研究生: |
白佩珊 Pai, Pei-Shan |
---|---|
論文名稱: |
固態電子式奈米孔製作之精確性探討及其應用於單分子檢測 Investigation of Accurate Fabrication of Solid-State Nanopores and Their Applications to Single Molecule Detection |
指導教授: |
洪健中
Hong, Chien-Chong 劉通敏 Liou, Tong-Miin |
口試委員: |
黃國柱
Hwang, Kuo-Chu 陳治平 Chen, Chie-Pein |
學位類別: |
碩士 Master |
系所名稱: |
工學院 - 動力機械工程學系 Department of Power Mechanical Engineering |
論文出版年: | 2019 |
畢業學年度: | 108 |
語文別: | 中文 |
論文頁數: | 120 |
中文關鍵詞: | 固態式奈米孔 、氮化矽 、電擊穿 、DNA螢光觀測 、易位訊號量測 |
外文關鍵詞: | Solid-state nanopore, Silicon nitride, Voltage breakdown, DNA fluorescence observation, Translocation signal measurement |
相關次數: | 點閱:3 下載:0 |
分享至: |
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報 |
在過去的二十年中,奈米孔吸引了越來越多學術研究的注意,其檢測屬於單分子實時檢測技術(Single molecule real time (SMRT) method),相較於傳統的檢測方法,在體積、成本、通量、讀長和準確度等皆具有優勢,當檢測物濃度極低,甚至是需要精準計算溶液中所含之待測物分子數量時,傳統方法尚不具有足夠之檢測空間解析度來獲得上述所需數據,透過單個分子通過單個奈米孔洞,進而在離子電流中產生可檢測的臨時阻塞,奈米孔分析反映了它的簡單性,而可檢測的分析物範圍從核酸、肽鏈、蛋白質和生物分子復合物到有機聚合物。
目前可以從文獻中獲得大量奈米孔相關的知識基礎,包括材料的選擇、奈米孔的製程到奈米元件整合、感測器訊號量測,有別於早期的奈米孔發展是以生物性薄膜為主,因其結構穩定性、孔洞一致性等問題逐漸開始被固態奈米孔所取代,在過去十年中,已經發展許多於固態膜中製造奈米孔的技術。當中,為因應不同的感測需求且追求以更有效率、方便的方式製作奈米孔,奈米孔製程不再侷限使用高能離子束或者電子束,做為較新穎的電擊穿奈米孔加工製程在一些文獻中已展示顯著降低了奈米孔製造的複雜性和成本的優勢,為固態奈米孔元件的製造提供了新的選擇,但其製程所面臨的困境為無法如聚焦離子束或者穿隧式電子顯微鏡精準的將奈米孔定位。
本論文預計將兩種奈米孔製程-鑽孔及電擊穿整合,以聚焦離子束在奈米孔薄膜上人工製作缺陷,再通過多次介電擊穿於定位位置形成奈米孔洞,探討固態電子式奈米孔製作之精確性,最後將其應用在生物單分子,透過離子電流訊號希望能夠辨識出在低濃度環境下單一分子通過時的特徵訊號,以期待達到實時、精確和高通量之相關裝置發展目標。
Over the past two decades, nanopore, with the capability of single molecule real time (SMRT) technique, has drawn more and more scientific interests. Compared with traditional methods, nanopore-based diagnostic tool could offer various advantages, such as high sensitivity, small sizes, and low cost. The most attractive is nanopore is able to detect target molecules at very low concentrations from very small sample volumes, even if it is necessary to accurately calculate the number of molecules in the solution, that traditional methods are unable to reach the level with not high enough resolution. As a single molecule enters a single nanopore, it interrupts the ionic current through the pore, resulting in a detectable temporary current blockage. Nanoporebased sensing allows for the detection of a wide range of analytes from nucleic acids and peptide to protein and bio-molecular complexes in a simple way.
There is a large number of literature based around nanopore, including membrane material selection, nanopore fabrication, system integration, and sensor signal measurement. Most of the early nanopore-based sensors adopted biological nanopores, solid-state nanopores have been gradually growing in popularity due to structural stability and pore consistency. Many approaches for the fabrication of solid-state nanopores have been developed in these years. To date, solid-state nanopores have been fabricated primarily through a focused-electronic or ions beam, however, they have been tried to substitute by other nanofabrication strategies because of the need to generate nanopore in a more efficient and convenient way. As a novel method, multilevel pulse electrical breakdown has shown the potential in reducing the complexity and cost of nanopore fabrication.
In this paper, we report an accurate fabrication of solid-state nanopores with integrating two nanopore fabrications – ions beam drilling and electrical breakdown. Nanopore was fabricated through multilevel pulse voltage at the direct position of artificial defect which is previously manufactured on the membrane by focusing the ion beam. We envision this fabrication strategy would improve accuracy of nanopore fabrication but retain the advantage in simplicity and low-cost. Furthermore, may be used for further single-molecule experiments.
[1] Leslie A. Pray, Discovery of DNA Structure and Function: Watson and Crick, Nature Education, 1(1):100, 2008
[2] Istemi Han Celik et al., What are the Cut-Off Levels for IL-6 and CRP in Neonatal Sepsis, Journal of Clinical Laboratory Analysis, 24, 407–412., 2010
[3] M. S. Pepe et al., Phases of biomarker development for early detection of cancer, Journal of the National Cancer Institute, 93, 1054-1061., 2001
[4] B. Clyne and J. S. Olshaker, The C-reactive protein, The Journal of emergency medicine, 17, 1019-1025., 1999
[5] S. G. Paquette et al., Interleukin-6 is a potential biomarker for severe pandemic H1N1 influenza A infection, PLoS One, 7, e38214., 2012
[6] O. H. Lowry et al., Protein measurement with the Folin phenol reagent, Journal of biological chemistry, 193, 265-275., 1951
[7] M. M. Bradford, A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Analytical biochemistry, 72, 248-254., 1976
[8] Donald M. Kirschenbaum, Molar Absorptivity and AC Values for Proteins at Selected Wavelengths of the Ultraviolet and Visible Regions, Analytical Biochemistry, 68, 465-484., 1975
[9] “Western Blotting”: Electrophoretic Transfer of Proteins from Sodium Dodecyl Sulfate-Polyacrylamide Gels to Unmodified Nitrocellulose and Radiographic Detection with Antibody and Radioiodinated Protein A, Analytical Biochemistry, 112, 195-203., 1981
[10] ELISA-Types-Applications, Online notes on microbiology
[11] Jodi Woan-Fei Law et al., Rapid Methods for the Detection of Foodborne Bacterial Pathogens: Principles, Applications, Advantages and Limitations, Frontiers in Microbiology, 5, 770, 2014
[12] Sulaiman Alnaimat and Saqer AbuShattal, Laboratory Manual in General Microbiology, 2012
[13] M Wanunu et al., et al., Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors, Nature Nanotechnology, 5, 807–814., 2010
[14] Yao Lin et al., Direct sensing of cancer biomarkers in clinical samples with a designed nanopore, Chem Commun., 53, 11564, 2017
[15] Makusu Tsutsui et al., Discriminating single-bacterial shape using low-aspect-ratio pores, Scientific Reports, 7, 17371, 2017
[16] Maxam, A.M. and W. Gilbert, A new method for sequencing DNA, Proc Natl Acad Sci USA, 74, 560-564., 1977
[17] Sanger, F. and A.R. Coulson, A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase, Journal of Molecular Biology, 94, 441-446., 1975
[18] Atlas of Oral Microbiology, 2015, figure 2.37. Sanger sequencing.
[19] Robert D. Fleischmann et al., Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd, Science, 269, 5223, 496-512., 1995
[20] Green, E.D., Strategies for the systematic sequencing of complex genomes. Nature Reviews Genetics, 2, 573-583., 2001
[21] W. H. Coulter, US Pat., 2656508, 1953
[22] E. Neher and B. Sakmann, Single-channel currents recorded from membrane of denervated frog muscle fibres, Nature, 260, 799–802., 1976
[23] H. Bayley and C. R. Martin, Resistive-Pulse Sensings from Microbes to Molecules, Chem. Rev., 100, 2575–2594., 2000
[24] S. Howorka and Z. Siwy, Nanopore analytics: sensing of single molecules, Chem. Soc. Rev., 38, 2360–2384., 2009
[25] YL Ying, C Cao and YT Long, Single molecule analysis by biological nanopore sensors, Analyst, 139, 3826–3835., 2014
[26] Kasianowicz JJ, Brandin E, Branton D, Characterization of individual polynucleotide molecules using a membrane channel, Proc Natl Acad Sci, 93, 13770–13773., 1996
[27] C Yang, L Liu et al., Highly Sensitive Simultaneous Detection of Lead(II) and Barium(II) with G-Quadruplex DNA in α-Hemolysin Nanopore, Anal. Chem., 85 (15), 7302-7307., 2013
[28] T C Sutherland, Y T Long et al., Structure of Peptides Investigated by Nanopore Analysis, Nano Lett., 4 (7), 1273-1277., 2004
[29] F. Haque et al., Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA, Nano Today, 8, 56—74., 2013
[30] Derrington et al., Nanopore DNA sequencing with MspA, PNAS, 107, 37, 16060–16065., 2010
[31] MJ Kim et al., Rapid Fabrication of Uniformly Sized Nanopores and Nanopore Arrays for Parallel DNA Analysis, Adv. Mater., 18, 3149–3153., 2006
[32] BM Venkatesan et al., DNA Sensing Using Nanocrystalline Surface‐Enhanced Al2O3 Nanopore Sensors, Adv. Funct. Mater, 20, 1266–1275., 2010
[33] Liu et al., Atomically Thin Molybdenum Disulfide Nanopores with High Sensitivity for DNA Translocation, Acsnano, 8, 3, 2504–2511., 2014
[34] Garaj S et al., Graphene as a subnanometre trans-electrode membrane, Nature, 467, 190–3.2010
[35] CJ Lo et al., Fabrication of symmetric sub-5 nm nanopores using focused ion and electron beams, Nanotechnology, 17, 3264–3267., 2006
[36] A. P. Ivanov et al., DNA tunneling detector embedded in a nanopore, Nano Lett, 11, 279-85., 2011
[37] T Deng et al., Development of solid-state nanopore fabrication technologies, Sci. Bull., 60, 3, 304–319., 2015
[38] J Li et al., Ion-beam sculpting at nanometre length scales, Nature, 412, 166–169., 2001
[39] Benjamin N. Miles et al., Single molecule sensing with solid-state nanopores: novel materials, methods, and applications, Chem. Soc. Rev., 42, 15-28., 2013
[40] Danelon et al., Fabrication and Functionalization of Nanochannels by Electron-Beam-Induced Silicon Oxide Deposition, Langmuir, 22, 10711-10715., 2006
[41] Lennart J. de Vreede et al., Nanopore Fabrication by Heating Au Particles on Ceramic Substrates, Nano Lett, 15, 727−731., 2015
[42] AJ Storm, Fabrication of solid-state nanopores with single-nanometre precision, nature materials, 2, 537-541., 2003
[43] MJ Kim et al., Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope, Nanotechnology, 18, 205302, 2007
[44] Patterson N et al., Controlled fabrication of nanopores using a direct focused ion beam approach with back face particle detection, Nanotechnology, 19, 235304, 2008
[45] Gierak J et al., Sub-5 nm FIB direct patterning of nanodevices, Microelectron Eng, 84, 779–783., 2007
[46] J Yang et al., Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection, Nanotechnology, 22, 285310, 2011
[47] HM Kim et al., Theoretical and experimental study of nanopore drilling by a focused electron beam in transmission electron microscopy, Nanotechnology, 22, 275303, 2011
[48] Park SR et al., Fabrication of nanopores in silicon chips using feedback chemical etching, Small, 3, 116–119., 2007
[49] Vlassiouk et al., Versatile ultrathin nanoporous silicon nitride membranes, PNAS, 106, 21039-21044., 2009
[50] Han A et al., Sensing protein molecules using nanofabricated pores, Appl Phys Lett, 88, 093901, 2006
[51] Beamish et al., Precise control of the size and noise of solid-state nanopores using high electric fields, Nanotechnology, 23, 405301, 2012
[52] Harold Kwok et al., Nanopore Fabrication by Controlled Dielectric Breakdown, PLoS ONE, 9, 3, e92880., 2014
[53] Kyle Briggs et al., Kinetics of nanopore fabrication during controlled breakdown of dielectric membranes in solution, Nanotechnology, 26, 084004, 2015
[54] Itaru Yanagi et al.,Two-step breakdown of a SiN membrane for nanopore fabrication: Formation of thin portion and penetration, Scientific Reports, 8:10129, 2018
[55] M. Wanunu, Nanopores: A journey towards DNA sequencing, Physics of Life Reviews, 9, 125–158., 2012
[56] Itaru Yanagi et al., Fabricating nanopores with diameters of sub-1 nm to 3 nm using multilevel pulse-voltage injection, Sci Rep, 4, 10, 1038, srep05000, 2014
[57] D. Fologea et al., Electrical characterization of protein molecules by a solid-state nanopore, Appl Phys Lett, 91, 539011-539013., 2007
[58] Hays S. Rye, Stephen Yue , et al., "Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: properties and applications " Nucleic Acids Research, vol. 20, no. 11, pp. 2803-2812, 1992.
[59] Thermo Fisher Scientific Inc. Available: https://www.thermofisher.com/
[60] Marcel Reuter and David T.F. Dryden, "The kinetics of YOYO-1 intercalation into single molecules of double-stranded DNA," 555, vol. 403, pp. 225-229, 2010.
[61] Katrin Günther et al., Mechanical and structural properties of YOYO-1 complexed DNA, Nucleic Acids Research, 38, 19, 6526–6532., 2010,
[62] Matt Krems et al., Ionic Memcapacitive Effects in Nanopores, Nano Lett., 10, 2674–2678., 2010
[63] Aleksij Aksimentiev et al., Microscopic Kinetics of DNA Translocation through Synthetic Nanopores, Biophysical Journal, 87, 2086–2097., 2004
[64] Jiunn B. Heng et al., Sizing DNA Using a Nanometer-Diameter Pore, Biophysical Journal, 87, 2905–2911., 2004
[65] Itaru Yanagi et al., Two-step breakdown of a SiN membrane for nanopore
fabrication: Formation of thin portion and penetration, Scientific Reports, 8, 10129, 2018
[66] Christopher A. Merchant et al., DNA Translocation through Graphene Nanopores, Nano Lett., 10, 2915–2921., 2010
[67] Calin Plesa et al., Data analysis methods for solid-state nanopores, Nanotechnology, 26, 084003, 2015
[68]S. P. Wang, Fabrication and Chreacterixation of Solid-state Nanopores on Molybdenum Disulfide Nanosheets for DNA Translacation, Master Degree Thesis, 2017
[69]M. X. Wu, Easy-to Embledded Nanopore Microfluidic Chips and their Applications to Bioeletronic Translocation Measurements, Master Degree Thesis, 2019
[70] B. Radisavljevic et al., Single-layer MoS2 transistors, Nature Nanotechnology, 6, 147-150., 2011
[71] Amir Barati Farimani et al., DNA Base Detection Using a Single-Layer MoS2, ACS Nano, 8, 8, 7914-7922., 2014
[72] Stephanie J. Heerema et al., Probing DNA Translocations with Inplane Current Signals in a Graphene Nanoribbon with a Nanopore, ACS Nano, 12, 3, 2623-2633., 2018