1
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Penkov B, Niedzwiecki D, Lari N, Drndić M, Shepard K. Time-domain event detection using single-instruction, multiple-thread gpGPU architectures in single-molecule biophysical data. COMPUTER PHYSICS COMMUNICATIONS 2024; 300:109191. [PMID: 38737416 PMCID: PMC11086699 DOI: 10.1016/j.cpc.2024.109191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Discrete amplitude levels in ordered, time-domain data often represent different underlying latent states of the system that is being interrogated. Analysis and feature extraction from these data sets generally require considering the order of each individual point; this approach cannot take advantage of contemporary general-purpose graphics processing units (gpGPU) and single-instruction multiple-data (SIMD) instruction set architectures. Two sources of such data from single-molecule biological measurements are nanopores and single-molecule field effect transistor (smFET) nanotube devices; both generate streams of time-ordered current or voltage data, typically sampled near 1 MS/s, with run times of minutes, yielding terabyte-scale datasets. Here, we present three gpGPU-based algorithms to overcome limitations associated with serial event detection in time series data, resulting in a 250× improvement in the rate with which we can detect salient features in nanopore and smFET datasets. The code is freely available.
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Affiliation(s)
- Boyan Penkov
- Department of Electrical Engineering, Columbia University, New York, NY, 10027
| | - David Niedzwiecki
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Nicolae Lari
- Department of Electrical Engineering, Columbia University, New York, NY, 10027
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Kenneth Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, 10027
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2
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Zhang LL, Zhong CB, Huang TJ, Zhang LM, Yan F, Ying YL. High-throughput single biomarker identification using droplet nanopore. Chem Sci 2024; 15:8355-8362. [PMID: 38846401 PMCID: PMC11151865 DOI: 10.1039/d3sc06795e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/28/2024] [Indexed: 06/09/2024] Open
Abstract
Biomarkers are present in various metabolism processes, demanding precise and meticulous analysis at the single-molecule level for accurate clinical diagnosis. Given the need for high sensitivity, biological nanopore have been applied for single biomarker sensing. However, the detection of low-volume biomarkers poses challenges due to their low concentrations in dilute buffer solutions, as well as difficulty in parallel detection. Here, a droplet nanopore technique is developed for low-volume and high-throughput single biomarker detection at the sub-microliter scale, which shows a 2000-fold volume reduction compared to conventional setups. To prove the concept, this nanopore sensing platform not only enables multichannel recording but also significantly lowers the detection limit for various types of biomarkers such as angiotensin II, to 42 pg. This advancement enables direct biomarker detection at the picogram level. Such a leap forward in detection capability positions this nanopore sensing platform as a promising candidate for point-of-care testing of biomarker at single-molecule level, while substantially minimizing the need for sample dilution.
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Affiliation(s)
- Lin-Lin Zhang
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Cheng-Bing Zhong
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Ting-Jing Huang
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Li-Min Zhang
- School of Electronic Science and Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Feng Yan
- School of Electronic Science and Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Yi-Lun Ying
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210023 P. R. China
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3
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Li X, Fu YH, Wei N, Yu RJ, Bhatti H, Zhang L, Yan F, Xia F, Ewing AG, Long YT, Ying YL. Emerging Data Processing Methods for Single-Entity Electrochemistry. Angew Chem Int Ed Engl 2024; 63:e202316551. [PMID: 38411372 DOI: 10.1002/anie.202316551] [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: 11/01/2023] [Revised: 02/12/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Single-entity electrochemistry is a powerful tool that enables the study of electrochemical processes at interfaces and provides insights into the intrinsic chemical and structural heterogeneities of individual entities. Signal processing is a critical aspect of single-entity electrochemical measurements and can be used for data recognition, classification, and interpretation. In this review, we summarize the recent five-year advances in signal processing techniques for single-entity electrochemistry and highlight their importance in obtaining high-quality data and extracting effective features from electrochemical signals, which are generally applicable in single-entity electrochemistry. Moreover, we shed light on electrochemical noise analysis to obtain single-molecule frequency fingerprint spectra that can provide rich information about the ion networks at the interface. By incorporating advanced data analysis tools and artificial intelligence algorithms, single-entity electrochemical measurements would revolutionize the field of single-entity analysis, leading to new fundamental discoveries.
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Affiliation(s)
- Xinyi Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ying-Huan Fu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Nannan Wei
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Ru-Jia Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, P. R. China
| | - Huma Bhatti
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Limin Zhang
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Feng Yan
- School of Electronic Science and Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, 430034, Wuhan, P. R. China
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41296, Gothenburg, Sweden
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, 210023, Nanjing, P. R. China
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4
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Jiang J, Li MY, Wu XY, Ying YL, Han HX, Long YT. Protein nanopore reveals the renin-angiotensin system crosstalk with single-amino-acid resolution. Nat Chem 2023; 15:578-586. [PMID: 36805037 DOI: 10.1038/s41557-023-01139-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 01/13/2023] [Indexed: 02/22/2023]
Abstract
The discovery of crosstalk effects on the renin-angiotensin system (RAS) is limited by the lack of approaches to quantitatively monitor, in real time, multiple components with subtle differences and short half-lives. Here we report a nanopore framework to quantitatively determine the effect of the hidden crosstalk between angiotensin-converting enzyme (ACE) and angiotensin-converting enzyme 2 (ACE2) on RAS. By developing an engineered aerolysin nanopore capable of single-amino-acid resolution, we show that the ACE can be selectively inhibited by ACE2 to prevent cleavage of angiotensin I, even when the concentration of ACE is more than 30-fold higher than that of ACE2. We also show that the activity of ACE2 for cleaving angiotensin peptides is clearly suppressed by the spike protein of SARS-CoV-2. This leads to the relaxation of ACE and the increased probability of accumulation of the principal effector angiotensin II. The spike protein of the SARS-CoV-2 Delta variant is demonstrated to have a much greater impact on the crosstalk than the wild type.
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Affiliation(s)
- Jie Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Xue-Yuan Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Huan-Xing Han
- Department of Pharmacy, Shanghai Changzheng Hospital, Shanghai, China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
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5
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Foster JC, Pham B, Pham R, Kim M, Moore MD, Chen M. An Engineered OmpG Nanopore with Displayed Peptide Motifs for Single-Molecule Multiplex Protein Detection. Angew Chem Int Ed Engl 2023; 62:e202214566. [PMID: 36457283 PMCID: PMC9898208 DOI: 10.1002/anie.202214566] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022]
Abstract
Molecular detection via nanopore, achieved by monitoring changes in ionic current arising from analyte interaction with the sensor pore, is a promising technology for multiplex sensing development. Outer Membrane Protein G (OmpG), a monomeric porin possessing seven functionalizable loops, has been reported as an effective sensing platform for selective protein detection. Using flow cytometry to screen unfavorable constructs, we identified two OmpG nanopores with unique peptide motifs displayed in either loop 3 or 6, which also exhibited distinct analyte signals in single-channel current recordings. We exploited these motif-displaying loops concurrently to facilitate single-molecule multiplex protein detection in a mixture. We additionally report a strategy to increase sensor sensitivity via avidity motif display. These sensing schemes may be expanded to more sophisticated designs utilizing additional loops to increase multiplicity and sensitivity.
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Affiliation(s)
- Joshua C Foster
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Bach Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Current address: Department of Chemistry, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Ryan Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Minji Kim
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Matthew D Moore
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Min Chen
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
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6
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Wang Y, Yuan J, Deng H, Zhang Z, Ma QDY, Wu L, Weng L. Procedural Data Processing for Single-Molecule Identification by Nanopore Sensors. BIOSENSORS 2022; 12:1152. [PMID: 36551119 PMCID: PMC9775113 DOI: 10.3390/bios12121152] [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: 10/26/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Nanopores are promising single-molecule sensing devices that have been successfully used for DNA sequencing, protein identification, as well as virus/particles detection. It is important to understand and characterize the current pulses collected by nanopore sensors, which imply the associated information of the analytes, including the size, structure, and surface charge. Therefore, a signal processing program, based on the MATLAB platform, was designed to characterize the ionic current signals of nanopore measurements. In a movable data window, the selected current segment was analyzed by the adaptive thresholds and corrected by multi-functions to reduce the noise obstruction of pulse signals. Accordingly, a set of single molecular events was identified, and the abundant information of current signals with the dwell time, amplitude, and current pulse area was exported for quantitative analysis. The program contributes to the efficient and fast processing of nanopore signals with a high signal-to-noise ratio, which promotes the development of the nanopore sensing devices in various fields of diagnosis systems and precision medicine.
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Affiliation(s)
- Yupeng Wang
- School of Materials Science & Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Jianxuan Yuan
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Haofeng Deng
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Ziang Zhang
- School of Materials Science & Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Qianli D. Y. Ma
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Lingzhi Wu
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Lixing Weng
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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7
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Dematties D, Wen C, Zhang SL. A Generalized Transformer-Based Pulse Detection Algorithm. ACS Sens 2022; 7:2710-2720. [PMID: 36039873 PMCID: PMC9513795 DOI: 10.1021/acssensors.2c01218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Pulse-like signals are ubiquitous in the field of single molecule analysis, e.g., electrical or optical pulses caused by analyte translocations in nanopores. The primary challenge in processing pulse-like signals is to capture the pulses in noisy backgrounds, but current methods are subjectively based on a user-defined threshold for pulse recognition. Here, we propose a generalized machine-learning based method, named pulse detection transformer (PETR), for pulse detection. PETR determines the start and end time points of individual pulses, thereby singling out pulse segments in a time-sequential trace. It is objective without needing to specify any threshold. It provides a generalized interface for downstream algorithms for specific application scenarios. PETR is validated using both simulated and experimental nanopore translocation data. It returns a competitive performance in detecting pulses through assessing them with several standard metrics. Finally, the generalization nature of the PETR output is demonstrated using two representative algorithms for feature extraction.
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Affiliation(s)
- Dario Dematties
- Northwestern
Argonne Institute of Science and Engineering, Northwestern University, 2205 Tech Drive Suite 1-160, Evanston, 60208 Illinois, United States,Mathematics
and Computer Science Division, Argonne National
Laboratory, 9700 S. Cass
Avenue, Lemont, 60439 Illinois, United States
| | - Chenyu Wen
- NanoDynamicsLab,
Laboratory of Biophysics, Wageningen University, Stippeneng 4, Wageningen 6708 WE, The
Netherlands,Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Shi-Li Zhang
- Department
of Electrical Engineering, Uppsala University, Lägerhyddsvägen 1,
752 37, SE-751 03 Uppsala, Sweden,
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8
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Lucas FLR, Willems K, Tadema MJ, Tych KM, Maglia G, Wloka C. Unbiased Data Analysis for the Parameterization of Fast Translocation Events through Nanopores. ACS OMEGA 2022; 7:26040-26046. [PMID: 35936408 PMCID: PMC9352258 DOI: 10.1021/acsomega.2c00871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single-molecule nanopore electrophysiology is an emerging technique for the detection of analytes in aqueous solutions with high sensitivity. These detectors have proven applicable for the enzyme-assisted sequencing of oligonucleotides. There has recently been an increased interest in the use of nanopores for the fingerprinting of peptides and proteins, referred to as single-molecule nanopore spectrometry. However, the analysis of the resulting electrophysiology traces remains complicated due to the fast unassisted translocation of such analytes, usually in the order of micro- to milliseconds, and the small ion current signal produced (in the picoampere range). Here, we present the application of a generalized normal distribution function (gNDF) for the characterization of short-lived ion current signals (blockades). We show that the gNDF can be used to determine if the observed blockades have adequate time to reach their maximum current plateau while also providing a description of each blockade based on the open pore current (I O), the difference caused by the pore blockade (ΔI B), the position in time (μ), the standard deviation (σ), and a shape parameter (β), leaving only the noise component. In addition, this method allows the estimation of an ideal range of low-pass filter frequencies that contains maximum information with minimal noise. In summary, we show a parameter-free and generalized method for the analysis of short-lived ion current blockades, which facilitates single-molecule nanopore spectrometry with minimal user bias.
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Affiliation(s)
- Florian L. R. Lucas
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9712 CP Groningen, The Netherlands
- Lab
for Nanobiology, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | | | - Matthijs J. Tadema
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Katarzyna M. Tych
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Carsten Wloka
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9712 CP Groningen, The Netherlands
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9
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Tang W, Fried JP, Tilley RD, Gooding JJ. Understanding and modelling the magnitude of the change in current of nanopore sensors. Chem Soc Rev 2022; 51:5757-5776. [PMID: 35748606 DOI: 10.1039/d1cs00972a] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanopores are promising sensing devices that can be used for the detection of analytes at the single molecule level. It is of importance to understand and model the current response of a nanopore sensor for improving the sensitivity of the sensor, a better interpretation of the behaviours of different analytes in confined nanoscale spaces, and quantitative analysis of the properties of the targets. The current response of a nanopore sensor, usually called a resistive pulse, results from the change in nanopore resistance when an analyte translocates through the nanopore. This article reviews the theoretical models used for the calculation of the resistance of the nanopore, and the corresponding change in nanopore resistance due to a translocation event. Models focus on the resistance of the pore cavity region and the access region of the nanopore. The influence of the sizes, shapes and surface charges of the translocating species and the nanopore, as well as the trajectory that the analyte follows are also discussed. This review aims to give a general guidance to the audience for understanding the current response of a nanopore sensor and the application of this class of sensor to a broad range of species with the theoretical models.
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Affiliation(s)
- Wenxian Tang
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jasper P Fried
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Richard D Tilley
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.,Electron Microscope Unit, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia
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10
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Das N, Chakraborty B, RoyChaudhuri C. A review on nanopores based protein sensing in complex analyte. Talanta 2022; 243:123368. [DOI: 10.1016/j.talanta.2022.123368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/30/2022] [Accepted: 03/03/2022] [Indexed: 11/26/2022]
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11
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Zhang L, Burns N, Jordan M, Jayasinghe L, Guo P. Macromolecule sensing and tumor biomarker detection by harnessing terminal size and hydrophobicity of viral DNA packaging motor channels into membranes and flow cells. Biomater Sci 2021; 10:167-177. [PMID: 34812812 DOI: 10.1039/d1bm01264a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biological nanopores for single-pore sensing have the advantage of size homogeneity, structural reproducibility, and channel amenability. In order to translate this to clinical applications, the functional biological nanopore must be inserted into a stable system for high-throughput analysis. Here we report factors that control the rate of pore insertion into polymer membrane and analyte translocation through the channel of viral DNA packaging motors of Phi29, T3 and T7. The hydrophobicity of aminol or carboxyl terminals and their relation to the analyte translocation were investigated. It was found that both the size and the hydrophobicity of the pore terminus are critical factors for direct membrane insertion. An N-terminus or C-terminus hydrophobic mutation is crucial for governing insertion orientation and subsequent macromolecule translocation due to the one-way traffic property. The N- or C-modification led to two different modes of application. The C-terminal insertion permits translocation of analytes such as peptides to enter the channel through the N terminus, while N-terminus insertion prevents translocation but offers the measurement of gating as a sensing parameter, thus generating a tool for detection of markers. A urokinase-type Plasminogen Activator Receptor (uPAR) binding peptide was fused into the C-terminal of Phi29 nanopore to serve as a probe for uPAR protein detection. The uPAR has proven to be a predictive biomarker in several types of cancer, including breast cancer. With an N-terminal insertion, the binding of the uPAR antigen to individual peptide probe induced discretive steps of current reduction due to the induction of channel gating. The distinctive current signatures enabled us to distinguish uPAR positive and negative tumor cell lines. This finding provides a theoretical basis for a robust biological nanopore sensing system for high-throughput macromolecular sensing and tumor biomarker detection.
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Affiliation(s)
- Long Zhang
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
| | - Michael Jordan
- Oxford Nanopore Technologies Ltd, Gosling Building, Edmund Halley Road, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Lakmal Jayasinghe
- Oxford Nanopore Technologies Ltd, Gosling Building, Edmund Halley Road, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
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12
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Liu SC, Xie BK, Zhong CB, Wang J, Ying YL, Long YT. An advanced optical-electrochemical nanopore measurement system for single-molecule analysis. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:121301. [PMID: 34972456 DOI: 10.1063/5.0067185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
Nanopore measurement has advanced in single-molecule analysis by providing a transient time and confined space window that only allows one interested molecule to exist. By optimization and integration of the electrical and optical analysis strategies in this transient window, the acquisition of comprehensive information could be achieved to resolve the intrinsic properties and heterogeneity of a single molecule. In this work, we present a roadmap to build a unified optical and electrochemical synchronous measurement platform for the research of a single molecule. We design a low-cost ultralow-current amplifier with low noise and high-bandwidth to measure the ionic current events as a single molecule translocates through a nanopore and combine a multi-functional optical system to implement the acquisition of the fluorescence, scattering spectrum, and photocurrent intensity of single molecule events in a nanopore confined space. Our system is a unified and unique platform for the protein nanopore, the solid-state nanopore, and the glass capillary nanopore, which has advantages in the comprehensive research of nanopore single-molecule techniques.
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Affiliation(s)
- Shao-Chuang Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Bao-Kang Xie
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Cheng-Bing Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jia Wang
- 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
| | - 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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13
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Wen C, Dematties D, Zhang SL. A Guide to Signal Processing Algorithms for Nanopore Sensors. ACS Sens 2021; 6:3536-3555. [PMID: 34601866 PMCID: PMC8546757 DOI: 10.1021/acssensors.1c01618] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/20/2021] [Indexed: 12/19/2022]
Abstract
Nanopore technology holds great promise for a wide range of applications such as biomedical sensing, chemical detection, desalination, and energy conversion. For sensing performed in electrolytes in particular, abundant information about the translocating analytes is hidden in the fluctuating monitoring ionic current contributed from interactions between the analytes and the nanopore. Such ionic currents are inevitably affected by noise; hence, signal processing is an inseparable component of sensing in order to identify the hidden features in the signals and to analyze them. This Guide starts from untangling the signal processing flow and categorizing the various algorithms developed to extracting the useful information. By sorting the algorithms under Machine Learning (ML)-based versus non-ML-based, their underlying architectures and properties are systematically evaluated. For each category, the development tactics and features of the algorithms with implementation examples are discussed by referring to their common signal processing flow graphically summarized in a chart and by highlighting their key issues tabulated for clear comparison. How to get started with building up an ML-based algorithm is subsequently presented. The specific properties of the ML-based algorithms are then discussed in terms of learning strategy, performance evaluation, experimental repeatability and reliability, data preparation, and data utilization strategy. This Guide is concluded by outlining strategies and considerations for prospect algorithms.
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Affiliation(s)
- Chenyu Wen
- Division
of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Dario Dematties
- Instituto
de Ciencias Humanas, Sociales y Ambientales, CONICET Mendoza Technological Scientific Center, Mendoza M5500, Argentina
| | - Shi-Li Zhang
- Division
of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, SE-751 03 Uppsala, Sweden
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14
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Abstract
Nanopores are single-molecule sensors used in nucleic acid analysis, whereas their applicability towards full protein identification has yet to be demonstrated. Here, we show that an engineered Fragaceatoxin C nanopore is capable of identifying individual proteins by measuring peptide spectra that are produced from hydrolyzed proteins. Using model proteins, we show that the spectra resulting from nanopore experiments and mass spectrometry share similar profiles, hence allowing protein fingerprinting. The intensity of individual peaks provides information on the concentration of individual peptides, indicating that this approach is quantitative. Our work shows the potential of a low-cost, portable nanopore-based analyzer for protein identification. Peptide mass fingerprinting is a traditional approach for protein identification by mass spectrometry. Here, the authors provide evidence that peptide mass fingerprinting is also feasible using FraC nanopores, demonstrating protein identification based on nanopore measurements of digested peptides.
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15
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Shorkey SA, Du J, Pham R, Strieter ER, Chen M. Real-Time and Label-Free Measurement of Deubiquitinase Activity with a MspA Nanopore. Chembiochem 2021; 22:2688-2692. [PMID: 34060221 PMCID: PMC8416795 DOI: 10.1002/cbic.202100092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/10/2021] [Indexed: 02/06/2023]
Abstract
Covalently attaching ubiquitin (Ub) to cellular proteins as a post-translational modification can result in altered function of modified proteins. Enzymes regulating Ub as a post-translational modification, such as ligases and deubiquitinases, are challenging to characterize in part due to the low throughput of in-vitro assays. Single-molecule nanopore based assays have the advantage of detecting proteins with high specificity and resolution, and in a label-free, real-time fashion. Here we demonstrate the use of a MspA nanopore for discriminating and quantifying Ub proteins. We further applied the MspA pore to measure the Ub-chain disassembly activity of UCH37, a proteasome associated deubiquitinase. The implementation of this MspA system into nanopore arrays could enable high throughput characterizations of unknown deubiquitinases as well as drug screening against disease related enzymes.
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Affiliation(s)
- Spencer A Shorkey
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Jiale Du
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Ryan Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Eric R Strieter
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Min Chen
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
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16
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Robertson JW, Ghimire M, Reiner JE. Nanopore sensing: A physical-chemical approach. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183644. [PMID: 33989531 PMCID: PMC9793329 DOI: 10.1016/j.bbamem.2021.183644] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022]
Abstract
Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.
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Affiliation(s)
- Joseph W.F. Robertson
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg MD. 20899, correspondence to:
| | - Madhav Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, VA
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA
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17
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Li MY, Ying YL, Yu J, Liu SC, Wang YQ, Li S, Long YT. Revisiting the Origin of Nanopore Current Blockage for Volume Difference Sensing at the Atomic Level. JACS AU 2021; 1:967-976. [PMID: 34467343 PMCID: PMC8395674 DOI: 10.1021/jacsau.1c00109] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Indexed: 05/21/2023]
Abstract
Changes in the nanopore ionic current during entry of a target molecule underlie the sensing capability and dominate the intensity and extent of applications of the nanopore approach. The volume exclusion model has been proposed and corrected to describe the nanopore current blockage. However, increasing evidence shows nonconformity with this model, suggesting that the ionic current within a nanopore should be entirely reconsidered. Here, we revisit the origin of nanopore current blockage from a theoretical perspective and propose that the noncovalent interactions between a nanopore and a target molecule affect the conductance of the solution inside the nanopore, leading to enhanced current blockage. Moreover, by considering the example of an aerolysin nanopore discriminating the cytosine DNA and methylcytosine DNA that differ by a single methyl group, we completely demonstrate, by nanopore experiments and molecular dynamics simulations, the essential nature of this noncovalent interaction for discrimination. Our conductance model suggests multiplicative effects of both volume exclusion and noncovalent interaction on the current blockage and provides a new strategy to achieve volume difference sensing at the atomic level with highly specific current events, which would promote the nanopore protein sequencing and its applications in real-life systems.
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Affiliation(s)
- Meng-Yin Li
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P.R. China
- Chemistry
and Biomedicine Innovation Center, Nanjing
University, Nanjing 210023, P.R. China
| | - Yi-Lun Ying
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P.R. China
- Chemistry
and Biomedicine Innovation Center, Nanjing
University, Nanjing 210023, P.R. China
| | - Jie Yu
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Shao-Chuang Liu
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P.R. China
| | - Ya-Qian Wang
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Shuang Li
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Yi-Tao Long
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P.R. China
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18
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Al Sulaiman D, Gatehouse A, Ivanov AP, Edel JB, Ladame S. Length-Dependent, Single-Molecule Analysis of Short Double-Stranded DNA Fragments through Hydrogel-Filled Nanopores: A Potential Tool for Size Profiling Cell-Free DNA. ACS APPLIED MATERIALS & INTERFACES 2021; 13:26673-26681. [PMID: 34085806 DOI: 10.1021/acsami.1c01145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Fast sampling followed by sequence-independent sensing and length-dependent detection of short double-stranded DNA fragments, the size of those found in blood and other bodily fluids, is achieved using engineered molecular sensors, dubbed hydrogel-filled nanopores (HFNs). Fragments as short as 100 base pairs were blindly sampled and concentrated at the tip of an HFN before reversing the applied potential to detect and distinguish individual molecules based on fragment length as they translocate out of the nanopore. A remarkable 16-fold increase in the signal-to-noise ratio was observed in the eject configuration compared to the load configuration, enabling the resolution of fragments with a size difference of 50 nucleotides in length. This fast and versatile technology offers great tunability for both sampling and detection. While increasing sampling time leads to an increase in the local DNA concentration at the tip prior to detection, a linear correlation between the peak current and DNA fragment size enables good resolution of fragments up to 250 bp long.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Alfie Gatehouse
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London W12 0BZ, U.K
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, Sir Michael Uren Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
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19
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Angevine CE, Robertson JWF, Dass A, Reiner JE. Laser-based temperature control to study the roles of entropy and enthalpy in polymer-nanopore interactions. SCIENCE ADVANCES 2021; 7:eabf5462. [PMID: 33883140 PMCID: PMC8059931 DOI: 10.1126/sciadv.abf5462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/04/2021] [Indexed: 05/05/2023]
Abstract
Single-molecule approaches for probing the free energy of confinement for polymers in a nanopore environment are critical for the development of nanopore biosensors. We developed a laser-based nanopore heating approach to monitor the free energy profiles of such a single-molecule sensor. Using this approach, we measure the free energy profiles of two distinct polymers, polyethylene glycol and water-soluble peptides, as they interact with the nanopore sensor. Polyethylene glycol demonstrates a retention mechanism dominated by entropy with little sign of interaction with the pore, while peptides show an enthalpic mechanism, which can be attributed to physisorption to the nanopore (e.g., hydrogen bonding). To manipulate the energetics, we introduced thiolate-capped gold clusters [Au25(SG)18] into the pore, which increases the charge and leads to additional electrostatic interactions that help dissect the contribution that enthalpy and entropy make in this modified environment. These observations provide a benchmark for optimization of single-molecule nanopore sensors.
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Affiliation(s)
| | - Joseph W F Robertson
- Biophysics Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Amala Dass
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA.
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20
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Li MY, Ying YL, Li S, Wang YQ, Wu XY, Long YT. Unveiling the Heterogenous Dephosphorylation of DNA Using an Aerolysin Nanopore. ACS NANO 2020; 14:12571-12578. [PMID: 32806044 DOI: 10.1021/acsnano.0c03215] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The simultaneous occurrence of multiple heterogeneous DNA phosphorylation statuses, which include 5' end phosphorylation, 5' end dephosphorylation, 3' end phosphorylation, and 3' end dephosphorylation, is crucial for regulating numerous cellular processes. Although there are many methods for detecting a single type of DNA phosphorylation, the direct and simultaneous identification of DNA phosphorylation/dephosphorylation on the 5' and/or 3' ends remains a challenge, let alone the unveiling of the heterogeneous catalysis processes of related phosphatases and kinases. Taking advantage of the charge-sensitive aerolysin nanopore interface, herein, an orientation-dependent sensing strategy is developed to enhance phosphorylation-site-dependent interaction with the nanopore sensing interface, enabling the direct and simultaneous electric identification of four heterogeneous phosphorylation statuses of a single DNA. By using this strategy, we can directly evaluate the heterogeneous dephosphorylation process of alkaline phosphatase (ALP) at the single-molecule level. Our results demonstrate that the ALP in fetal bovine serum preferentially catalyzes the 3' phosphate rather than both ends. The quantification of endogenous ALP activity in fetal bovine serum could reach the submilli-IU/L level. Our aerolysin measurements provide a direct look at the heterogeneous phosphorylation status of DNA, allowing the unveiling of the dynamic single-molecule functions of kinase and phosphatase.
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Affiliation(s)
- Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P.R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P.R. China
| | - Shuang Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Ya-Qian Wang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Xue-Yuan Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
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21
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Hu F, Angelov B, Li S, Li N, Lin X, Zou A. Single‐Molecule Study of Peptides with the Same Amino Acid Composition but Different Sequences by Using an Aerolysin Nanopore. Chembiochem 2020; 21:2467-2473. [DOI: 10.1002/cbic.202000119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/09/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Fangzhou Hu
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Borislav Angelov
- Institute of Physics, ELI BeamlinesAcademy of Sciences of the Czech Republic Na Slovance 2 18221 Prague Czech Republic
| | - Shuang Li
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Na Li
- National Center for Protein Science in ShanghaiZhangjiang LabShanghai Advanced Research Institute, CAS Shanghai 200120 P. R. China
| | - Xubo Lin
- Institute of Single Cell EngineeringBeijing Advanced Innovation Center for Biomedical EngineeringBeihang University Beijing 100191 P. R. China
| | - Aihua Zou
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
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22
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He L, Karau P, Tabard-Cossa V. Fast capture and multiplexed detection of short multi-arm DNA stars in solid-state nanopores. NANOSCALE 2019; 11:16342-16350. [PMID: 31386731 DOI: 10.1039/c9nr04566j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fast and multiplexed detection of low-abundance disease biomarkers at the point-of-need would transform medicine. Nanopores have gained attention as single-molecule counters to electrically detect a range of biological molecules in a handheld format, but challenges remain before diagnostic applications can emerge. For solid-state nanopore sensors, the specificity of the ionic current signatures and the rate of target capture required to simultaneously recognize and rapidly count a mixture of molecular targets in a complex sample are active areas of research. Herein, we study the capture and translocation characteristics of short N-arm star shaped DNA nanostructures to evaluate their potential as a family of surrogate label molecules for biomarkers of interest, designed for fast and reliable multiplexed detection based on conductance blockages. Simple hybridization of a varying number of short, easily synthesized 50 bp ssDNA strands allows the number of arms in the star shape DNA to be controlled from N = 3 to 12. By introducing more arms to the nanostructures, we show that we can controllably increase the nanopore signal-to-noise ratio for a range of pore sizes, producing conductance blockages which increase linearly with the number of arms, and we demonstrate conductance-based multiplexing through simultaneous detection of three such nanostructures. Moreover, the increased molecular signal strength facilitates detection under salt concentration asymmetries, allowing for a capture rate enhancement of two orders of magnitude without compromising the nanopore temporal and ionic signals. Together, these attributes (strong signal, multiplexing potential and increased counting rate) make the N-arm star DNA-based nanostructures promising candidates as proxy labels for the detection of multiple biomarkers of interest in future high sensitivity single-molecule solid-state nanopore-based assays.
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Affiliation(s)
- Liqun He
- Department of Physics, University of Ottawa, Ottawa, ON, Canada.
| | - Philipp Karau
- Department of Physics, University of Ottawa, Ottawa, ON, Canada.
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23
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Li MY, Wang YQ, Lu Y, Ying YL, Long YT. Single Molecule Study of Hydrogen Bond Interactions Between Single Oligonucleotide and Aerolysin Sensing Interface. Front Chem 2019; 7:528. [PMID: 31417894 PMCID: PMC6684785 DOI: 10.3389/fchem.2019.00528] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/11/2019] [Indexed: 01/06/2023] Open
Abstract
The aerolysin nanopore displays a charming sensing capability for single oligonucleotide discrimination. When reading from the electrochemical signal, stronger interaction between the aerolysin nanopore and oligonucleotide represent prolonged duration time, thereby amplifying the hidden but intrinsic signal thus improving the sensitivity. In order to further understand and optimize the performance of the aerolysin nanopore, we focus on the investigation of the hydrogen bond interaction between nanopore, and analytes. Taking advantage of site-direct mutagenesis, single residue is replaced. According to whole protein sequence screening, the region near K238 is one of the key sensing regions. Such a positively charged amino acid is then mutagenized into cysteine and tyrosine denoted as K238C, and K238Y. As (dA)4 traverses the pores, K238C dramatically produces a six times longer duration time than the WT aerolysin nanopore at the voltage of +120 mV. However, K238Y shortens the dwell time which suggests the acceleration of the translocation causing poor sensitivity. Referring to our previous findings in K238G, and K238F, our results suggest that the hydrogen bond does not dominate the dynamic translocation process, but enhances the interaction between pores and analytes confined in such nanopore space. These insights give detailed information for the rational design of the sensing mechanism of the aerolysin nanopore, thereby providing further understanding for the weak interactions between biomolecules and the confined space for nanopore sensing.
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Affiliation(s)
- Meng-Yin Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Ya-Qian Wang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yao Lu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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24
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Gao R, Lin Y, Ying YL, Long YT. Nanopore-based sensing interface for single molecule electrochemistry. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9509-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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25
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Wei ZX, Ying YL, Li MY, Yang J, Zhou JL, Wang HF, Yan BY, Long YT. Learning Shapelets for Improving Single-Molecule Nanopore Sensing. Anal Chem 2019; 91:10033-10039. [PMID: 31083925 DOI: 10.1021/acs.analchem.9b01896] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nanopore technique employs a nanoscale cavity to electrochemically confine individual molecules, achieving ultrasensitive single-molecule analysis based on evaluating the amplitude and duration of the ionic current. However, each nanopore sensing interface has its own intrinsic sensing ability, which does not always efficiently generate distinctive blockade currents for multiple analytes. Therefore, analytes that differ at only a single site often exhibit similar blockade currents or durations in nanopore experiments, which often produces serious overlap in the resulting statistical graphs. To improve the sensing ability of nanopores, herein we propose a novel shapelet-based machine learning approach to discriminate mixed analytes that exhibit nearly identical blockade current amplitudes and durations. DNA oligomers with a single-nucleotide difference, 5'-AAAA-3' and 5'-GAAA-3', are employed as model analytes that are difficult to identify in aerolysin nanopores at 100 mV. First, a set of the most informative and discriminative segments are learned from the time-series data set of blockade current signals using the learning time-series shapelets (LTS) algorithm. Then, the shapelet-transformed representation of the signals is obtained by calculating the minimum distance between the shapelets and the original signals. A simple logistic classifier is used to identify the two types of DNA oligomers in accordance with the corresponding shapelet-transformed representation. Finally, an evaluation is performed on the validation data set to show that our approach can achieve a high F1 score of 0.933. In comparison with the conventional statistical methods for the analysis of duration and residual current, the shapelet-transformed representation provides clearly discriminated distributions for multiple analytes. Taking advantage of the robust LTS algorithm, one could anticipate the real-time analysis of nanopore events for the direct identification and quantification of multiple biomolecules in a complex real sample (e.g., serum) without labels and time-consuming mutagenesis.
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Affiliation(s)
- Zi-Xuan Wei
- School of Information and Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Yi-Lun Ying
- School of Chemistry and Molecule Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China.,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
- School of Chemistry and Molecule Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Jie Yang
- School of Chemistry and Molecule Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Jia-Le Zhou
- School of Information and Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Hui-Feng Wang
- School of Information and Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Bing-Yong Yan
- School of Information and Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Yi-Tao Long
- School of Chemistry and Molecule Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China.,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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26
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Wang H, Kasianowicz JJ, Robertson JWF, Poster DL, Ettedgui J. A comparison of ion channel current blockades caused by individual poly(ethylene glycol) molecules and polyoxometalate nanoclusters. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:83. [PMID: 31250227 DOI: 10.1140/epje/i2019-11838-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Proteinaceous nanometer-scale pores have been used to detect and physically characterize many different types of analytes at the single-molecule limit. The method is based on the ability to measure the transient reduction in the ionic channel conductance caused by molecules that partition into the pore. The distribution of blockade depth amplitudes and residence times of the analytes in the pore are used to physically and chemically characterize them. Here we compare the current blockade events caused by flexible linear polymers of ethylene glycol (PEGs) and structurally well-defined tungsten polyoxymetallate nanoparticles in the nanopores formed by Staphylococcus aureusα-hemolysin and Aeromonas hydrophila aerolysin. Surprisingly, the variance in the ionic current blockade depth values for the relatively rigid metallic nanoparticles is much greater than that for the flexible PEGs, possibly because of multiple charged states of the polyoxymetallate clusters.
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Affiliation(s)
- Haiyan Wang
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
- Shenzhen Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, 508060, Shenzhen, China
| | - John J Kasianowicz
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA.
- Columbia University, Department of Applied Physics Applied Mathematics, 10027, New York, NY, USA.
| | - Joseph W F Robertson
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
| | - Dianne L Poster
- National Institute of Standards and Technology, Material Measurement Laboratory, 20899, Gaithersburg, MD, USA
| | - Jessica Ettedgui
- National Institute of Standards and Technology, Physical Measurement Laboratory, 20899, Gaithersburg, MD, USA
- Columbia University, Department of Chemical Engineering, 10027, New York, NY, USA
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27
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Meng FN, Ying YL, Yang J, Long YT. A Wild-Type Nanopore Sensor for Protein Kinase Activity. Anal Chem 2019; 91:9910-9915. [DOI: 10.1021/acs.analchem.9b01570] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Fu-Na Meng
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jie Yang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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28
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Cressiot B, Ouldali H, Pastoriza-Gallego M, Bacri L, Van der Goot FG, Pelta J. Aerolysin, a Powerful Protein Sensor for Fundamental Studies and Development of Upcoming Applications. ACS Sens 2019; 4:530-548. [PMID: 30747518 DOI: 10.1021/acssensors.8b01636] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nanopore electrical approach is a breakthrough in single molecular level detection of particles as small as ions, and complex as biomolecules. This technique can be used for molecule analysis and characterization as well as for the understanding of confined medium dynamics in chemical or biological reactions. Altogether, the information obtained from these kinds of experiments will allow us to address challenges in a variety of biological fields. The sensing, design, and manufacture of nanopores is crucial to realize these objectives. For some time now, aerolysin, a pore forming toxin, and its mutants have shown high potential in real time analytical chemistry, size discrimination of neutral polymers, oligosaccharides, oligonucleotides and peptides at monomeric resolution, sequence identification, chemical modification on DNA, potential biomarkers detection, and protein folding analysis. This review focuses on the results obtained with aerolysin nanopores on the fields of chemistry, biology, physics, and biotechnology. We discuss and compare as well the results obtained with other protein channel sensors.
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Affiliation(s)
- Benjamin Cressiot
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | - Hadjer Ouldali
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Manuela Pastoriza-Gallego
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Laurent Bacri
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | | | - Juan Pelta
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
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29
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Olivares-Quiroz L, Vélez-Pérez JA. Translocation of non-interacting heteropolymer protein chains in terms of single helical propensity and size. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:565-574. [PMID: 30885619 DOI: 10.1016/j.bbapap.2019.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/27/2019] [Accepted: 03/13/2019] [Indexed: 11/29/2022]
Abstract
In this work we present an analytical framework to calculate the average translocation time τ required for an ideal proteinogenic polypeptide chain to cross over a small pore on a membrane. Translocation is considered to proceed as a chain of non-interacting amino acid residues of sequence {Xj} diffuses through the pore against an energy barrier Δℱ, set by chain entropy and unfolding-folding energetics. We analyze the effect of sequence heterogeneity on the dynamics of translocation by means of helical propensity of amino acid residues. In our calculations we use sequences of fifteen well-known proteins that are translocated which span two orders of magnitude in size according to the number of residues N. Results show non-symmetric free energy barriers as a consequence of sequence heterogeneity, such asymmetry in energy may be useful in differentiated directions of translocation. For the fifteen polypeptide chains considered we found conditions when sequence heterogeneity has not a significant effect on the time scale of translocation leading to a scaling law τ ∝ Nν, where ν ∼ 1.6 is an exponent that holds for most ground state energies. We also identify conditions when sequence heterogeneity has a great impact on the time scale of translocation, in consequence, no more scaling laws for τ there exist.
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Affiliation(s)
- L Olivares-Quiroz
- Departamento de Fisica and Posgrado en Ciencias de la Complejidad, Universidad Autonoma de la Ciudad de Mexico, CP 09760 Mexico City, Mexico; Centro de Ciencias de la Complejidad C3, UNAM, Circuito Mario de la Cueva 20, CP 04510 Mexico City, Mexico.
| | - José Antonio Vélez-Pérez
- Depto. Matemáticas y Mecánica, I.I.M.A.S., Universidad Nacional Autónoma de México, Apdo. Postal 20-726, 01000 Cd. México, Mexico; Posgrado en Nanociencias y Nanotecnología, Centro de Investigación y de Estudios Avanzados del IPN, Ap. Postal: 14-740, 07000 México, DF, Mexico.
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30
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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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31
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Sahu S, Zwolak M. Colloquium: Ionic phenomena in nanoscale pores through 2D materials. REVIEWS OF MODERN PHYSICS 2019; 91:10.1103/RevModPhys.91.021004. [PMID: 31579274 PMCID: PMC6774369 DOI: 10.1103/revmodphys.91.021004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Ion transport through nanopores permeates through many areas of science and technology, from cell behavior to sensing and separation to catalysis and batteries. Two-dimensional materials, such as graphene, molybdenum disulfide (MoS2), and hexagonal boron nitride (hBN), are recent additions to these fields. Low-dimensional materials present new opportunities to develop filtration, sensing, and power technologies, encompassing ion exclusion membranes, DNA sequencing, single molecule detection, osmotic power generation, and beyond. Moreover, the physics of ionic transport through pores and constrictions within these materials is a distinct realm of competing many-particle interactions (e.g., solvation/dehydration, electrostatic blockade, hydrogen bond dynamics) and confinement. This opens up alternative routes to creating biomimetic pores and may even give analogues of quantum phenomena, such as quantized conductance, in the classical domain. These prospects make membranes of 2D materials - i.e., 2D membranes - fascinating. We will discuss the physics and applications of ionic transport through nanopores in 2D membranes.
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Affiliation(s)
- Subin Sahu
- Biophysics Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Maryland NanoCenter, University of Maryland, College Park, Maryland 20742, USA
| | - Michael Zwolak
- Biophysics Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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32
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Yang J, Wang YQ, Li MY, Ying YL, Long YT. Direct Sensing of Single Native RNA with a Single-Biomolecule Interface of Aerolysin Nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14940-14945. [PMID: 30462509 DOI: 10.1021/acs.langmuir.8b03264] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
RNA sensing is of vital significance to advance our comprehension of gene expression and to further benefit medical diagnostics. Taking advantage of the excellent sensing capability of the aerolysin nanopore as a single-biomolecule interface, we for the first time achieved the direct characterization of single native RNA of Poly(A)4 and Poly(U)4. Poly(A)4 induces ∼10% larger blockade current amplitude than Poly(U)4. The statistical duration of Poly(A)4 is 18.83 ± 1.08 ms, which is 100 times longer than that of Poly(U)4. Our results demonstrated that the capture of RNA homopolymers is restricted by the biased diffusion. The translocation of RNA needs to overcome a lower free-energy barrier than that of DNA. Moreover, the strong RNA-aerolysin interaction is attributed to the hydroxyl in pentose, which prolongs the translocation time. This study opens an avenue for aerolysin nanopores to directly achieve RNA sensing, including discrimination of RNA epigenetic modification and selective detection of miRNA.
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Affiliation(s)
- Jie Yang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Ya-Qian Wang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Meng-Yin Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
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33
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Roman J, Le Pioufle B, Auvray L, Pelta J, Bacri L. From current trace to the understanding of confined media. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:99. [PMID: 30159758 DOI: 10.1140/epje/i2018-11709-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Nanopores constitute devices for the sensing of nano-objects such as ions, polymer chains, proteins or nanoparticles. We describe what information we can extract from the current trace. We consider the entrance of polydisperse chains into the nanopore, which leads to a conductance drop. We describe the detection of these current blockades according to their shape. Finally, we explain how data analysis can be used to enhance our understanding of physical processes in confined media.
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Affiliation(s)
- Jean Roman
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, F-91025, Evry, France
| | - Bruno Le Pioufle
- ENS Paris-Saclay, CNRS, Institut d'Alembert, SATIE, Université Paris-Saclay, F-94230, Cachan, France
| | - Loïc Auvray
- Matière et Systèmes Complexes, Université Paris Diderot/CNRS (UMR 7057), 75205, Paris, Cedex 13, France
| | - Juan Pelta
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, F-91025, Evry, France
| | - Laurent Bacri
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, F-91025, Evry, France.
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34
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Karau P, Tabard-Cossa V. Capture and Translocation Characteristics of Short Branched DNA Labels in Solid-State Nanopores. ACS Sens 2018; 3:1308-1315. [PMID: 29874054 DOI: 10.1021/acssensors.8b00165] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The challenge when employing solid-state nanopores as single-molecule sensors in a given assay is the specificity of the ionic current signal during the translocation of target molecules. Here we present the capture and translocation characteristics of short structurally defined DNA molecules that could serve as effective surrogate labels in biosensing applications. We produced T-shaped or Y-shaped DNA molecules with a 50 bp double-stranded DNA (dsDNA) backbone and a 25 bp dsDNA branch in the middle, as improved labels over short linear DNA fragments. We show that molecular topologies can be distinguished from linear DNA by analyzing ionic current blockades produced as these DNA labels translocate through nanopores fabricated by controlled breakdown on 10-nm-thick SiN membranes and ranging in diameter from 4 to 10 nm. Event signatures are shown to be a direct result of the structure of the label and lead to an increased signal-to-noise ratio over that of short linear dsDNA, in addition to well resolved dwell times for the pore size in this range. These results show that structurally defined branched DNA molecules can be robustly detected for a broad range of pore size, and thus represent promising candidates as surrogate labels in a variety of nanopore-based molecular or immunoassay schemes.
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Affiliation(s)
- Philipp Karau
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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35
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Mapping the sensing spots of aerolysin for single oligonucleotides analysis. Nat Commun 2018; 9:2823. [PMID: 30026547 PMCID: PMC6053387 DOI: 10.1038/s41467-018-05108-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/05/2018] [Indexed: 12/05/2022] Open
Abstract
Nanopore sensing is a powerful single-molecule method for DNA and protein sequencing. Recent studies have demonstrated that aerolysin exhibits a high sensitivity for single-molecule detection. However, the lack of the atomic resolution structure of aerolysin pore has hindered the understanding of its sensing capabilities. Herein, we integrate nanopore experimental results and molecular simulations based on a recent pore structural model to precisely map the sensing spots of this toxin for ssDNA translocation. Rationally probing ssDNA length and composition upon pore translocation provides new important insights for molecular determinants of the aerolysin nanopore. Computational and experimental results reveal two critical sensing spots (R220, K238) generating two constriction points along the pore lumen. Taking advantage of the sensing spots, all four nucleobases, cytosine methylation and oxidation of guanine can be clearly identified in a mixture sample. The results provide evidence for the potential of aerolysin as a nanosensor for DNA sequencing. Nanopores are an emerging powerful single-molecule method of DNA sequencing. Here the authors map the structure of aerolysin for use as a nanopore and show detection of modified and unmodified nucleobases.
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36
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Talarimoghari M, Baaken G, Hanselmann R, Behrends JC. Size-dependent interaction of a 3-arm star poly(ethylene glycol) with two biological nanopores. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:77. [PMID: 29926213 DOI: 10.1140/epje/i2018-11687-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
We use two pore-forming proteins, alpha-hemolysin and aerolysin, to compare the polymer size-dependence of ionic current block by two types of ethyleneglycol polymers: 1) linear and 2) 3-arm star poly(ethylene glycol), both applied as a polydisperse mixture of average mass 1kDa under high salt conditions. The results demonstrate that monomer size sensitivity, as known for linear PEGs, is conserved for the star polymers with only subtle differences in the dependence of the residual conductance on monomer number. To explain this absence of a dominant effect of polymer architecture, we propose that PEG adsorbs to the inner pore wall in a collapsed, salted-out state, likely due to the effect of hydrophobic residues in the pore wall on the availability of water for hydration.
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Affiliation(s)
- Monasadat Talarimoghari
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
| | - Gerhard Baaken
- Ionera Technologies GmbH, Hermann-Herder-Str. 7, 79104, Freiburg, Germany
| | - Ralf Hanselmann
- Institute for Macromolecular Chemistry, Stefan-Meier-Str. 31, 79104, Freiburg, Germany
- Freiburg Materials Research Centre, University of Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Hermann-Herder-Str. 7, 79104, Freiburg, Germany.
- Freiburg Materials Research Centre, University of Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany.
- Freiburg Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany.
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37
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Liao DF, Cao C, Ying YL, Long YT. A General Strategy of Aerolysin Nanopore Detection for Oligonucleotides with the Secondary Structure. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1704520. [PMID: 29603609 DOI: 10.1002/smll.201704520] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/01/2018] [Indexed: 06/08/2023]
Abstract
An aerolysin nanopore is employed as a sensitive tool for single-molecule analysis of short oligonucleotides (≤10 nucleotides), poly(ethylene glycol) (PEGs), peptides, and proteins. However, the direct analysis of long oligonucleotides with the secondary structure (e.g., G-quadruplex topology) remains a challenge, which impedes the further practical applications of the aerolysin nanopore. Here, a simple and applicable method of aerolysin nanopore is presented to achieve a direct analysis of structured oligonucleotides that are extended to 30 nucleotides long by a cation-regulation mechanism. By regulating the cation type in electrolyte solution, the structured oligonucleotides are unfolded into linear form which ensures the successive translocation. The results show that each model oligonucleotide of 5'-(TTAGGG)n -3' can produce a well-resolved current blockade in its unfolded solution of MgCl2 . The length between 6 and 30 nucleotides long of model oligonucleotides is proportional to the duration time, showing a translocation velocity as low as 0.70-0.13 ms nt-1 at +140 mV. This method exhibits an excellent sensitivity and a sufficient temporal resolution, provides insight into the aerolysin nanopore methodology for genetic and epigenetic biosensing, making aerolysin applicable in practical diagnosing with long and structured nucleic acids.
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Affiliation(s)
- Dong-Fang Liao
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
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38
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Wang H, Ettedgui J, Forstater J, Robertson JWF, Reiner JE, Zhang H, Chen S, Kasianowicz JJ. Determining the Physical Properties of Molecules with Nanometer-Scale Pores. ACS Sens 2018; 3:251-263. [PMID: 29381331 DOI: 10.1021/acssensors.7b00680] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nanometer-scale pores have been developed for the detection, characterization, and quantification of a wide range of analytes (e.g., ions, polymers, proteins, anthrax toxins, neurotransmitters, and synthetic nanoparticles) and for DNA sequencing. We describe the key requirements that made this method possible and how the technique evolved. Finally, we show that, despite sound theoretical work, which advanced both the conceptual framework and quantitative capability of the method, there are still unresolved questions that need to be addressed to further improve the technique.
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Affiliation(s)
- Haiyan Wang
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - Jessica Ettedgui
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Chemical Engineering, Columbia University New York, New York 10027, United States
| | - Jacob Forstater
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Chemical Engineering, Columbia University New York, New York 10027, United States
| | - Joseph W. F. Robertson
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
| | - Joseph E. Reiner
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Huisheng Zhang
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - Siping Chen
- Shenzhen
Key Laboratory of Biomedical Engineering, School of Medicine, Shenzhen University, 3688 Nanhai Road, Shenzhen 508060, China
| | - John J. Kasianowicz
- National Institute
of Standards and Technology Physical Measurement Laboratory, Gaithersburg, Maryland 20899, United States
- Department
of Applied Physics Applied Mathematics, Columbia University New York, New York 10027, United States
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39
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Briggs K, Madejski G, Magill M, Kastritis K, de Haan HW, McGrath JL, Tabard-Cossa V. DNA Translocations through Nanopores under Nanoscale Preconfinement. NANO LETTERS 2018; 18:660-668. [PMID: 29087723 PMCID: PMC5814347 DOI: 10.1021/acs.nanolett.7b03987] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
To reduce unwanted variation in the passage speed of DNA through solid-state nanopores, we demonstrate nanoscale preconfinement of translocating molecules using an ultrathin nanoporous silicon nitride membrane separated from a single sensing nanopore by a nanoscale cavity. We present comprehensive experimental and simulation results demonstrating that the presence of an integrated nanofilter within nanoscale distances of the sensing pore eliminates the dependence of molecular passage time distributions on pore size, revealing a global minimum in the coefficient of variation of the passage time. These results provide experimental verification that the inter- and intramolecular passage time variation depends on the conformational entropy of each molecule prior to translocation. Furthermore, we show that the observed consistently narrower passage time distributions enables a more reliable DNA length separation independent of pore size and stability. We also demonstrate that the composite nanofilter/nanopore devices can be configured to suppress the frequency of folded translocations, ensuring single-file passage of captured DNA molecules. By greatly increasing the rate at which usable data can be collected, these unique attributes will offer significant practical advantages to many solid-state nanopore-based sensing schemes, including sequencing, genomic mapping, and barcoded target detection.
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Affiliation(s)
- Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, ON, Canada
| | - Gregory Madejski
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - Martin Magill
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
| | | | - Hendrick W. de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, ON, Canada
| | - James L. McGrath
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
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40
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Cao C, Yu J, Li MY, Wang YQ, Tian H, Long YT. Direct Readout of Single Nucleobase Variations in an Oligonucleotide. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13. [PMID: 29024329 DOI: 10.1002/smll.201702011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/16/2017] [Indexed: 05/08/2023]
Abstract
Direct, low-cost, label-free, and enzyme-free identification of single nucleobase is a great challenge for genomic studies. Here, this study reports that wild-type aerolysin can directly identify the difference of four types of single nucleobase (adenine, thymine, cytosine, and guanine) in a free DNA oligomer while avoiding the operations of additional DNA immobilization, adapter incorporation, and the use of the processing enzyme. The nanoconfined space of aerolysin enables DNA molecules to be limited in the narrow pore. Moreover, aerolysin exhibits an unexpected capability of detecting DNA oligomers at the femtomolar concentration. In the future, by virtue of the high sensitivity of aerolysin and its high capture ability for DNA oligomers, aerolysin will play an important role in the studies of single nucleobase variations and open up new avenues for a broad range of nucleic-acid-based sensing and disease diagnosis.
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Affiliation(s)
- Chan Cao
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jie Yu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Meng-Yin Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Ya-Qian Wang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
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41
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Yu J, Cao C, Long YT. Selective and Sensitive Detection of Methylcytosine by Aerolysin Nanopore under Serum Condition. Anal Chem 2017; 89:11685-11689. [DOI: 10.1021/acs.analchem.7b03133] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jie Yu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P.R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P.R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P.R. China
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Gu Z, Wang H, Ying YL, Long YT. Ultra-low noise measurements of nanopore-based single molecular detection. Sci Bull (Beijing) 2017; 62:1245-1250. [PMID: 36659452 DOI: 10.1016/j.scib.2017.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/29/2017] [Accepted: 09/04/2017] [Indexed: 01/21/2023]
Abstract
Nanopore is an ultra-sensitive electrochemical technique for single molecular detection in confined space. To suppress the noise in detection of the weak current of nanopore, we investigated the influence of membrane capacitance and applied voltage on the noise of the current signal by model analysis, simulation and experiment. The obtained results demonstrated that membrane capacitance affects the noise by amplifying the noise of the applied voltage. Therefore, suppression of applied voltage noise is an efficient approach for reducing the noise in nanopore detection. Here, we developed an ultra-low noise instrument system for detecting the single molecule signal in nanopores. As demonstrated by nanopore experiments, the p-p noise of the developed system during the recording is reduced to 3.26pA using the filter of 5kHz. Therefore, the developed system could be applied in highly sensitive nanopore detection.
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Affiliation(s)
- Zhen Gu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Huifeng Wang
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
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43
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Bodrenko IV, Wang J, Salis S, Winterhalter M, Ceccarelli M. Sensing Single Molecule Penetration into Nanopores: Pushing the Time Resolution to the Diffusion Limit. ACS Sens 2017; 2:1184-1190. [PMID: 28730802 DOI: 10.1021/acssensors.7b00311] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To quantify small molecule penetration into and eventually permeation through nanopores, we applied an improved excess-noise analysis of the ion current fluctuation caused by entering molecules. The kinetic parameters of substrate entry and exit are derived from a two-state Markov model, analyzing the substrate concentration dependence of the average ion current and its variance. Including filter corrections allows one to detect the transition rates beyond the cutoff frequency, fc, of the instrumental ion-current filter. As an application of the method, we performed an analysis of the single-channel ion current of Meropenem, an antibiotic of the carbapenem family, interacting with OmpF, the major general outer membrane channel of Escherichia coli bacteria. At 40 °C we detected the residence time of Meropenem inside OmpF of about 500 ns-more than 2 orders of magnitude smaller than fc-1 and close to the diffusion limit of few hundred nanoseconds. We also have established theoretical limit conditions under which the substrate-induced channel blockages can be detected and suggest that submicrosecond-scale gating kinetic parameters are accessible with existing experimental equipment.
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Affiliation(s)
- Igor V. Bodrenko
- Department
of Physics, University of Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042, Monserrato, Cagliari, Italy
| | - Jiajun Wang
- Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Samuele Salis
- Department
of Physics, University of Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042, Monserrato, Cagliari, Italy
| | | | - Matteo Ceccarelli
- Department
of Physics, University of Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042, Monserrato, Cagliari, Italy
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44
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Construction of an aerolysin nanopore in a lipid bilayer for single-oligonucleotide analysis. Nat Protoc 2017; 12:1901-1911. [PMID: 28837133 DOI: 10.1038/nprot.2017.077] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nanopore techniques offer the possibility to study biomolecules at the single-molecule level in a low-cost, label-free and high-throughput manner. By analyzing the level, duration and frequency of ionic current blockades, information regarding the structural conformation, mass, length and concentration of single molecules can be obtained in physiological conditions. Aerolysin monomers assemble into small pores that provide a confined space for effective electrochemical control of a single molecule interacting with the pore, which significantly improves the temporal resolution of this technique. In comparison with other reported protein nanopores, aerolysin maintains its functional stability in a wide range of pH conditions, which allows for the direct discrimination of oligonucleotides between 2 and 10 nt in length and the monitoring of the stepwise cleavage of oligonucleotides by exonuclease I (Exo I) in real time. This protocol describes the process of activating proaerolysin using immobilized trypsin to obtain the aerolysin monomer, the construction of a lipid membrane and the insertion of an individual aerolysin nanopore into this membrane. A step-by-step description is provided of how to perform single-oligonucleotide analyses and how to process the acquired data. The total time required for this protocol is ∼3 d.
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45
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Sahu S, Zwolak M. Ionic selectivity and filtration from fragmented dehydration in multilayer graphene nanopores. NANOSCALE 2017; 9:11424-11428. [PMID: 28767109 PMCID: PMC5604754 DOI: 10.1039/c7nr03838k] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Selective ion transport is a hallmark of biological ion channel behavior but is a major challenge to engineer into artificial membranes. Here, we demonstrate, with all-atom molecular dynamics simulations, that bare graphene nanopores yield measurable ion selectivity that varies over one to two orders of magnitude simply by changing the pore radius and number of graphene layers. Monolayer graphene does not display dehydration-induced selectivity until the pore radius is small enough to exclude the first hydration layer from inside the pore. Bi- and tri-layer graphene, though, display such selectivity already for a pore size that barely encroaches on the first hydration layer, which is due to the more significant water loss from the second hydration layer. Measurement of selectivity and activation barriers from both first and second hydration layer barriers will help elucidate the behavior of biological ion channels. Moreover, the energy barriers responsible for selectivity - while small on the scale of hydration energies - are already relatively large, i.e., many kBT. For separation of ions from water, therefore, one can exchange longer, larger radius pores for shorter, smaller radius pores, giving a practical method for maintaining exclusion efficiency while enhancing other properties (e.g., water throughput).
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Affiliation(s)
- Subin Sahu
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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46
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Zhang J, Liu X, Ying YL, Gu Z, Meng FN, Long YT. High-bandwidth nanopore data analysis by using a modified hidden Markov model. NANOSCALE 2017; 9:3458-3465. [PMID: 28232981 DOI: 10.1039/c6nr09135k] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nanopore-based sensing is an emerging analytical technique with a number of important applications, including single-molecule detection and DNA sequencing. In this paper, we developed a Modified Hidden Markov Model (MHMM) to analyze directly the raw (unfiltered) nanopore current blockade data, which significantly reduced the filtering-induced distortion of the nanopore events. Traditionally, prior to further analysis, the measured nanopore data need to be pre-filtered to supress the strong noises. Nonetheless, this would result in the distortion of the shape of the blockade current especially for rapid translocations and bumping blockades. The HMM has been proved to be robust with respect to highly noisy data and thus ideally suitable for processing raw nanopore data directly. Unfortunately, its performance is somehow sensitive to the initial parameters usually preset arbitrarily. To overcome this problem, we use the Fuzzy c-Means (FCM) algorithm to initialize the HMM parameters automatically. Then we use the Viterbi training algorithm to optimize the HMM. Finally, the application results on both the simulated and experimental data are presented to demonstrate the practicability of the developed method for accurate detection of the nanopore current blockade events. The proposed method enables detection of the nanopore events at the highest bandwidth of the commercial instruments to extract the true useful information about the single molecules under analysis.
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Affiliation(s)
- Jianhua Zhang
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China.
| | - Xiuling Liu
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China.
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, P.R. China.
| | - Zhen Gu
- Key Laboratory for Advanced Materials and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, P.R. China.
| | - Fu-Na Meng
- Key Laboratory for Advanced Materials and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, P.R. China.
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials and Department of Chemistry, East China University of Science and Technology, Shanghai 200237, P.R. China.
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Tahvildari R, Beamish E, Briggs K, Chagnon-Lessard S, Sohi AN, Han S, Watts B, Tabard-Cossa V, Godin M. Manipulating Electrical and Fluidic Access in Integrated Nanopore-Microfluidic Arrays Using Microvalves. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602601. [PMID: 28026148 DOI: 10.1002/smll.201602601] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/06/2016] [Indexed: 06/06/2023]
Abstract
On-chip microvalves regulate electrical and fluidic access to an array of nanopores integrated within microfluidic networks. This configuration allows for on-chip sequestration of biomolecular samples in various flow channels and analysis by independent nanopores.
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Affiliation(s)
- Radin Tahvildari
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Eric Beamish
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | | | - Ali Najafi Sohi
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shuo Han
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Benjamin Watts
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | | | - Michel Godin
- Department of Physics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Mechanical Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Ottawa-Carleton Institute for Biomedical Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
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48
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Vélez-Pérez JA, Olivares-Quiroz L. Jump transition observed in translocation time for ideal poly-X proteinogenic chains as a result of competing folding and anchoraging contributions. Phys Rev E 2017; 95:012407. [PMID: 28208414 DOI: 10.1103/physreve.95.012407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Indexed: 01/07/2023]
Abstract
In this work we analyze the translocation of homopolymer chains poly-X, where X represents any of the 20 naturally occurring amino acid residues, in terms of size N and single-helical propensity ω. We provide an analytical framework to calculate both the free energy F of translocation and the translocation time τ as a function of chain size N, energies U and ε of the unfolded and folded states, respectively. Our results show that free energy F has a characteristic bell-shaped barrier as function of the percentage of monomers translocated. Inclusion of single-helical propensity ω associated to monomer X and chain's native energy ε in the translocation model increases the energy barrier ΔF up to one order of magnitude as compared with the well-known Gaussian chain model. Computation of the mean first-passage time as function of chain size N shows that the translocation time τ exhibits a significant jump of several orders of magnitude at a critical chain size N. This jump markedly slows down translocation of chains larger than N. Existence of the transition jump of τ has been observed experimentally at least in poly(ethylene oxide) chains [R. P. Choudhury, P. Galvosas, and M. Schönhoff, J. Phys. Chem. B 112, 13245 (2008)]JPCBFK1520-610610.1021/jp804680q. Our results suggest the transition jump of τ as a function of N may be a very well spread feature throughout translocation of poly-X chains.
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Affiliation(s)
- José Antonio Vélez-Pérez
- Posgrado en Nanociencias y Nanotecnología, Centro de Investigación y de Estudios Avanzados del IPN, Ap. Postal 14-740, 07000 México, DF, México
| | - Luis Olivares-Quiroz
- Colegio de Ciencia y Tecnologia and Posgrado en Ciencias de la Complejidad, Universidad Autonoma de la Ciudad de México, CP 09760 México City, México
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49
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Ying YL, Ding Z, Zhan D, Long YT. Advanced electroanalytical chemistry at nanoelectrodes. Chem Sci 2017; 8:3338-3348. [PMID: 28507703 PMCID: PMC5416909 DOI: 10.1039/c7sc00433h] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 02/16/2017] [Indexed: 01/10/2023] Open
Abstract
Nanoelectrodes, with dimensions below 100 nm, have the advantages of high sensitivity and high spatial resolution. These electrodes have attracted increasing attention in various fields such as single cell analysis, single-molecule detection, single particle characterization and high-resolution imaging. The rapid growth of novel nanoelectrodes and nanoelectrochemical methods brings enormous new opportunities in the field. In this perspective, we discuss the challenges, advances, and opportunities for nanoelectrode fabrication, real-time characterizations and high-performance electrochemical instrumentation.
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Affiliation(s)
- Yi-Lun Ying
- School of Chemistry & Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China .
| | - Zhifeng Ding
- Department of Chemistry , University of Western Ontario , 1151 Richmond Street , London , ON N6A 5B7 , Canada
| | - Dongping Zhan
- State Key Laboratory of Physical Chemistry of Solid Surfaces , Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM) , Department of Chemistry , College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , 361005 , P. R. China
| | - Yi-Tao Long
- School of Chemistry & Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China .
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50
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Zhang JH, Liu XL, Hu ZL, Ying YL, Long YT. Intelligent identification of multi-level nanopore signatures for accurate detection of cancer biomarkers. Chem Commun (Camb) 2017; 53:10176-10179. [DOI: 10.1039/c7cc04745b] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We combined a modified DBSCAN algorithm with the Hidden Markov Model (HMM) for the intelligent recognition of multi-level current blockage events from the measured nanopore data of serum samples.
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Affiliation(s)
- Jian-Hua Zhang
- School of Information Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Xiu-Ling Liu
- School of Information Science and Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Zheng-Li Hu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P. R. China
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