纳米孔DNA单分子测序★

doi:10.6023/A25050179

化学学报 ›› 2025, Vol. 83 ›› Issue (9): 1089-1102.DOI: 10.6023/A25050179 上一篇下一篇

综述

纳米孔DNA单分子测序^★

白宏震, 谭皓璟, 冯建东^*()

浙江大学化学系物理生物学实验室杭州 310058

投稿日期:2025-05-19 发布日期:2025-07-09

作者简介:

白宏震, 浙江大学化学系副研究员, 主要从事功能高分子、纳米材料和单分子测量等方面研究. 发展面向生命科学和精准医学的分子传感技术和药物输送系统, 实现对生物过程和疾病通路的解析及调控.

谭皓璟, 浙江大学化学系博士研究生, 研究内容为基于纳米孔的单分子测量以及纳米尺度流体传输现象和物理机制探索.

冯建东, 浙江大学求是特聘教授, 化学、光学工程博导, 主要从事单分子操控、测量、超分辨成像方法和科学装置研究. 发展单分子电学、光学、化学、量子测量等实验手段, 研制精密测量科学装置, 实现面向物质、信息极限的分子测量和数字化认知.

^★ “中国青年化学家”专辑.

基金资助:
国家重点研发计划(2020YFA0211200); 国家自然科学基金面上(22175153); 新基石科学基金会科学探索奖资助

Nanopore-based Single-molecule DNA Sequencing^★

Hongzhen Bai, Haojing Tan, Jiandong Feng^*()

Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, Hangzhou 310058

Received:2025-05-19 Published:2025-07-09
Contact: * E-mail: jiandong.feng@zju.edu.cn
About author:
^★ For the VSI “Rising Stars in Chemistry”.
Supported by:
National Key R&D Program of China(2020YFA0211200); National Natural Science Foundation of China(22175153); New Cornerstone Science Foundation through the XPLORER Prize

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摘要/Abstract

纳米孔测序技术作为一种革命性的单分子测序方法, 利用限域纳米孔与DNA分子的非共价相互作用解析碱基信息, 进而从单分子水平读取DNA序列. 这种直接的物理读取方法具有无标记、长读长、高通量、低成本和实时检测等独特优势, 在基因组学、医学研究等领域展现出巨大应用潜力. 本文系统性综述了纳米孔单分子测序的原理与发展历程, 重点阐述了纳米孔测量空间分辨率提升策略、基于马达蛋白的测序时间分辨率控制策略、纳米孔测序系统的构建, 并探讨这些关键因素之间的相互关系及影响. 在此基础上, 讨论纳米孔测序技术的应用现状与发展趋势.

关键词: 单分子测量, 生物纳米孔, DNA测序, 基因组学

As a revolutionary single-molecule sequencing technology, nanopore DNA sequencing technology leverages the non-covalent interactions between nano-confined sensing interfaces and DNA molecules to parse the base information, then reading the DNA sequence at the single-molecule level. This physical method for direct reading of DNA offers unique advantages such as label-free, long reads, high-throughput, cost-effective, and real-time detection, demonstrating immense potential in genomics research and medicine science. This review summarizes the principles and development history of biological nanopore-based single-molecule DNA sequencing, focusing on key aspects including the engineering of biological nanopores for spatial resolution improvement, motor protein-based strategies of DNA translocation for time resolution control, and the construction of nanopore sequencing systems, then going deep into the underlying connection of these factors. Based on these, the current application and future development of nanopore-based single-molecule sequencing technology has been discussed.

Key words: single-molecule measurement, biological nanopores, DNA sequencing, genomics

引用此文

白宏震, 谭皓璟, 冯建东. 纳米孔DNA单分子测序^★[J]. 化学学报, 2025, 83(9): 1089-1102.

Hongzhen Bai, Haojing Tan, Jiandong Feng. Nanopore-based Single-molecule DNA Sequencing^★[J]. Acta Chimica Sinica, 2025, 83(9): 1089-1102.

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图/表 7

图1. 纳米孔测序的基本概念与原理示意图. (a)纳米孔单分子测序平台示意图. 在测量槽中注入电解质溶液(通常为KCl缓冲液), 由一片特氟龙薄膜分割为两个腔室. 薄膜中间有一个直径约100 μm的支撑孔, 用来结合磷脂双分子层. 随后加入生物纳米孔, 使其自发插入磷脂层, 形成测量通道[86]. 灰色为磷脂膜, 蓝色孔道为生物纳米孔. (b) MspA纳米孔结构及传感区示意图. 在磷脂双分子层的两侧插入电极, cis侧为负电压, trans侧为正电压. I0表示没有分析物穿孔时的纳米孔内离子电流. (c) MspA纳米孔测序示意图: 单链DNA与DNA聚合酶phi29形成复合物, 这种复合物能稳定保持在纳米孔端口. 在聚合酶的作用下, 单链DNA开始合成双螺旋结构. 在该过程中, 聚合酶的引物延伸“力量”驱动单链DNA在纳米孔内的步进易位, 逐个碱基地从纳米孔向上拉出单链DNA. 单链DNA分子进入传感区后阻塞孔道使得离子电流降低, 从而产生阻塞电流信号Ib. (d)纳米孔阻塞电流与测序: 不同序列的单链DNA穿过纳米孔时产生不同持续时间和幅度的阻塞电流[31]. 通过分析堵孔深度和堵孔时间, 可以在单分子水平上对DNA进行直接传感, 通过碱基识别算法分析DNA序列信息.

Figure 1. Schematic illustration of the basic concepts and principles of nanopore DNA sequencing. (a) Schematic diagram of the nanopore single-molecule sequencing platform. The electrolyte solution (usually KCl buffer) is injected into the measurement tank, and the tank is divided into two chambers by a Teflon film. There is a support pore with a diameter of approximately 100 μm in the middle of the film, which is used to bind the phospholipid bilayer. Subsequently, biological nanopores are added in the solution to spontaneously insert into the phospholipid layer, forming a nanoscale measurement channel[86]. Phospholipid membrane is shown in gray, and the biological nanopores are presented as blue channels. (b) Schematic diagram of the structure and sensing area of MspA nanopores. A pair of electrodes is inserted into the two sides of the phospholipid bilayer, with a negative voltage on the cis side and a positive voltage on the trans side. I0 represents the ion current within the nanopores when no analyte is perforated. (c) Schematic of MspA nanopore sequencing. Single-stranded DNA (ssDNA) forms a complex with the DNA polymerase phi29, and this complex can stably remain at the nanopore port. Under the action of polymerase, ssDNA begins to synthesize the double helix structure. During this process, the primer extension "force" of the polymerase drives the stepped-translocation of ssDNA within the nanopores, pulling out the ssDNA from the nanopores one base at a time. When ssDNA molecules enter the sensing region, they block the nano-channels, reducing the ionic current and thereby generating the blocking current signal Ib. (d) Nanopore blockade current and sequencing. When ssDNA molecules with different sequences pass through nanopores, blocking currents with different durations and amplitudes are generated[31]. By analyzing the depth and time of blockade currents, DNA can be directly sensed at the single-molecule level, and the DNA sequence information can be analyzed through base calling algorithms.

图2. 五种生物纳米孔的发现时间、结构与关键位点. 从左到右依次为α-HL、Aerolysin、MspA、FraC和CsgG纳米孔. 纳米孔蛋白质骨架以灰色表示, 关键突变位点范德华面表示, 传感区以绿色透明区域表示. 图中蛋白结构来自RCSB Protein Data Bank数据库. α-HL纳米孔是最早被应用于DNA单分子测量的生物纳米孔[24], 其传感区的空间分辨率能够区分嘌呤与吡啶片段. Aerolysin纳米孔具有类似于α-HL纳米孔的长且狭窄的传感区. 但相较于α-HL纳米孔, Aerolysin纳米孔的传感区内部具有更多的关键位点, 有利于构建多样的功能化孔道[60]. 相比于前两者, MspA纳米孔具有更短和更窄的单分子传感区, 在DNA测序方面表现出高分辨率优势[31]. FraC纳米孔特点是其跨膜域由α-螺旋而非β-桶构成, 具有可调的孔径[77]. CsgG纳米孔被开发应用于牛津纳米孔的商业化DNA测序平台, 其特点是可与CsgF形成CsgG-CsgF复合纳米孔[85], 该复合孔具有一个次级传感区域用以增强传感性能.

Figure 2. Discovery, structure, and key mutation sites of five biological nanopores. From left to right: schematic diagrams of the structure and key mutation sites of α-HL, Aerolysin, MspA, FraC, and CsgG nanopores. Protein backbones of these nanopores are shown in grey, amino acids at key mutation sites are shown as van der Waals surfaces, and the sensing regions are presented with Green transparent areas. Protein structures in the schematic diagram are from RCSB PDB database. α-HL nanopores are the earliest biological nanopores to be applied in DNA single-molecule measurement[24], and the spatial resolution of their sensing regions can distinguish between purine and pyridine fragments. Aerolysin nanopores have long and narrow sensing regions similar to α-HL nanopores. Compared with α-HL nanopores, the sensing regions of Aerolysin nanopores have more key sites, which is conducive to the construction of diverse functional channels[60]. Compared with the former two, MspA nanopores exhibit high-resolution advantages in DNA sequencing due to their shorter and narrower single-molecule sensing regions[31]. Frac nanopores are characterized by their α-helix-typed transmembrane domains rather than β-folding structures[77], which endows the Frac nanopores with tunable pore sizes. CsgG nanopores have been developed and applied to the commercial DNA sequencing platform of ONT. They can form CsgG-CsgF composite nanopores with CsgF[85], and this kind of composite nanopores has a secondary sensing region to enhance the sensing performance.

纳米孔	直径/nm	长度/nm	孔径/nm	来源
α-HL	10	10	1.4	Staphylococcus aureus
Aerolysin	16	10	1.8	Aeromonas hydrophila
MspA	8.8	9.6	1.2	Mycobacterium smegmatis
FraC	11	7.0	1.6	Actinia fragacea
CsgG	9.4	9.6	1.2	Escherichia coli

表1. 五种生物纳米孔的结构信息表. 结构数据源于RCSB Protein Data Bank数据库(α-HL, PDB ID: 3ANZ; Aerolysin, PDB ID: 5JZH; MspA, PDB ID: 1UUN; FraC, PDB ID: 4TSY; CsgG, PDB ID: 4UV3)

Table 1. Structural information table of five types of biological nanopores. The structural data is originated from the RCSB Protein Data Bank database (α-HL, PDB ID: 3ANZ; Aerolysin, PDB ID: 5JZH; MspA, PDB ID: 1UUN; FraC, PDB ID: 4TSY; CsgG, PDB ID: 4UV3)

图3. 马达蛋白调控DNA孔内易位动力学示意图. MspA纳米孔以蓝色表示, 马达蛋白以黄色表示. (a) phi29控速机制及特点: 通过聚合反应, phi29在合成DNA双链的同时将待测DNA单链步进牵引穿过纳米孔. 箭头指示待测DNA的运动方向. (b) Hel308控速机制及特点: 通过ATP水解循环, Hel308步进解开DNA双螺旋, 使得待测DNA步进易位穿过纳米孔. 箭头指示待测DNA链的运动方向.

Figure 3. Schematic diagram of motor proteins controlling the kinetics of DNA translocation within nanopores. MspA nanopores are presented in blue, and motor proteins are shown in yellow. (a) phi29 speed control mechanism and characteristics: Through polymerization reaction, phi29 gradually pulls the single strand of the DNA translocating through the nanopore while synthesizing the double strands of DNA. The arrow indicates the movement direction of the DNA. (b) Hel308 speed control mechanism and characteristics: Through the ATP hydrolysis cycle, Hel308 step by step unties the DNA double helix, allowing the DNA translocation in the nanopore. The arrow indicates the movement direction of the DNA.

图4. 影响纳米孔单分子平台的测序准确性和测序效率的关键因素, 包括: 基于纳米孔结构改造的测序空间分辨率优化(正上, 突变型CytK纳米孔, 蛋白结构数据来自RCSB PDB网站 https://www.rcsb.org)、基于马达蛋白的DNA易位动力学控制及测序时间分辨率优化(左中, phi29聚合酶-DNA复合物, 结构数据来自Alamy网站 https://www.alamy.com)、碱基识别算法及测序程序(右中, base calling算法流程示意图)、基于多通道流体槽并行工作的高通量测序技术(左下, 高通量测序系统示意图)、基于in-chip构架的集成化测序系统(右下, 集成化纳米孔测序平台示意图).

Figure 4. The key factors affecting the sequencing accuracy and efficiency of nanopore single-molecule platforms include: Sequencing spatial resolution optimization based on nanopore structure modification (top, mutant CytK nanopore, protein structure data from RCSB PDB website, https://www.rcsb.org), DNA translocation dynamics control and sequencing time resolution optimization based on motor proteins (middle left, phi29 polymerase-DNA complex, structural model data from Alamy website, https://www.alamy.com), base calling algorithm and sequencing program (middle right, schematic diagram of base calling algorithm flow), high-throughput sequencing technology based on the parallel operation of multi-channel fluid channels (lower left, high-throughput sequencing system schematic diagram) and integrated sequencing system based on in-chip architecture (lower right, integrated nanopore sequencing platform).

图5. 纳米孔DNA测序技术应用场景, 包括: 基因组学、精准医学与疫情监测和实时实地测序. 基因组学研究示意图及新型冠状病毒序列示意图分别引用自参考文献[137]、[143]并获得许可. 空间站测序示意图来自网站新闻图片(www.nasaspaceflight.com).

Figure 5. The application scenarios of nanopore DNA sequencing technology include: genomics research, precision medicine and epidemic supervision, and real-time on-site sequencing. The schematic diagrams of genomic research and the sequence diagrams of the novel coronavirus are respectively cited from references [137] and [143] and have been granted permission. The schematic diagram of the space station's sequencing is from the news photo at www.nasaspaceflight.com.

公司	测序仪	读长	吞吐量	准确率	应用举例
华大智造	CycloneSEQ-WT02	Mb	50 Gb×2	97%	病原检测
普译生物	PolyseqOne	200 kb	20 Gb	97%	环境测序
齐碳科技	QNome-3841hex	Mb	5 Gb×6	90%	组学研究
	QPursue-6khex	Mb	60 Gb×6	97%	临床诊断
安序源	AXP100	100 kb	100 Gb	99%	基因筛查

表2. 近三年我国企业研发的纳米孔单分子测序仪仪器信息表. CycloneSEQ-WT02发布于2024年9月, PolyseqOne发布于2024年1月, QNome-3841hex发布于2022年6月, QPursue-6khex发布于2023年8月, AXP100发布于2023年5月.

Table 2. Information table of nanopore single-molecule sequencers developed by Chinese enterprises in the past three years. CycloneSEQ-WT02 was released in September 2024, PolyseqOne in January 2024, QNome-3841hex in June 2022, QPursue-6khex in August 2023, and AXP100 in May 2023.

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[2]	曹婵, 廖冬芳, 应佚伦, 龙亿涛. Aerolysin纳米孔道对寡聚核苷酸的高灵敏单分子检测[J]. 化学学报, 2016, 74(9): 734-737.
[3]	赵超, 汪海林. DNA羟甲基化测序技术[J]. 化学学报, 2013, 71(01): 26-35.

纳米孔DNA单分子测序★

Nanopore-based Single-molecule DNA Sequencing★

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纳米孔DNA单分子测序^★

Nanopore-based Single-molecule DNA Sequencing^★