Progress in Biological Nanopore-based Analysis Technology
- Corresponding author: XI Dongmei, dongmxi@126.com ZHANG Shusheng, shushzhang@126.com
Citation:
SHANG Jizhen, LI Zhi, XI Dongmei, ZHANG Shusheng. Progress in Biological Nanopore-based Analysis Technology[J]. Chinese Journal of Applied Chemistry,
;2017, 34(8): 855-867.
doi:
10.11944/j.issn.1000-0518.2017.08.170103
Kasianowicz J J, Brandin E, Branton D. Characterization of Individual Polynucleotide Molecules Using a Membrane Channel[J]. Proc Natl Acad Sci USA, 1996,93(24):13770-13773. doi: 10.1073/pnas.93.24.13770
Branton D, Deamer D W, Marziali A. The Potential and Challenges of Nanopore Sequencing[J]. Nat Biotechnol, 2008,26(10):1146-1153. doi: 10.1038/nbt.1495
Ying Y L, Zhang J, Gao R. Nanopore-based Sequencing and Detection of Nucleic Acids[J]. Angew Chem Int Ed, 2013,52(50):13154-13161. doi: 10.1002/anie.201303529
Ying Y L, Cao C, Long Y T. Single Molecule Analysis by Biological Nanopore Sensors[J]. Analyst, 2014,139(16):3826-3835. doi: 10.1039/C4AN00706A
Stefureac R, Long Y T, Kraatz H B. Transport of Alpha-helical Peptides Through Alpha-hemolysin and Aerolysin Pores[J]. Biochemistry, 2006,45(30):9172-9179. doi: 10.1021/bi0604835
Butler T Z, Pavlenok M, Derrington I M. Single-molecule DNA Detection with an Engineered MspA Protein Nanopore[J]. Proc Natl Acad Sci USA, 2008,105(52):20647-20652. doi: 10.1073/pnas.0807514106
Wendell D, Jing P, Geng J. Translocation of Double-stranded DNA Through Membrane-adapted phi29 Motor Protein Nanopores[J]. Nat Nanotechnol, 2009,4(11):765-772. doi: 10.1038/nnano.2009.259
Wang H Y, Ying Y L, Li Y. Peering into Biological Nanopore:A Practical Technology to Single-molecule Analysis[J]. Chem Asian J, 2010,5(9):1952-1961. doi: 10.1002/asia.201000279
Iacovache I, Paumard P, Scheib H. A Rivet Model for Channel Formation by Aerolysin-like Pore-forming Toxins[J]. EMBO J, 2006,25(3):457-466. doi: 10.1038/sj.emboj.7600959
Song L, Hobaugh M R, Shustak C. Structure of Staphylococcal Alpha-hemolysin, a Heptameric Transmembrane Pore[J]. Science, 1996,274(5294):1859-1866. doi: 10.1126/science.274.5294.1859
Akeson M, Branton D, Kasianowicz J J. Microsecond Time-scale Discrimination Among Polycytidylic Acid, Polyadenylic Acid, and Polyuridylic Acid as Homopolymers or as Segments Within Single RNA Molecules[J]. Biophys J, 1999,77(6):3227-3233. doi: 10.1016/S0006-3495(99)77153-5
Pastoriza-Gallego M, Rabah L, Gibrat G. Dynamics of Unfolded Protein Transport Through an Aerolysin Pore[J]. J Am Chem Soc, 2011,133(9):2923-2931. doi: 10.1021/ja1073245
Gouaux J E, Braha O, Hobaugh M R. Subunit Stoichiometry of Staphylococcal Alpha-hemolysin in Crystals and on Membranes:A Heptameric Transmembrane Pore[J]. Proc Natl Acad Sci USA, 1994,91(26):12828-12831. doi: 10.1073/pnas.91.26.12828
Braha O, Walker B, Cheley S. Designed Protein Pores as Components for Biosensors[J]. Chem Biol, 1997,4(7):497-505. doi: 10.1016/S1074-5521(97)90321-5
Parker M W, Buckley J T, Postma J P. Structure of the Aeromonas Toxin Proaerolysin in Its Water-soluble and Membrane-channel States[J]. Nature, 1994,367(6460):292-295. doi: 10.1038/367292a0
Degiacomi M T, Iacovache I, Pernot L. Molecular Assembly of the Aerolysin Pore Reveals a Swirling Membrane-insertion Mechanism[J]. Nat Chem Biol, 2013,9(10):623-629. doi: 10.1038/nchembio.1312
Merstorf C, Cressiot B, Pastoriza-Gallego M. Wild Type, Mutant Protein Unfolding and Phase Transition Detected by Single-nanopore Recording[J]. ACS Chem Biol, 2012,7(4):652-658. doi: 10.1021/cb2004737
Cressiot B, Braselmann E, Oukhaled A. Dynamics and Energy Contributions for Transport of Unfolded Pertactin Through a Protein Nanopore[J]. ACS Nano, 2015,9(9):9050-9061. doi: 10.1021/acsnano.5b03053
Fennouri A, Daniel R, Pastoriza-Gallego M. Kinetics of Enzymatic Degradation of High Molecular Weight Polysaccharides Through a Nanopore:Experiments and Data-modeling[J]. Anal Chem, 2013,85(18):8488-8492. doi: 10.1021/ac4020929
Derrington I M, Butler T Z, Collins M D. Nanopore DNA Sequencing with MspA[J]. Proc Natl Acad Sci USA, 2010,107(37):16060-16065. doi: 10.1073/pnas.1001831107
Heinz C, Karosi S, Niederweis M. High-level Expression of the Mycobacterial Porin MspA in Escherichia coli and Purification of the Recombinant Protein[J]. J Chromatogr B Analyt Technol Biomed Life Sci, 2003,790(1/2):337-348.
Guasch A, Pous J, Ibarra B. Detailed Architecture of a DNA Translocating Machine:The High-resolution Structure of the Bacteriophage phi29 Connector Particle[J]. J Mol Biol, 2002,315(4):663-676. doi: 10.1006/jmbi.2001.5278
Jing P, Haque F, Vonderheide A P. Robust Properties of Membrane-embedded Connector Channel of Bacterial Virus phi29 DNA Packaging Motor[J]. Mol Biosyst, 2010,6(10):1844-1852. doi: 10.1039/c003010d
Kawano R, Schibel A E, Cauley C. Controlling the Translocation of Single-stranded DNA Through Alpha-hemolysin Ion Channels Using Viscosity[J]. Langmuir, 2009,25(2):1233-1237. doi: 10.1021/la803556p
Meller A, Nivon L, Brandin E. Rapid Nanopore Discrimination Between Single Polynucleotide Molecules[J]. Proc Natl Acad Sci USA, 2000,97(3):1079-1084. doi: 10.1073/pnas.97.3.1079
Rincon-Restrepo M, Mikhailova E, Bayley H. Controlled Translocation of Individual DNA Molecules Through Protein Nanopores with Engineered Molecular Brakes[J]. Nano Lett, 2011,11(2):746-750. doi: 10.1021/nl1038874
Cherf G M, Lieberman K R, Rashid H. Automated forward and Reverse Ratcheting of DNA in a Nanopore at 5-A Precision[J]. Nat Biotechnol, 2012,30(4):344-348. doi: 10.1038/nbt.2147
Lieberman K R, Cherf G M, Doody M J. Processive Replication of Single DNA Molecules in a Nanopore Catalyzed by phi29 DNA Polymerase[J]. J Am Chem Soc, 2010,132(50):17961-17972. doi: 10.1021/ja1087612
Stoddart D, Maglia G, Mikhailova E. Multiple Base-recognition Sites in a Biological Nanopore:Two Heads are Better than One[J]. Angew Chem Int Ed, 2010,49(3):556-559. doi: 10.1002/anie.200905483
Gu L Q, Cheley S, Bayley H. Capture of a Single Molecule in a Nanocavity[J]. Science, 2001,291(5504):636-640. doi: 10.1126/science.291.5504.636
Gu L Q, Braha O, Conlan S. Stochastic Sensing of Organic Analytes by a Pore-forming Protein Containing a Molecular Adapter[J]. Nature, 1999,398(6729):686-690. doi: 10.1038/19491
Clarke J, Wu H C, Jayasinghe L. Continuous Base Identification for Single-molecule Nanopore DNA Sequencing[J]. Nat Nanotechnol, 2009,4(4):265-270. doi: 10.1038/nnano.2009.12
Kumar S, Tao C, Chien M. PEG-labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis[J]. Sci Rep, 2012,2684. doi: 10.1038/srep00684
Manrao E A, Derrington I M, Laszlo A H. Reading DNA at Single-nucleotide Resolution with a Mutant MspA Nanopore and phi29 DNA Polymerase[J]. Nat Biotechnol, 2012,30(4):349-353. doi: 10.1038/nbt.2171
Pennisi E. Genome Sequencing[J]. Science, 2012,336(6081):534-537. doi: 10.1126/science.336.6081.534
Stranges P B, Palla M, Kalachikov S. Design and Characterization of a Nanopore-coupled Polymerase for Single-molecule DNA Sequencing by Synthesis on an Electrode Array[J]. Proc Natl Acad Sci USA, 2016,113(44):E6749-E6756. doi: 10.1073/pnas.1608271113
Henrickson S E, Misakian M, Robertson B. Driven DNA Transport into an Asymmetric Nanometer-scale Pore[J]. Phys Rev Lett, 2000,85(14):3057-3060. doi: 10.1103/PhysRevLett.85.3057
Sauer-Budge A F, Nyamwanda J A, Lubensky D K. Unzipping Kinetics of Double-stranded DNA in a Nanopore[J]. Phys Rev Lett, 2003,90(23)238101. doi: 10.1103/PhysRevLett.90.238101
Bates M, Burns M, Meller A. Dynamics of DNA Molecules in a Membrane Channel Probed by Active Control Techniques[J]. Biophys J, 2003,84(4):2366-2372. doi: 10.1016/S0006-3495(03)75042-5
Wang Y, Zheng D, Tan Q. Nanopore-based Detection of Circulating MicroRNAs in Lung Cancer Patients[J]. Nat Nanotechnol, 2011,6(10):668-674. doi: 10.1038/nnano.2011.147
Xi D, Shang J, Fan E. Nanopore-Based Selective Discrimination of MicroRNAs with Single-Nucleotide Difference Using Locked Nucleic Acid-Modified Probes[J]. Anal Chem, 2016,88(21):10540-10546. doi: 10.1021/acs.analchem.6b02620
Tian K, Decker K, Aksimentiev A. Interference-Free Detection of Genetic Biomarkers Using Synthetic Dipole-Facilitated Nanopore Dielectrophoresis[J]. ACS Nano, 2017,11(2):1204-1213. doi: 10.1021/acsnano.6b07570
Cao C, Ying Y L, Hu Z L. Discrimination of Oligonucleotides of Different Lengths with a Wild-type Aerolysin Nanopore[J]. Nat Nanotechnol, 2016,11(8):713-718. doi: 10.1038/nnano.2016.66
Movileanu L, Schmittschmitt J P, Scholtz J M. Interactions of Peptides with a Protein Pore[J]. Biophys J, 2005,89(2):1030-1045. doi: 10.1529/biophysj.104.057406
Mohammad M M, Prakash S, Matouschek A. Controlling a Single Protein in a Nanopore Through Electrostatic Traps[J]. J Am Chem Soc, 2008,130(12):4081-4088. doi: 10.1021/ja710787a
Wolfe A J, Mohammad M M, Cheley S. Catalyzing the Translocation of Polypeptides Through Attractive Interactions[J]. J Am Chem Soc, 2007,129(45):14034-14041. doi: 10.1021/ja0749340
Wang H Y, Ying Y L, Li Y. Nanopore Analysis of Beta-amyloid Peptide Aggregation Transition Induced by Small Molecules[J]. Anal Chem, 2011,83(5):1746-1752. doi: 10.1021/ac1029874
Wang H Y, Gu Z, Cao C. Analysis of a Single Alpha-synuclein Fibrillation by the Interaction with a Protein Nanopore[J]. Anal Chem, 2013,85(17):8254-8261. doi: 10.1021/ac401496x
Rodriguez-Larrea D, Bayley H. Multistep Protein Unfolding During Nanopore Translocation[J]. Nat Nanotechnol, 2013,8(4):288-295. doi: 10.1038/nnano.2013.22
Rosen C B, Rodriguez-Larrea D, Bayley H. Single-molecule Site-specific Detection of Protein Phosphorylation with a Nanopore[J]. Nat Biotechnol, 2014,32(2):179-181. doi: 10.1038/nbt.2799
Soskine M, Biesemans A, De Maeyer M. Tuning the Size and Properties of ClyA Nanopores Assisted by Directed Evolution[J]. J Am Chem Soc, 2013,135(36):13456-13463. doi: 10.1021/ja4053398
Fahie M, Chisholm C, Chen M. Resolved Single-molecule Detection of Individual Species Within a Mixture of Anti-biotin Antibodies Using an Engineered Monomeric Nanopore[J]. ACS Nano, 2015,9(2):1089-1098. doi: 10.1021/nn506606e
Zhang X, Xu X, Yang Z. Mimicking Ribosomal Unfolding of RNA Pseudoknot in a Protein Channel[J]. J Am Chem Soc, 2015,137(50):15742-15752. doi: 10.1021/jacs.5b07910
Zhang L, Zhang K, Liu G. Label-free Nanopore Proximity Bioassay for Platelet-derived Growth Factor Detection[J]. Anal Chem, 2015,87(11):5677-5682. doi: 10.1021/acs.analchem.5b00791
Li T, Liu L, Li Y. A Universal Strategy for Aptamer-based Nanopore Sensing Through Host-guest Interactions Inside Alpha-hemolysin[J]. Angew Chem Int Ed, 2015,54(26):7568-7571. doi: 10.1002/anie.201502047
Braha O, Webb J, Gu L Q. Carriers Versus Adapters in Stochastic Sensing[J]. ChemPhysChem, 2005,6(5):889-892. doi: 10.1002/(ISSN)1439-7641
Braha O, Gu L Q, Zhou L. Simultaneous Stochastic Sensing of Divalent Metal Ions[J]. Nat Biotechnol, 2000,18(9):1005-1007. doi: 10.1038/79275
Wen S, Zeng T, Liu L. Highly Sensitive and Selective DNA-based Detection of Mercury(Ⅱ) with Alpha-hemolysin Nanopore[J]. J Am Chem Soc, 2011,133(45):18312-18317. doi: 10.1021/ja206983z
Yang C, Liu L, Zeng T. Highly Sensitive Simultaneous Detection of Lead(Ⅱ) and Barium(Ⅱ) with G-quadruplex DNA in Alpha-hemolysin Nanopore[J]. Anal Chem, 2013,85(15):7302-7307. doi: 10.1021/ac401198d
Huang S, Romero-Ruiz M, Castell O K. High-throughput Optical Sensing of Nucleic Acids in a Nanopore Array[J]. Nat Nanotechnol, 2015,10(11):986-991. doi: 10.1038/nnano.2015.189
Gu Z, Ying Y L, Cao C. Accurate Data Process for Nanopore Analysis[J]. Anal Chem, 2015,87(2):907-913. doi: 10.1021/ac5028758
Zhang J, Liu X, Ying Y L. High-bandwidth Nanopore Data Analysis by Using a Modified Hidden Markov Model[J]. Nanoscale, 2017,9(10):3458-3465. doi: 10.1039/C6NR09135K
Gao R, Ying Y L, Yan B Y. An Integrated Current Measurement System for Nanopore Analysis[J]. Chinese Sci Bull, 2014,59(35):4968-4973. doi: 10.1007/s11434-014-0656-0
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A.α-HL[8]; B.Aerolysin[9]; C.MspA[6]; D.Phi29connector[7]
A.the structure of α-HL modified by cyclodextrin; B.residual current histogram of nucleotide; C.discrimination of the nucleotides based on the residual current
A.diagram of the combination between MspA nanopore and phi29 DNA polymerase; B.reading DNA with the nanopore