1
|
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.
Collapse
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
| |
Collapse
|
2
|
Acharjee MC, Ledden B, Thomas B, He X, Messina T, Giurleo J, Talaga D, Li J. Aggregation and Oligomerization Characterization of ß-Lactoglobulin Protein Using a Solid-State Nanopore Sensor. SENSORS (BASEL, SWITZERLAND) 2023; 24:81. [PMID: 38202943 PMCID: PMC10781269 DOI: 10.3390/s24010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024]
Abstract
Protein aggregation is linked to many chronic and devastating neurodegenerative human diseases and is strongly associated with aging. This work demonstrates that protein aggregation and oligomerization can be evaluated by a solid-state nanopore method at the single molecule level. A silicon nitride nanopore sensor was used to characterize both the amyloidogenic and native-state oligomerization of a model protein ß-lactoglobulin variant A (βLGa). The findings from the nanopore measurements are validated against atomic force microscopy (AFM) and dynamic light scattering (DLS) data, comparing βLGa aggregation from the same samples at various stages. By calibrating with linear and circular dsDNA, this study estimates the amyloid fibrils' length and diameter, the quantity of the βLGa aggregates, and their distribution. The nanopore results align with the DLS and AFM data and offer additional insight at the level of individual protein molecular assemblies. As a further demonstration of the nanopore technique, βLGa self-association and aggregation at pH 4.6 as a function of temperature were measured at high (2 M KCl) and low (0.1 M KCl) ionic strength. This research highlights the advantages and limitations of using solid-state nanopore methods for analyzing protein aggregation.
Collapse
Affiliation(s)
- Mitu C. Acharjee
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Brad Ledden
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Brian Thomas
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Xianglan He
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
| | - Troy Messina
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Department of Physics, Berea College, Berea, KY 40404, USA
| | - Jason Giurleo
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - David Talaga
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (X.H.); (J.G.)
- Department of Chemistry, Sokol Institute, Montclair State University, Montclair, NJ 07043, USA
| | - Jiali Li
- Material Science and Engineering, University of Arkansas, Fayetteville, AR 72701, USA
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
| |
Collapse
|
3
|
Hu R, Zhu R, Wei G, Wang Z, Gu ZY, Wanunu M, Zhao Q. Solid-State Quad-Nanopore Array for High-Resolution Single-Molecule Analysis and Discrimination. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211399. [PMID: 37037423 DOI: 10.1002/adma.202211399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/12/2023] [Indexed: 06/16/2023]
Abstract
The ability to detect and distinguish biomolecules at the single-molecule level is at the forefront of today's biomedicine and analytical chemistry research. Increasing the dwell time of individual biomolecules in the sensing spot can greatly enhance the sensitivity of single-molecule methods. This is particularly important in solid-state nanopore sensing, where the detection of small molecules is often limited by the transit dwell time and insufficient temporal resolution. Here, a quad-nanopore is introduced, a square array of four nanopores (with a space interval of 30-50 nm) to improve the detection sensitivity through electric field manipulation in the access region. It is shown that dwell times of short DNA strands (200 bp) are prolonged in quad-nanopores as compared to single nanopores of the same diameter. The dependence of dwell times on the quad-pore spacing is investigated and it is found that the "retarding effect" increases with decreasing space intervals. Furthermore, ultra-short DNA (50 bp) detection is demonstrated using a 10 nm diameter quad-nanopore array, which is hardly detected by a single nanopore. Finally, the general utility of quad-nanopores has been verified by successful discrimination of two kinds of small molecules, metal-organic cage and bovine serum albumin (BSA).
Collapse
Affiliation(s)
- Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Rui Zhu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Guanghao Wei
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Zhan Wang
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Zhi-Yuan Gu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, USA
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu, 226010, China
- Collaborative Innovation Center of Quantum Matter, Beijing, 100084, China
| |
Collapse
|
4
|
Tian R, Weng T, Chen S, Wu J, Yin B, Ma W, Liang L, Xie W, Wang Y, Zeng X, Yin Y, Wang D. DNA nanostructure-assisted detection of carcinoembryonic antigen with a solid-state nanopore. Bioelectrochemistry 2023; 149:108284. [PMID: 36244111 DOI: 10.1016/j.bioelechem.2022.108284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/15/2022] [Accepted: 10/01/2022] [Indexed: 11/07/2022]
Abstract
In this paper, a novel detection technique for tumor marker carcinoembryonic antigen (CEA) has been developed by using a solid-state nanopore as a tool. The system utilizes the specific affinity between aptamer-modified magnetic Fe3O4 and CEA, rather than directly detecting the translocation of CEA through the nanopore. The aptamer-modified magnetic Fe3O4 was hybridized with tetrahedral DNA nanostructures (TDNs), and TDNs were released after CEA was added. We investigate the translocation behavior of individual TDNs through solid-state nanopores. The frequency of the blockage signals for TDNs is recorded for indirect detection of CEA. We realized the detection of CEA with a concentration as low as 0.1 nM and proved the specificity of the interaction between the aptamer. In addition, our designed nanopore sensing strategy can detect CEA in real samples.
Collapse
Affiliation(s)
- Rong Tian
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China
| | - Ting Weng
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China
| | - Shanchuan Chen
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China
| | - Ji Wu
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China
| | - Bohua Yin
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China; Changchun University of Science and Technology, Changchun, China
| | - Wenhao Ma
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China
| | - Liyuan Liang
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China
| | - Wanyi Xie
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China
| | - Yunjiao Wang
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoqing Zeng
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China; Chongqing University, Chongqing, China
| | - Yajie Yin
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China.
| | - Deqiang Wang
- Chongqing School, University of Chinese Academy of Sciences, Beijing, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
5
|
Maheshwaram SK, Shet D, David SR, Lakshminarayana MB, Soni GV. Nanopore Sensing of DNA-Histone Complexes on Nucleosome Arrays. ACS Sens 2022; 7:3876-3884. [PMID: 36441954 DOI: 10.1021/acssensors.2c01865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The location of nucleosomes in DNA and their structural stability are critical in regulating DNA compaction, site accessibility, and epigenetic gene regulation. Here, we combine the nanopore platform-based fast and label-free single-molecule detection technique with a voltage-dependent force rupture assay to detect distinct structures on nucleosomal arrays and then to induce breakdown of individual nucleosome complexes. Specifically, we demonstrate direct measurement of distinct nucleosome structures present on individual 12-mer arrays. A detailed event analysis showed that nucleosomes are present as a combination of complete and partial structures, during translocation through the pore. By comparing with the voltage-dependent translocation of the mononucleosomes, we find that the partial nucleosomes result from voltage-dependent structural disintegration of nucleosomes. High signal-to-noise detection of heterogeneous levels in translocation of 12-mer array molecules quantifies the heterogeneity and nucleosomal substructure sizes on the arrays. These results facilitate the understanding of electrostatic interactions responsible for the integrity of the nucleosome structure and possible mechanisms of its unraveling by chromatin remodeling enzymes. This study also has potential applications in chromatin profiling.
Collapse
Affiliation(s)
| | - Divya Shet
- Raman Research Institute, Bangalore, Karnataka 560080, India
| | - Serene R David
- Raman Research Institute, Bangalore, Karnataka 560080, India
| | | | - Gautam V Soni
- Raman Research Institute, Bangalore, Karnataka 560080, India
| |
Collapse
|
6
|
Tripathi P, Chandler M, Maffeo CM, Fallahi A, Makhamreh A, Halman J, Aksimentiev A, Afonin KA, Wanunu M. Discrimination of RNA fiber structures using solid-state nanopores. NANOSCALE 2022; 14:6866-6875. [PMID: 35441627 PMCID: PMC9520586 DOI: 10.1039/d1nr08002d] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
RNA fibers are a class of biomaterials that can be assembled using HIV-like kissing loop interactions. Because of the programmability of molecular design and low immunorecognition, these structures present an interesting opportunity to solve problems in nanobiotechnology and synthetic biology. However, the experimental tools to fully characterize and discriminate among different fiber structures in solution are limited. Herein, we utilize solid-state nanopore experiments and Brownian dynamics simulations to characterize and distinguish several RNA fiber structures that differ in their degrees of branching. We found that, regardless of the electrolyte type and concentration, fiber structures that have more branches produce longer and deeper ionic current blockades in comparison to the unbranched fibers. Experiments carried out at temperatures ranging from 20-60 °C revealed almost identical distributions of current blockade amplitudes, suggesting that the kissing loop interactions in fibers are resistant to heating within this range.
Collapse
Affiliation(s)
- Prabhat Tripathi
- Department of Physics, Northeastern University, Boston, MA, 02115, USA.
| | - Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | | | - Ali Fallahi
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Amr Makhamreh
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - Justin Halman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Aleksei Aksimentiev
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, USA.
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| |
Collapse
|
7
|
Hu R, Liu C, Lu W, Wei G, Yu D, Li W, Chen P, Li G, Zhao Q. Probing the Effect of Ubiquitinated Histone on Mononucleosomes by Translocation Dynamics Study through Solid-State Nanopores. NANO LETTERS 2022; 22:888-895. [PMID: 35060726 DOI: 10.1021/acs.nanolett.1c02978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Post-translational modifications (PTMs), such as ubiquitination, are critically important in regulating genetic expressions by adjusting the nucleosome stability. A fast and label-free technology inspecting dynamic nucleosome structures can facilitate the interrogation of PTMs effects. Here we leverage the advantages of mechanically stable solid-state nanopores and detect the effect of a ubiquitinated histone on mononucleosomes at the single-molecule level. By comparing the translocation dynamics of natural and cross-linked mononucleosomes, we verified that the nucleosomal DNA unravelled from histones in natural mononucleosomes. Furthermore, we found that a turning point of voltage corresponds to the onset of nucleosome rupture. More importantly, we reveal that ubH2A stabilizes the nucleosome by shifting the turning point to a larger value and investigated the effect of ubiquitination on different histones (ubH2A and ubH2B). These findings open promising possibilities for developing a miniaturized and portable device for the fast screening of PTMs on nucleosomes.
Collapse
Affiliation(s)
- Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics School of Physics, Peking University, Beijing 100871, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenlong Lu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics School of Physics, Peking University, Beijing 100871, China
| | - Guanghao Wei
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics School of Physics, Peking University, Beijing 100871, China
| | - Dapeng Yu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics School of Physics, Peking University, Beijing 100871, China
- Institute for Quantum Science and Technology and Department of Physics, South University of Science and Technology of China (SUSTech), Shenzhen 518055, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Ping Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics School of Physics, Peking University, Beijing 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, China
| |
Collapse
|
8
|
Wang Z, Lv TY, Shi ZB, Yang SS, Gu ZY. Two-dimensional materials as solid-state nanopores for chemical sensing. Dalton Trans 2021; 50:13608-13619. [PMID: 34518861 DOI: 10.1039/d1dt02206g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solid-state nanopores as a versatile alternative to biological nanopores have grown tremendously over the last two decades. They exhibit unique characteristics including mechanical robustness, thermal and chemical stability, easy modifications and so on. Moreover, the pore size of a solid-state nanopore could be accurately controlled from sub-nanometers to hundreds of nanometers based on the experimental requirements, presenting better adaptability than biological nanopores. Two-dimensional (2D) materials with single layer thicknesses and highly ordered structures have great potential as solid-state nanopores. In this perspective, we introduced three kinds of substrate-supported 2D material solid-state nanopores, including graphene, MoS2 and MOF nanosheets, which exhibited big advantages compared to traditional solid-state nanopores and other biological counterparts. Besides, we suggested the fabrication and modulation of 2D material solid-state nanopores. We also discussed the applications of 2D materials as solid-state nanopores for ion transportation, DNA sequencing and biomolecule detection.
Collapse
Affiliation(s)
- Zhan Wang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Tian-Yi Lv
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Zi-Bo Shi
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China. .,Henan Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, P. R. China.
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| |
Collapse
|
9
|
Liang S, Zhang W, Xiang F. The effect of laser irradiation on reducing the noise of solid-state nanopore. NANOTECHNOLOGY 2021; 32:345301. [PMID: 33979783 DOI: 10.1088/1361-6528/ac007f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
The performance of solid-state nanopore is affected by the noise level. This study aimed to investigate the effect of laser irradiation on the noise performance of solid-state nanoporein situ. Laser irradiation is applied to fresh and contaminated nanopores. The measurement results show that the noise of fresh and contaminated nanopores decreases with the laser power and there is a threshold of laser power in reducing the noise of contaminated nanopores. The possible reasons for reducing noise in the laser irradiation process are discussed. The laser treatment is proven to provide a convenient method for reducing the noise of solid-state nanopore.
Collapse
Affiliation(s)
- Shengfa Liang
- Key Lab of Microelectronic Devices & Integrated Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Wenchang Zhang
- Key Lab of Microelectronic Devices & Integrated Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029, People's Republic of China
| | - Feibin Xiang
- Key Lab of Microelectronic Devices & Integrated Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029, People's Republic of China
- School of Electronic Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| |
Collapse
|
10
|
Fahie MA, Candido J, Andree G, Chen M. Tuning Protein Discrimination Through Altering the Sampling Interface Formed between the Analyte and the OmpG Nanopore. ACS Sens 2021; 6:1286-1294. [PMID: 33599487 DOI: 10.1021/acssensors.0c02580] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nanopore sensors capable of distinguishing homologous protein analytes are highly desirable tools for proteomics research and disease diagnostics. Recently, an engineered outer membrane protein G (OmpG) nanopore with a high-affinity ligand attached to a gating loop 6 showed specificity for distinguishing homologous proteins in complex mixtures. Here, we report the development of OmpG nanopores with the other six loops used as the anchoring point to host an affinity ligand for protein sensing. We investigated how the analyte binding to the affinity ligand located at different loops affects the detection sensitivity, selectivity, and specificity. Our results reveal that analytes weakly attracted to the OmpG nanopore surface are only detectable when the ligand is tethered to loop 6. In contrast, protein analytes that form a strong interaction with the OmpG surface via electrostatic attractions are distinguishable by all seven OmpG nanopore constructs. In addition, the same analyte can generate distinct binding signals with different OmpG nanopore constructs. The ability to exploit all seven OmpG loops will aid the design of a new generation of OmpG sensors with increased sensitivity, selectivity, and specificity for biomarker sensing.
Collapse
Affiliation(s)
- Monifa A. Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Jonathan Candido
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Gisele Andree
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Min Chen
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| |
Collapse
|
11
|
Nazarian R, Lee E, Siegel B, Kuo C, Acharya S, Schmidt J. Quantitative Measurements of Protein Volume and Concentration using Hydrogel-Backed Nanopores. ACS Sens 2021; 6:722-726. [PMID: 33703889 DOI: 10.1021/acssensors.1c00284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate identification and quantification of proteins in solution using nanopores is technically challenging in part because of the large fraction of missed translocation events due to short event times and limitations of conventional current amplifiers. Previously, we have shown that a nanopore interfaced with a poly(ethylene glycol)-dimethacrylate hydrogel with an average mesh size of 3.1 nm significantly enhances the protein residence time within the pore, reducing the number of missed events. We used hydrogel-backed nanopores to sense unlabeled proteins as small as 5.5 kDa in size and 10 fM in concentration. We show that the frequency of protein translocation events linearly scales with bulk concentration over a wide range of concentrations and that unknown protein concentrations can be determined from an interpolation of the frequency-concentration curve with less than 10% error. Further, we show an iterative method to determine a protein volume accurately from measurement data for proteins with a diameter comparable to a nanopore diameter. Our measurements and analysis also suggest several competing mechanisms for the detection enhancement enabled by the presence of the hydrogel.
Collapse
Affiliation(s)
- Reyhaneh Nazarian
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Eric Lee
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Brian Siegel
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Chance Kuo
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Shiv Acharya
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Jacob Schmidt
- Department of Bioengineering, UCLA, 420 Westwood Plaza, Los Angeles, California 90095, United States
| |
Collapse
|
12
|
Houghtaling J, Ying C, Eggenberger OM, Fennouri A, Nandivada S, Acharjee M, Li J, Hall AR, Mayer M. Estimation of Shape, Volume, and Dipole Moment of Individual Proteins Freely Transiting a Synthetic Nanopore. ACS NANO 2019; 13:5231-5242. [PMID: 30995394 DOI: 10.1021/acsnano.8b09555] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This paper demonstrates that high-bandwidth current recordings in combination with low-noise silicon nitride nanopores make it possible to determine the molecular volume, approximate shape, and dipole moment of single native proteins in solution without the need for labeling, tethering, or other chemical modifications of these proteins. The analysis is based on current modulations caused by the translation and rotation of single proteins through a uniform electric field inside of a nanopore. We applied this technique to nine proteins and show that the measured protein parameters agree well with reference values but only if the nanopore walls were coated with a nonstick fluid lipid bilayer. One potential challenge with this approach is that an untethered protein is able to diffuse laterally while transiting a nanopore, which generates increasingly asymmetric disruptions in the electric field as it approaches the nanopore walls. These "off-axis" effects add an additional noise-like element to the electrical recordings, which can be exacerbated by nonspecific interactions with pore walls that are not coated by a fluid lipid bilayer. We performed finite element simulations to quantify the influence of these effects on subsequent analyses. Examining the size, approximate shape, and dipole moment of unperturbed, native proteins in aqueous solution on a single-molecule level in real time while they translocate through a nanopore may enable applications such as identifying or characterizing proteins in a mixture, or monitoring the assembly or disassembly of transient protein complexes based on their shape, volume, or dipole moment.
Collapse
Affiliation(s)
- Jared Houghtaling
- Department of Biomedical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Cuifeng Ying
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Olivia M Eggenberger
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Aziz Fennouri
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Santoshi Nandivada
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Mitu Acharjee
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Jiali Li
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Adam R Hall
- Wake Forest University School of Medicine , Winston Salem , North Carolina 27157 , United States
| | - Michael Mayer
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| |
Collapse
|
13
|
Roudini L, NayebZadeh Eidgahi N, Rahimi HR, Saberi MR, Amiri Tehranizadeh Z, Beigoli S, Chamani J. Determining the interaction behavior of calf thymus DNA with berberine hydrochloride in the presence of linker histone: a biophysical study. J Biomol Struct Dyn 2019; 38:364-381. [DOI: 10.1080/07391102.2019.1574240] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Louisa Roudini
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Negar NayebZadeh Eidgahi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Hamid Reza Rahimi
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Modern Sciences & Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zeinab Amiri Tehranizadeh
- Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sima Beigoli
- Endoscopic and Minimally Invasive Surgery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| |
Collapse
|
14
|
Kaur H, Nandivada S, Acharjee MC, McNabb DS, Li J. Estimating RNA Polymerase Protein Binding Sites on λ DNA Using Solid-State Nanopores. ACS Sens 2019; 4:100-109. [PMID: 30561195 DOI: 10.1021/acssensors.8b00976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, using a silicon nitride nanopore based device, we measure the binding locations of RNA Polymerase (RNAP) on 48.5 kbp (16.5 μm) long λ DNA. To prevent the separation of bound RNAPs from a λ DNA molecule in the high electric field inside a nanopore, we cross-linked RNAP proteins to λ DNA by formaldehyde. We compare the current blockage event data measured with a mixture of λ DNA and RNAP under cross-link conditions with our control samples: RNAP, λ DNA, RNAP, and λ DNA incubated in formaldehyde separately and in a mixture. By analyzing the time durations and amplitudes of current blockage signals of events and their subevents, as well as subevent starting times, we can estimate the binding efficiency and locations of RNAPs on a λ DNA. Our data analysis shows that under the conditions of our experiment with the ratio of 6 to 1 for RNAP to λ DNA molecules, the probability of an RNAP molecule to bind a λ DNA is ∼42%, and that RNAP binding has a main peak at 3.51 μm ± 0.53 μm, most likely corresponding to the two strong promoter regions at 3.48 and 4.43 μm of λ DNA. However, individual RNAP binding sites were not distinguished with this nanopore setup. This work brings out new perspectives and complications to study transcription factor RNAP binding at various positions on very long DNA molecules.
Collapse
|
15
|
Varongchayakul N, Hersey J, Squires A, Meller A, Grinstaff M. A Solid-State Hard Microfluidic-Nanopore Biosensor with Multilayer Fluidics and On-Chip Bioassay/Purification Chamber. ADVANCED FUNCTIONAL MATERIALS 2018; 28:1804182. [PMID: 31632230 PMCID: PMC6800661 DOI: 10.1002/adfm.201804182] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Indexed: 05/21/2023]
Abstract
Solid-state nanopores are an emerging biosensor for nucleic acid and protein characterization. For use in a clinical setting, solid-state nanopore sensing requires sample preparation and purification, fluid handling, a heating element, electrical noise insulators, and an electrical readout detector, all of which hamper its translation to a point-of-care diagnostic device. A stand-alone microfluidic-based nanopore device is described that combines a bioassay reaction/purification chamber with a solid-state nanopore sensor. The microfluidic device is composed of the high-temperature/solvent resistance Zeonex plastic, formed via micro-machining and heat bonding, enabling the use of both a heat regulator and a magnetic controller. Fluid control through the microfluidic channels and chambers is controlled via fluid port selector valves and allows up-to eight different solutions. Electrical noise measurements and DNA translocation experiments demonstrate the integrity of the device, with performance comparable to a conventional stand-alone nanopore setup. However, the microfluidic-nanopore setup is superior in terms of ease of use. To showcase the utility of the device, single molecule detection of a DNA PCR product, after magnetic bead DNA separation, is accomplished on chip.
Collapse
Affiliation(s)
- Nitinun Varongchayakul
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston MA, 02215, USA
| | - Joseph Hersey
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston MA, 02215, USA
| | - Allison Squires
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Amit Meller
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston MA, 02215, USA
| | - Mark Grinstaff
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston MA, 02215, USA
| |
Collapse
|
16
|
Houghtaling J, List J, Mayer M. Nanopore-Based, Rapid Characterization of Individual Amyloid Particles in Solution: Concepts, Challenges, and Prospects. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802412. [PMID: 30225962 DOI: 10.1002/smll.201802412] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/15/2018] [Indexed: 06/08/2023]
Abstract
Aggregates of misfolded proteins are associated with several devastating neurodegenerative diseases. These so-called amyloids are therefore explored as biomarkers for the diagnosis of dementia and other disorders, as well as for monitoring disease progression and assessment of the efficacy of therapeutic interventions. Quantification and characterization of amyloids as biomarkers is particularly demanding because the same amyloid-forming protein can exist in different states of assembly, ranging from nanometer-sized monomers to micrometer-long fibrils that interchange dynamically both in vivo and in samples from body fluids ex vivo. Soluble oligomeric amyloid aggregates, in particular, are associated with neurotoxic effects, and their molecular organization, size, and shape appear to determine their toxicity. This concept article proposes that the emerging field of nanopore-based analytics on a single molecule and single aggregate level holds the potential to account for the heterogeneity of amyloid samples and to characterize these particles-rapidly, label-free, and in aqueous solution-with regard to their size, shape, and abundance. The article describes the concept of nanopore-based resistive pulse sensing, reviews previous work in amyloid analysis, and discusses limitations and challenges that will need to be overcome to realize the full potential of amyloid characterization on a single-particle level.
Collapse
Affiliation(s)
- Jared Houghtaling
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700, Fribourg, Switzerland
| | - Jonathan List
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700, Fribourg, Switzerland
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700, Fribourg, Switzerland
| |
Collapse
|
17
|
Shi X, Li Q, Gao R, Si W, Liu SC, Aksimentiev A, Long YT. Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore. J Phys Chem Lett 2018; 9:4686-4694. [PMID: 30058336 PMCID: PMC6252057 DOI: 10.1021/acs.jpclett.8b01755] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Docking of a protein-DNA complex onto a nanopore can provide ample observation time, and has enabled collection of analytic applications of biological nanopores, including DNA sequencing. However, the application of the same principle to solid-state nanopores is tempered by poor understanding of the docking process. Here, we elucidate the behavior of individual protein-DNA complexes docked onto a solid-state nanopore by monitoring the nanopore ionic current. Repeat docking of monovalent streptavidin-DNA complexes is found to produce ionic current blockades that fluctuate between discrete levels. We elucidate the roles of the protein plug and the DNA tether in the docking process, finding the docking configurations to determine the multitude of the current blockade levels, whereas the frequency of the current level switching is determined by the interactions between the molecules and the solid-state membrane. Finally, we prove the feasibility of using the nanopore docking principle for single-molecule sensing using solid-state nanopores by detecting conformational changes of a tethered DNA molecule from a random coil to an i-motif state.
Collapse
Affiliation(s)
- Xin Shi
- Key Laboratory for Advanced Materials, School of Chemistry &Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China,
| | - Qiao Li
- Key Laboratory for Advanced Materials, School of Chemistry &Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China,
| | - Rui Gao
- Key Laboratory for Advanced Materials, School of Chemistry &Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China,
| | - Wei Si
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, 1110 W Green St, Urbana, IL 61801, USA
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing 210096, P. R. China
| | - Shao-Chuang Liu
- Key Laboratory for Advanced Materials, School of Chemistry &Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China,
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, 1110 W Green St, Urbana, IL 61801, USA
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry &Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China,
| |
Collapse
|
18
|
Hu R, Rodrigues JV, Pradeep Waduge J, Yamazaki H, Cressiot B, Chishti Y, Makowski L, Yu D, Shakhnovich E, Zhao Q, Wanunu M. Differential Enzyme Flexibility Probed Using Solid-State Nanopores. ACS NANO 2018; 12:4494-4502. [PMID: 29630824 PMCID: PMC9016714 DOI: 10.1021/acsnano.8b00734] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enzymes and motor proteins are dynamic macromolecules that coexist in a number of conformations of similar energies. Protein function is usually accompanied by a change in structure and flexibility, often induced upon binding to ligands. However, while measuring protein flexibility changes between active and resting states is of therapeutic significance, it remains a challenge. Recently, our group has demonstrated that breadth of signal amplitudes in measured electrical signatures as an ensemble of individual protein molecules is driven through solid-state nanopores and correlates with protein conformational dynamics. Here, we extend our study to resolve subtle flexibility variation in dihydrofolate reductase mutants from unlabeled single molecules in solution. We first demonstrate using a canonical protein system, adenylate kinase, that both size and flexibility changes can be observed upon binding to a substrate that locks the protein in a closed conformation. Next, we investigate the influence of voltage bias and pore geometry on the measured electrical pulse statistics during protein transport. Finally, using the optimal experimental conditions, we systematically study a series of wild-type and mutant dihydrofolate reductase proteins, finding a good correlation between nanopore-measured protein conformational dynamics and equilibrium bulk fluorescence probe measurements. Our results unequivocally demonstrate that nanopore-based measurements reliably probe conformational diversity in native protein ensembles.
Collapse
Affiliation(s)
- Rui Hu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
| | - João V. Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - J Pradeep Waduge
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Hirohito Yamazaki
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Yasmin Chishti
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Dapeng Yu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
- Corresponding Authors:.,
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Corresponding Authors:.,
| |
Collapse
|
19
|
Shakibapour N, Dehghani Sani F, Beigoli S, Sadeghian H, Chamani J. Multi-spectroscopic and molecular modeling studies to reveal the interaction between propyl acridone and calf thymus DNA in the presence of histone H1: binary and ternary approaches. J Biomol Struct Dyn 2018; 37:359-371. [DOI: 10.1080/07391102.2018.1427629] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Niloufar Shakibapour
- Faculty of Sciences, Department of Biology, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Farzad Dehghani Sani
- Faculty of Sciences, Department of Biology, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Sima Beigoli
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamid Sadeghian
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Faculty of Sciences, Department of Biology, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| |
Collapse
|
20
|
Celaya G, Perales-Calvo J, Muga A, Moro F, Rodriguez-Larrea D. Label-Free, Multiplexed, Single-Molecule Analysis of Protein-DNA Complexes with Nanopores. ACS NANO 2017; 11:5815-5825. [PMID: 28530800 DOI: 10.1021/acsnano.7b01434] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Protein interactions with specific DNA sequences are crucial in the control of gene expression and the regulation of replication. Single-molecule methods offer excellent capabilities to unravel the mechanism and kinetics of these interactions. Here, we develop a nanopore approach where a target DNA sequence is contained in a hairpin followed by a ssDNA. This system allows DNA-protein complexes to be distinguished from bare DNA molecules as they are pulled through a single nanopore detector, providing both equilibrium and kinetic information. We show that this approach can be used to test the inhibitory effect of small molecules on complex formation and their mechanisms of action. In a proof of concept, we use DNAs with different sequence patterns to probe the ability of the nanopore to distinguish the effects of an inhibitor in a complex mixture of target DNAs and proteins. We anticipate that the use of this technology with arrays of thousands of nanopores will contribute to the development of transcription factor binding inhibitors.
Collapse
Affiliation(s)
- Garbiñe Celaya
- Biofisika Institute (CSIC, UPV/EHU) , Department of Biochemistry and Molecular Biology (UPV/EHU), Leioa 48940, Spain
| | - Judit Perales-Calvo
- Biofisika Institute (CSIC, UPV/EHU) , Department of Biochemistry and Molecular Biology (UPV/EHU), Leioa 48940, Spain
| | - Arturo Muga
- Biofisika Institute (CSIC, UPV/EHU) , Department of Biochemistry and Molecular Biology (UPV/EHU), Leioa 48940, Spain
| | - Fernando Moro
- Biofisika Institute (CSIC, UPV/EHU) , Department of Biochemistry and Molecular Biology (UPV/EHU), Leioa 48940, Spain
| | - David Rodriguez-Larrea
- Biofisika Institute (CSIC, UPV/EHU) , Department of Biochemistry and Molecular Biology (UPV/EHU), Leioa 48940, Spain
| |
Collapse
|
21
|
Arcadia CE, Reyes CC, Rosenstein JK. In Situ Nanopore Fabrication and Single-Molecule Sensing with Microscale Liquid Contacts. ACS NANO 2017; 11:4907-4915. [PMID: 28485922 DOI: 10.1021/acsnano.7b01519] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In this article, we introduce a flexible technique for high-throughput solid-state nanopore analysis of single biomolecules. By confining the electrolyte to a micron-scale liquid meniscus at the tip of a glass micropipette, we enable automation and reuse of a single solid-state membrane chip for measurements with hundreds of distinct nanopores per day. In addition to overcoming important experimental bottlenecks, the microscale liquid contact dramatically reduces device capacitance, which is a key limiting factor to the speed and fidelity of solid-state nanopore sensor recordings.
Collapse
Affiliation(s)
- Christopher E Arcadia
- School of Engineering, Brown University , Providence, Rhode Island 02912, United States
| | - Carlos C Reyes
- School of Engineering, Brown University , Providence, Rhode Island 02912, United States
| | - Jacob K Rosenstein
- School of Engineering, Brown University , Providence, Rhode Island 02912, United States
| |
Collapse
|
22
|
Lian J, Liu Q, Jin Y, Li B. Histone–DNA interaction: an effective approach to improve the fluorescence intensity and stability of DNA-templated Cu nanoclusters. Chem Commun (Camb) 2017; 53:12568-12571. [DOI: 10.1039/c7cc07424g] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The histone–DNA interaction is found to greatly improve the fluorescence intensity and stability of DNA-templated Cu nanoclusters (CuNCs).
Collapse
Affiliation(s)
- Jinyu Lian
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- China
| | - Qiang Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- China
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- China
| | - Baoxin Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry & Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- China
| |
Collapse
|
23
|
Vu T, Davidson SL, Borgesi J, Maksudul M, Jeon TJ, Shim J. Piecing together the puzzle: nanopore technology in detection and quantification of cancer biomarkers. RSC Adv 2017. [DOI: 10.1039/c7ra08063h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This mini-review paper is a comprehensive outline of nanopore technology applications in the detection and study of various cancer causal factors.
Collapse
Affiliation(s)
- Trang Vu
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Shanna-Leigh Davidson
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Julia Borgesi
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Mowla Maksudul
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| | - Tae-Joon Jeon
- Department of Biological Engineering
- Inha University
- Incheon 22212
- Republic of Korea
| | - Jiwook Shim
- Department of Biomedical Engineering
- Henry M. Rowan College of Engineering
- Rowan University
- Glassboro
- USA
| |
Collapse
|
24
|
Squires AH, Gilboa T, Torfstein C, Varongchayakul N, Meller A. Single-Molecule Characterization of DNA-Protein Interactions Using Nanopore Biosensors. Methods Enzymol 2016; 582:353-385. [PMID: 28062042 DOI: 10.1016/bs.mie.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Detection and characterization of nucleic acid-protein interactions, particularly those involving DNA and proteins such as transcription factors, enzymes, and DNA packaging proteins, remain significant barriers to our understanding of genetic regulation. Nanopores are an extremely sensitive and versatile sensing platform for label-free detection of single biomolecules. Analyte molecules are drawn to and through a nanoscale aperture by an electrophoretic force, which acts upon their native charge while in the sensing region of the pore. When the nanopore's diameter is only slightly larger than the biopolymer's cross section (typically a few nm); the latter must translocate through the pore in a linear fashion due to the constricted geometry in this region. These features allow nanopores to interrogate protein-nucleic acids in multiple sensing modes: first, by scanning and mapping the locations of binding sites along an analyte molecule, and second, by probing the strength of the bond between a protein and nucleic acid, using the native charge of the nucleic acid to apply an electrophoretic force to the complex while the protein is geometrically prevented from passing through the nanopore. In this chapter, we describe progress toward nanopore sensing of protein-nucleic acid complexes in the context of both mapping binding sites and performing force spectroscopy to determine the strength of interactions. We conclude by reviewing the strengths and challenges of the nanopore technique in the context of studying DNA-protein interactions.
Collapse
Affiliation(s)
- A H Squires
- Stanford University, Stanford, CA, United States
| | | | | | | | - A Meller
- The Technion, Haifa, Israel; Boston University, Boston, MA, United States.
| |
Collapse
|
25
|
Liu L, Wu HC. DNA-Based Nanopore Sensing. Angew Chem Int Ed Engl 2016; 55:15216-15222. [DOI: 10.1002/anie.201604405] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/13/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| |
Collapse
|
26
|
Franceschini L, Brouns T, Willems K, Carlon E, Maglia G. DNA Translocation through Nanopores at Physiological Ionic Strengths Requires Precise Nanoscale Engineering. ACS NANO 2016; 10:8394-402. [PMID: 27513592 PMCID: PMC5221729 DOI: 10.1021/acsnano.6b03159] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Many important processes in biology involve the translocation of a biopolymer through a nanometer-scale pore. Moreover, the electrophoretic transport of DNA across nanopores is under intense investigation for single-molecule DNA sequencing and analysis. Here, we show that the precise patterning of the ClyA biological nanopore with positive charges is crucial to observe the electrophoretic translocation of DNA at physiological ionic strength. Surprisingly, the strongly electronegative 3.3 nm internal constriction of the nanopore did not require modifications. Further, DNA translocation could only be observed from the wide entry of the nanopore. Our results suggest that the engineered positive charges are important to align the DNA in order to overcome the entropic and electrostatic barriers for DNA translocation through the narrow constriction. Finally, the dependencies of nucleic acid translocations on the Debye length of the solution are consistent with a physical model where the capture of double-stranded DNA is diffusion-limited while the capture of single-stranded DNA is reaction-limited.
Collapse
|
27
|
Affiliation(s)
- Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety; Institute of High Energy Physics; Chinese Academy of Sciences; Peking 100049 China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety; Institute of High Energy Physics; Chinese Academy of Sciences; Peking 100049 China
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Peking 100190 China
| |
Collapse
|
28
|
Hu R, Diao J, Li J, Tang Z, Li X, Leitz J, Long J, Liu J, Yu D, Zhao Q. Intrinsic and membrane-facilitated α-synuclein oligomerization revealed by label-free detection through solid-state nanopores. Sci Rep 2016; 6:20776. [PMID: 26865505 PMCID: PMC4749980 DOI: 10.1038/srep20776] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/12/2016] [Indexed: 11/09/2022] Open
Abstract
α-Synuclein (α-Syn) is an abundant cytosolic protein involved in the release of neurotransmitters in presynaptic terminal and its aberrant aggregation is found to be associated with Parkinson’s disease. Recent study suggests that the oligomers formed at the initial oligomerization stage may be the root cause of cytotoxicity. While characterizing this stage is challenging due to the inherent difficulties in studying heterogeneous and transient systems by conventional biochemical technology. Here we use solid-state nanopores to study the time-dependent kinetics of α-Syn oligomerization through a label-free and single molecule approach. A tween 20 coating method is developed to inhibit non-specific adsorption between α-Syn and nanopore surface to ensure successful and continuous detection of α-Syn translocation. We identify four types of oligomers formed in oligomerization stage and find an underlying consumption mechanism that the formation of large oligomers consumes small oligomers. Furthermore, the effect of lipid membrane on oligomerization of α-Syn is also investigated and the results show that 1,2-dioleoyl-sn-glycero-3-[phospho-L-serine] (DOPS) small unilamellar vesicles (SUVs) dramatically enhances the aggregation rate of α-Syn while do not alter the aggregation pathway.
Collapse
Affiliation(s)
- Rui Hu
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, People's Republic of China.,Collaborative Innovation Center of Quantum Matter, 100084 Beijing, China
| | - Jiajie Diao
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Life Science, Frontier Institute of Science and Technology (FIST), Xi'an Jiaotong University, Xi'an 710049, China
| | - Ji Li
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, People's Republic of China.,Collaborative Innovation Center of Quantum Matter, 100084 Beijing, China
| | - Zhipeng Tang
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, People's Republic of China.,Collaborative Innovation Center of Quantum Matter, 100084 Beijing, China
| | - Xiaoqing Li
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, People's Republic of China.,Collaborative Innovation Center of Quantum Matter, 100084 Beijing, China
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Jiangang Long
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Life Science, Frontier Institute of Science and Technology (FIST), Xi'an Jiaotong University, Xi'an 710049, China
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Life Science, Frontier Institute of Science and Technology (FIST), Xi'an Jiaotong University, Xi'an 710049, China
| | - Dapeng Yu
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, People's Republic of China.,Collaborative Innovation Center of Quantum Matter, 100084 Beijing, China
| | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, People's Republic of China.,Collaborative Innovation Center of Quantum Matter, 100084 Beijing, China
| |
Collapse
|
29
|
Carson S, Wick ST, Carr PA, Wanunu M, Aguilar CA. Direct Analysis of Gene Synthesis Reactions Using Solid-State Nanopores. ACS NANO 2015; 9:12417-24. [PMID: 26580227 PMCID: PMC5154552 DOI: 10.1021/acsnano.5b05782] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Synthetic nucleic acids offer rich potential to understand and engineer new cellular functions, yet an unresolved limitation in their production and usage is deleterious products, which restrict design complexity and add cost. Herein, we employ a solid-state nanopore to differentiate molecules of a gene synthesis reaction into categories of correct and incorrect assemblies. This new method offers a solution that provides information on gene synthesis reactions in near-real time with higher complexity and lower costs. This advance can permit insights into gene synthesis reactions such as kinetics monitoring, real-time tuning, and optimization of factors that drive reaction-to-reaction variations as well as open venues between nanopore-sensing, synthetic biology, and DNA nanotechnology.
Collapse
Affiliation(s)
- Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Scott T. Wick
- Massachusetts Institute of Technology Lincoln Laboratory, Massachusetts Institute of Technology, 244 Wood Street, Lexington, Massachusetts 02420, United States
| | - Peter A. Carr
- Massachusetts Institute of Technology Lincoln Laboratory, Massachusetts Institute of Technology, 244 Wood Street, Lexington, Massachusetts 02420, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Carlos A. Aguilar
- Massachusetts Institute of Technology Lincoln Laboratory, Massachusetts Institute of Technology, 244 Wood Street, Lexington, Massachusetts 02420, United States
| |
Collapse
|
30
|
Bulushev RD, Marion S, Radenovic A. Relevance of the Drag Force during Controlled Translocation of a DNA-Protein Complex through a Glass Nanocapillary. NANO LETTERS 2015; 15:7118-25. [PMID: 26393370 DOI: 10.1021/acs.nanolett.5b03264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Combination of glass nanocapillaries with optical tweezers allowed us to detect DNA-protein complexes in physiological conditions. In this system, a protein bound to DNA is characterized by a simultaneous change of the force and ionic current signals from the level observed for the bare DNA. Controlled displacement of the protein away from the nanocapillary opening revealed decay in the values of the force and ionic current. Negatively charged proteins EcoRI, RecA, and RNA polymerase formed complexes with DNA that experienced electrophoretic force lower than the bare DNA inside nanocapillaries. Force profiles obtained for DNA-RecA in our system were different than those in the system with nanopores in membranes and optical tweezers. We suggest that such behavior is due to the dominant impact of the drag force comparing to the electrostatic force acting on a DNA-protein complex inside nanocapillaries. We explained our results using a stochastic model taking into account the conical shape of glass nanocapillaries.
Collapse
Affiliation(s)
- Roman D Bulushev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| | - Sanjin Marion
- Institute of Physics , Bijenicka cesta 46, HR-10000 Zagreb, Croatia
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
| |
Collapse
|
31
|
Squires A, Atas E, Meller A. Nanopore sensing of individual transcription factors bound to DNA. Sci Rep 2015; 5:11643. [PMID: 26109509 PMCID: PMC4479991 DOI: 10.1038/srep11643] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/02/2015] [Indexed: 01/05/2023] Open
Abstract
Transcription factor (TF)-DNA interactions are the primary control point in regulation of gene expression. Characterization of these interactions is essential for understanding genetic regulation of biological systems and developing novel therapies to treat cellular malfunctions. Solid-state nanopores are a highly versatile class of single-molecule sensors that can provide rich information about local properties of long charged biopolymers using the current blockage patterns generated during analyte translocation, and provide a novel platform for characterization of TF-DNA interactions. The DNA-binding domain of the TF Early Growth Response Protein 1 (EGR1), a prototypical zinc finger protein known as zif268, is used as a model system for this study. zif268 adopts two distinct bound conformations corresponding to specific and nonspecific binding, according to the local DNA sequence. Here we implement a solid-state nanopore platform for direct, label- and tether-free single-molecule detection of zif268 bound to DNA. We demonstrate detection of single zif268 TFs bound to DNA according to current blockage sublevels and duration of translocation through the nanopore. We further show that the nanopore can detect and discriminate both specific and nonspecific binding conformations of zif268 on DNA via the distinct current blockage patterns corresponding to each of these two known binding modes.
Collapse
Affiliation(s)
- Allison Squires
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215 U.S.A
| | - Evrim Atas
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215 U.S.A
| | - Amit Meller
- 1] Department of Biomedical Engineering Boston University Boston, Massachusetts 02215 U.S.A. [2] Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel, 32000
| |
Collapse
|
32
|
Plesa C, Ruitenberg JW, Witteveen MJ, Dekker C. Detection of Individual Proteins Bound along DNA Using Solid-State Nanopores. NANO LETTERS 2015; 15:3153-8. [PMID: 25928590 DOI: 10.1021/acs.nanolett.5b00249] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
DNA in cells is heavily covered with all types of proteins that regulate its genetic activity. Detection of DNA-bound proteins is a challenge that is well suited to solid-state nanopores as they provide a linear readout of the DNA and DNA-protein volume in the pore constriction along the entire length of a molecule. Here, we demonstrate that we can realize the detection of even individual DNA-bound proteins at the single-DNA-molecule level using solid-state nanopores. We introduce and use a new model system of anti-DNA antibodies bound to lambda phage DNA. This system provides several advantages since the antibodies bind individually, tolerate high salt concentrations, and will, because of their positive charge, not translocate through the pore unless bound to the DNA. Translocation of DNA-antibody samples reveals the presence of short 12 μs current spikes within the DNA traces, with amplitudes that are about 4.5 times larger than that of dsDNA, which are associated with individual antibodies. We conclude that transient interactions between the pore and the antibodies are the primary mechanism by which bound antibodies are observed. This work provides a proof-of-concept for how nanopores could be used for future sensing applications.
Collapse
Affiliation(s)
- Calin Plesa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Justus W Ruitenberg
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Menno J Witteveen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| |
Collapse
|
33
|
Langecker M, Ivankin A, Carson S, Kinney SM, Simmel FC, Wanunu M. Nanopores suggest a negligible influence of CpG methylation on nucleosome packaging and stability. NANO LETTERS 2015; 15:783-90. [PMID: 25495735 PMCID: PMC4296928 DOI: 10.1021/nl504522n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 12/09/2014] [Indexed: 05/21/2023]
Abstract
Nucleosomes are the fundamental repeating units of chromatin, and dynamic regulation of their positioning along DNA governs gene accessibility in eukaryotes. Although epigenetic factors have been shown to influence nucleosome structure and dynamics, the impact of DNA methylation on nucleosome packaging remains controversial. Further, all measurements to date have been carried out under zero-force conditions. In this paper, we present the first automated force measurements that probe the impact of CpG DNA methylation on nucleosome stability. In solid-state nanopore force spectroscopy, a nucleosomal DNA tail is captured into a pore and pulled on with a time-varying electrophoretic force until unraveling is detected. This is automatically repeated for hundreds of nucleosomes, yielding statistics of nucleosome lifetime vs electrophoretic force. The force geometry, which is similar to displacement forces exerted by DNA polymerases and helicases, reveals that nucleosome stability is sensitive to DNA sequence yet insensitive to CpG methylation. Our label-free method provides high-throughput data that favorably compares with other force spectroscopy experiments and is suitable for studying a variety of DNA-protein complexes.
Collapse
Affiliation(s)
- Martin Langecker
- Lehrstuhl für
Bioelektronik, Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Andrey Ivankin
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Spencer Carson
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Shannon
R. M. Kinney
- Department
of Pharmaceutical and Administrative Sciences, Western New England University, Springfield, Massachusetts 01119, United States
| | - Friedrich C. Simmel
- Lehrstuhl für
Bioelektronik, Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
- E-mail:
| | - Meni Wanunu
- Departments of Physics and Chemistry/Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- E-mail:
| |
Collapse
|
34
|
Plesa C, van Loo N, Ketterer P, Dietz H, Dekker C. Velocity of DNA during translocation through a solid-state nanopore. NANO LETTERS 2015; 15:732-7. [PMID: 25496458 DOI: 10.1021/nl504375c] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
While understanding translocation of DNA through a solid-state nanopore is vital for exploiting its potential for sensing and sequencing at the single-molecule level, surprisingly little is known about the dynamics of the propagation of DNA through the nanopore. Here we use linear double-stranded DNA molecules, assembled by the DNA origami technique, with markers at known positions in order to determine for the first time the local velocity of different segments along the length of the molecule. We observe large intramolecular velocity fluctuations, likely related to changes in the drag force as the DNA blob unfolds. Furthermore, we observe an increase in the local translocation velocity toward the end of the translocation process, consistent with a speeding up due to unfolding of the last part of the DNA blob. We use the velocity profile to estimate the uncertainty in determining the position of a feature along the DNA given its temporal location and demonstrate the error introduced by assuming a constant translocation velocity.
Collapse
Affiliation(s)
- Calin Plesa
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology , Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | | | | | | | | |
Collapse
|
35
|
Krasniqi B, Lee JS. RNase A does not translocate the alpha-hemolysin pore. PLoS One 2014; 9:e88004. [PMID: 24505349 PMCID: PMC3913706 DOI: 10.1371/journal.pone.0088004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/02/2014] [Indexed: 11/24/2022] Open
Abstract
The application of nanopore sensing utilizing the α-hemolysin pore to probe proteins at single-molecule resolution has expanded rapidly. In some studies protein translocation through the α-hemolysin has been reported. However, there is no direct evidence, as yet, that proteins can translocate the α-hemolysin pore. The biggest challenge to obtaining direct evidence is the lack of a highly sensitive assay to detect very low numbers of protein molecules. Furthermore, if an activity based assay is applied then the proteins translocating by unfolding should refold back to an active confirmation for the assay technique to work. To overcome these challenges we selected a model enzyme, ribonuclease A, that readily refolds to an active conformation even after unfolding it with denaturants. In addition we have developed a highly sensitive reverse transcription polymerase chain reaction based activity assay for ribonuclease A. Initially, ribonuclease A, a protein with a positive net charge and dimensions larger than the smallest diameter of the pore, was subjected to nanopore analysis under different experimental conditions. Surprisingly, although the protein was added to the cis chamber (grounded) and a positive potential was applied, the interaction of ribonuclease A with α-hemolysin pore induced small and large blockade events in the presence and the absence of a reducing and/or denaturing agent. Upon measuring the zeta potential, it was found that the protein undergoes a charge reversal under the experimental conditions used for nanopore sensing. From the investigation of the effect of voltage on the interaction of ribonuclease A with the α-hemolysin pore, it was impossible to conclude if the events observed were translocations. However, upon testing for ribonuclease A activity on the trans chamber it was found that ribonuclease A does not translocate the α-hemolysin pore.
Collapse
Affiliation(s)
- Besnik Krasniqi
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jeremy S. Lee
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
- * E-mail:
| |
Collapse
|
36
|
Gibb TR, Ivanov AP, Edel JB, Albrecht T. Single Molecule Ionic Current Sensing in Segmented Flow Microfluidics. Anal Chem 2014; 86:1864-71. [DOI: 10.1021/ac403921m] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Thomas R. Gibb
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7
2AZ, United Kingdom
| | - Aleksandar P. Ivanov
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7
2AZ, United Kingdom
| | - Joshua B. Edel
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7
2AZ, United Kingdom
| | - Tim Albrecht
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7
2AZ, United Kingdom
| |
Collapse
|