1
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Xia Z, Patchin M, McKay CP, Drndić M. Deoxyribonucleic Acid Extraction from Mars Analog Soils and Their Characterization with Solid-State Nanopores. ASTROBIOLOGY 2022; 22:992-1008. [PMID: 35731031 DOI: 10.1089/ast.2021.0051] [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
Life detection on Mars is an important topic that includes a direct search for biomarkers. This requires instruments for in situ biomarker detection that are compact, lightweight, and able to withstand operations in space. Solid-state nanopores are excellent candidates that allow fast single-molecule detection. They can withstand high temperatures and be sterilized to minimize planetary contamination. The instruments are portable with low-power requirements. We demonstrate a few key results in advancing the use of nanopores for in-space applications. First, we developed modified deoxyribonucleic acid (DNA) extraction protocols to extract DNA from Mars analog soils. Second, we used silicon nitride nanopores to demonstrate the detection of extracted DNA and corresponding current characteristics. The yields and properties of extracted DNA (e.g., estimated diameters) varied somewhat by soil types, extraction methods, and nanopores used. The yields varied from a minimum of 0.9 ng DNA/g soil for a magnesium carbonate sample from Lake Salda to a maximum of 210 ng DNA/g soil for a calcium carbonate sample from Trona Pinnacles. For a given soil type, yields from different methods varied by a factor of up to 50. These observations motivate future studies with a broader range of Mars-like soils and improved instruments to increase signal-to-noise-ratio at higher measurement bandwidths.
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Affiliation(s)
- Zehui Xia
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Margaret Patchin
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Christopher P McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Marija Drndić
- David Rittenhouse Laboratory, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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2
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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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Chen X, Zhao X, Ma R, Hu Y, Cui C, Mi Z, Dou R, Pan D, Shan X, Wang L, Fan C, Lu X. Ionic Current Fluctuation and Orientation of Tetrahedral DNA Nanostructures in a Solid-State Nanopore. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107237. [PMID: 35092143 DOI: 10.1002/smll.202107237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Understanding the dynamic behavior of a nanostructure translocating through a nanopore is important for various applications. In this paper, the characteristics in ion current traces of tetrahedral DNA nanostructures (TDN) translocating through a solid-state nanopore are examined, by combined experimental and theoretical simulations. The results of finite element analysis reveal the correlation between orientation of TDN and the conductance blockade. The experimentally measured fluctuations in the conductance blockade, expressed as voltage-dependent histogram profiles, are consistent with the simulation, revealing the nature of a random distribution in orientation and weak influence of electrostatic and viscous torques. The step changes in orientation of a TDN during translocation are further explained by the collision with the nanopore, while the gradual changes in orientation illustrate the impact of a weak torque field in the nano-fluidic channel. The results demonstrate a general method and basic understanding in the dynamic behavior of nanostructures translocating through solid-state nanopores.
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Affiliation(s)
- Xiaoyu Chen
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xinjia Zhao
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Ruiping Ma
- Beijing Normal University, Beijing, 100088, China
| | - Ying Hu
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Chengjun Cui
- Shanghai Frontier Innovation Research Institute, Shanghai, 201108, China
| | - Zhuang Mi
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Ruifen Dou
- Beijing Normal University, Beijing, 100088, China
| | - Dun Pan
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University Shanghai, Shanghai, 200030, China
| | - Xinyan Shan
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Lihua Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinghua Lu
- Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
- Center for Excellence in Topological Quantum Computation, Beijing, 100190, China
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4
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Xia Z, Lin CY, Drndić M. Protein-enabled detection of ibuprofen and sulfamethoxazole using solid-state nanopores. Proteomics 2022; 22:e2100071. [PMID: 34974637 DOI: 10.1002/pmic.202100071] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 02/01/2023]
Abstract
Enabled by proteins, we present an all-electrical method for rapid detection of small pharmaceuticals (ibuprofen and sulfamethoxazole [SMZ]) in aqueous media using silicon nitride pores. Specifically, we use carrier proteins, bovine serum albumin (BSA), and take advantage of their interactions with two small drug molecules to form BSA-drug complexes which can be detected by nm-diameter pores, thereby confirming the presence of small pharmaceuticals. We demonstrate detection of ibuprofen and SMZ at concentrations down to 100 nM (∼21 μg/L) and 48.5 nM (12 μg/L), respectively. We observe changes in electrical signal characteristics (reflected in event durations, rates, current magnitudes, and estimated particle diameters) of BSA-drug complexes compared to BSA-only, and differences between these two small pharmaceuticals, possibly paving a path toward developing selective sensors by identifying "electrical fingerprints" of these molecules in the future. These distinct electrical signals are likely a combined result of diffusion, electrophoretic and electroosmotic effects, interactions between the pore and particles, which depend on pore diameters, pH, and the resulting surface charges. The use of single-molecule-counting nanopores allows sensing of small pharmaceuticals, studies of protein conformational changes, and may aid in efforts to evaluate the impact of small drug molecules on aquatic and human life.
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Affiliation(s)
- Zehui Xia
- Goeppert LLC, Philadelphia, Pennsylvania, USA
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marija Drndić
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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5
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Zeng X, Xiang Y, Liu Q, Wang L, Ma Q, Ma W, Zeng D, Yin Y, Wang D. Nanopore Technology for the Application of Protein Detection. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1942. [PMID: 34443773 PMCID: PMC8400292 DOI: 10.3390/nano11081942] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/19/2023]
Abstract
Protein is an important component of all the cells and tissues of the human body and is the material basis of life. Its content, sequence, and spatial structure have a great impact on proteomics and human biology. It can reflect the important information of normal or pathophysiological processes and promote the development of new diagnoses and treatment methods. However, the current techniques of proteomics for protein analysis are limited by chemical modifications, large sample sizes, or cumbersome operations. Solving this problem requires overcoming huge challenges. Nanopore single molecule detection technology overcomes this shortcoming. As a new sensing technology, it has the advantages of no labeling, high sensitivity, fast detection speed, real-time monitoring, and simple operation. It is widely used in gene sequencing, detection of peptides and proteins, markers and microorganisms, and other biomolecules and metal ions. Therefore, based on the advantages of novel nanopore single-molecule detection technology, its application to protein sequence detection and structure recognition has also been proposed and developed. In this paper, the application of nanopore single-molecule detection technology in protein detection in recent years is reviewed, and its development prospect is investigated.
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Affiliation(s)
- Xiaoqing Zeng
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yang Xiang
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianyun Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Wenhao Ma
- Chongqing University, 174 Shazheng Street, Shapingba District, Chongqing 400044, China; (X.Z.); (Y.X.); (W.M.)
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Delin Zeng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Yajie Yin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (Q.L.); (L.W.); (Q.M.); (D.Z.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
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6
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Synthetic heparan sulfate standards and machine learning facilitate the development of solid-state nanopore analysis. Proc Natl Acad Sci U S A 2021; 118:2022806118. [PMID: 33688052 DOI: 10.1073/pnas.2022806118] [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] [Indexed: 11/18/2022] Open
Abstract
The application of solid-state (SS) nanopore devices to single-molecule nucleic acid sequencing has been challenging. Thus, the early successes in applying SS nanopore devices to the more difficult class of biopolymer, glycosaminoglycans (GAGs), have been surprising, motivating us to examine the potential use of an SS nanopore to analyze synthetic heparan sulfate GAG chains of controlled composition and sequence prepared through a promising, recently developed chemoenzymatic route. A minimal representation of the nanopore data, using only signal magnitude and duration, revealed, by eye and image recognition algorithms, clear differences between the signals generated by four synthetic GAGs. By subsequent machine learning, it was possible to determine disaccharide and even monosaccharide composition of these four synthetic GAGs using as few as 500 events, corresponding to a zeptomole of sample. These data suggest that ultrasensitive GAG analysis may be possible using SS nanopore detection and well-characterized molecular training sets.
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7
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Application of Solid-State Nanopore in Protein Detection. Int J Mol Sci 2020; 21:ijms21082808. [PMID: 32316558 PMCID: PMC7215903 DOI: 10.3390/ijms21082808] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/11/2020] [Accepted: 04/14/2020] [Indexed: 11/17/2022] Open
Abstract
A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks.
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8
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Si W, Zhang Y, Wu G, Kan Y, Zhang Y, Sha J, Chen Y. Discrimination of Protein Amino Acid or Its Protonated State at Single-Residue Resolution by Graphene Nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900036. [PMID: 30848871 DOI: 10.1002/smll.201900036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/24/2019] [Indexed: 05/03/2023]
Abstract
The function of a protein is determined by the composition of amino acids and is essential to proteomics. However, protein sequencing remains challenging due to the protein's irregular charge state and its high-order structure. Here, a proof of principle study on the capability of protein sequencing by graphene nanopores integrated with atomic force microscopy is performed using molecular dynamics simulations. It is found that nanopores can discriminate a protein sequence and even its protonation state at single-residue resolution. Both the pulling forces and current blockades induced by the permeation of protein residues are found to be highly correlated with the type of amino acids, which makes the residues identifiable. It is also found that aside from the dimension, both the conformation and charge state of the residue can significantly influence the force and current signal during its permeation through the nanopore. In particular, due to the electro-osmotic flow effect, the blockade current for the double-protonated histidine is slightly smaller than that for single-protonated histidine, which makes it possible for discrimination of different protonation states of amino acids. The results reported here present a novel protein sequencing scheme using graphene nanopores combined with nanomanipulation technology.
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Affiliation(s)
- Wei Si
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yin Zhang
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Yajing Kan
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yan Zhang
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Jingjie Sha
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yunfei Chen
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
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9
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Nicolaï A, Barrios Pérez MD, Delarue P, Meunier V, Drndić M, Senet P. Molecular Dynamics Investigation of Polylysine Peptide Translocation through MoS2 Nanopores. J Phys Chem B 2019; 123:2342-2353. [DOI: 10.1021/acs.jpcb.8b10634] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Adrien Nicolaï
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
| | - Maria Daniela Barrios Pérez
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
| | - Patrice Delarue
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
| | - Vincent Meunier
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Patrick Senet
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
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10
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Shekar S, Chien CC, Hartel A, Ong P, Clarke OB, Marks A, Drndic M, Shepard KL. Wavelet Denoising of High-Bandwidth Nanopore and Ion-Channel Signals. NANO LETTERS 2019; 19:1090-1097. [PMID: 30601669 PMCID: PMC6904930 DOI: 10.1021/acs.nanolett.8b04388] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recent work has pushed the noise-limited bandwidths of solid-state nanopore conductance recordings to more than 5 MHz and of ion channel conductance recordings to more than 500 kHz through the use of integrated complementary metal-oxide-semiconductor (CMOS) integrated circuits. Despite the spectral spread of the pulse-like signals that characterize these recordings when a sinusoidal basis is employed, Bessel filters are commonly used to denoise these signals to acceptable signal-to-noise ratios (SNRs) at the cost of losing many of the faster temporal features. Here, we report improvements to the SNR that can be achieved using wavelet denoising instead of Bessel filtering. When combined with state-of-the-art high-bandwidth CMOS recording instrumentation, we can reduce baseline noise levels by over a factor of 4 compared to a 2.5 MHz Bessel filter while retaining transient properties in the signal comparable to this filter bandwidth. Similarly, for ion-channel recordings, we achieve a temporal response better than a 100 kHz Bessel filter with a noise level comparable to that achievable with a 25 kHz Bessel filter. Improvements in SNR can be used to achieve robust statistical analyses of these recordings, which may provide important insights into nanopore translocation dynamics and mechanisms of ion-channel function.
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Affiliation(s)
| | - Chen-Chi Chien
- Department of Physics and Astronomy , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | | | | | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics , Columbia University , New York , New York 10032 , United States
| | - Andrew Marks
- Department of Physiology and Cellular Biophysics , Columbia University , New York , New York 10032 , United States
| | - Marija Drndic
- Department of Physics and Astronomy , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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11
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Yu JS, Hong SC, Wu S, Kim HM, Lee C, Lee JS, Lee JE, Kim KB. Differentiation of selectively labeled peptides using solid-state nanopores. NANOSCALE 2019; 11:2510-2520. [PMID: 30672547 DOI: 10.1039/c8nr09315f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Determination of the amino acid sequence of a protein is critical for understanding various biological processes. Mass spectrometry has mainly been used for protein identification; however, there are limitations to its sensitivity when detecting low abundance proteins. In this study, we attempted to distinguish between three similar peptide sequences (∼40 amino acids, ∼5 kDa) that differed only by the location or number of cysteine residues with solid-state nanopores. The cysteine residues are located at one end, one at the center, and at both ends for each of the three peptides. We found that differentiation of the three types of peptides by nanopore signals was difficult. However, when the cysteine residue was labeled with a negatively charged molecule, Flamma® 496, the labeled peptides showed distinct signals for each peptide. Comparing the relative current blockades of labeled peptides with applied voltages, we found that the label was able to change peptide conformations and the resulting ionic current signals from the three labeled peptides were distinguished based on the relative current blockade, full width at half-maximum of the current blockade distribution, and single-molecule level peak shape analysis. Our results suggest that solid-state nanopores combined with a targeted labeling strategy could be used to obtain characteristic peptide signatures that could ultimately be used for protein identification.
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Affiliation(s)
- Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
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12
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Varongchayakul N, Song J, Meller A, Grinstaff MW. Single-molecule protein sensing in a nanopore: a tutorial. Chem Soc Rev 2018; 47:8512-8524. [PMID: 30328860 DOI: 10.1039/c8cs00106e] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Proteins are the structural elements and machinery of cells responsible for a functioning biological architecture and homeostasis. Advances in nanotechnology are catalyzing key breakthroughs in many areas, including the analysis and study of proteins at the single-molecule level. Nanopore sensing is at the forefront of this revolution. This tutorial review provides readers a guidebook and reference for detecting and characterizing proteins at the single-molecule level using nanopores. Specifically, the review describes the key materials, nanoscale features, and design requirements of nanopores. It also discusses general design requirements as well as details on the analysis of protein translocation. Finally, the article provides the background necessary to understand current research trends and to encourage the identification of new biomedical applications for protein sensing using nanopores.
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13
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Robertson JWF, Reiner JE. The Utility of Nanopore Technology for Protein and Peptide Sensing. Proteomics 2018; 18:e1800026. [PMID: 29952121 PMCID: PMC10935609 DOI: 10.1002/pmic.201800026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/13/2018] [Indexed: 04/29/2024]
Abstract
Resistive pulse nanopore sensing enables label-free single-molecule analysis of a wide range of analytes. An increasing number of studies have demonstrated the feasibility and usefulness of nanopore sensing for protein and peptide characterization. Nanopores offer the potential to study a variety of protein-related phenomena that includes unfolding kinetics, differences in unfolding pathways, protein structure stability, and free-energy profiles of DNA-protein and RNA-protein binding. In addition to providing a tool for fundamental protein characterization, nanopores have also been used as highly selective protein detectors in various solution mixtures and conditions. This review highlights these and other developments in the area of nanopore-based protein and peptide detection.
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Affiliation(s)
- Joseph W F Robertson
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA, 23284, USA
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14
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Luan B, Zhou R. Single-File Protein Translocations through Graphene-MoS 2 Heterostructure Nanopores. J Phys Chem Lett 2018; 9:3409-3415. [PMID: 29870254 DOI: 10.1021/acs.jpclett.8b01340] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Successfully threading unfolded protein molecules through nanopores whose sizes are comparable to that of an amino acid is a prerequisite for the nanopore-based protein sequencing method that promises to be high-throughput and low-cost. While the electric driving method can be effective for a homogeneously charged DNA molecule, it fails to drive an unfolded protein through a nanopore because the net charge of a protein fragment inside of the pore (where the electric field exists) can be positive, negative, or neutral. Here we propose and demonstrate by molecular dynamics simulations protein transport through a nanopore in a quasi-two-dimensional heterostructure stacked together by graphene and molybdenum disulfide (MoS2) nanosheets. Thanks to different van der Waals interactions ( U) between a protein molecule and different 2D surfaces, it is energetically favorable for protein to progressively move from the MoS2 surface to the graphene surface (more negative U) through a nanopore in the heterostructure.
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Affiliation(s)
- Binquan Luan
- Computational Biological Center, IBM Thomas J. Watson Research , Yorktown Heights , New York 10598 , United States
| | - Ruhong Zhou
- Computational Biological Center, IBM Thomas J. Watson Research , Yorktown Heights , New York 10598 , United States
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15
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Hu R, Rodrigues JV, Pradeep Waduge J, Yamazaki H, Cressiot B, Chishti Y, Makowski L, Yu D, Shakhnovich E, Zhao Q, Wanunu M. Differential Enzyme Flexibility Probed Using Solid-State Nanopores. ACS NANO 2018; 12:4494-4502. [PMID: 29630824 PMCID: PMC9016714 DOI: 10.1021/acsnano.8b00734] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enzymes and motor proteins are dynamic macromolecules that coexist in a number of conformations of similar energies. Protein function is usually accompanied by a change in structure and flexibility, often induced upon binding to ligands. However, while measuring protein flexibility changes between active and resting states is of therapeutic significance, it remains a challenge. Recently, our group has demonstrated that breadth of signal amplitudes in measured electrical signatures as an ensemble of individual protein molecules is driven through solid-state nanopores and correlates with protein conformational dynamics. Here, we extend our study to resolve subtle flexibility variation in dihydrofolate reductase mutants from unlabeled single molecules in solution. We first demonstrate using a canonical protein system, adenylate kinase, that both size and flexibility changes can be observed upon binding to a substrate that locks the protein in a closed conformation. Next, we investigate the influence of voltage bias and pore geometry on the measured electrical pulse statistics during protein transport. Finally, using the optimal experimental conditions, we systematically study a series of wild-type and mutant dihydrofolate reductase proteins, finding a good correlation between nanopore-measured protein conformational dynamics and equilibrium bulk fluorescence probe measurements. Our results unequivocally demonstrate that nanopore-based measurements reliably probe conformational diversity in native protein ensembles.
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Affiliation(s)
- Rui Hu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
| | - João V. Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - J Pradeep Waduge
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Hirohito Yamazaki
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Yasmin Chishti
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Dapeng Yu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
- Corresponding Authors:.,
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Corresponding Authors:.,
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16
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Varongchayakul N, Huttner D, Grinstaff MW, Meller A. Sensing Native Protein Solution Structures Using a Solid-state Nanopore: Unraveling the States of VEGF. Sci Rep 2018; 8:1017. [PMID: 29343861 PMCID: PMC5772516 DOI: 10.1038/s41598-018-19332-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/27/2017] [Indexed: 01/01/2023] Open
Abstract
Monitoring individual proteins in solution while simultaneously obtaining tertiary and quaternary structural information is challenging. In this study, translocation of the vascular endothelial growth factor (VEGF) protein through a solid-state nanopore (ssNP) produces distinct ion-current blockade amplitude levels and durations likely corresponding to monomer, dimer, and higher oligomeric states. Upon changing from a non-reducing to a reducing condition, ion-current blockage events from the monomeric state dominate, consistent with the expected reduction of the two inter-chain VEGF disulfide bonds. Cleavage by plasmin and application of either a positive or a negative NP bias results in nanopore signals corresponding either to the VEGF receptor recognition domain or to the heparin binding domain, accordingly. Interestingly, multi-level analysis of VEGF events reveals how individual domains affect their translocation pattern. Our study shows that careful characterization of ssNP results elucidates real-time structural information about the protein, thereby complementing classical techniques for structural analysis of proteins in solution with the added advantage of quantitative single-molecule resolution of native proteins.
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Affiliation(s)
- Nitinun Varongchayakul
- Departments of Biomedical Engineering, Boston University, Boston, 02215, Massachusetts, USA
| | - Diana Huttner
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Mark W Grinstaff
- Departments of Biomedical Engineering, Boston University, Boston, 02215, Massachusetts, USA. .,Department of Chemistry, Boston University, Boston, 02215, Massachusetts, USA. .,School of Medicine, Boston University, Boston, 02215, Massachusetts, USA.
| | - Amit Meller
- Departments of Biomedical Engineering, Boston University, Boston, 02215, Massachusetts, USA. .,Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel.
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17
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Tadaki D, Yamaura D, Araki S, Yoshida M, Arata K, Ohori T, Ishibashi KI, Kato M, Ma T, Miyata R, Tozawa Y, Yamamoto H, Niwano M, Hirano-Iwata A. Mechanically stable solvent-free lipid bilayers in nano- and micro-tapered apertures for reconstitution of cell-free synthesized hERG channels. Sci Rep 2017; 7:17736. [PMID: 29255199 PMCID: PMC5735097 DOI: 10.1038/s41598-017-17905-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/01/2017] [Indexed: 01/08/2023] Open
Abstract
The self-assembled bilayer lipid membrane (BLM) is the basic component of the cell membrane. The reconstitution of ion channel proteins in artificially formed BLMs represents a well-defined system for the functional analysis of ion channels and screening the effects of drugs that act on them. However, because BLMs are unstable, this limits the experimental throughput of BLM reconstitution systems. Here we report on the formation of mechanically stable solvent-free BLMs in microfabricated apertures with defined nano- and micro-tapered edge structures. The role of such nano- and micro-tapered structures on the stability of the BLMs was also investigated. Finally, this BLM system was combined with a cell-free synthesized human ether-a-go-go-related gene channel, a cardiac potassium channel whose relation to arrhythmic side effects following drug treatment is well recognized. Such stable BLMs as these, when combined with a cell-free system, represent a potential platform for screening the effects of drugs that act on various ion-channel genotypes.
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Affiliation(s)
- Daisuke Tadaki
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Daichi Yamaura
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Shun Araki
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Miyu Yoshida
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Kohei Arata
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Takeshi Ohori
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Ken-Ichi Ishibashi
- Hang-Ichi Corporation, 1-7-315 Honcho, Naka-ku, Yokohama, Kanagawa, 231-0005, Japan
| | - Miki Kato
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Teng Ma
- Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Ryusuke Miyata
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Yuzuru Tozawa
- Department of Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Hideaki Yamamoto
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Michio Niwano
- Kansei Fukushi Research Institute, Tohoku Fukushi University, 6-149-1 Kunimi-ga-oka, Aoba-ku, Sendai, Miyagi, 989-3201, Japan
| | - Ayumi Hirano-Iwata
- Laboratory for Nanoelectronics and Spintronics, Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan. .,Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.
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18
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Feliciano GT, Sanz-Navarro C, Coutinho-Neto MD, Ordejón P, Scheicher RH, Rocha AR. Addressing the Environment Electrostatic Effect on Ballistic Electron Transport in Large Systems: A QM/MM-NEGF Approach. J Phys Chem B 2017; 122:485-492. [DOI: 10.1021/acs.jpcb.7b03475] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gustavo T. Feliciano
- Instituto
de Química, Departamento de Fisico-Química, Universidade Estadual Paulista (UNESP), 14800-060, Araraquara, SP, Brazil
| | - Carlos Sanz-Navarro
- Catalan Institute
of Nanoscience and Nanotechnology (ICN2), CSIC, and The Barcelona
Institute of Science and Technology, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | | | - Pablo Ordejón
- Catalan Institute
of Nanoscience and Nanotechnology (ICN2), CSIC, and The Barcelona
Institute of Science and Technology, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Ralph H. Scheicher
- Division
of Materials Theory, Department of Physics and Astronomy, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Alexandre Reily Rocha
- Instituto
de Fı́sica Teorica, Universidade Estadual Paulista (UNESP), 01140-070, São Paulo, SP, Brazil
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19
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Waduge P, Hu R, Bandarkar P, Yamazaki H, Cressiot B, Zhao Q, Whitford PC, Wanunu M. Nanopore-Based Measurements of Protein Size, Fluctuations, and Conformational Changes. ACS NANO 2017; 11:5706-5716. [PMID: 28471644 DOI: 10.1021/acsnano.7b01212] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Proteins are structurally dynamic macromolecules, and it is challenging to quantify the conformational properties of their native state in solution. Nanopores can be efficient tools to study proteins in a solution environment. In this method, an electric field induces electrophoretic and/or electro-osmotic transport of protein molecules through a nanopore slightly larger than the protein molecule. High-bandwidth ion current measurement is used to detect the transit of each protein molecule. First, our measurements reveal a correlation between the mean current blockade amplitude and the radius of gyration for each protein. Next, we find a correlation between the shape of the current signal amplitude distributions and the protein fluctuation as obtained from molecular dynamics simulations. Further, the magnitude of the structural fluctuations, as probed by experiments and simulations, correlates with the ratio of α-helix to β-sheet content. We highlight the resolution of our measurements by resolving two states of calmodulin, a canonical protein that undergoes a conformational change in response to calcium binding.
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Affiliation(s)
| | - Rui Hu
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University , Beijing 100871, People's Republic of China
| | | | - Hirohito Yamazaki
- Graduate School of Science and Technology, Keio University , 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | | | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University , Beijing 100871, People's Republic of China
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20
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Lin X, Ivanov AP, Edel JB. Selective single molecule nanopore sensing of proteins using DNA aptamer-functionalised gold nanoparticles. Chem Sci 2017; 8:3905-3912. [PMID: 28626560 PMCID: PMC5465561 DOI: 10.1039/c7sc00415j] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/14/2017] [Indexed: 01/26/2023] Open
Abstract
Single molecule detection methods, such as nanopore sensors have found increasing importance in applications ranging from gaining a better understanding of biophysical processes to technology driven solutions such as DNA sequencing. However, challenges remain especially in relation to improving selectivity to probe specific targets or to alternatively enable detection of smaller molecules such as small-sized proteins with a sufficiently high signal-to-noise ratio. In this article, we propose a solution to these technological challenges by using DNA aptamer-modified gold nanoparticles (AuNPs) that act as a molecular carrier through the nanopore sensor. We show that this approach offers numerous advantages including: high levels of selectivity, efficient capture from a complex mixture, enhanced signal, minimized analyte-sensor surface interactions, and finally can be used to enhance the event detection rate. This is demonstrated by incorporating a lysozyme binding aptamer to a 5 nm AuNP carrier to selectively probe lysozyme within a cocktail of proteins. We show that nanopores can reveal sub-complex molecular information, by discriminating the AuNP from the protein analyte, indicating the potential use of this technology for single molecule analysis of different molecular analytes specifically bound to AuNP.
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Affiliation(s)
- Xiaoyan Lin
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
| | - Aleksandar P Ivanov
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
| | - Joshua B Edel
- Department of Chemistry , Imperial College London , South Kensington , London SW7 2AZ , UK . ;
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21
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Ji Z, Wang S, Zhao Z, Zhou Z, Haque F, Guo P. Fingerprinting of Peptides with a Large Channel of Bacteriophage Phi29 DNA Packaging Motor. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:4572-8. [PMID: 27435806 PMCID: PMC5166430 DOI: 10.1002/smll.201601157] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/16/2016] [Indexed: 05/27/2023]
Abstract
Nanopore technology has become a highly sensitive and powerful tool for single molecule sensing of chemicals and biopolymers. Protein pores have the advantages of size amenability, channel homogeneity, and fabrication reproducibility. But most well-studied protein pores for sensing are too small for passage of peptide analytes that are typically a few nanometers in dimension. The funnel-shaped channel of bacteriophage phi29 DNA packaging motor has previously been inserted into a lipid membrane to serve as a larger pore with a narrowest N-terminal constriction of 3.6 nm and a wider C-terminal end of 6 nm. Here, the utility of phi29 motor channel for fingerprinting of various peptides using single molecule electrophysiological assays is reported. The translocation of peptides is proved unequivocally by single molecule fluorescence imaging. Current blockage percentage and distinctive current signatures are used to distinguish peptides with high confidence. Each peptide generated one or two distinct current blockage peaks, serving as typical fingerprint for each peptide. The oligomeric states of peptides can also be studied in real time at single molecule level. The results demonstrate the potential for further development of phi29 motor channel for detection of disease-associated peptide biomarkers.
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22
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Fahie MA, Yang B, Pham B, Chen M. Tuning the selectivity and sensitivity of an OmpG nanopore sensor by adjusting ligand tether length. ACS Sens 2016; 1:614-622. [PMID: 27500277 DOI: 10.1021/acssensors.6b00014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We have previously shown that a biotin ligand tethered to the rim of an OmpG nanopore can be used to detect biotin-binding proteins. Here, we investigate the effect of the length of the polyethylene glycol tether on the nanopore's sensitivity and selectivity. When the tether length was increased from 2 to 45 ethylene repeats, sensitivity decreased substantially for a neutral protein streptavidin and slightly for a positively charged protein (avidin). In addition, we found that two distinct avidin binding conformations were possible when using a long tether. These conformations were sensitive to the salt concentration and applied voltage. Finally, a longer tether resulted in reduced sensitivity due to slower association for a monoclonal anti-biotin antibody. Our results highlight the importance of electrostatic, electroosmotic and electrophoretic forces on nanopore binding kinetics and sensor readout.
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Affiliation(s)
- Monifa A. Fahie
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Bib Yang
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Bach Pham
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Min Chen
- Molecular and Cellular Biology Program and ‡Department of
Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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23
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Kwak DK, Chae H, Lee MK, Ha JH, Goyal G, Kim MJ, Kim KB, Chi SW. Probing the Small-Molecule Inhibition of an Anticancer Therapeutic Protein-Protein Interaction Using a Solid-State Nanopore. Angew Chem Int Ed Engl 2016; 55:5713-7. [DOI: 10.1002/anie.201511601] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/25/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Dong-Kyu Kwak
- Structural Biology & Nanopore Research Laboratory; Disease Target Structure Research Center; KRIBB; 125 Gwahak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
- Department of Bio-Analytical Sciences; Korea University of Science and Technology; 217 Gajeong-ro, Yuseong-gu Daejeon 34113 Republic of Korea
| | - Hongsik Chae
- Department of Materials Science and Engineering; Seoul National University; 599 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Mi-Kyung Lee
- Structural Biology & Nanopore Research Laboratory; Disease Target Structure Research Center; KRIBB; 125 Gwahak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Ji-Hyang Ha
- Structural Biology & Nanopore Research Laboratory; Disease Target Structure Research Center; KRIBB; 125 Gwahak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Gaurav Goyal
- School of Biomedical Engineering; Science and Health Systems Drexel University; 3701 Market Street Philadelphia PA 19104 USA
| | - Min Jun Kim
- School of Biomedical Engineering; Science and Health Systems Drexel University; 3701 Market Street Philadelphia PA 19104 USA
- Department of Mechanical Engineering and Mechanics; Drexel University; 3701 Market Street Philadelphia PA 19104 USA
| | - Ki-Bum Kim
- Department of Materials Science and Engineering; Seoul National University; 599 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Seung-Wook Chi
- Structural Biology & Nanopore Research Laboratory; Disease Target Structure Research Center; KRIBB; 125 Gwahak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
- Department of Bio-Analytical Sciences; Korea University of Science and Technology; 217 Gajeong-ro, Yuseong-gu Daejeon 34113 Republic of Korea
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24
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Kwak DK, Chae H, Lee MK, Ha JH, Goyal G, Kim MJ, Kim KB, Chi SW. Probing the Small-Molecule Inhibition of an Anticancer Therapeutic Protein-Protein Interaction Using a Solid-State Nanopore. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dong-Kyu Kwak
- Structural Biology & Nanopore Research Laboratory; Disease Target Structure Research Center; KRIBB; 125 Gwahak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
- Department of Bio-Analytical Sciences; Korea University of Science and Technology; 217 Gajeong-ro, Yuseong-gu Daejeon 34113 Republic of Korea
| | - Hongsik Chae
- Department of Materials Science and Engineering; Seoul National University; 599 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Mi-Kyung Lee
- Structural Biology & Nanopore Research Laboratory; Disease Target Structure Research Center; KRIBB; 125 Gwahak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Ji-Hyang Ha
- Structural Biology & Nanopore Research Laboratory; Disease Target Structure Research Center; KRIBB; 125 Gwahak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Gaurav Goyal
- School of Biomedical Engineering; Science and Health Systems Drexel University; 3701 Market Street Philadelphia PA 19104 USA
| | - Min Jun Kim
- School of Biomedical Engineering; Science and Health Systems Drexel University; 3701 Market Street Philadelphia PA 19104 USA
- Department of Mechanical Engineering and Mechanics; Drexel University; 3701 Market Street Philadelphia PA 19104 USA
| | - Ki-Bum Kim
- Department of Materials Science and Engineering; Seoul National University; 599 Gwanak-ro, Gwanak-gu Seoul 08826 Republic of Korea
| | - Seung-Wook Chi
- Structural Biology & Nanopore Research Laboratory; Disease Target Structure Research Center; KRIBB; 125 Gwahak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
- Department of Bio-Analytical Sciences; Korea University of Science and Technology; 217 Gajeong-ro, Yuseong-gu Daejeon 34113 Republic of Korea
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25
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Zahid OK, Hall AR. Helium Ion Microscope Fabrication of Solid-State Nanopore Devices for Biomolecule Analysis. HELIUM ION MICROSCOPY 2016. [DOI: 10.1007/978-3-319-41990-9_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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26
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Balan A, Chien CC, Engelke R, Drndić M. Suspended Solid-state Membranes on Glass Chips with Sub 1-pF Capacitance for Biomolecule Sensing Applications. Sci Rep 2015; 5:17775. [PMID: 26644307 PMCID: PMC4672352 DOI: 10.1038/srep17775] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/04/2015] [Indexed: 02/04/2023] Open
Abstract
Solid-state membranes are finding use in many applications in nanoelectronics and nanomedicine, from single molecule sensors to water filtration, and yet many of their electronics applications are limited by the relatively high current noise and low bandwidth stemming from the relatively high capacitance (>10 pF) of the membrane chips. To address this problem, we devised an integrated fabrication process to grow and define circular silicon nitride membranes on glass chips that successfully lower the chip capacitance to below 1 pF. We use these devices to demonstrate low-noise, high-bandwidth DNA translocation measurements. We also make use of this versatile, low-capacitance platform to suspend other thin, two-dimensional membrane such as graphene.
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Affiliation(s)
- Adrian Balan
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Chen-Chi Chien
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Rebecca Engelke
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
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27
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Kasianowicz JJ, Balijepalli AK, Ettedgui J, Forstater JH, Wang H, Zhang H, Robertson JWF. Analytical applications for pore-forming proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:593-606. [PMID: 26431785 DOI: 10.1016/j.bbamem.2015.09.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/28/2015] [Accepted: 09/25/2015] [Indexed: 01/13/2023]
Abstract
Proteinaceous nanometer-scale pores are ubiquitous in biology. The canonical ionic channels (e.g., those that transport Na(+), K(+), Ca(2+), and Cl(-) across cell membranes) play key roles in many cellular processes, including nerve and muscle activity. Another class of channels includes bacterial pore-forming toxins, which disrupt cell function, and can lead to cell death. We describe here the recent development of these toxins for a wide range of biological sensing applications. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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Affiliation(s)
- John J Kasianowicz
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States.
| | | | - Jessica Ettedgui
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Jacob H Forstater
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Haiyan Wang
- NIST, Physical Measurement Laboratory, Gaithersburg, MD 20899, United States
| | - Huisheng Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Dept. of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
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