1
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Si W, Chen J, Zhang Z, Wu G, Zhao J, Sha J. Electroosmotic Sensing of Uncharged Peptides and Differentiating Their Phosphorylated States Using Nanopores. Chemphyschem 2024; 25:e202400281. [PMID: 38686913 DOI: 10.1002/cphc.202400281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/14/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
The correct characterization and identification of different kinds of proteins is crucial for the survival and development of living organisms, and proteomics research promotes the analysis and understanding of future genome functions. Nanopore technique has been proved to accurately identify individual nucleotides. However, accurate and rapid protein sequencing is difficult due to the variability of protein structures that contains more than 20 amino acids, and it remains very challenging especially for uncharged peptides as they can not be electrophoretically driven through the nanopore. Graphene nanopores have the advantages of high accuracy, sensitivity and low cost in identifying protein phosphorylation modifications. Here, by using all-atom molecular dynamics simulations, charged graphene nanopores are employed to electroosmotically capture and sense uncharged peptides. By further mimicking AFM manipulation of single molecules, it is also found that the uncharged peptides and their phosphorylated states could also be differentiated by both the ionic current and pulling force signals during their pulling processes through the nanopore with a slow and constant velocity. The results shows ability of using nanopores to detect and discriminate single amino acid and its phosphorylation, which is essential for the future low-cost and high-throughput sequencing of protein residues and their post-translational modifications.
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Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Jiayi Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Zhen Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiajia Zhao
- Department of Pharmacology, Key Laboratory of Neuropsychiatric Diseases, China Pharmaceutical University, Nanjing, 211198, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
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2
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Chen H, Huang C, Liao Z, Ma X, Fan J. The Role of MXene Surface Terminations on Peptide Transportation in Nanopore Sensing. J Phys Chem Lett 2024; 15:3900-3906. [PMID: 38564363 DOI: 10.1021/acs.jpclett.4c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Nanopores with two-dimensional materials have various advantages in sensing, but the fast translocation of molecules hinders their scale-up applications. In this work, we investigate the influence of -F, -O, and -OH surface terminations on the translocation of peptides through MXene nanopores. We find that the longest dwell time always occurs when peptides pass through the Ti3C2O2 nanopores. This elongated dwell time is induced by the strongest interaction between peptides and the Ti3C2O2 membrane, in which the van der Waals interactions dominate. Compared to the other two MXene nanopores, the braking effect is indicated during the whole translocation process, which evidence the advantage of Ti3C2O2 in nanopore sensing. Our work demonstrates that membrane surface chemistry has a great influence on the translocation of peptides, which can be introduced in the design of nanopores for a better performance.
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Affiliation(s)
- Huan Chen
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Changxiong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Zhenyu Liao
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Xinyao Ma
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
- Department of Mechanical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
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3
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Si W, Lin X, Wang L, Wu G, Zhang Y, Chen Y, Sha J. Nanopore actuation of a DNA-tracked nanovehicle. NANOSCALE 2023; 15:14659-14668. [PMID: 37622615 DOI: 10.1039/d3nr02633g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
As a kind of nanomachine that has great potential for applications in nanoscale sensing and manipulation, nanovehicles with unique shapes and functions have received extensive attention in recent years. Different from the existing common method of using synthetic chemistry to design and manufacture a nanovehicle, here we theoretically report a molecularly assembled DNA-tracked nanovehicle that can move on a solid-state surface using molecular dynamics simulations. A graphene membrane with four nanopores acts as the chassis of the nanoscale vehicle, and two circular ssDNAs across the nanopores serve as the wheels. The electroosmotic flows induced by independently charged nanopores with different surface charge densities under external electric fields were found to be the main power to actuate the controlled rotary motion of circular ssDNAs across every two nanopores. By tuning the rotary speed of each circular ssDNA, the linear and turning movements of the designed nanovehicle were realized. The designed nanovehicle makes it possible to have access to almost everywhere in the human body, which would lead to significant breakthroughs in the fields of nanoscale surgery, drug delivery and so on. The research not only enriches the family of nanorobots, but also opens another way for designing nanovehicles.
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Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Xiaojing Lin
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Liwei Wang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
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4
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Chen Y, Zhu F, Leng J, Ying T, Jiang JW, Zhou Q, Chang T, Guo W, Gao H. Fluctuotaxis: Nanoscale directional motion away from regions of fluctuation. Proc Natl Acad Sci U S A 2023; 120:e2220500120. [PMID: 37487105 PMCID: PMC10401016 DOI: 10.1073/pnas.2220500120] [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: 12/13/2022] [Accepted: 06/27/2023] [Indexed: 07/26/2023] Open
Abstract
Regulating the motion of nanoscale objects on a solid surface is vital for a broad range of technologies such as nanotechnology, biotechnology, and mechanotechnology. In spite of impressive advances achieved in the field, there is still a lack of a robust mechanism which can operate under a wide range of situations and in a controllable manner. Here, we report a mechanism capable of controllably driving directed motion of any nanoobjects (e.g., nanoparticles, biomolecules, etc.) in both solid and liquid forms. We show via molecular dynamics simulations that a nanoobject would move preferentially away from the fluctuating region of an underlying substrate, a phenomenon termed fluctuotaxis-for which the driving force originates from the difference in atomic fluctuations of the substrate behind and ahead of the object. In particular, we find that the driving force can depend quadratically on both the amplitude and frequency of the substrate and can thus be tuned flexibly. The proposed driving mechanism provides a robust and controllable way for nanoscale mass delivery and has potential in various applications including nanomotors, molecular machines, etc.
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Affiliation(s)
- Yang Chen
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Fangyan Zhu
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Jiantao Leng
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Tianquan Ying
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Jin-Wu Jiang
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
- Joint-Research Center for Computational Materials, Zhejiang Laboratory, Hangzhou311100, China
| | - Quan Zhou
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
| | - Tienchong Chang
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Frontier Science Center of Mechanoinformatics, School of Mechanics and Engineering Science, Shanghai University, Shanghai200072, China
- Joint-Research Center for Computational Materials, Zhejiang Laboratory, Hangzhou311100, China
- Shanghai Institute of Aircraft Mechanics and Control, Tongji University, Shanghai200092, China
| | - Wanlin Guo
- Key Laboratory for Intelligent Nano Materials and Devices of the Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, Institute of Nanoscience of Nanjing University of Aeronautics and Astronautics, Nanjing210016, China
| | - Huajian Gao
- School of Mechanical and Aerospace Engineering, College of Engineering, Nanyang Technological University, Singapore639798, Singapore
- Institute of High Performance Computing, Agency for Science, Technology and Research, Singapore138632, Singapore
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5
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Hu G, Yan H, Xi G, Gao Z, Wu Z, Lu Z, Tu J. Nanopore sensors for single molecular protein detection: Research progress based on computer simulations. IET Nanobiotechnol 2023; 17:257-268. [PMID: 36924083 DOI: 10.1049/nbt2.12124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
As biological macromolecules, proteins are involved in important cellular functions ranging from DNA replication and biosynthesis to metabolic signalling and environmental sensing. Protein sequencing can help understand the relationship between protein function and structure, and provide key information for disease diagnosis and new drug design. Nanopore sensors are a novel technology to achieve the goal of label-free and high-throughput protein sequencing. In recent years, nanopore-based biosensors have been widely used in the detection and analysis of biomolecules such as DNA, RNA, and proteins. At the same time, computer simulations can describe the transport of proteins through nanopores at the atomic level. This paper reviews the applications of nanopore sensors in protein sequencing over the past decade and the solutions to key problems from a computer simulation perspective, with the aim of pointing the way to the future of nanopore protein sequencing.
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Affiliation(s)
- Gang Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Han Yan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Guohao Xi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhuwei Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Ziqing Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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6
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Kim D, Byun S, Pu Y, Huh H, Jung Y, Kim S, Lee KY. Design of a Current Sensing System with TIA Gain of 160 dBΩ and Input-Referred Noise of 1.8 pA rms for Biosensor. SENSORS (BASEL, SWITZERLAND) 2023; 23:3019. [PMID: 36991734 PMCID: PMC10051069 DOI: 10.3390/s23063019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
This paper proposes a high-gain low-noise current signal detection system for biosensors. When the biomaterial is attached to the biosensor, the current flowing through the bias voltage is changed so that the biomaterial can be sensed. A resistive feedback transimpedance amplifier (TIA) is used for the biosensor requiring a bias voltage. Current changes in the biosensor can be checked by plotting the current value of the biosensor in real time on the self-made graphical user interface (GUI). Even if the bias voltage changes, the input voltage of the analog to digital converter (ADC) does not change, so it is designed to plot the current of the biosensor accurately and stably. In particular, for multi-biosensors with an array structure, a method of automatically calibrating the current between biosensors by controlling the gate bias voltage of the biosensors is proposed. Input-referred noise is reduced using a high-gain TIA and chopper technique. The proposed circuit achieves 1.8 pArms input-referred noise with a gain of 160 dBΩ and is implemented in a TSMC 130 nm CMOS process. The chip area is 2.3 mm2, and the power consumption of the current sensing system is 12 mW.
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Affiliation(s)
- Donggyu Kim
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sungjun Byun
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Younggun Pu
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Hyungki Huh
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Yeonjae Jung
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Seokkee Kim
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
| | - Kang-Yoon Lee
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKAIChips Co., Ltd., Suwon 16419, Republic of Korea
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7
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Mittal S, Manna S, Pathak B. Machine Learning Prediction of the Transmission Function for Protein Sequencing with Graphene Nanoslit. ACS APPLIED MATERIALS & INTERFACES 2022; 14:51645-51655. [PMID: 36374991 DOI: 10.1021/acsami.2c13405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein sequencing has rapidly changed the landscape of healthcare and life science by accelerating the growth of diagnostics and personalized medicines for a variety of fatal diseases. Next-generation nanopore/nanoslit sequencing is promising to achieve single-molecule resolution with chromosome-size-long readability. However, due to inherent complexity, high-throughput sequencing of all 20 amino acids demands different approaches. Aiming to accelerate the detection of amino acids, a general machine learning (ML) method has been developed for quick and accurate prediction of the transmission function for amino acid sequencing. Among the utilized ML models, the XGBoost regression model is found to be the most effective algorithm for fast prediction of the transmission function with a very low test root-mean-square error (RMSE ∼0.05). In addition, using the random forest ML classification technique, we are able to classify the neutral amino acids with a prediction accuracy of 100%. Therefore, our approach is an initiative for the prediction of the transmission function through ML and can provide a platform for the quick identification of amino acids with high accuracy.
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Affiliation(s)
- Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh453552, India
| | - Souvik Manna
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh453552, India
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8
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Gu Z, He Z, Chen F, Meng L, Feng J, Zhou R. Ionic Liquid Decelerates Single-Stranded DNA Transport through Molybdenum Disulfide Nanopores. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32618-32624. [PMID: 35798544 DOI: 10.1021/acsami.2c03335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nanopores in two-dimensional (2D) materials have emerged to offer in principle necessary spatial resolution for high-throughput DNA sequencing. However, their fidelity is severely limited by the fast DNA translocation. A recent experiment indicates that introducing ionic liquids could slow down DNA translocation in a MoS2 nanopore. However, the corresponding in-depth molecular mechanism underlying the experimental findings is not fully understood, which is crucial for the future improvement of rational DNA translocation control. Here, we computationally investigate and then experimentally identify the effect of BmimCl ionic liquid on the retardation of ssDNA translocation through a single-layer MoS2 nanopore. Our all-atom molecular dynamics simulations demonstrate that the strong interaction between Bmim+ and ssDNA offers a considerable dragging force to decelerate the electrophoretic motion of ssDNA in the BmimCl solution. Moreover, we show that Bmim+ ions exhibit preferential binding on the sulfur edges of the nanopore. These Bmim+ in the pore region can not only act as a steric blockage but also form π-π stackings with nucleobases, which provide a further restriction on the ssDNA motion. Therefore, our molecular dynamics simulation investigations deepen the understanding of the critical role of ionic liquid in DNA translocation through a nanopore from a molecular landscape, which may benefit practical implementations of ionic liquids in nanopore sequencing.
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Affiliation(s)
- Zonglin Gu
- Institute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China
| | - Zhi He
- Institute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China
| | - Fanfan Chen
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027 Hangzhou, China
| | - Lijun Meng
- Institute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China
| | - Jiandong Feng
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027 Hangzhou, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, 201203 Shanghai, China
- Department of Chemistry, Colombia University, New York City, New York 10027, United States
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9
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Wei G, Hu R, Li Q, Lu W, Liang H, Nan H, Lu J, Li J, Zhao Q. Oligonucleotide Discrimination Enabled by Tannic Acid-Coordinated Film-Coated Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6443-6453. [PMID: 35544765 DOI: 10.1021/acs.langmuir.2c00638] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Discrimination of nucleotides serves as the basis for DNA sequencing using solid-state nanopores. However, the translocation of DNA is usually too fast to be detected, not to mention nucleotide discrimination. Here, we utilized polyphenolic TA and Fe3+, an attractive metal-organic thin film, and achieved a fast and robust surface coating for silicon nitride nanopores. The hydrophilic coating layer can greatly reduce the low-frequency noise of an original unstable nanopore, and the nanopore size can be finely tuned in situ at the nanoscale by simply adjusting the relative ratio of Fe3+ and TA monomers. Moreover, the hydrogen bonding interaction formed between the hydroxyl groups provided by TA and the phosphate groups of DNAs significantly increases the residence time of a short double-strand (100 bp) DNA. More importantly, we take advantage of the different strengths of hydrogen bonding interactions between the hydroxyl groups provided by TA and the analytes to discriminate between two oligonucleotide samples (oligodeoxycytidine and oligodeoxyadenosine) with similar sizes and lengths, of which the current signal patterns are significantly different using the coated nanopore. The results shed light on expanding the biochemical functionality of surface coatings on solid-state nanopores for future biomedical applications.
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Affiliation(s)
- Guanghao Wei
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Qiuhui Li
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Wenlong Lu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
| | - Hanyu Liang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, 310022 Hangzhou, China
| | - Hexin Nan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, 310022 Hangzhou, China
| | - Jing Lu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, 226010 Jiangsu, China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, China
| | - Juan Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, 310022 Hangzhou, China
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-Optoelectronics, School of Physics, Peking University, Beijing 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, 226010 Jiangsu, China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, China
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10
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Si W, Yuan R, Wu G, Kan Y, Sha J, Chen Y, Zhang Y, Shen Y. Navigated Delivery of Peptide to the Nanopore Using In-Plane Heterostructures of MoS 2 and SnS 2 for Protein Sequencing. J Phys Chem Lett 2022; 13:3863-3872. [PMID: 35467868 DOI: 10.1021/acs.jpclett.2c00533] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The impressive success of DNA sequencing using nanopores makes it possible to realize nanopore based protein sequencing. Well-controlled capture and linear movement of the protein are essential for accurate nanopore protein sequencing. Here, by taking advantage of different binding affinities of protein to two isomorphic materials, we theoretically designed a heterostructual platform for delivering the unfolded peptide to the nanopore sensing region. Due to the stronger binding between the peptide and SnS2 compared to MoS2, the peptide would adsorb to the SnS2 nanostripe and keep its threadlike conformation in the MoS2/SnS2/MoS2 heterostructure. Through switching the direction of the applied electric field in real time, the peptide was strategically driven to move along the designed path to the target nanopore. The ionic current blockades were also found to be different as the compositions of the peptide were changed, indicating the possibility for differentiating different peptides using this platform.
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Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Runyi Yuan
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yajing Kan
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Yang Shen
- Department of Obstetrics and Gynaecology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
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11
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Li JG, Li MY, Li XY, Wu XY, Ying YL, Long YT. Full Width at Half Maximum of Nanopore Current Blockage Controlled by a Single-Biomolecule Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1188-1193. [PMID: 35019652 DOI: 10.1021/acs.langmuir.1c02900] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A biological nanopore is one of the predominant single-molecule approaches as a result of its controllable single-biomolecule interface, which could reflect the "intrinsic" information on an individual molecule in a label-free way. Because the current blockage is normally treated as the most important parameter for nanopore identification of every single molecule, the fluctuation of current blockage for certain types of molecules, defined as full width at half maximum (fwhm) of current blockage, actually owns a dominant influence on nanopore resolution. Therefore, controlling the fwhm of current blockage of molecules is critical for the sensing capability of the nanopore. Here, taking an aerolysin nanopore as a model, by precisely controlling the functional group in this single-biomolecule interface, we could narrow the fwhm of nanopore current blockage for DNA identification and prolong the duration inside the nanopore. Moreover, a substantial correlation between fwhm of current blockage and duration is established, showing a non-monotonic variation. Besides, the mechanism is also clarified with studying the detailed current blockage events. This proposed correlation is further demonstrated to be applied uniformly across different mutant aerolysins for a certain DNA. This study proposes a new strategy for regulating molecular sensing from the duration of the analyte, which could guide the resolution of heterogeneity analysis using nanopores.
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Affiliation(s)
- Jun-Ge Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xin-Yi Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xue-Yuan Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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Saikia N. Probing the adsorption behavior and free energy landscape of single-stranded DNA oligonucleotides on single-layer MoS 2with molecular dynamics. NANOTECHNOLOGY 2021; 33:105602. [PMID: 34823233 DOI: 10.1088/1361-6528/ac3d61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Interfacing single-stranded DNA (ssDNA) with 2D transition metal dichalcogenides are important for numerous technological advancements. However, the molecular mechanism of this process, including the nature of intermolecular association and conformational details of the self-assembled hybrids is still not well understood. Here, atomistic molecular dynamics simulation is employed to study the distinct adsorption behavior of ssDNA on a single-layer MoS2in aqueous environment. The ssDNA sequences [T10, G10, A10, C10, U10, (GT)5, and (AC)5] are chosen on the basis that short ssDNA segments can undergo a spontaneous conformational change upon adsorption and allow efficient sampling of the conformational landscape. Differences in hybridization is attributed to the inherent molecular recognition ability of the bases. While the binding appears to be primarily driven by energetically favorable van der Waalsπ-stacking interactions, equilibrium structures are modulated by the ssDNA conformational changes. The poly-purines demonstrate two concurrently competingπ-stacking interactions: nucleobase-nucleobase (intramolecular) and nucleobase-MoS2(intermolecular). The poly-pyrimidines, on the other hand, reveal enhancedπ-stacking interactions, thereby maximizing the number of contacts. The results provide new molecular-level understanding of ssDNA adsorption on the MoS2surface and facilitate future studies in design of functional DNA/MoS2structure-based platforms for DNA sequencing, biosensing (optical, electrochemical, and electronic), and drug delivery.
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Affiliation(s)
- Nabanita Saikia
- School of Science, Navajo Technical University, Chinle Site, AZ 86503, United States of America
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