• 综述 •
林子涵, 陈煌, 董嘉伟, 赵道辉, 李理波. 纳米孔生物分子检测研究[J]. 化学进展, 2020, 32(5): 562-580.
Zihan Lin, Huang Chen, Jiawei Dong, Daohui Zhao, Libo Li. Nanopore-Based Biomolecular Detection[J]. Progress in Chemistry, 2020, 32(5): 562-580.
纳米孔单分子检测技术是一种集操作简单、灵敏度高、检测速度快、无需标记等优点的传感检测技术,广泛应用于蛋白质检测、基因测序和标志物检测等领域。基因测序的费用、灵敏度和精度是该检测技术的发展中亟待解决的主要问题,而开发新型的纳米孔材料则是解决这些问题的关键手段。本文从纳米孔材料的选择和设计角度出发,综述了三种不同的纳米孔,即蛋白质等生物纳米孔、固态纳米孔和新型二维材料纳米孔在生物分子检测方面的应用现状,并比较了生物纳米孔与固态纳米孔的差别。本文也重点阐述了二维材料纳米孔在生物分子检测中的实验和模拟研究进展。最后,对纳米孔检测技术的发展前景进行了展望。
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Company | Detection length | Application range | Website |
---|---|---|---|
454/Roche | 400 bp(single end) | Bacterial and viral genomes, multiplex PCR products, verification of point mutations, target detection of somatic mutations | http://www.454.com/ |
Illumina | 150~300 bp(paired end) | Complex genomes(human, mouse and plant) and a wide range of gene applications, RNA sequences, hybrid or multiplex PCR products, somatic mutation detection, forensics, noninvasive prenatal diagnosis | http://www.illumina.com/ |
ABI SOLiD | 75 bp(single end) or 50 bp(paired end) | Complex genomes(human, mouse and plant) and a wide range of gene applications, RNA sequences, hybrid or multiplex PCR products, somatic mutation detection | http://www.thermofisher.com/ |
Pacific Biosciences | Up to 40 kb(single end or circular consensus) | Complex genomes(human, mouse and plant), microbial and infectious disease genes, transcriptional fusion detection, methylation detection | http://www.pacb.com/ |
Ion Torrent | 200~400 bp(single end) | Multiplex PCR products, microbial and infectious disease genes, somatic mutation detection, point mutation verification | http://www.thermofisher.com/ |
Oxford Nanopore | Variable(1D or 2D reads) | Pathogen monitoring, targeted mutations, metagenomics, bacterial and viral genes | http://nanoporetech.com/ |
Qiagen GenReader | 107 bp(single end) | Targeted mutation detection, liquid biopsy in cancer | http://www.genereaderngs.com/ |
Detection technology | Detection principle | Advantage | ref |
---|---|---|---|
| By removing ions in the nanopore, the resistance of the nanopore ρL/πr 2(ρ, solution resistivity; L, pore length, and r, radius) is increased. The electric signal is obtained by changing the ion current of the Ag/AgCl electrode at the top and bottom of the nanopore. | The experimental device is simple, requiring only a single molecular size nanopore. Although the current depends on the concentration of the electrolyte, a relatively large current can be observed. | 26 |
| The tunneling current(It ) is detected during the perforation of the test object. The conductivity of the target single molecule is measured by the nanogap electrode embedded in the nanopore. | High spatial resolution is obtained by tunneling current, and DNA sensing based on single base recognition has been confirmed. | 29 |
| The potential change in the nanopore caused by the analyte molecule with charge q can be detected as the modulation of the gate voltage(ΔVg =Δq/C) by using a MOSFET device embedded in the nanopore. | The embedded MOSFET has high-speed performance and fast operation is feasible. The bottom-up process can be integrated by using the nanowire FET and graphene nanoribbon. | 30 |
Nanopore | pore | size/nm | Analyte | ref |
---|---|---|---|---|
α-HL | 1.4 | Metal ions, organic small molecules, RNA, ssDNA, amino acids, unfolded proteins, polymers, gold nanoparticles | [7AHL] | 45 |
MspA | 1.2 | ssDNA、dsDNA | [1UUN] | 51 |
Aerolysin | 1~1.7 | peptide, protein, DNA, RNA, organic small molecule | [5JZT] | 49, 52~61 |
OmpG | ~2 | Protein, antibody | [2F1C] | 62 |
FhuA | ~2.4 | Protein, Protein-ssDNA, polymer | [1BY3] | 63 |
Phi29 | 3.6 | ssDNA, dsDNA, Thioester antibody | [1FOU] | 64 |
SP1 | ~3 | ssDNA | [1TRO] | 65 |
ClyA | 3.3~4.2 | ssDNA, protein | [2WCD] | 66 |
VDAC | 2.5~3 | Tubulin, organic small molecule, dsDNA | [2JK4] | 67 |
Material | Minimum pore size | Analyte | ref |
---|---|---|---|
SiN | 3 nm | RNA + drug | 92 |
3.7 nm | dsDNA + γ-PNA | 93 | |
3~20 nm | RNAP + DNA | 94 | |
SiN/SiO2/SiN | 20 nm | histone nucleosome | 95 |
HfO2/SiNx | < 2 nm(HfO2) | ssDNA | 96 |
dsDNA | |||
graphene/SiO2 | 22 nm(single layer) | λ-DNA | 97 |
graphene/SiNx | 5 nm(1~2 layers) | 10 kb-DNA | 12 |
Al2O3/graphene/Al2O3 | 9 nm(graphene) | dsDNA | 98 |
dsDNA+protein | |||
TiO2/graphene/SiN/SiO2 | 8 nm(3~15 layers) | 15 kb-DNA | 99 |
chemical modified graphene | 5~15 nm | ssDNA | 100 |
MoS2/SiNx | 5 nm(few-layer MoS2) | λ-DNA | 101 |
DNA Origami/SiN | 15 nm(DNA origami) | dsDNA | 102 |
chemical modified SiN | 40 nm(SiN) | protein | 103 |
25 nm(modified SiN) | |||
chemical modified Au/SiN | 20~25 nm(modified Au) | His-tagged protein | 104 |
IgG-antiboby |
Material | Nano device | Signal characteristics | Biomolecular size | Ion concentration | ref |
---|---|---|---|---|---|
Graphene | Nanopore(5~25 nm) | Unfolded > partial folded > fully folded | λ-dsDNA(16 μm long) | 1 M KCl | 97 |
Graphene | Nanopore(5~10 nm) | Low SNR, fully folded > unfolded | dsDNA(15 kbp) | 1 M KCl | 99 |
Graphene | Nanopore(5 nm) | folded > unfolded | dsDNA | 3 M KCl | 12 |
Graphene | Nanopore(15~20 nm) | precision:1 M LiCl > 1 M KCl ≈ 1 M NaCl | dsDNA(48.5 kbp) | 1 M KCl, 1 M NaCl, 1 M LiCl | 131 |
Graphene | Nanoribbon | Blocking current + transverse current | dsDNA(2.7 kbp) | 1 M KCl | 132 |
Graphene | Nanopore | folded > unfolded | dsDNA | 3 M KCl | 100 |
Graphene | Nanopore(2.5~5 nm) | Aperture dependent | dsDNA(10 kbp) | 3 M KCl | 133 |
Graphene | Nanopore | Conductivity + ionic current | dsDNA(2.7 kbp) | 1 M KCl | 132 |
MoS2 | Nanopore(5 nm) | High SNR(> 10) | dsDNA(48 kbp) | 2 M KCl | 101 |
MoS2 | Nanopore(~2.8 nm) | polyA30 > polyT30 > polyC30 > polyG30 | dsDNA(48.5 kbp) | 2 M KCl | 14 |
h-BN | Nanopore(12.3 nm) | Unfolded > Partially folded | dsDNA(10 kbp) | 3 M KCl | 13 |
Au | Transistor | Conductivity | poly(GATC)x | 134 |
Material | Pore size (nm) | Simulation method | Signal characteristics | Molecular size | Ion concentration | ref | |
---|---|---|---|---|---|---|---|
graphene | 2.4 | MD | poly(G-C) > poly(A-T) | 45 bases | 1 M KCl | 142 | |
graphene | 1.1~1.5 | MD+BD | poly(A)≈poly(G)< poly(T) < poly(C) | 20 bases | 1.7 M KCl | 143 | |
graphene | 1.6~5.0 | MD | The SNR increases with the decrease of aperture | 45 bases | 1.0 M KCl | 144 | |
graphene | 2.0~3.0 | MD | Conductivity is related to pore thickness | 12 bases | 1.0 M NaCl | 129 | |
graphene | 2.4 | MD | The fluctuation of signal is related to the DNA structure | 48 bases | 1.0 M NaCl | 145 | |
graphene | 1.5 | MD | Increasing the number of graphene layers can improve the accuracy | 45 bases | 1.0 M KCl | 146 | |
graphene | 1.6 | MD | The charge regulates DNA perforation | 20 bases | 1.0 M KCl | 147 | |
graphene | 2.1 | MD | Hybrid hole can improve the detection accuracy | 20 bases | 1.0 M NaCl | 148 | |
graphene | 1.6 | MD | Ion current + perforation time | 15 bases | 1.0 M KCl | 149 | |
graphene | 2.2 | MD | The perforation rate is related to the type of polypeptide and the number of graphene layers | 48 residues | 1.0 M KCl | 150 | |
graphene | 10 | MD | IgG3 > IgG2 | IgG | 0.5 M NaCl | 151 | |
MoS2 | 2.3 | MD+DFT | SNR > 15 | 16 bases | 1.0 M NaCl | 130 | |
MoS2 | 2.5 | MD+DFT | Pull force + ionic current | 6 bases | 5 mM KCl | 152 | |
h-BN | 2.4 | MD | poly(A-T)40 <poly(G-C)40 | 40 bases | 1.0 M KCl | 153 | |
graphene | 1.5 | SMD | Pull force + ionic current | Thioredoxin | 2 M KCl | 154 | |
graphene | 1.0 | SMD | G > A > T > C | 11 bases | 155 | ||
graphene | 1.0 | SMD | G > A > T > C | 12 bases | 156 | ||
graphene | 1.1 | SMD | Dependent on the structure of the hole | 6 bases | 157 | ||
graphene | 1.6, 2.4 | SMD | Independent of pore size and shape | 14 bases | 1 M KCl | 158 |
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