed to integrate kinetic data obtained from different experimental constructs and/or from molecular dynamics simulations of a biomolecule of interest.
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Affiliation(s)
- Jason Hon
- Department of Chemistry, Columbia University, New York, New York
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, New York.
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26
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Weng R, Lou S, Li L, Zhang Y, Qiu J, Su X, Qian Y, Walter NG. Single-Molecule Kinetic Fingerprinting for the Ultrasensitive Detection of Small Molecules with Aptasensors. Anal Chem 2019; 91:1424-1431. [PMID: 30562003 DOI: 10.1021/acs.analchem.8b04145] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aptamers have emerged as promising molecular tools for small-molecule analyte sensing. However, the performance of such aptasensors is generally limited by leakage since it has been difficult to completely suppress signal in the absence of analyte, resulting in a compromise between sensitivity and specificity. Here, we describe a methodology for the ultrasensitive detection of analytes combining aptasensors with single-molecule kinetic fingerprinting. A short, fluorescently labeled DNA probe is utilized to detect the structural changes upon ligand binding to the designed hairpin-shaped aptasensor probe. The Poisson statistics of binding and dissociation events of the DNA probe to single surface-immobilized aptasensor molecules is monitored by total internal reflection fluorescence microscopy, permitting the high-accuracy discrimination of the ligand bound and ligand-free states, resulting in zero background. The programmable dynamics of the hairpin enables fine-tuning of the hybridization kinetics of the fluorescent probe, rendering the acquisition time sufficiently flexible to optimize discrimination. Remarkable detection limits are achieved for a diverse set of analytes when spiked into chicken meat extract: the nucleotide adenosine (0.3 pM), the insecticide acetamiprid (0.35 pM), and the dioxin-like toxin PCB-77 (0.72 pM), which is superior to recently reported aptasensors. Our generalizable method significantly improves the performance of aptasensors, with the potential to extend to other molecular biomarkers.
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Affiliation(s)
- Rui Weng
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standards and Testing Technology for Agro-Products , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Shengting Lou
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Lidan Li
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yi Zhang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Jing Qiu
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standards and Testing Technology for Agro-Products , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Xin Su
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yongzhong Qian
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standards and Testing Technology for Agro-Products , Chinese Academy of Agricultural Sciences , Beijing 100081 , China
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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27
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Direct observation of single-molecule hydrogen-bond dynamics with single-bond resolution. Nat Commun 2018; 9:807. [PMID: 29476061 PMCID: PMC5825177 DOI: 10.1038/s41467-018-03203-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/26/2018] [Indexed: 12/18/2022] Open
Abstract
The hydrogen bond represents a fundamental interaction widely existing in nature, which plays a key role in chemical, physical and biochemical processes. However, hydrogen bond dynamics at the molecular level are extremely difficult to directly investigate. Here, in this work we address direct electrical measurements of hydrogen bond dynamics at the single-molecule and single-event level on the basis of the platform of molecular nanocircuits, where a quadrupolar hydrogen bonding system is covalently incorporated into graphene point contacts to build stable supramolecule-assembled single-molecule junctions. The dynamics of individual hydrogen bonds in different solvents at different temperatures are studied in combination with density functional theory. Both experimental and theoretical results consistently show a multimodal distribution, stemming from the stochastic rearrangement of the hydrogen bond structure mainly through intermolecular proton transfer and lactam-lactim tautomerism. This work demonstrates an approach of probing hydrogen bond dynamics with single-bond resolution, making an important contribution to broad fields beyond supramolecular chemistry.
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28
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Guan J, Jia C, Li Y, Liu Z, Wang J, Yang Z, Gu C, Su D, Houk KN, Zhang D, Guo X. Direct single-molecule dynamic detection of chemical reactions. SCIENCE ADVANCES 2018; 4:eaar2177. [PMID: 29487914 PMCID: PMC5817934 DOI: 10.1126/sciadv.aar2177] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/16/2018] [Indexed: 05/03/2023]
Abstract
Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.
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Affiliation(s)
- Jianxin Guan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Chuancheng Jia
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Yanwei Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Environment Research Institute, Shandong University, Jinan 250100, P. R. China
| | - Zitong Liu
- Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Jinying Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Zhongyue Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Chunhui Gu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Dingkai Su
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Deqing Zhang
- Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, P. R. China
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29
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Patra S, Anders C, Schummel PH, Winter R. Antagonistic effects of natural osmolyte mixtures and hydrostatic pressure on the conformational dynamics of a DNA hairpin probed at the single-molecule level. Phys Chem Chem Phys 2018; 20:13159-13170. [DOI: 10.1039/c8cp00907d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Osmolyte mixtures from deep sea organisms are able to rescue nucleic acids from pressure-induced unfolding.
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Affiliation(s)
- Satyajit Patra
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Christian Anders
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Paul Hendrik Schummel
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
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30
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Li J, He G, Hiroshi U, Liu W, Noji H, Qi C, Guo X. Direct Measurement of Single-Molecule Adenosine Triphosphatase Hydrolysis Dynamics. ACS NANO 2017; 11:12789-12795. [PMID: 29215860 DOI: 10.1021/acsnano.7b07639] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
F1-ATPase (F1) is a bidirectional molecular motor that hydrolyzes nearly all ATPs to fuel the cellular processes. Optical observation of labeled F1 rotation against the α3β3 hexamer ring revealed the sequential mechanical rotation steps corresponding to ATP binding/ADP release and ATP hydrolysis/Pi release. These substeps originate from the F1 rotation but with heavy load on the γ shaft due to fluorescent labeling and the photophysical limitation of an optical microscope, which hampers better understanding of the intrinsic kinetic behavior of ATP hydrolysis. In this work, we present a method capable of electrically monitoring ATP hydrolysis of a single label-free F1 in real time by using a high-gain silicon nanowire-based field-effect transistor circuit. We reproducibly observe the regular current signal fluctuations with two distinct levels, which are induced by the binding dwell and the catalytic dwell, respectively, in both concentration- and temperature-dependent experiments. In comparison with labeled F1, the hydrolysis rate of nonlabeled F1 used in this study is 1 order of magnitude faster (1.69 × 108 M-1 s-1 at 20 °C), and the differences between two sequential catalytic rates are clearer, demonstrating the ability of nanowire nanocircuits to directly probe the intrinsic dynamic processes of the biological activities with single-molecule/single-event sensitivity. This approach is complementary to traditional optical methods, offering endless opportunities to unravel molecular mechanisms of a variety of dynamic biosystems under realistic physiological conditions.
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Affiliation(s)
- Jie Li
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, P. R. China
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, P. R. China
| | - Gen He
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, P. R. China
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, P. R. China
| | - Ueno Hiroshi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo , Tokyo 113-8654, Japan
| | - Wenzhe Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, P. R. China
| | - Hiroyuki Noji
- Department of Applied Chemistry, School of Engineering, The University of Tokyo , Tokyo 113-8654, Japan
| | - Chuanmin Qi
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University , Beijing 100875, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, P. R. China
- Department of Materials Science and Engineering, College of Engineering, Peking University , Beijing 100871, P. R. China
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31
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Zhang JX, Fang JZ, Duan W, Wu LR, Zhang AW, Dalchau N, Yordanov B, Petersen R, Phillips A, Zhang DY. Predicting DNA hybridization kinetics from sequence. Nat Chem 2017; 10:91-98. [PMID: 29256499 PMCID: PMC5739081 DOI: 10.1038/nchem.2877] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 09/21/2017] [Indexed: 12/17/2022]
Abstract
Hybridization is a key molecular process in biology and biotechnology, but so far there is no predictive model for accurately determining hybridization rate constants based on sequence information. Here, we report a weighted neighbour voting (WNV) prediction algorithm, in which the hybridization rate constant of an unknown sequence is predicted based on similarity reactions with known rate constants. To construct this algorithm we first performed 210 fluorescence kinetics experiments to observe the hybridization kinetics of 100 different DNA target and probe pairs (36 nt sub-sequences of the CYCS and VEGF genes) at temperatures ranging from 28 to 55 °C. Automated feature selection and weighting optimization resulted in a final six-feature WNV model, which can predict hybridization rate constants of new sequences to within a factor of 3 with ∼91% accuracy, based on leave-one-out cross-validation. Accurate prediction of hybridization kinetics allows the design of efficient probe sequences for genomics research.
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Affiliation(s)
- Jinny X Zhang
- Department of Bioengineering, Rice University, Houston, Texas 77030, USA.,Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77030, USA
| | - John Z Fang
- Department of Bioengineering, Rice University, Houston, Texas 77030, USA
| | - Wei Duan
- Department of Bioengineering, Rice University, Houston, Texas 77030, USA
| | - Lucia R Wu
- Department of Bioengineering, Rice University, Houston, Texas 77030, USA
| | - Angela W Zhang
- Department of Bioengineering, Rice University, Houston, Texas 77030, USA
| | | | | | | | | | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, Texas 77030, USA.,Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77030, USA
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32
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He G, Li J, Qi C, Guo X. Single Nucleotide Polymorphism Genotyping in Single-Molecule Electronic Circuits. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2017; 4:1700158. [PMID: 29201610 PMCID: PMC5700462 DOI: 10.1002/advs.201700158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/20/2017] [Indexed: 05/08/2023]
Abstract
Establishing low-cost, high-throughput, simple, and accurate single nucleotide polymorphism (SNP) genotyping techniques is beneficial for understanding the intrinsic relationship between individual genetic variations and their biological functions on a genomic scale. Here, a straightforward and reliable single-molecule approach is demonstrated for precise SNP authentication by directly measuring the fluctuations in electrical signals in an electronic circuit, which is fabricated from a high-gain field-effect silicon nanowire decorated with a single hairpin DNA, in the presence of different target DNAs. By simply comparing the proportion difference of a probe-target duplex structure throughout the process, this study implements allele-specific and accurate SNP detection. These results are supported by the statistical analyses of different dynamic parameters such as the mean lifetime and the unwinding probability of the duplex conformation. In comparison with conventional polymerase chain reaction and optical methods, this convenient and label-free method is complementary to existing optical methods and also shows several advantages, such as simple operation and no requirement for fluorescent labeling, thus promising a futuristic route toward the next-generation genotyping technique.
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Affiliation(s)
- Gen He
- Beijing National Laboratory for Molecular SciencesState Key Laboratory for Structural Chemistry of Unstable and Stable SpeciesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
- Key Laboratory of RadiopharmaceuticalsMinistry of EducationCollege of ChemistryBeijing Normal UniversityBeijing100875P. R. China
| | - Jie Li
- Beijing National Laboratory for Molecular SciencesState Key Laboratory for Structural Chemistry of Unstable and Stable SpeciesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
- Key Laboratory of RadiopharmaceuticalsMinistry of EducationCollege of ChemistryBeijing Normal UniversityBeijing100875P. R. China
| | - Chuanmin Qi
- Key Laboratory of RadiopharmaceuticalsMinistry of EducationCollege of ChemistryBeijing Normal UniversityBeijing100875P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular SciencesState Key Laboratory for Structural Chemistry of Unstable and Stable SpeciesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
- Department of Materials Science and EngineeringCollege of EngineeringPeking UniversityBeijing100871P. R. China
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33
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Patra S, Anders C, Erwin N, Winter R. Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701420] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Satyajit Patra
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Christian Anders
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Nelli Erwin
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
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34
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Patra S, Anders C, Erwin N, Winter R. Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions. Angew Chem Int Ed Engl 2017; 56:5045-5049. [DOI: 10.1002/anie.201701420] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/03/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Satyajit Patra
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Christian Anders
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Nelli Erwin
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Physikalische Chemie I - Biophysikalische Chemie; Fakultät für Chemie und Chemische Biologie; TU Dortmund; Otto-Hahn Str. 4a 44227 Dortmund Germany
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35
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Li J, He G, Ueno H, Jia C, Noji H, Qi C, Guo X. Direct real-time detection of single proteins using silicon nanowire-based electrical circuits. NANOSCALE 2016; 8:16172-16176. [PMID: 27714062 DOI: 10.1039/c6nr04103e] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present an efficient strategy through surface functionalization to build a single silicon nanowire field-effect transistor-based biosensor that is capable of directly detecting protein adsorption/desorption at the single-event level. The step-wise signals in real-time detection of His-tag F1-ATPases demonstrate a promising electrical biosensing approach with single-molecule sensitivity, thus opening up new opportunities for studying single-molecule biophysics in broad biological systems.
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Affiliation(s)
- Jie Li
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China. and Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.
| | - Gen He
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China. and Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.
| | - Hiroshi Ueno
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8654, Japan.
| | - Chuancheng Jia
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.
| | - Hiroyuki Noji
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8654, Japan.
| | - Chuanmin Qi
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China. and Department of Materials Science and Engineering, College of Engineering, Peking University, Beijing 100871, P. R. China
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