1
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Kumawat RL, Jena MK, Mittal S, Pathak B. Advancement of Next-Generation DNA Sequencing through Ionic Blockade and Transverse Tunneling Current Methods. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2401112. [PMID: 38716623 DOI: 10.1002/smll.202401112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/05/2024] [Indexed: 10/04/2024]
Abstract
DNA sequencing is transforming the field of medical diagnostics and personalized medicine development by providing a pool of genetic information. Recent advancements have propelled solid-state material-based sequencing into the forefront as a promising next-generation sequencing (NGS) technology, offering amplification-free, cost-effective, and high-throughput DNA analysis. Consequently, a comprehensive framework for diverse sequencing methodologies and a cross-sectional understanding with meticulous documentation of the latest advancements is of timely need. This review explores a broad spectrum of progress and accomplishments in the field of DNA sequencing, focusing mainly on electrical detection methods. The review delves deep into both the theoretical and experimental demonstrations of the ionic blockade and transverse tunneling current methods across a broad range of device architectures, nanopore, nanogap, nanochannel, and hybrid/heterostructures. Additionally, various aspects of each architecture are explored along with their strengths and weaknesses, scrutinizing their potential applications for ultrafast DNA sequencing. Finally, an overview of existing challenges and future directions is provided to expedite the emergence of high-precision and ultrafast DNA sequencing with ionic and transverse current approaches.
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Affiliation(s)
- Rameshwar L Kumawat
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
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2
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Xie Z, Chen Z, Li A, Huang B, Guo C, Zhai Y. Specific Small-Molecule Detection Using Designed Nucleic Acid Nanostructure Carriers and Nanopores. Anal Chem 2024; 96:8528-8533. [PMID: 38728651 DOI: 10.1021/acs.analchem.4c00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
In the realm of nanopore sensor technology, an enduring challenge lies in achieving the discerning detection of small biomolecules with a sufficiently high signal-to-noise ratio. This study introduces a method for reliably quantifying the concentration of target small molecules, utilizing tetrahedral DNA nanostructures as surrogates for the captured molecules through a magnetic-bead-based competition substitution mechanism. Magnetic Fe3O4-DNA tetrahedron nanoparticles (MNPs) are incorporated into a nanopore electrochemical system for small-molecule sensing. In the presence of the target, the DNA tetrahedron, featuring an aptamer tail acting as a molecular carrier, detaches from the MNPs due to aptamer deformation. Following removal of the MNPs, the DNA tetrahedron bound to the target traversed the nanopore by applying a positive potential. This approach exhibits various advantages, including heightened sensitivity, selectivity, an improved signal-to-noise ratio (SNR), and robust anti-interference capabilities. Our findings demonstrate that this innovative methodology has the potential to significantly enhance the sensing of various small-molecule targets by nanopores, thereby advancing the sensitivity and dynamic range. This progress holds promise for the development of precise clinical diagnostic tools.
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Affiliation(s)
- Zhipeng Xie
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, Hubei, P. R. China
| | - Zihao Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, Hubei, P. R. China
| | - Aijia Li
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, Hubei, P. R. China
| | - Bing Huang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei, P. R. China
| | - Cunlan Guo
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei, P. R. China
| | - Yueming Zhai
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, Hubei, P. R. China
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3
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Ji CM, Feng XY, Huang YW, Chen RA. The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research. Viruses 2024; 16:798. [PMID: 38793679 PMCID: PMC11125791 DOI: 10.3390/v16050798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, an increasing number of viruses have triggered outbreaks that pose a severe threat to both human and animal life, as well as caused substantial economic losses. It is crucial to understand the genomic structure and epidemiology of these viruses to guide effective clinical prevention and treatment strategies. Nanopore sequencing, a third-generation sequencing technology, has been widely used in genomic research since 2014. This technology offers several advantages over traditional methods and next-generation sequencing (NGS), such as the ability to generate ultra-long reads, high efficiency, real-time monitoring and analysis, portability, and the ability to directly sequence RNA or DNA molecules. As a result, it exhibits excellent applicability and flexibility in virus research, including viral detection and surveillance, genome assembly, the discovery of new variants and novel viruses, and the identification of chemical modifications. In this paper, we provide a comprehensive review of the development, principles, advantages, and applications of nanopore sequencing technology in animal and human virus research, aiming to offer fresh perspectives for future studies in this field.
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Affiliation(s)
- Chun-Miao Ji
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
| | - Xiao-Yin Feng
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
| | - Yao-Wei Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rui-Ai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
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4
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Yao G, Ke W, Xia B, Gao Z. Nanopore-based glycan sequencing: state of the art and future prospects. Chem Sci 2024; 15:6229-6243. [PMID: 38699252 PMCID: PMC11062086 DOI: 10.1039/d4sc01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Sequencing of biomacromolecules is a crucial cornerstone in life sciences. Glycans, one of the fundamental biomolecules, derive their physiological and pathological functions from their structures. Glycan sequencing faces challenges due to its structural complexity and current detection technology limitations. As a highly sensitive sensor, nanopores can directly convert nucleic acid sequence information into electrical signals, spearheading the revolution of third-generation nucleic acid sequencing technologies. However, their potential for deciphering complex glycans remains untapped. Initial attempts demonstrated the significant sensitivity of nanopores in glycan sensing, which provided the theoretical basis and insights for the realization of nanopore-based glycan sequencing. Here, we present three potential technical routes to employ nanopore technology in glycan sequencing for the first time. The three novel technical routes include: strand sequencing, capturing glycan chains as they translocate through nanopores; sequential hydrolysis sequencing, capturing released monosaccharides one by one; splicing sequencing, mapping signals from hydrolyzed glycan fragments to an oligosaccharide database/library. Designing suitable nanopores, enzymes, and motors, and extracting characteristic signals pose major challenges, potentially aided by artificial intelligence. It would be highly desirable to design an all-in-one high-throughput glycan sequencer instrument by integrating a sample processing unit, nanopore array, and signal acquisition system into a microfluidic device. The nanopore sequencer invention calls for intensive multidisciplinary cooperation including electrochemistry, glycochemistry, engineering, materials, enzymology, etc. Advancing glycan sequencing will promote the development of basic research and facilitate the discovery of glycan-based drugs and disease markers, fostering progress in glycoscience and even life sciences.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- School of Life Science and Technology, Shanghai Tech University 201210 Shanghai China
- Lingang Laboratory 200031 Shanghai China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 528400 Zhongshan China
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5
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Xia B, Fang J, Ma S, Ma M, Yao G, Li T, Cheng X, Wen L, Gao Z. Mapping the Acetylamino and Carboxyl Groups on Glycans by Engineered α-Hemolysin Nanopores. J Am Chem Soc 2023; 145:18812-18824. [PMID: 37527445 DOI: 10.1021/jacs.3c03563] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Glycan is a crucial class of biological macromolecules with important biological functions. Functional groups determine the chemical properties of glycans, which further affect their biological activities. However, the structural complexity of glycans has set a technical hurdle for their direct identification. Nanopores have emerged as highly sensitive biosensors that are capable of detecting and characterizing various analytes. Here, we identified the functional groups on glycans with a designed α-hemolysin nanopore containing arginine mutations (M113R), which is specifically sensitive to glycans with acetamido and carboxyl groups. Molecular dynamics simulations indicated that the acetamido and carboxyl groups of the glycans produce unique electrical signatures by forming polar and electrostatic interactions with the M113R nanopores. Using these electrical features as the fingerprints, we mapped the length of the glycans containing acetamido and carboxyl groups at the monosaccharide, disaccharide, and trisaccharide levels. This proof-of-concept study provides a promising foundation for developing single-molecule glycan fingerprinting libraries and demonstrates the capability of biological nanopores in glycan sequencing.
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Affiliation(s)
- Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jie Fang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Shengzhou Ma
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mengyao Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- Lingang Laboratory, School of Life Science and Technology, Shanghai Tech University, Shanghai 200031, China
| | - Tiehai Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, China
| | - Liuqing Wen
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China
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6
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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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7
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Chapman R, Jones L, D'Angelo A, Suliman A, Anwar M, Bagby S. Nanopore-Based Metagenomic Sequencing in Respiratory Tract Infection: A Developing Diagnostic Platform. Lung 2023; 201:171-179. [PMID: 37009923 PMCID: PMC10067523 DOI: 10.1007/s00408-023-00612-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/14/2023] [Indexed: 04/04/2023]
Abstract
Respiratory tract infection (RTI) remains a significant cause of morbidity and mortality across the globe. The optimal management of RTI relies upon timely pathogen identification via evaluation of respiratory samples, a process which utilises traditional culture-based methods to identify offending microorganisms. This process can be slow and often prolongs the use of broad-spectrum antimicrobial therapy, whilst also delaying the introduction of targeted therapy as a result. Nanopore sequencing (NPS) of respiratory samples has recently emerged as a potential diagnostic tool in RTI. NPS can identify pathogens and antimicrobial resistance profiles with greater speed and efficiency than traditional sputum culture-based methods. Increased speed to pathogen identification can improve antimicrobial stewardship by reducing the use of broad-spectrum antibiotic therapy, as well as improving overall clinical outcomes. This new technology is becoming more affordable and accessible, with some NPS platforms requiring minimal sample preparation and laboratory infrastructure. However, questions regarding clinical utility and how best to implement NPS technology within RTI diagnostic pathways remain unanswered. In this review, we introduce NPS as a technology and as a diagnostic tool in RTI in various settings, before discussing the advantages and limitations of NPS, and finally what the future might hold for NPS platforms in RTI diagnostics.
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Affiliation(s)
- Robert Chapman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK.
| | - Luke Jones
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Alberto D'Angelo
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Ahmed Suliman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Muhammad Anwar
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
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8
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Liang L, Qin F, Wang S, Wu J, Li R, Wang Z, Ren M, Liu D, Wang D, Astruc D. Overview of the materials design and sensing strategies of nanopore devices. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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9
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MacKenzie M, Argyropoulos C. An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations. MICROMACHINES 2023; 14:459. [PMID: 36838159 PMCID: PMC9966803 DOI: 10.3390/mi14020459] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
There has been significant progress made in the field of nanopore biosensor development and sequencing applications, which address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making the platforms a mainstay in contemporary research laboratories. Equipped with the ability to provide long- and short read sequencing information, with quick turn-around times and simple sample preparation, nanopore sequencers are rapidly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We present examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.
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Affiliation(s)
- Morgan MacKenzie
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Christos Argyropoulos
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
- Clinical & Translational Science Center, Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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10
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Chen P, Sun Z, Wang J, Liu X, Bai Y, Chen J, Liu A, Qiao F, Chen Y, Yuan C, Sha J, Zhang J, Xu LQ, Li J. Portable nanopore-sequencing technology: Trends in development and applications. Front Microbiol 2023; 14:1043967. [PMID: 36819021 PMCID: PMC9929578 DOI: 10.3389/fmicb.2023.1043967] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.
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Affiliation(s)
- Pin Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zepeng Sun
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Jiawei Wang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Xinlong Liu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yun Bai
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jiang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Anna Liu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Feng Qiao
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Chenyan Yuan
- Clinical Laboratory, Southeast University Zhongda Hospital, Nanjing, China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, China
| | - Jinghui Zhang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Li-Qun Xu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China,*Correspondence: Li-Qun Xu, ✉
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China,Jian Li, ✉
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11
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Wang Y, Li Y, Zhou X, Zhang W, Zhang S, Xi D. Detection of Tobacco Bacterial Wilt Caused by Ralstonia solanacearum by Combining Polymerase Chain Reaction with an α-Hemolysin Nanopore. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:332. [PMID: 36678085 PMCID: PMC9863824 DOI: 10.3390/nano13020332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Tobacco bacterial wilt is a serious disease caused by the soil-borne bacterium Ralstonia solanacearum (R. solanacearum). Herein, a rapid and purification-free α-hemolysin (α-HL) nanopore-sensing strategy based on polymerase chain reaction (PCR) and lambda exonuclease digestion was established to detect R. solanacearum. A 198-nucleotide-long single-stranded DNA was obtained via asymmetric PCR or the lambda exonuclease-mediated digestion of the PCR product. The DNA fragment produced unique long-lived, current-blocking signals when it passed through the α-HL nanopore. This sensing approach can allow for the determination of R. solanacearum in tobacco samples and can be conveniently extended to other DNA monitoring because of the extremely wide range of PCR applications.
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Affiliation(s)
- Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Linyi 276005, China
| | - Yusen Li
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Linyi 276005, China
| | - Xin Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Linyi 276005, China
| | - Wenna Zhang
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi 276000, China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Linyi 276005, China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Linyi 276005, China
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12
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Zhang K, Chen YJ, Wilde D, Doroschak K, Strauss K, Ceze L, Seelig G, Nivala J. A nanopore interface for higher bandwidth DNA computing. Nat Commun 2022; 13:4904. [PMID: 35987925 PMCID: PMC9392746 DOI: 10.1038/s41467-022-32526-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 08/04/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractDNA has emerged as a powerful substrate for programming information processing machines at the nanoscale. Among the DNA computing primitives used today, DNA strand displacement (DSD) is arguably the most popular, with DSD-based circuit applications ranging from disease diagnostics to molecular artificial neural networks. The outputs of DSD circuits are generally read using fluorescence spectroscopy. However, due to the spectral overlap of typical small-molecule fluorescent reporters, the number of unique outputs that can be detected in parallel is limited, requiring complex optical setups or spatial isolation of reactions to make output bandwidths scalable. Here, we present a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies’ MinION device). These results increase DSD output bandwidth by an order of magnitude over what is currently feasible with fluorescence spectroscopy.
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13
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Seth S, Bhattacharya A. DNA barcode by flossing through a cylindrical nanopore. RSC Adv 2021; 11:20781-20787. [PMID: 34178311 PMCID: PMC8190898 DOI: 10.1039/d1ra00349f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves the measurements to almost 100% accuracy. The heavier protein tags along the DNA backbone introduce a large speed variation in the chain that can be understood using the idea of non-equilibrium tension propagation theory. However, from an initial rough characterization of velocities into “fast” (nucleotides) and “slow” (protein tags) domains, we introduce a physically motivated interpolation scheme that enables us to determine the barcode velocities rather accurately. Our theoretical analysis of the motion of the DNA through a cylindrical nanopore opens up the possibility of its experimental realization and carries over to multi-nanopore devices used for barcoding. We report a method for DNA barcoding from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive scheme to improve the measurements to almost 100% accuracy.![]()
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Affiliation(s)
- Swarnadeep Seth
- Department of Physics, University of Central Florida Orlando FL 32816-2385 USA
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida Orlando FL 32816-2385 USA
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14
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The Nanopore-Tweezing-Based, Targeted Detection of Nucleobases on Short Functionalized Peptide Nucleic Acid Sequences. Polymers (Basel) 2021; 13:polym13081210. [PMID: 33918592 PMCID: PMC8069169 DOI: 10.3390/polym13081210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023] Open
Abstract
The implication of nanopores as versatile components in dedicated biosensors, nanoreactors, or miniaturized sequencers has considerably advanced single-molecule investigative science in a wide range of disciplines, ranging from molecular medicine and nanoscale chemistry to biophysics and ecology. Here, we employed the nanopore tweezing technique to capture amino acid-functionalized peptide nucleic acids (PNAs) with α-hemolysin-based nanopores and correlated the ensuing stochastic fluctuations of the ionic current through the nanopore with the composition and order of bases in the PNAs primary structure. We demonstrated that while the system enables the detection of distinct bases on homopolymeric PNA or triplet bases on heteropolymeric strands, it also reveals rich insights into the conformational dynamics of the entrapped PNA within the nanopore, relevant for perfecting the recognition capability of single-molecule sequencing.
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15
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Pereiro I, Aubert J, Kaigala GV. Micro-scale technologies propel biology and medicine. BIOMICROFLUIDICS 2021; 15:021302. [PMID: 33948133 PMCID: PMC8081554 DOI: 10.1063/5.0047196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/05/2021] [Indexed: 05/05/2023]
Abstract
Historically, technology has been central to new discoveries in biology and progress in medicine. Among various technologies, microtechnologies, in particular, have had a prominent role in the revolution experienced by the life sciences in the last few decades, which will surely continue in the years to come. In this Perspective, we illustrate how microtechnologies, with a focus on microfluidics, have evolved in trends/waves to tackle the boundary of knowledge in the life sciences. We provide illustrative examples of technology-enabled biological breakthroughs and their current and future use in clinics. Finally, we take a closer look at the translational process to understand why the incorporation of new micro-scale technologies in medicine has been comparatively slow so far.
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16
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Crnković A, Srnko M, Anderluh G. Biological Nanopores: Engineering on Demand. Life (Basel) 2021; 11:life11010027. [PMID: 33466427 PMCID: PMC7824896 DOI: 10.3390/life11010027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.
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17
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Mereuta L, Asandei A, Dragomir IS, Bucataru IC, Park J, Seo CH, Park Y, Luchian T. Sequence-specific detection of single-stranded DNA with a gold nanoparticle-protein nanopore approach. Sci Rep 2020; 10:11323. [PMID: 32647249 PMCID: PMC7347621 DOI: 10.1038/s41598-020-68258-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Fast, cheap and easy to use nucleic acids detection methods are crucial to mitigate adverse impacts caused by various pathogens, and are essential in forensic investigations, food safety monitoring or evolution of infectious diseases. We report here a method based on the α-hemolysin (α-HL) nanopore, working in conjunction to unmodified citrate anion-coated gold nanoparticles (AuNPs), to detect nanomolar concentrations of short single-stranded DNA sequences (ssDNA). The core idea was to use charge neutral peptide nucleic acids (PNA) as hybridization probe for complementary target ssDNAs, and monitor at the single-particle level the PNA-induced aggregation propensity AuNPs during PNA–DNA duplexes formation, by recording ionic current blockades signature of AuNP–α-HL interactions. This approach offers advantages including: (1) a simple to operate platform, producing clear-cut readout signals based on distinct size differences of PNA-induced AuNPs aggregates, in relation to the presence in solution of complementary ssDNAs to the PNA fragments (2) sensitive and selective detection of target ssDNAs (3) specific ssDNA detection in the presence of interference DNA, without sample labeling or signal amplification. The powerful synergy of protein nanopore-based nanoparticle detection and specific PNA–DNA hybridization introduces a new strategy for nucleic acids biosensing with short detection time and label-free operation.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, 'Alexandru I. Cuza' University, 700506, Iasi, Romania.
| | - Alina Asandei
- Sciences Department, Interdisciplinary Research Institute, 'Alexandru I. Cuza' University, 700506, Iasi, Romania
| | - Isabela S Dragomir
- Sciences Department, Interdisciplinary Research Institute, 'Alexandru I. Cuza' University, 700506, Iasi, Romania
| | - Ioana C Bucataru
- Department of Physics, 'Alexandru I. Cuza' University, 700506, Iasi, Romania
| | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, Kongju, 32588, Republic of Korea
| | - Chang Ho Seo
- Department of Bioinformatics, Kongju National University, Kongju, 32588, Republic of Korea
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, 61452, Republic of Korea.
| | - Tudor Luchian
- Department of Physics, 'Alexandru I. Cuza' University, 700506, Iasi, Romania.
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18
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Hu F, Angelov B, Li S, Li N, Lin X, Zou A. Single‐Molecule Study of Peptides with the Same Amino Acid Composition but Different Sequences by Using an Aerolysin Nanopore. Chembiochem 2020; 21:2467-2473. [DOI: 10.1002/cbic.202000119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/09/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Fangzhou Hu
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Borislav Angelov
- Institute of Physics, ELI BeamlinesAcademy of Sciences of the Czech Republic Na Slovance 2 18221 Prague Czech Republic
| | - Shuang Li
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Na Li
- National Center for Protein Science in ShanghaiZhangjiang LabShanghai Advanced Research Institute, CAS Shanghai 200120 P. R. China
| | - Xubo Lin
- Institute of Single Cell EngineeringBeijing Advanced Innovation Center for Biomedical EngineeringBeihang University Beijing 100191 P. R. China
| | - Aihua Zou
- Shanghai Key Laboratory of Functional Materials ChemistryState Key Laboratory of Bioreactor Engineering and Institute of Applied ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
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19
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Murphy TW, Hsieh YP, Zhu B, Naler LB, Lu C. Microfluidic Platform for Next-Generation Sequencing Library Preparation with Low-Input Samples. Anal Chem 2020; 92:2519-2526. [PMID: 31894965 PMCID: PMC7002211 DOI: 10.1021/acs.analchem.9b04086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Advances in next-generation sequencing (NGS) have made available a wealth of information that had previously been inaccessible to researchers and clinicians. NGS has been applied to understand genomic, transcriptomic, and epigenomic changes and gained traction as a significant tool capable of accelerating diagnosis, prognosis, and biomarker discovery. However, these NGS assays have yet to be practical methods for patient stratification or diagnosis because of the gap between the tiny quantities of biomaterials provided by a clinical sample and the large DNA input required by most of these assays. Current library preparation methodologies typically require large input amounts of DNA and a long and complicated manual process. Here, we present a microfluidic droplet-based system for NGS library preparation, capable of reducing the number of pipetting steps significantly, reducing reagent consumption by 10×, and automating much of the process, while supporting an extremely low DNA input requirement (10 pg per library). This semiautomated technology will allow for low-input preparations of 8 libraries simultaneously while reducing batch-to-batch variation and operator hands-on time.
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Affiliation(s)
- Travis W. Murphy
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061
| | - Yuan-Pang Hsieh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061
| | - Lynette B. Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061
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20
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Abstract
The molecular scale pore structure, called nanopore, can be formed from protein ion channels by genetic engineering or fabricated on solid substrates using fashion nanotechnology. Target molecules in interaction with the functionalized lumen of nanopore, can produce characteristic changes in the pore conductance, which act as fingerprints, allowing us to identify single molecules and simultaneously quantify each target species in the mixture. Nanopore sensors have been created for tremendous biomedical detections, with targets ranging from metal ions, drug compounds and cellular second messengers, to proteins and DNAs. Recently, we have used the nanopore technique to dissect folding and unfolding mechanism of a single G-quadruplex DNA aptamer regulated by a variety of ions; we also created a portable and durable molecular device that integrated a protein pore sensor with a solidified lipid membrane for real-time detection.
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Affiliation(s)
- L Q Gu
- Biological Engineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, USA
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21
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Sultan M, Kanavarioti A. Nanopore device-based fingerprinting of RNA oligos and microRNAs enhanced with an Osmium tag. Sci Rep 2019; 9:14180. [PMID: 31578367 PMCID: PMC6775150 DOI: 10.1038/s41598-019-50459-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/12/2019] [Indexed: 12/19/2022] Open
Abstract
Protein and solid-state nanopores are used for DNA/RNA sequencing as well as for single molecule analysis. We proposed that selective labeling/tagging may improve base-to-base resolution of nucleic acids via nanopores. We have explored one specific tag, the Osmium tetroxide 2,2'-bipyridine (OsBp), which conjugates to pyrimidines and leaves purines intact. Earlier reports using OsBp-tagged oligodeoxyribonucleotides demonstrated proof-of-principle during unassisted voltage-driven translocation via either alpha-Hemolysin or a solid-state nanopore. Here we extend this work to RNA oligos and a third nanopore by employing the MinION, a commercially available device from Oxford Nanopore Technologies (ONT). Conductance measurements demonstrate that the MinION visibly discriminates oligoriboadenylates with sequence A15PyA15, where Py is an OsBp-tagged pyrimidine. Such resolution rivals traditional chromatography, suggesting that nanopore devices could be exploited for the characterization of RNA oligos and microRNAs enhanced by selective labeling. The data also reveal marked discrimination between a single pyrimidine and two consecutive pyrimidines in OsBp-tagged AnPyAn and AnPyPyAn. This observation leads to the conjecture that the MinION/OsBp platform senses a 2-nucleotide sequence, in contrast to the reported 5-nucleotide sequence with native nucleic acids. Such improvement in sensing, enabled by the presence of OsBp, may enhance base-calling accuracy in enzyme-assisted DNA/RNA sequencing.
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Affiliation(s)
- Madiha Sultan
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA
| | - Anastassia Kanavarioti
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA.
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22
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Mereuta L, Asandei A, Schiopu I, Park Y, Luchian T. Nanopore-Assisted, Sequence-Specific Detection, and Single-Molecule Hybridization Analysis of Short, Single-Stranded DNAs. Anal Chem 2019; 91:8630-8637. [PMID: 31194518 DOI: 10.1021/acs.analchem.9b02080] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report here on the ability of the α-hemolysin (α-HL) nanopore to achieve label-free, selective, and real-time detection of 15 nt long ssDNA fragments in solution, by exploiting their hybridization with freely added, polycationic peptides-functionalized PNAs. At the core of our work lies the paradigm that when PNAs and ssDNA are mixed together, the bulk concentration of free PNA decreases, depending upon the (mis)match degree between complementary strands and their relative concentrations. We demonstrate that the ssDNA sensing principle and throughput of the method are determined by the rate at which nonhybridized, polycationic peptides-functionalized PNA molecules arrive at the α-HL's vestibule entrance and thread into the nanopore. We found that with the application of a 30-fold salt gradient across the nanopore, the method enhances single-molecule detection sensitivity in the nanomolar range of ssDNA concentrations. This study demonstrates that the transmembrane potential-dependent unzip of single PNA-DNA duplexes at the α-HL's β-barrel entry permits discrimination between sequences that differ by one base pair.
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Affiliation(s)
| | | | | | - Yoonkyung Park
- Department of Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM) , Chosun University , Gwangju 61452 , Republic of Korea
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23
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Luchian T, Park Y, Asandei A, Schiopu I, Mereuta L, Apetrei A. Nanoscale Probing of Informational Polymers with Nanopores. Applications to Amyloidogenic Fragments, Peptides, and DNA-PNA Hybrids. Acc Chem Res 2019; 52:267-276. [PMID: 30605305 DOI: 10.1021/acs.accounts.8b00565] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The decades long advances in nanotechnology, biomolecular sciences, and protein engineering ushered the introduction of groundbreaking technologies devoted to understanding how matter behaves at single particle level. Arguably, one of the simplest in concept is the nanopore-based paradigm, with deep roots in what is originally known as the Coulter counter, resistive-pulse technique. Historically, a nanopore system comprising the oligomeric protein generated by Staphylococcus aureus toxin α-hemolysin (α-HL) was first applied to detecting polynucleotides, as revealed in 1996 by John J. Kasianowicz, Eric Brandin, Daniel Branton, and David W. Deamer, in the Proceedings of the National Academy of Sciences. Nowadays, a wide variety of other solid-state or protein-based nanopores have emerged as efficient tools for stochastic sensing of analytes as small as single metal ions, handling single molecules, or real-time, label-free probing of chemical reactions at single-molecule level. In this Account, we demonstrate the usefulness of the α-HL nanopore on probing metal-induced folding of peptides, and to investigating the reversible binding of various metals to physiologically relevant amyloid fragments. The widely recognized Achilles heel of the approach, is the relatively short dwell time of the analytes inside the nanopore. This hinders the collection of sufficient data required to infer statistically meaningful conclusions about the physical or chemical state of the studied analyte. To mitigate this, various approaches were successfully applied in particular experiments, including but not restricted to altering physical parameters of the aqueous solution, downsizing the nanopore geometry, the controlled tuning of the balance between the electrostatic and electro-osmotic forces, coating nanopores with a fluid lipid bilayer, employing a pressure-voltage biased pore. From our perspective, in this Account, we will present two strategies aimed at controlling the analyte passage across the α-HL. First, we will reveal how the electroosmotic flow can be harnessed to control residence time, direction, and the sequence of spatiotemporal dynamics of a single peptide along the nanopore. This also allows one to identify the mesoscopic trajectory of a peptide exiting the nanopore through either the vestibule or β-barrel moiety. Second, we lay out the principles of an approach dubbed "nanopore tweezing", enabling simultaneous capture rate increase and escape rate decrease of a peptide from the α-HL, with the applied voltage. At its core, this method requires the creation of an electrical dipole on the peptide under study, via engineering positive and negative amino acid residues at the two ends of the peptide. Concise applications of this approach are being demonstrated, as in proof-of-concept experiments we probed the primary structure exploration of polypeptides, via discrimination between selected neutral amino acid residues. Another useful venue provided by the nanopores is represented by single-molecule force experiments on captured analytes inside the nanopore, which proved useful in exploring force-induced rupture of nucleic acids duplexes, hairpins, or various nucleic acids-ligand conjugates. We will show that when applied to oppositely charged, polypeptide-functionalized PNA-DNA duplexes, the nanopore tweezing introduces a new generation of force-spectroscopy nanopore-based platforms, facilitating unzipping of a captured duplex and enabling the duplex hybridization energy estimation.
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Affiliation(s)
- Tudor Luchian
- Department of Physics, ‘Alexandru I. Cuza’ University, Iasi, Romania 700506
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, Republic of Korea 61452
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, ‘Alexandru I. Cuza’ University, Iasi, Romania 700506
| | - Irina Schiopu
- Interdisciplinary Research Institute, Sciences Department, ‘Alexandru I. Cuza’ University, Iasi, Romania 700506
| | - Loredana Mereuta
- Department of Physics, ‘Alexandru I. Cuza’ University, Iasi, Romania 700506
| | - Aurelia Apetrei
- Department of Physics, ‘Alexandru I. Cuza’ University, Iasi, Romania 700506
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24
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Willems K, Van Meervelt V, Wloka C, Maglia G. Single-molecule nanopore enzymology. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630164 DOI: 10.1098/rstb.2016.0230] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Biological nanopores are a class of membrane proteins that open nanoscale water conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. In addition, a more recent nanopore application is the analysis of single proteins and enzymes. Monitoring enzymatic reactions with nanopores, i.e. nanopore enzymology, has the unique advantage that it allows long-timescale observations of native proteins at the single-molecule level. Here, we describe the approaches and challenges in nanopore enzymology.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Kherim Willems
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.,Department of Life Sciences and Imaging, IMEC, Kapeldreef 75, 3001 Leuven, Belgium
| | - Veerle Van Meervelt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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25
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Fu K, Bohn PW. Nanopore Electrochemistry: A Nexus for Molecular Control of Electron Transfer Reactions. ACS CENTRAL SCIENCE 2018; 4:20-29. [PMID: 29392173 PMCID: PMC5785767 DOI: 10.1021/acscentsci.7b00576] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Indexed: 05/12/2023]
Abstract
Pore-based structures occur widely in living organisms. Ion channels embedded in cell membranes, for example, provide pathways, where electron and proton transfer are coupled to the exchange of vital molecules. Learning from mother nature, a recent surge in activity has focused on artificial nanopore architectures to effect electrochemical transformations not accessible in larger structures. Here, we highlight these exciting advances. Starting with a brief overview of nanopore electrodes, including the early history and development of nanopore sensing based on nanopore-confined electrochemistry, we address the core concepts and special characteristics of nanopores in electron transfer. We describe nanopore-based electrochemical sensing and processing, discuss performance limits and challenges, and conclude with an outlook for next-generation nanopore electrode sensing platforms and the opportunities they present.
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Affiliation(s)
- Kaiyu Fu
- Department
of Chemistry and Biochemistry and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Paul W. Bohn
- Department
of Chemistry and Biochemistry and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
- E-mail: . Tel: +1 574 631 1849. Fax: +1 574 631 8366
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26
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Asandei A, Rossini AE, Chinappi M, Park Y, Luchian T. Protein Nanopore-Based Discrimination between Selected Neutral Amino Acids from Polypeptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:14451-14459. [PMID: 29178796 DOI: 10.1021/acs.langmuir.7b03163] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nanopore probing of biological polymers has the potential to achieve single-molecule sequencing at low cost, high throughput, portability, and minimal sample preparation and apparatus. In this article, we explore the possibility of discrimination between neutral amino acid residues from the primary structure of 30 amino acids long, engineered peptides, through the analysis of single-molecule ionic current fluctuations accompanying their slowed-down translocation across the wild type α-hemolysin (α-HL) nanopore, and molecular dynamics simulations. We found that the transient presence inside the α-HL of alanine or tryptophan residues from the primary sequence of engineered peptides results in distinct features of the ionic current fluctuation pattern associated with the peptide reversibly blocking the nanopore. We propose that α-HL sensitivity to the molecular exclusion at the most constricted region mediates ionic current blockade events correlated with the volumes that are occluded by at least three alanine or tryptophan residues, and provides the specificity needed to discriminate between groups of neutral amino acids. Further, we find that the pattern of current fluctuations depends on the orientation of the threaded amino acid residues, suggestive of a conformational anisotropy of the ensemble of conformations of the peptide on the restricted nanopore region, related to its relative axial orientation inside the nanopore.
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Affiliation(s)
| | - Aldo E Rossini
- Department of Basic and Applied Science for Engineering, Sapienza University of Rome , Via A. Scarpa14, 00161 Rome, Italy
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata , Via del Politecnico 1, 00133 Rome, Italy
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia , Via Regina Elena 291, 00161 Rome, Italy
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University , Gwangju, Korea
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28
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Fleming SJ, Lu B, Golovchenko JA. Charge, Diffusion, and Current Fluctuations of Single-Stranded DNA Trapped in an MspA Nanopore. Biophys J 2017; 112:368-375. [PMID: 28122222 PMCID: PMC5266147 DOI: 10.1016/j.bpj.2016.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/03/2016] [Accepted: 12/05/2016] [Indexed: 10/20/2022] Open
Abstract
We report effective charges and diffusion constants of several different single-stranded DNA oligonucleotides trapped in an MspA nanopore. Nucleotide identity is found to have a substantial influence on effective charges and diffusion constants. These quantities are determined from escape time experiments for a DNA molecule attached to a NeutrAvidin molecule that, unlike the DNA, does not pass through the pore. Correlations are reported between oligonucleotide effective charges and current blockages, and between their diffusion constants and DNA-induced current blockage fluctuations. We also report an unanticipated source of current fluctuations that reflects a discrete blockage current level structure. We posit that this is associated with interactions between the NeutrAvidin molecule and the MspA nanopore.
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Affiliation(s)
| | - Bo Lu
- Department of Physics, Harvard University, Cambridge, Massachusetts
| | - Jene A Golovchenko
- Department of Physics, Harvard University, Cambridge, Massachusetts; School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts.
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29
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Piguet F, Ouldali H, Discala F, Breton MF, Behrends JC, Pelta J, Oukhaled A. High Temperature Extends the Range of Size Discrimination of Nonionic Polymers by a Biological Nanopore. Sci Rep 2016; 6:38675. [PMID: 27924860 PMCID: PMC5141499 DOI: 10.1038/srep38675] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/11/2016] [Indexed: 01/29/2023] Open
Abstract
We explore the effect of temperature on the interaction of polydisperse mixtures of nonionic poly(ethylene glycol) (PEG) polymers of different average molar masses with the biological nanopore α-hemolysin. In contrast with what has been previously observed with various nanopores and analytes, we find that, for PEGs larger than a threshold molar mass (2000 g/mol, PEG 2000), increasing temperature increases the duration of the PEG/nanopore interaction. In the case of PEG 3400 the duration increases by up to a factor of 100 when the temperature increases from 5 °C to 45 °C. Importantly, we find that increasing temperature extends the polymer size range of application of nanopore-based single-molecule mass spectrometry (Np-SMMS)-type size discrimination. Indeed, in the case of PEG 3400, discrimination of individual molecular species of different monomer number is impossible at room temperature but is achieved when the temperature is raised to 45 °C. We interpret our observations as the consequence of a decrease of PEG solubility and a collapse of PEG molecules with higher temperatures. In addition to expanding the range of application of Np-SMMS to larger nonionic polymers, our findings highlight the crucial role of the polymer solubility for the nanopore detection.
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Affiliation(s)
- Fabien Piguet
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France.,LPTM UMR 8089 CNRS, Cergy University, France
| | - Hadjer Ouldali
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France
| | | | | | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Faculty of Medicine, Department of Physiology, University of Freiburg, Germany.,Freiburg Materials Research Centre, University of Freiburg, Germany.,Centre for Interactive Materials and Bioinspired Technologies, University of Freiburg, Germany
| | - Juan Pelta
- LAMBE UMR 8587 CNRS, Cergy and Évry Universities, France
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Kanavarioti A. False positives and false negatives measure less than 0.001% in labeling ssDNA with osmium tetroxide 2,2'-bipyridine. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:1434-1446. [PMID: 27826518 PMCID: PMC5082614 DOI: 10.3762/bjnano.7.135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 09/23/2016] [Indexed: 06/06/2023]
Abstract
Osmium tetroxide 2,2'-bipyridine (OsBp) is known to react with pyrimidines in ssDNA and preferentially label deoxythymine (T) over deoxycytosine (C). The product, osmylated DNA, was proposed as a surrogate for nanopore-based DNA sequencing due to OsBp's "perfect" label attributes. Osmylated deoxyoligos translocate unassisted and measurably slow via sub-2 nm SiN solid-state nanopores, as well as via the alpha-hemolysin (α-HL) pore. Both nanopores discriminate clearly between osmylated and intact nucleobase; α-HL was also shown to discriminate between osmylated T and osmylated C. Experiments presented here confirm that the kinetics of osmylation are comparable for short oligos and long ssDNA and show that pyrimidine osmylation is practically complete in two hours at room temperature with less than 15 mM OsBp. Under the proposed labeling conditions: deoxyoligo backbone degradation measures less than 1/1,000,000; false positives such as osmylated deoxyadenine (A) and osmylated deoxyguanine (G) measure less than 1/100,000; false negatives, i.e., unosmylated C measure less than 1/10,000; and unosmylated T must measure substantially lower than 1/10,000 due to the 27-fold higher reactivity of T compared to C. However, osmylated C undergoes degradation that amounts to about 1-2% for the duration of the labeling protocol. This degradation may be further characterized, possibly suppressed, and the properties of the degradation products via nanopore translocation can be evaluated to assure base calling quality in a DNA sequencing effort.
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Comer J, Aksimentiev A. DNA sequence-dependent ionic currents in ultra-small solid-state nanopores. NANOSCALE 2016; 8:9600-13. [PMID: 27103233 PMCID: PMC4860951 DOI: 10.1039/c6nr01061j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computational approaches, here we show how the sequence, molecular conformation, and pore geometry affect the blockade ionic current in model solid-state nanopores. We demonstrate that the blockade current from a DNA molecule is determined by the chemical identities and conformations of at least three consecutive nucleotides. We find the blockade currents produced by the nucleotide triplets to vary considerably with their nucleotide sequences despite having nearly identical molecular conformations. Encouragingly, we find blockade current differences as large as 25% for single-base substitutions in ultra small (1.6 nm × 1.1 nm cross section; 2 nm length) solid-state nanopores. Despite the complex dependence of the blockade current on the sequence and conformation of the DNA triplets, we find that, under many conditions, the number of thymine bases is positively correlated with the current, whereas the number of purine bases and the presence of both purines and pyrimidines in the triplet are negatively correlated with the current. Based on these observations, we construct a simple theoretical model that relates the ion current to the base content of a solid-state nanopore. Furthermore, we show that compact conformations of DNA in narrow pores provide the greatest signal-to-noise ratio for single base detection, whereas reduction of the nanopore length increases the ionic current noise. Thus, the sequence dependence of the nanopore blockade current can be theoretically rationalized, although the predictions will likely need to be customized for each nanopore type.
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Affiliation(s)
- Jeffrey Comer
- Department of Anatomy and Physiology, Kansas State University, P-213 Mosier Hall, 1800 Denison Ave, Manhattan, Kansas, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W Green St, Urbana, IL, USA.
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32
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Ding Y, Kanavarioti A. Single pyrimidine discrimination during voltage-driven translocation of osmylated oligodeoxynucleotides via the α-hemolysin nanopore. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:91-101. [PMID: 26925357 PMCID: PMC4734350 DOI: 10.3762/bjnano.7.11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 01/08/2016] [Indexed: 06/05/2023]
Abstract
The influence of an electric field on an isolated channel or nanopore separating two compartments filled with electrolytes produces a constant ion flux through the pore. Nucleic acids added to one compartment traverse the pore, and modulate the current in a sequence-dependent manner. While translocation is faster than detection, the α-hemolysin nanopore (α-HL) successfully senses base modifications in ssDNA immobilized within the pore. With the assistance of a processing enzyme to slow down translocation, nanopore-based DNA sequencing is now a commercially available platform. However, accurate base calling is challenging because α-HL senses a sequence, and not a single nucleotide. Osmylated DNA was recently proposed as a surrogate for nanopore-based sequencing. Osmylation is the addition of osmium tetroxide 2,2'-bipyridine (OsBp) to the C5-C6 pyrimidine double bond. The process is simple, selective for deoxythymidine (dT) over deoxycytidine (dC), unreactive towards the purines, practically 100% effective, and strikingly independent of length, sequence, and composition. Translocation of an oligodeoxynucleotide (oligo) dA10XdA9 via α-HL is relatively slow, and exhibits distinct duration as well as distinct residual current when X = dA, dT(OsBp), or dC(OsBp). The data indicate that the α-HL constriction zone/β-barrel interacts strongly with both OsBp and the base. A 23 nucleotide long oligo with four dT(OsBp) traverses 18-times slower, and the same oligo with nine (dT+dC)(OsBp) moieties traverses 84-times slower compared to dA20, suggesting an average rate of 40 or 180 μs/base, respectively. These translocation speeds are well above detection limits, may be further optimized, and clear the way for nanopore-based sequencing using osmylated DNA.
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Affiliation(s)
- Yun Ding
- Chemistry Department, University of Utah, Salt Lake City, UT, USA
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33
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Martin HSC, Jha S, Howorka S, Coveney PV. Determination of Free Energy Profiles for the Translocation of Polynucleotides through α-Hemolysin Nanopores using Non-Equilibrium Molecular Dynamics Simulations. J Chem Theory Comput 2015; 5:2135-48. [PMID: 26613153 DOI: 10.1021/ct9000894] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The translocation of polynucleotides through transmembrane protein pores is a fundamental biological process with important technological and medical relevance. The translocation process is complex, and it is influenced by a range of factors including the diameter and inner surface of the pore, the secondary structure of the polymer, and the interactions between the polymer and protein. In this paper, we perform nonequilibrium constant velocity-steered molecular dynamics simulations of nucleic acid molecule translocation through the protein nanopore α-hemolysin and use Jarzynski's identity to determine the associated free energy profiles. With this approach we are able to explain the observed differences in experimental translocation time through the nanopore between polyadenosine and polydeoxycytidine. The translocation of polynucleotides and single nucleotides through α-hemolysin is investigated. These simulations are computationally intensive as they employ models with atomistic level resolution; in addition to their size, these systems are challenging to study due to the time scales of translocation of large asymmetric molecules. Our simulations provide insight into the role of the interactions between the nucleic acid molecules and the protein pore. Mutated protein pores provide confirmation of residue-specific interactions between nucleotides and the protein pore. By harnessing such molecular dynamics simulations, we gain new physicochemical insight into the translocation process.
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Affiliation(s)
- Hugh S C Martin
- Centre for Computational Science and Department of Chemistry, University College London, 20 Gordon Street, London, United Kingdom, and Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Shantenu Jha
- Centre for Computational Science and Department of Chemistry, University College London, 20 Gordon Street, London, United Kingdom, and Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Stefan Howorka
- Centre for Computational Science and Department of Chemistry, University College London, 20 Gordon Street, London, United Kingdom, and Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Peter V Coveney
- Centre for Computational Science and Department of Chemistry, University College London, 20 Gordon Street, London, United Kingdom, and Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803
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Biesemans A, Soskine M, Maglia G. A Protein Rotaxane Controls the Translocation of Proteins Across a ClyA Nanopore. NANO LETTERS 2015; 15:6076-6081. [PMID: 26243210 PMCID: PMC4606981 DOI: 10.1021/acs.nanolett.5b02309] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Rotaxanes, pseudorotaxanes, and catenanes are supramolecular complexes with potential use in nanomachinery, molecular computing, and single-molecule studies. Here we constructed a protein rotaxane in which a polypeptide thread is encircled by a Cytolysin A (ClyA) nanopore and capped by two protein stoppers. The rotaxane could be switched between two states. At low negative applied potentials (<-50 mV) one of the protein stoppers resided inside the nanopore indefinitely. Under this configuration the rotaxane prevents the diffusion of protein molecules across the lipid bilayer and provides a useful platform for single-molecule analysis. High negative applied potentials (-100 mV) dismantled the interlocked rotaxane system by the forceful translocation of the protein stopper, allowing new proteins to be trapped inside or transported across the nanopore. The observed voltage threshold for the translocation of the protein stopper through the nanopore related well to the biphasic voltage dependence of the residence time measured for the freely diffusing protein stopper. We propose a model in which molecules translocate through a nanopore when the average dwell time decreases with the applied potential.
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Affiliation(s)
- Annemie Biesemans
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
| | - Misha Soskine
- Groningen Biomolecular Sciences & Biotechnology (GBB) Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology (GBB) Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Department of Chemistry, University of Leuven, Leuven, 3001, Belgium
- Corresponding author:
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Abstract
The α-hemolysin (αHL) protein nanopore has been investigated previously as a base detector for the strand sequencing of DNA and RNA. Recent findings have suggested that shorter pores might provide improved base discrimination. New work has also shown that truncated-barrel mutants (TBM) of αHL form functional pores in lipid bilayers. Therefore, we tested TBM pores for the ability to recognize bases in DNA strands immobilized within them. In the case of TBMΔ6, in which the barrel is shortened by ∼16 Å, one of the three recognition sites found in the wild-type pore, R1, was almost eliminated. With further mutagenesis (Met113 → Gly), R1 was completely removed, demonstrating that TBM pores can mediate sharpened recognition. Remarkably, a second mutant of TBMΔ6 (Met113 → Phe) was able to bind the positively charged β-cyclodextrin, am7βCD, unusually tightly, permitting the continuous recognition of individual nucleoside monophosphates, which would be required for exonuclease sequencing mediated by nanopore base identification.
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Affiliation(s)
- Mariam Ayub
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | | | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
- Corresponding Author:
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36
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Asandei A, Chinappi M, Kang HK, Seo CH, Mereuta L, Park Y, Luchian T. Acidity-Mediated, Electrostatic Tuning of Asymmetrically Charged Peptides Interactions with Protein Nanopores. ACS APPLIED MATERIALS & INTERFACES 2015; 7:16706-16714. [PMID: 26144534 DOI: 10.1021/acsami.5b04406] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Despite success in probing chemical reactions and dynamics of macromolecules on submillisecond time and nanometer length scales, a major impasse faced by nanopore technology is the need to cheaply and controllably modulate macromolecule capture and trafficking across the nanopore. We demonstrate herein that tunable charge separation engineered at the both ends of a macromolecule very efficiently modulates the dynamics of macromolecules capture and traffic through a nanometer-size pore. In the proof-of-principle approach, we employed a 36 amino acids long peptide containing at the N- and C-termini uniform patches of glutamic acids and arginines, flanking a central segment of asparagines, and we studied its capture by the α-hemolysin (α-HL) and the mean residence time inside the pore in the presence of a pH gradient across the protein. We propose a solution to effectively control the dynamics of peptide interaction with the nanopore, with both association and dissociation reaction rates of peptide-α-HL interactions spanning orders of magnitude depending upon solution acidity on the peptide addition side and the transmembrane electric potential, while preserving the amplitude of the blockade current signature.
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Affiliation(s)
- Alina Asandei
- †Department of Interdisciplinary Research, Alexandru I. Cuza University, Iasi, Romania
| | - Mauro Chinappi
- ‡Center for Life Nano Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Hee-Kyoung Kang
- §Department of Biomedical Science and Research Center for Proteineous Materials, Chosun University, Gwangju, South Korea
| | - Chang Ho Seo
- ∥Department of Bioinformatics, Kongju National University, Kongju, South Korea
| | - Loredana Mereuta
- ⊥Department of Physics, Alexandru I. Cuza University, Iasi, Romania
| | - Yoonkyung Park
- §Department of Biomedical Science and Research Center for Proteineous Materials, Chosun University, Gwangju, South Korea
| | - Tudor Luchian
- ⊥Department of Physics, Alexandru I. Cuza University, Iasi, Romania
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37
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Liu N, Yang Z, Ou X, Wei B, Zhang J, Jia Y, Xia F. Nanopore-based analysis of biochemical species. Mikrochim Acta 2015; 183:955-963. [PMID: 27013767 PMCID: PMC4778144 DOI: 10.1007/s00604-015-1560-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/30/2015] [Indexed: 12/11/2022]
Abstract
Biological nanochannels or nanopores play a crucial role in basic biochemical processes in cells. Artificial nanopores possessing dimensions comparable to the size of biological molecules and mimicking the function of biological ion channels are of particular interest with respect to the design of biosensors with a sensitivity that can go down to the fM level and even to single molecule detection. Nanopore-based analysis (NPA) is currently a new research field with fascinating prospects. This review (with 118 refs.) summarizes the progress made in this field in the recent 10 years. Following an introduction into the fundamentals of NPA, we demonstrate its potential by describing selected methods for sensing (a) proteins such as streptavidin, certain antibodies, or thrombin via aptamers; (b) oligomers, larger nucleic acids, or micro-RNA; (c) small molecules, (d) ions such as K(I) which is vital to the maintenance of life, or Hg(II) which is dangerous to health. We summarize the results and discuss the merits and limitations of the various methods at last. Graphical abstractSchematic of a signal-off system and a signal-on system in nanopore analysis. The effective diameter of nanopores decreases when targets undergo certain interactions with receptors attached on the inner surface of the nanopore. Correspondingly, the current will drop on appearance of the analyte. This is referred to as a "signal-off" system. Conversely, it is called a "signal-on" system.
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Affiliation(s)
- Nannan Liu
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Zekun Yang
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Xiaowen Ou
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Benmei Wei
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Juntao Zhang
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Yongmei Jia
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
| | - Fan Xia
- />Key Laboratory for Large-Format Battery Materials and Systems, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074 China
- />National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan, 430074 China
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38
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Fabrication of nanopores in multi-layered silicon-based membranes using focused electron beam induced etching with XeF2 gas. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1557-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Rovigatti U. Cancer modelling in the NGS era - Part I: Emerging technology and initial modelling. Crit Rev Oncol Hematol 2015; 96:274-307. [PMID: 26427785 DOI: 10.1016/j.critrevonc.2015.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 04/14/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023] Open
Abstract
It is today indisputable that great progresses have been made in our molecular understanding of cancer cells, but an effective implementation of such knowledge into dramatic cancer-cures is still belated and yet desperately needed. This review gives a snapshot at where we stand today in this search for cancer understanding and definitive treatments, how far we have progressed and what are the major obstacles we will have to overcome both technologically and for disease modelling. In the first part, promising 3rd/4th Generation Sequencing Technologies will be summarized (particularly IonTorrent and OxfordNanopore technologies). Cancer modelling will be then reviewed from its origin in XIX Century Germany to today's NGS applications for cancer understanding and therapeutic interventions. Developments after Molecular Biology revolution (1953) are discussed as successions of three phases. The first, PH1, labelled "Clonal Outgrowth" (from 1960s to mid 1980s) was characterized by discoveries in cytogenetics (Nowell, Rowley) and viral oncology (Dulbecco, Bishop, Varmus), which demonstrated clonality. Treatments were consequently dominated by a "cytotoxic eradication" strategy with chemotherapeutic agents. In PH2, (from the mid 1980s to our days) the description of cancer as "Gene Networks" led to targeted-gene-therapies (TGTs). TGTs are the focus of Section 3: in view of their apparent failing (Ephemeral Therapies), alternative strategies will be discussed in review part II (particularly cancer immunotherapy, CIT). Additional Pitfalls impinge on the concepts of tumour heterogeneity (inter/intra; ITH). The described pitfalls set the basis for a new phase, PH3, which is called "NGS Era" and will be also discussed with ten emerging cancer models in the Review 2nd part.
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Affiliation(s)
- Ugo Rovigatti
- University of Pisa Medical School, Oncology Department, via Roma 55, 56127 Pisa, Italy.
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40
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Behera H, Ramkumar V, Madhavan N. Cation-Transporting Peptides: Scaffolds for Functionalized Pores? Chemistry 2015; 21:10179-84. [DOI: 10.1002/chem.201500881] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Indexed: 01/09/2023]
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41
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Placement of oppositely charged aminoacids at a polypeptide termini determines the voltage-controlled braking of polymer transport through nanometer-scale pores. Sci Rep 2015; 5:10419. [PMID: 26029865 PMCID: PMC4450769 DOI: 10.1038/srep10419] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/13/2015] [Indexed: 11/09/2022] Open
Abstract
Protein and solid-state nanometer-scale pores are being developed for the detection, analysis, and manipulation of single molecules. In the simplest embodiment, the entry of a molecule into a nanopore causes a reduction in the latter's ionic conductance. The ionic current blockade depth and residence time have been shown to provide detailed information on the size, adsorbed charge, and other properties of molecules. Here we describe the use of the nanopore formed by Staphylococcus aureus α-hemolysin and polypeptides with oppositely charged segments at the N- and C-termini to increase both the polypeptide capture rate and mean residence time of them in the pore, regardless of the polarity of the applied electrostatic potential. The technique provides the means to improve the signal to noise of single molecule nanopore-based measurements.
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42
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Hadi-Alijanvand H, Rouhani M. Journey of poly-nucleotides through OmpF porin. J Phys Chem B 2015; 119:6113-28. [PMID: 25965338 DOI: 10.1021/acs.jpcb.5b00763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OmpF is an abundant porin in many bacteria which attracts attention as a promising biological nanopore for DNA sequencing. We study the interactions of OmpF with pentameric poly-nucleotides (poly-Ns) in silico. The poly-N molecule is forced to translocate through the lumen of OmpF. Subsequently, the structural and dynamical effects of translocation steps on protein and poly-N molecules are explored in detail. The external loops of OmpF are introduced as the main region for discrimination of poly-Ns based on their organic bases. Structural network analyses of OmpF in the presence or absence of poly-Ns characterize special residues in the structural network of porin. These residues pave the way for engineering OmpF protein. The poly-N-specific pattern of OmpF's local conductance is detected in the current study. Computing the potential of mean force for translocation steps, we define the energetic barrier ahead of poly-N to move through OmpF's lumen. We suggest that fast translocation of the examined poly-N molecules through OmpF seems unattainable by small external driving forces. Our computational results suggest some abilities for OmpF porin like OmpF's potential for being used in poly-N sequencing.
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Affiliation(s)
- Hamid Hadi-Alijanvand
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
| | - Maryam Rouhani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
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43
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Ferrari AC, Bonaccorso F, Fal'ko V, Novoselov KS, Roche S, Bøggild P, Borini S, Koppens FHL, Palermo V, Pugno N, Garrido JA, Sordan R, Bianco A, Ballerini L, Prato M, Lidorikis E, Kivioja J, Marinelli C, Ryhänen T, Morpurgo A, Coleman JN, Nicolosi V, Colombo L, Fert A, Garcia-Hernandez M, Bachtold A, Schneider GF, Guinea F, Dekker C, Barbone M, Sun Z, Galiotis C, Grigorenko AN, Konstantatos G, Kis A, Katsnelson M, Vandersypen L, Loiseau A, Morandi V, Neumaier D, Treossi E, Pellegrini V, Polini M, Tredicucci A, Williams GM, Hong BH, Ahn JH, Kim JM, Zirath H, van Wees BJ, van der Zant H, Occhipinti L, Di Matteo A, Kinloch IA, Seyller T, Quesnel E, Feng X, Teo K, Rupesinghe N, Hakonen P, Neil SRT, Tannock Q, Löfwander T, Kinaret J. Science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems. NANOSCALE 2015; 7:4598-810. [PMID: 25707682 DOI: 10.1039/c4nr01600a] [Citation(s) in RCA: 991] [Impact Index Per Article: 110.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We present the science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems, targeting an evolution in technology, that might lead to impacts and benefits reaching into most areas of society. This roadmap was developed within the framework of the European Graphene Flagship and outlines the main targets and research areas as best understood at the start of this ambitious project. We provide an overview of the key aspects of graphene and related materials (GRMs), ranging from fundamental research challenges to a variety of applications in a large number of sectors, highlighting the steps necessary to take GRMs from a state of raw potential to a point where they might revolutionize multiple industries. We also define an extensive list of acronyms in an effort to standardize the nomenclature in this emerging field.
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Affiliation(s)
- Andrea C Ferrari
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK.
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44
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Linas S, Fulcrand R, Cauwet F, Poinsot B, Brioude A. Nanochannel arrays etched into hexagonal boron nitride meso-membranes by a focused ion beam. RSC Adv 2015. [DOI: 10.1039/c5ra05325k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Nanochannel arrays are etched into h-BN membranes by a focused ion beam for nanofluidic applications.
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Affiliation(s)
- S. Linas
- LMI
- Univ. Lyon 1 and CNRS UMR5615
- 69622 Villeurbanne Cedex
- France
| | - R. Fulcrand
- ILM
- Univ. Lyon 1 and CNRS UMR5306
- 69622 Villeurbanne Cedex
- France
| | - F. Cauwet
- LMI
- Univ. Lyon 1 and CNRS UMR5615
- 69622 Villeurbanne Cedex
- France
| | - B. Poinsot
- LMI
- Univ. Lyon 1 and CNRS UMR5615
- 69622 Villeurbanne Cedex
- France
| | - A. Brioude
- LMI
- Univ. Lyon 1 and CNRS UMR5615
- 69622 Villeurbanne Cedex
- France
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45
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Affiliation(s)
- Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK.
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46
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Ding Y, Fleming AM, White HS, Burrows CJ. Internal vs fishhook hairpin DNA: unzipping locations and mechanisms in the α-hemolysin nanopore. J Phys Chem B 2014; 118:12873-82. [PMID: 25333648 PMCID: PMC4234443 DOI: 10.1021/jp5101413] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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Studies
on the interaction of hairpin DNA with the α-hemolysin
(α-HL) nanopore have determined hairpin unzipping kinetics,
thermodynamics, and sequence-dependent DNA/protein interactions. Missing
from these results is a systematic study comparing the unzipping process
for fishhook (one-tail) vs internal (two-tail) hairpins when they
are electrophoretically driven from the cis to the trans side of α-HL via a 30-mer single-stranded tail.
In the current studies, fishhook hairpins showed long unzipping times
with one deep blockage current level. In contrast, the internal hairpins
demonstrated relatively fast unzipping and a characteristic pulse-like
current pattern. These differences were further explored with respect
to stem length and sequence context. Further, a series of internal
hairpins with asymmetric tails were studied, for which it was determined
that a second tail longer than 12 nucleotides results in internal
hairpin unzipping behavior, while tail lengths of 6 nucleotides behaved
like fishhook hairpins. Interestingly, these studies were able to
resolve a current difference of ∼6% between hairpin DNA immobilized
in the nanopore waiting to unzip vs the translocating unzipped DNA,
with the latter showing a deeper current blockage level. This demonstration
of different currents for immobilized and translocating DNA has not
been described previously. These results were interpreted as fishhook
hairpins unzipping inside the vestibule, while the internal hairpins
unzip outside the vestibule of α-HL. Lastly, we used this knowledge
to study the unzipping of a long double-stranded DNA (>50 base
pairs)
outside the vestibule of α-HL. The conclusions drawn from these
studies are anticipated to be beneficial in future application of
nanopore analysis of nucleic acids.
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Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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47
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Buermans H, den Dunnen J. Next generation sequencing technology: Advances and applications. Biochim Biophys Acta Mol Basis Dis 2014; 1842:1932-1941. [DOI: 10.1016/j.bbadis.2014.06.015] [Citation(s) in RCA: 460] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 06/05/2014] [Accepted: 06/15/2014] [Indexed: 12/12/2022]
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Gurnev PA, Nestorovich EM. Channel-forming bacterial toxins in biosensing and macromolecule delivery. Toxins (Basel) 2014; 6:2483-540. [PMID: 25153255 PMCID: PMC4147595 DOI: 10.3390/toxins6082483] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 12/19/2022] Open
Abstract
To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on "Intracellular Traffic and Transport of Bacterial Protein Toxins", reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their "second life" in a variety of developing medical and technological applications.
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Affiliation(s)
- Philip A Gurnev
- Physics Department, University of Massachusetts, Amherst, MA 01003, USA.
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49
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Martin HSC, Jha S, Coveney PV. Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force. J Comput Chem 2014; 35:692-702. [PMID: 24403093 PMCID: PMC4274958 DOI: 10.1002/jcc.23525] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/13/2013] [Accepted: 12/07/2013] [Indexed: 12/17/2022]
Abstract
The translocation of nucleotide molecules across biological and synthetic nanopores has attracted attention as a next generation technique for sequencing DNA. Computer simulations have the ability to provide atomistic-level insight into important states and processes, delivering a means to develop a fundamental understanding of the translocation event, for example, by extracting the free energy of the process. Even with current supercomputing facilities, the simulation of many-atom systems in fine detail is limited to shorter timescales than the real events they attempt to recreate. This imposes the need for enhanced simulation techniques that expand the scope of investigation in a given timeframe. There are numerous free energy calculation and translocation methodologies available, and it is by no means clear which method is best applied to a particular problem. This article explores the use of two popular free energy calculation methodologies in a nucleotide-nanopore translocation system, using the α-hemolysin nanopore. The first uses constant velocity-steered molecular dynamics (cv-SMD) in conjunction with Jarzynski's equality. The second applies an adaptive biasing force (ABF), which has not previously been applied to the nucleotide-nanpore system. The purpose of this study is to provide a comprehensive comparison of these methodologies, allowing for a detailed comparative assessment of the scientific merits, the computational cost, and the statistical quality of the data obtained from each technique. We find that the ABF method produces results that are closer to experimental measurements than those from cv-SMD, whereas the net errors are smaller for the same computational cost.
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Affiliation(s)
- Hugh S C Martin
- Department of Chemistry, Centre for Computational ScienceUCL, 20 Gordon Street, London, United Kingdom
| | - Shantenu Jha
- Department of Electrical Engineering BuildingRutgers, 94 Brett Road, Piscataway, New Jersey
| | - Peter V Coveney
- Department of Chemistry, Centre for Computational ScienceUCL, 20 Gordon Street, London, United Kingdom
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50
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Ervin EN, Barrall GA, Pal P, Bean MK, Schibel AEP, Hibbs AD. Creating a Single Sensing Zone within an Alpha-Hemolysin Pore Via Site Directed Mutagenesis. BIONANOSCIENCE 2014; 4:78-84. [PMID: 24678449 PMCID: PMC3963172 DOI: 10.1007/s12668-013-0119-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Although significant progress has recently been made towards realizing the goal of direct nanopore based DNA sequencing [1], there are still numerous hurdles that need to be overcome. One such hurdle associated with the use of the biological nanopore α-hemolysin (αHL) is the fact that the wild type channel contains three very distinct recognition or sensing regions within the β-barrel [2, 3], making identification of the bases residing within or moving through the pore very difficult. Through site directed mutagenesis, we have been able to selectively remove one of two sensing regions while simultaneously enhancing the third. Our approach has led to the creation of αHL pores containing single sensing zones and provides the basis for engineering αHL pores suitable for direct DNA sequencing.
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Affiliation(s)
- Eric N. Ervin
- Electronic BioSciences, Inc., 5754 Pacific Center Blvd. Suite 204, San Diego, CA 92121
| | - Geoffrey A. Barrall
- Electronic BioSciences, Inc., 5754 Pacific Center Blvd. Suite 204, San Diego, CA 92121
| | - Prithwish Pal
- Electronic BioSciences, Inc., 5754 Pacific Center Blvd. Suite 204, San Diego, CA 92121
| | - Megan K. Bean
- Electronic BioSciences, Inc., 5754 Pacific Center Blvd. Suite 204, San Diego, CA 92121
| | - Anna E. P. Schibel
- Electronic BioSciences, Inc., 5754 Pacific Center Blvd. Suite 204, San Diego, CA 92121
| | - Andrew D. Hibbs
- Electronic BioSciences, Inc., 5754 Pacific Center Blvd. Suite 204, San Diego, CA 92121
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