1
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Salehirozveh M, Kure Larsen AK, Stojmenovic M, Thei F, Dong M. In-situ PLL-g-PEG Functionalized Nanopore for Enhancing Protein Characterization. Chem Asian J 2023; 18:e202300515. [PMID: 37497831 DOI: 10.1002/asia.202300515] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/03/2023] [Indexed: 07/28/2023]
Abstract
Single-molecule nanopore detection technology has revolutionized proteomics research by enabling highly sensitive and label-free detection of individual proteins. Herein, we designed a small, portable, and leak-free flowcell made of PMMA for nanopore experiments. In addition, we developed an in situ functionalizing PLL-g-PEG approach to produce non-sticky nanopores for measuring the volume of diseases-relevant biomarker, such as the Alpha-1 antitrypsin (AAT) protein. The in situ functionalization method allows continuous monitoring, ensuring adequate functionalization, which can be directly used for translocation experiments. The functionalized nanopores exhibit improved characteristics, including an increased nanopore lifetime and enhanced translocation events of the AAT proteins. Furthermore, we demonstrated the reduction in the translocation event's dwell time, along with an increase in current blockade amplitudes and translocation numbers under different voltage stimuli. The study also successfully measures the single AAT protein volume (253 nm3 ), which closely aligns with the previously reported hydrodynamic volume. The real-time in situ PLL-g-PEG functionalizing method and the developed nanopore flowcell hold great promise for various nanopores applications involving non-sticky single-molecule characterization.
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Affiliation(s)
- Mostafa Salehirozveh
- Department Of Physics And Astronomy, University of Bologna, Bologna, Italy
- Elements srl, Cesena, Italy
| | - Anne-Kathrine Kure Larsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Sino-Danish Center for Education and Research, Aarhus, Denmark
- University of the Chinese Academy of Sciences, Beijing, China
| | | | | | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Department of Biology - Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
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2
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Hong H, Wei J, Lei X, Chen H, Sarro PM, Zhang G, Liu Z. Study on the controllability of the fabrication of single-crystal silicon nanopores/nanoslits with a fast-stop ionic current-monitored TSWE method. MICROSYSTEMS & NANOENGINEERING 2023; 9:63. [PMID: 37206700 PMCID: PMC10188523 DOI: 10.1038/s41378-023-00532-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 03/28/2023] [Indexed: 05/21/2023]
Abstract
The application of single-crystal silicon (SCS) nanopore structures in single-molecule-based analytical devices is an emerging approach for the separation and analysis of nanoparticles. The key challenge is to fabricate individual SCS nanopores with precise sizes in a controllable and reproducible way. This paper introduces a fast-stop ionic current-monitored three-step wet etching (TSWE) method for the controllable fabrication of SCS nanopores. Since the nanopore size has a quantitative relationship with the corresponding ionic current, it can be regulated by controlling the ionic current. Thanks to the precise current-monitored and self-stop system, an array of nanoslits with a feature size of only 3 nm was obtained, which is the smallest size ever reported using the TSWE method. Furthermore, by selecting different current jump ratios, individual nanopores of specific sizes were controllably prepared, and the smallest deviation from the theoretical value was 1.4 nm. DNA translocation measurement results revealed that the prepared SCS nanopores possessed the excellent potential to be applied in DNA sequencing.
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Affiliation(s)
- Hao Hong
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
| | - Jiangtao Wei
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
| | - Xin Lei
- School of Chemistry, Beihang University, 100084 Beijing, China
| | - Haiyun Chen
- School of Electronic and Information Engineering, Beijing Jiaotong University, 100084 Beijing, China
| | - Pasqualina M. Sarro
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Guoqi Zhang
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Zewen Liu
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
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3
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Chen Y, Tian X, Xu X, Xu WS, Chen J. Investigation of Markovian and Non-Markovian Search Processes of Monomers of a Rouse Chain Confined in a Spherical Cavity. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c01877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Ye Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun130022, P. R. China
- University of Science and Technology of China, Hefei230026, P. R. China
| | - Xiaofei Tian
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun130022, P. R. China
- University of Science and Technology of China, Hefei230026, P. R. China
| | - Xiaolei Xu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun130022, P. R. China
| | - Wen-Sheng Xu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun130022, P. R. China
- University of Science and Technology of China, Hefei230026, P. R. China
| | - Jizhong Chen
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou510006, P. R. China
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4
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Burck N, Gilboa T, Gadi A, Patkin Nehrer M, Schneider RJ, Meller A. Nanopore Identification of Single Nucleotide Mutations in Circulating Tumor DNA by Multiplexed Ligation. Clin Chem 2021; 67:753-762. [PMID: 33496315 DOI: 10.1093/clinchem/hvaa328] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Circulating tumor DNAs (ctDNAs) are highly promising cancer biomarkers, potentially applicable for noninvasive liquid biopsy and disease monitoring. However, to date, sequencing of ctDNAs has proven to be challenging primarily due to small sample size and high background of fragmented cell-free DNAs (cfDNAs) derived from normal cells in the circulation, specifically in early stage cancer. METHODS Solid-state nanopores (ssNPs) have recently emerged as a highly efficient tool for single-DNA sensing and analysis. Herein, we present a rapid nanopore genotyping strategy to enable an amplification-free identification and classification of ctDNA mutations. A biochemical ligation detection assay was used for the creation of specific fluorescently-labelled short DNA reporter molecules. Color conjugation with multiple fluorophores enabled a unique multi-color signature for different mutations, offering multiplexing potency. Single-molecule readout of the fluorescent labels was carried out by electro-optical sensing via solid-state nanopores drilled in titanium oxide membranes. RESULTS As proof of concept, we utilized our method to detect the presence of low-quantity ERBB2 F310S and PIK3Ca H1047R breast cancer mutations from both plasmids and xenograft mice blood samples. We demonstrated an ability to distinguish between a wild type and a mutated sample, and between the different mutations in the same sample. CONCLUSIONS Our method can potentially enable rapid and low cost ctDNA analysis that completely circumvents PCR amplification and library preparation. This approach will thus meet a currently unmet demand in terms of sensitivity, multiplexing and cost, opening new avenues for early diagnosis of cancer.
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Affiliation(s)
- Nitza Burck
- Department of Biomedical Engineering, Technion- IIT, Haifa, Israel
| | - Tal Gilboa
- Department of Biomedical Engineering, Technion- IIT, Haifa, Israel.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Abhilash Gadi
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | | | | | - Amit Meller
- Department of Biomedical Engineering, Technion- IIT, Haifa, Israel.,Russell Berrie Nanotechnology Institute, Technion- IIT, Haifa, Israel
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5
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Fragasso A, Schmid S, Dekker C. Comparing Current Noise in Biological and Solid-State Nanopores. ACS NANO 2020; 14:1338-1349. [PMID: 32049492 PMCID: PMC7045697 DOI: 10.1021/acsnano.9b09353] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 05/16/2023]
Abstract
Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio (SNR) and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the SNR, the important figure of merit, by measuring translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR > 160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.
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Affiliation(s)
- Alessio Fragasso
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sonja Schmid
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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6
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Liu X, Zimny P, Zhang Y, Rana A, Nagel R, Reisner W, Dunbar WB. Flossing DNA in a Dual Nanopore Device. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905379. [PMID: 31858745 DOI: 10.1002/smll.201905379] [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] [Received: 10/20/2019] [Revised: 11/12/2019] [Indexed: 05/16/2023]
Abstract
Solid-state nanopores are a single-molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single-molecule data. Here, an active control technique termed "flossing" that uses a dual nanopore device is presented to trap a proteintagged DNA molecule and up to 100's of back-and-forth electrical scans of the molecule are performed in a few seconds. The protein motifs bound to 48.5 kb λ-DNA are used as detectable features for active triggering of the bidirectional control. Molecular noise is suppressed by averaging the multiscan data to produce averaged intertag distance estimates that are comparable to their known values. Since nanopore feature-mapping applications require DNA linearization when passing through the pore, a key advantage of flossing is that trans-pore linearization is increased to >98% by the second scan, compared to 35% for single nanopore passage of the same set of molecules. In concert with barcoding methods, the dual-pore flossing technique could enable genome mapping and structural variation applications, or mapping loci of epigenetic relevance.
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Affiliation(s)
- Xu Liu
- Ontera Inc., Santa Cruz, CA, 95060, USA
| | | | - Yuning Zhang
- Department of Physics, McGill University Montreal, QC H3A 2T8, Canada
| | | | | | - Walter Reisner
- Department of Physics, McGill University Montreal, QC H3A 2T8, Canada
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7
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Waugh M, Briggs K, Gunn D, Gibeault M, King S, Ingram Q, Jimenez AM, Berryman S, Lomovtsev D, Andrzejewski L, Tabard-Cossa V. Solid-state nanopore fabrication by automated controlled breakdown. Nat Protoc 2019; 15:122-143. [DOI: 10.1038/s41596-019-0255-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/10/2019] [Indexed: 11/09/2022]
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8
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Fragasso A, Pud S, Dekker C. 1/f noise in solid-state nanopores is governed by access and surface regions. NANOTECHNOLOGY 2019; 30:395202. [PMID: 31247592 DOI: 10.1088/1361-6528/ab2d35] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The performance of solid-state nanopores as promising biosensors is severely hampered by low-frequency 1/f noise in the through-pore ionic current recordings. Here, we develop a model for the 1/f noise in such nanopores, that, unlike previous reports, accounts for contributions from both the pore-cylinder, pore-surface, and access regions. To test our model, we present measurements of the open-pore current noise through solid-state nanopores of different diameters (1-50 nm). To describe the observed trends, it appears essential to include the access resistance in the modeling of the 1/f noise. We attribute a different Hooge constant for the charge carrier fluctuations occurring in the bulk electrolyte and at the pore surface. The model reported here can be used to accurately analyze different contributions to the nanopore low-frequency noise, rendering it a powerful tool for characterizing and comparing different membrane materials in terms of their 1/f noise properties.
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Affiliation(s)
- Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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9
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Madejski GR, Briggs K, DesOrmeaux JP, Miller JJ, Roussie JA, Tabard-Cossa V, McGrath JL. Monolithic Fabrication of NPN/SiN x Dual Membrane Cavity for Nanopore-based DNA Sensing. ADVANCED MATERIALS INTERFACES 2019; 6:1900684. [PMID: 32577337 PMCID: PMC7310959 DOI: 10.1002/admi.201900684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Indexed: 06/11/2023]
Abstract
Nanoscale preconfinement of DNA has been shown to reduce the variation of passage times through solid-state nanopores. Preconfinement has been previously achieved by forming a femtoliter-sized cavity capped with a highly porous layer of nanoporous silicon nitride (NPN). This cavity was formed by sealing a NPN nanofilter membrane against a substrate chip using water vapor delamination. Ultimately, this method of fabrication cannot keep a consistent spacing between the filter and solid-state nanopore due to thermal fluctuations and wrinkles in the membrane, nor can it be fabricated on thousands of individual devices reliably. To overcome these issues, we present a method to fabricate the femtoliter cavity monolithically, using a selective XeF2 etch to hollow out a polysilicon spacer sandwiched between silicon nitride layers. These monolithically fabricated cavities behave identically to their counterparts formed by vapor delamination, exhibiting similar translocation passage time variation reduction and folding suppression of DNA without requiring extensive manual assembly. The ability to form nanocavity sensors with nanometer-scale precision and to reliably manufacture them at scale using batch wafer processing techniques will find numerous applications, including motion control of polymers for single-molecule detection applications, filtering of dirty samples prior to nanopore detection, and simple fabrication of single-molecule nanobioreactors.
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Affiliation(s)
- Gregory R. Madejski
- Department of Biomedical Engineering, University of Rochester, Robert B. Goergen Hall Box 270168 Rochester, NY 14627, USA
| | - Kyle Briggs
- Department of Physics, University of Ottawa, 150 Louis-Pasteur Pvt, Ottawa, ON, K1N6N5, Canada
| | | | - Joshua J. Miller
- SiMPore Inc, 150 Lucius Gordon Dr, West Henrietta, NY, 14586, USA
| | - James A. Roussie
- SiMPore Inc, 150 Lucius Gordon Dr, West Henrietta, NY, 14586, USA
| | - Vincent Tabard-Cossa
- Department of Physics, University of Ottawa, 150 Louis-Pasteur Pvt, Ottawa, ON, K1N6N5, Canada
| | - James L. McGrath
- Department of Biomedical Engineering, University of Rochester, Robert B. Goergen Hall Box 270168 Rochester, NY 14627, USA
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10
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Wang R, Gilboa T, Song J, Huttner D, Grinstaff MW, Meller A. Single-Molecule Discrimination of Labeled DNAs and Polypeptides Using Photoluminescent-Free TiO 2 Nanopores. ACS NANO 2018; 12:11648-11656. [PMID: 30372037 DOI: 10.1021/acsnano.8b07055] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Multicolor fluorescence substantially expands the sensing capabilities of nanopores by complementing or substituting the resistive pulsing signals. However, to date single-fluorophore detection in multiple color channels has proven to be challenging primarily due to high photoluminescence (PL) emanating from the silicon nitride (SiN x) membrane. We hypothesize that the high bandgap of titanium oxide (TiO2) would eliminate the PL background when used as a substrate for a nanopore, and hence enable individual fluorophore sensing during the fast passage of biomolecules through the pore. Herein, we introduce a method for fabricating locally supported, free-standing, TiO2 membranes, in which solid-state nanopores can be readily drilled. These devices produce essentially no PL in the blue-to-red visible spectral range, even when excited by multiple lasers simultaneously. At the same time, the TiO2 nanopores exhibit low electrical noise comparable with standard SiN x devices. Importantly, the optical signal-to-background ratio (SBR) in single-molecule sensing is improved by an order of magnitude, enabling the differentiation among labeled DNA molecules of similar length based solely on their labeling scheme. Finally, the increased SBR of the TiO2 devices allows detection of single fluorophores conjugated to the lysine or cysteine residues of short polypeptides, thus introducing the possibility for optical based peptide/protein discrimination in nanopores.
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Affiliation(s)
- Rui Wang
- Department of Biomedical Engineering, Technion-IIT , Haifa , 32000 , Israel
| | - Tal Gilboa
- Department of Biomedical Engineering, Technion-IIT , Haifa , 32000 , Israel
| | - Jiaxi Song
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Diana Huttner
- Department of Biomedical Engineering, Technion-IIT , Haifa , 32000 , Israel
| | - Mark W Grinstaff
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - Amit Meller
- Department of Biomedical Engineering, Technion-IIT , Haifa , 32000 , Israel
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
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11
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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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12
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Cheng F, Su L, Qian C. Circulating tumor DNA: a promising biomarker in the liquid biopsy of cancer. Oncotarget 2018; 7:48832-48841. [PMID: 27223063 PMCID: PMC5217053 DOI: 10.18632/oncotarget.9453] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 04/24/2016] [Indexed: 12/15/2022] Open
Abstract
Tissue biopsy is the standard diagnostic procedure for cancers and also provides a material for genotyping, which can assist in the targeted therapies of cancers. However, tissue biopsy-based cancer diagnostic procedures have limitations in their assessment of cancer development, prognosis and genotyping, due to tumor heterogeneity and evolution. Circulating tumor DNA (ctDNA) is single- or double-stranded DNA released by the tumor cells into the blood and it thus harbors the mutations of the original tumor. In recent years, liquid biopsy based on ctDNA analysis has shed a new light on the molecular diagnosis and monitoring of cancer. Studies found that the screening of genetic mutations using ctDNA is highly sensitive and specific, suggesting that ctDNA analysis may significantly improve current systems of tumor diagnosis, even facilitating early-stage detection. Moreover, ctDNA analysis is capable of accurately determining the tumor progression, prognosis and assisting in targeted therapy. Therefore, using ctDNA as a liquid biopsy may herald a revolution for tumor management. Herein, we review the biology of ctDNA, its detection methods and potential applications in tumor diagnosis, treatment and prognosis.
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Affiliation(s)
- Feifei Cheng
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China.,School of Life Science, Zhejiang Sci-Tech University, Hangzhou, China
| | - Li Su
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Cheng Qian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
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13
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Zhang Y, Rana A, Stratton Y, Czyzyk-Krzeska MF, Esfandiari L. Sequence-Specific Detection of MicroRNAs Related to Clear Cell Renal Cell Carcinoma at fM Concentration by an Electroosmotically Driven Nanopore-Based Device. Anal Chem 2017; 89:9201-9208. [PMID: 28832110 DOI: 10.1021/acs.analchem.7b01944] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRs) are small noncoding RNAs that play a critical role in gene regulation. Recently, traces of cancer-related miRs have been identified in body fluids, which make them remarkable noninvasive biomarkers. In this study, a new nanopore-based detection scheme utilizing a borosilicate micropipette and an assay of complementary γ-peptide nucleic acid (γ-PNA) probes conjugated to polystyrene beads have been reported for the detection of miR-204 and miR-210 related to the clear cell Renal Cell Carcinoma (ccRCC). Electroosmotic flow (EOF) is induced as the driving force to transport PNA-beads harboring target miRs to the tip of the pore (sensing zone), which results in pore blockades with unique and easily distinguishable serrated shape electrical signals. The concentration detection limit is investigated to be 1 and 10 fM for miR-204 and miR-210, respectively. The EOF transport mechanism enables highly sensitive detection of molecules with low surface charge density with 97.6% detection accuracy compared to the conventional electrophoretically driven methods. Furthermore, resistive-pulse experiments are conducted to study the correlation of the particles' surface charge density with their translocation time and verify the detection principle.
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Affiliation(s)
- Yuqian Zhang
- Department of Electrical Engineering and Computing Systems, University of Cincinnati , Cincinnati, Ohio 45221, United States
| | - Ankit Rana
- Department of Electrical Engineering and Computing Systems, University of Cincinnati , Cincinnati, Ohio 45221, United States
| | - Yiwen Stratton
- Department of Cancer Biology, University of Cincinnati , Cincinnati, Ohio 45267, United States
| | - Maria F Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati , Cincinnati, Ohio 45267, United States.,Department of Veterans Affairs, VA Research Service , Cincinnati, Ohio 45220, United States
| | - Leyla Esfandiari
- Department of Electrical Engineering and Computing Systems, University of Cincinnati , Cincinnati, Ohio 45221, United States.,Department of Biomedical Chemical and Environmental Engineering, University of Cincinnati , Cincinnati, Ohio 45221, United States
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14
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Karouia F, Peyvan K, Pohorille A. Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth. Biotechnol Adv 2017; 35:905-932. [PMID: 28433608 DOI: 10.1016/j.biotechadv.2017.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 12/18/2022]
Abstract
Space biotechnology is a nascent field aimed at applying tools of modern biology to advance our goals in space exploration. These advances rely on our ability to exploit in situ high throughput techniques for amplification and sequencing DNA, and measuring levels of RNA transcripts, proteins and metabolites in a cell. These techniques, collectively known as "omics" techniques have already revolutionized terrestrial biology. A number of on-going efforts are aimed at developing instruments to carry out "omics" research in space, in particular on board the International Space Station and small satellites. For space applications these instruments require substantial and creative reengineering that includes automation, miniaturization and ensuring that the device is resistant to conditions in space and works independently of the direction of the gravity vector. Different paths taken to meet these requirements for different "omics" instruments are the subjects of this review. The advantages and disadvantages of these instruments and technological solutions and their level of readiness for deployment in space are discussed. Considering that effects of space environments on terrestrial organisms appear to be global, it is argued that high throughput instruments are essential to advance (1) biomedical and physiological studies to control and reduce space-related stressors on living systems, (2) application of biology to life support and in situ resource utilization, (3) planetary protection, and (4) basic research about the limits on life in space. It is also argued that carrying out measurements in situ provides considerable advantages over the traditional space biology paradigm that relies on post-flight data analysis.
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Affiliation(s)
- Fathi Karouia
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA; NASA Ames Research Center, Flight Systems Implementation Branch, Moffett Field, CA 94035, USA.
| | | | - Andrew Pohorille
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA.
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15
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Magill M, Falconer C, Waller E, de Haan HW. Translocation Time through a Nanopore with an Internal Cavity Is Minimal for Polymers of Intermediate Length. PHYSICAL REVIEW LETTERS 2016; 117:247802. [PMID: 28009178 DOI: 10.1103/physrevlett.117.247802] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Indexed: 06/06/2023]
Abstract
The translocation of polymers through nanopores with large internal cavities bounded by two narrow pores is studied via Langevin dynamics simulations. The total translocation time is found to be a nonmonotonic function of polymer length, reaching a minimum at intermediate length, with both shorter and longer polymers taking longer to translocate. The location of the minimum is shown to shift with the magnitude of the applied force, indicating that the pore can be dynamically tuned to favor different polymer lengths. A simple model balancing the effects of entropic trapping within the cavity against the driving force is shown to agree well with simulations. Beyond the nonmonotonicity, detailed analysis of translocation uncovers rich dynamics in which factors such as going to a high force regime and the emergence of a tail for long polymers dramatically change the behavior of the system. These results suggest that nanopores with internal cavities can be used for applications such as selective extraction of polymers by length and filtering of polymer solutions, extending the uses of nanopores within emerging nanofluidic technologies.
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Affiliation(s)
- Martin Magill
- University of Ontario Institute of Technology, Faculty of Science, 2000 Simcoe Street North, Oshawa, ON L1H 7K4, Canada
| | - Cory Falconer
- University of Ontario Institute of Technology, Faculty of Science, 2000 Simcoe Street North, Oshawa, ON L1H 7K4, Canada
| | - Ed Waller
- University of Ontario Institute of Technology, Faculty of Energy Systems and Nuclear Science, 2000 Simcoe Street North, Oshawa, ON L1H 7K4, Canada
| | - Hendrick W de Haan
- University of Ontario Institute of Technology, Faculty of Science, 2000 Simcoe Street North, Oshawa, ON L1H 7K4, Canada
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16
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Shi X, Gao R, Ying YL, Si W, Chen YF, Long YT. A Scattering Nanopore for Single Nanoentity Sensing. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00408] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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
| | - Rui Gao
- Key Laboratory for Advanced Materials, School of Chemistry & 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 & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Wei Si
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, Southeast University, Nanjing 210096, P. R. China
| | - Yun-Fei Chen
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, Southeast University, Nanjing 210096, P. R. China
| | - 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
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17
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18
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Kudr J, Skalickova S, Nejdl L, Moulick A, Ruttkay-Nedecky B, Adam V, Kizek R. Fabrication of solid-state nanopores and its perspectives. Electrophoresis 2015; 36:2367-79. [DOI: 10.1002/elps.201400612] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 05/13/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Jiri Kudr
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Sylvie Skalickova
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Lukas Nejdl
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Branislav Ruttkay-Nedecky
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
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19
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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.
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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
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Harrer S, Kim SC, Schieber C, Kannam S, Gunn N, Moore S, Scott D, Bathgate R, Skafidas S, Wagner JM. Label-free screening of single biomolecules through resistive pulse sensing technology for precision medicine applications. NANOTECHNOLOGY 2015; 26:182502. [PMID: 25875197 DOI: 10.1088/0957-4484/26/18/182502] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Employing integrated nano- and microfluidic circuits for detecting and characterizing biological compounds through resistive pulse sensing technology is a vibrant area of research at the interface of biotechnology and nanotechnology. Resistive pulse sensing platforms can be customized to study virtually any particle of choice which can be threaded through a fluidic channel and enable label-free single-particle interrogation with the primary read-out signal being an electric current fingerprint. The ability to perform label-free molecular screening with single-molecule and even single binding site resolution makes resistive pulse sensing technology a powerful tool for analyzing the smallest units of biological systems and how they interact with each other on a molecular level. This task is at the core of experimental systems biology and in particular 'omics research which in combination with next-generation DNA-sequencing and next-generation drug discovery and design forms the foundation of a novel disruptive medical paradigm commonly referred to as personalized medicine or precision medicine. DNA-sequencing has approached the 1000-Dollar-Genome milestone allowing for decoding a complete human genome with unmatched speed and at low cost. Increased sequencing efficiency yields massive amounts of genomic data. Analyzing this data in combination with medical and biometric health data eventually enables understanding the pathways from individual genes to physiological functions. Access to this information triggers fundamental questions for doctors and patients alike: what are the chances of an outbreak for a specific disease? Can individual risks be managed and if so how? Which drugs are available and how should they be applied? Could a new drug be tailored to an individual's genetic predisposition fast and in an affordable way? In order to provide answers and real-life value to patients, the rapid evolvement of novel computing approaches for analyzing big data in systems genomics has to be accompanied by an equally strong effort to develop next-generation DNA-sequencing and next-generation drug screening and design platforms. In that context lab-on-a-chip devices utilizing nanopore- and nanochannel based resistive pulse-sensing technology for DNA-sequencing and protein screening applications occupy a key role. This paper describes the status quo of resistive pulse sensing technology for these two application areas with a special focus on current technology trends and challenges ahead.
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Affiliation(s)
- S Harrer
- IBM Research-Australia, 204 Lygon Street, 3053 Carlton, VIC, Australia. University of Melbourne, 3010 Parkville, VIC, Australia
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21
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Carson S, Wanunu M. Challenges in DNA motion control and sequence readout using nanopore devices. NANOTECHNOLOGY 2015; 26:074004. [PMID: 25642629 PMCID: PMC4710574 DOI: 10.1088/0957-4484/26/7/074004] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nanopores are being hailed as a potential next-generation DNA sequencer that could provide cheap, high-throughput DNA analysis. In this review we present a detailed summary of the various sensing techniques being investigated for use in DNA sequencing and mapping applications. A crucial impasse to the success of nanopores as a reliable DNA analysis tool is the fast and stochastic nature of DNA translocation. We discuss the incorporation of biological motors to step DNA through a pore base-by-base, as well as the many experimental modifications attempted for the purpose of slowing and controlling DNA transport.
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22
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Sean D, de Haan HW, Slater GW. Translocation of a polymer through a nanopore starting from a confining nanotube. Electrophoresis 2015; 36:682-91. [DOI: 10.1002/elps.201400418] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/29/2014] [Accepted: 11/11/2014] [Indexed: 11/12/2022]
Affiliation(s)
- David Sean
- Department of Physics; University of Ottawa; Ottawa Ontario Canada
| | - Hendrick W. de Haan
- Faculty of Science; University of Ontario Institute of Technology; Oshawa Ontario Canada
| | - Gary W. Slater
- Faculty of Science; University of Ontario Institute of Technology; Oshawa Ontario Canada
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23
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Lv W, Liu S, Li X, Wu R. Spatial blockage of ionic current for electrophoretic translocation of DNA through a graphene nanopore. Electrophoresis 2014; 35:1144-51. [PMID: 24459097 DOI: 10.1002/elps.201300501] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 01/10/2014] [Accepted: 01/10/2014] [Indexed: 11/11/2022]
Abstract
Graphene nanopore has been promising the ultra-high resolution for DNA sequencing due to the atomic thickness and excellent electronic properties of the graphene monolayer. The dynamical translocation phenomena and/or behaviors underneath the blocked ionic current, however, have not been well unveiled to date for the translocation of DNA electrophoretically through a graphene nanopore. In this report, the assessment on the sensitivity of ionic current to instantaneous statuses of DNA in a 2.4 nm graphene nanopore was carried out based on the all-atom molecular dynamics simulations. By filtering out the thermal noise of ionic current, the instantaneous conformational variations of DNA in a graphene nanopore have been unveiled from the fluctuations of ionic current, because of the spatial blockage effect of DNA against ionic current. Interestingly, the neighborhood effect of DNA against ionic current was also observed within a distance of 1.5 nm nearby the graphene nanopore, suggesting the further precise control for DNA translocation through a graphene nanopore in gene sequencing. Moreover, the sensitivity of the blocked ionic current toward the instantaneous conformations of DNA in a graphene nanopore demonstrates the great potential of graphene nanopores in the dynamics analysis of single molecules.
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Affiliation(s)
- Wenping Lv
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, P. R. China
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24
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Niedzwiecki’ DJ, Iyer R, Borer PN, Movileanu L. Sampling a biomarker of the human immunodeficiency virus across a synthetic nanopore. ACS NANO 2013; 7:3341-50. [PMID: 23445080 PMCID: PMC3634884 DOI: 10.1021/nn400125c] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
One primary goal in nanobiotechnology is designing new methodologies for molecular biomedical diagnosis at stages much earlier than currently possible and without use of expensive reagents and sophisticated equipment. In this work, we show the proof of principle for single-molecule detection of the nucleocapsid protein 7 (NCp7), a protein biomarker of the HIV-1 virus, using synthetic nanopores and the resistive-pulse technique. The biosensing mechanism relied upon specific interactions between NCp7 and aptamers of stem-loop 3 (SL3) in the packaging domain of the retroviral RNA genome. One critical step of this study was the choice of the optimal size of the nanopores for accurate, label-free determinations of the dissociation constant of the NCp7 protein-SL3 RNA aptamer complex. Therefore, we systematically investigated the NCp7 protein-SL3 RNA aptamer complex employing two categories of nanopores in a silicon nitride membrane: (i) small, whose internal diameter was smaller than 6 nm, and (ii) large, whose internal diameter was in the range of 7 to 15 nm. Here, we demonstrate that only the use of nanopores with an internal diameter that is smaller than or comparable with the largest cross-sectional size of the NCp7-SL3 aptamer complex enables accurate measurement of the dissociation constant between the two interacting partners. Notably, this determination can be accomplished without the need for prior nanopore functionalization. Moreover, using small solid-state nanopores, we demonstrate the ability to detect drug candidates that inhibit the binding interactions between NCp7 and SL3 RNA by using a test case of N-ethylmaleimide.
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Affiliation(s)
| | - Raghuvaran Iyer
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, New York 13244-4100, USA
| | - Philip N. Borer
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, New York 13244-4100, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
- Syracuse Biomaterials Institute, Syracuse University, 121 Link Hall, Syracuse, New York 13244, USA
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