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Wiswedel R, Bui ATN, Kim J, Lee MK. Beta-Barrel Nanopores as Diagnostic Sensors: An Engineering Perspective. BIOSENSORS 2024; 14:345. [PMID: 39056622 PMCID: PMC11274599 DOI: 10.3390/bios14070345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/13/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024]
Abstract
Biological nanopores are ultrasensitive and highly attractive platforms for disease diagnostics, including the sequencing of viral and microbial genes and the detection of biomarkers and pathogens. To utilize biological nanopores as diagnostic sensors, they have been engineered through various methods resulting in the accurate and highly sensitive detection of biomarkers and disease-related biomolecules. Among diverse biological nanopores, the β-barrel-containing nanopores have advantages in nanopore engineering because of their robust structure, making them well-suited for modifications. In this review, we highlight the engineering approaches for β-barrel-containing nanopores used in single-molecule sensing for applications in early diagnosis and prognosis. In the highlighted studies, β-barrel nanopores can be modified by genetic mutation to change the structure; alter charge distributions; or add enzymes, aptamers, and protein probes to enhance sensitivity and accuracy. Furthermore, this review discusses challenges and future perspectives for advancing nanopore-based diagnostic sensors.
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Affiliation(s)
- Rani Wiswedel
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Anh Thi Ngoc Bui
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
| | - Jinhyung Kim
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Mi-Kyung Lee
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
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2
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Liu B, Dong X, Zheng C, Keener D, Chen Z, Cheng H, Watts JK, Xue W, Sontheimer EJ. Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates. Nat Biotechnol 2024; 42:1039-1045. [PMID: 37709915 DOI: 10.1038/s41587-023-01947-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 08/15/2023] [Indexed: 09/16/2023]
Abstract
Reverse transcriptases, used in prime editing systems, exhibit lower fidelity, processivity and dNTP affinity than many DNA-dependent DNA polymerases. We report that a DNA-dependent DNA polymerase (phi29), untethered from Cas9, enables editing from a synthetic, end-stabilized DNA-containing template at up to 60% efficiency in human cells. Compared to prime editing, DNA polymerase editing avoids autoinhibitory intramolecular base pairing of the template, facilitates template synthesis and supports larger insertions (>100 nucleotides).
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Affiliation(s)
- Bin Liu
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Xiaolong Dong
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Tessera Therapeutics, Somerville, MA, USA
| | - Chunwei Zheng
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - David Keener
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Haoyang Cheng
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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3
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Huster D, Maiti S, Herrmann A. Phospholipid Membranes as Chemically and Functionally Tunable Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312898. [PMID: 38456771 DOI: 10.1002/adma.202312898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/12/2024] [Indexed: 03/09/2024]
Abstract
The sheet-like lipid bilayer is the fundamental structural component of all cell membranes. Its building blocks are phospholipids and cholesterol. Their amphiphilic structure spontaneously leads to the formation of a bilayer in aqueous environment. Lipids are not just structural elements. Individual lipid species, the lipid membrane structure, and lipid dynamics influence and regulate membrane protein function. An exciting field is emerging where the membrane-associated material properties of different bilayer systems are used in designing innovative solutions for widespread applications across various fields, such as the food industry, cosmetics, nano- and biomedicine, drug storage and delivery, biotechnology, nano- and biosensors, and computing. Here, the authors summarize what is known about how lipids determine the properties and functions of biological membranes and how this has been or can be translated into innovative applications. Based on recent progress in the understanding of membrane structure, dynamics, and physical properties, a perspective is provided on how membrane-controlled regulation of protein functions can extend current applications and even offer new applications.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107, Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400 005, India
| | - Andreas Herrmann
- Freie Universität Berlin, Department Chemistry and Biochemistry, SupraFAB, Altensteinstr. 23a, D-14195, Berlin, Germany
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4
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Zhang H, Jiang H, Liu X, Wang X. A review of innovative electrochemical strategies for bioactive molecule detection and cell imaging: Current advances and challenges. Anal Chim Acta 2024; 1285:341920. [PMID: 38057043 DOI: 10.1016/j.aca.2023.341920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 12/08/2023]
Abstract
Cellular heterogeneity poses a major challenge for tumor theranostics, requiring high-resolution intercellular bioanalysis strategies. Over the past decades, the advantages of electrochemical analysis, such as high sensitivity, good spatio-temporal resolution, and ease of use, have made it the preferred method to uncover cellular differences. To inspire more creative research, herein, we highlight seminal works in electrochemical techniques for biomolecule analysis and bioimaging. Specifically, micro/nano-electrode-based electrochemical techniques enable real-time quantitative analysis of electroactive substances relevant to life processes in the micro-nanostructure of cells and tissues. Nanopore-based technique plays a vital role in biosensing by utilizing nanoscale pores to achieve high-precision detection and analysis of biomolecules with exceptional sensitivity and single-molecule resolution. Electrochemiluminescence (ECL) technology is utilized for real-time monitoring of the behavior and features of individual cancer cells, enabling observation of their dynamic processes due to its capability of providing high-resolution and highly sensitive bioimaging of cells. Particularly, scanning electrochemical microscopy (SECM) and scanning ion conductance microscopy (SICM) which are widely used in real-time observation of cell surface biological processes and three-dimensional imaging of micro-nano structures, such as metabolic activity, ion channel activity, and cell morphology are introduced in this review. Furthermore, the expansion of the scope of cellular electrochemistry research by innovative functionalized electrodes and electrochemical imaging models and strategies to address future challenges and potential applications is also discussed in this review.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Hui Jiang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Xiaohui Liu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China.
| | - Xuemei Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China.
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5
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Sampath G. Identifying residues in unfolded whole proteins with a nanopore: a theoretical model based on linear inequalities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555759. [PMID: 37693569 PMCID: PMC10491143 DOI: 10.1101/2023.08.31.555759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
A theoretical model is proposed for the identification of individual amino acids (AAs) in an unfolded whole protein's primary sequence. It is based in part on a recent report (Nat. Biotech. 41, 1130-1139, 2023) that describes the unfolding and translocation of whole proteins at constant speed through a biological nanopore (alpha-Hemolysin) of length 5 nm with a residue dwell time inside the pore of ~10 μs. Here current blockade levels in the pore due to the translocating protein are assumed to be measured with a limited precision of 70 nm3 and a bandwidth of 20 KHz for measurement with a low-bandwidth detector. Exclusion volumes in two pores of slightly different lengths are used as a computational proxy for the blockade signal; subsequence exclusion volume differences along the protein sequence are computed from the sampled translocation signals in the two pores relatively shifted multiple times. These are then converted into a system of linear inequalities that can be solved with linear programming and related methods; residues are coarsely identified as belonging to one of 4 subsets of the 20 standard AAs. To obtain the exact identity of a residue an artifice analogous to the use of base-specific tags for DNA sequencing with a nanopore (PNAS 113, 5233-5238, 2016) is used. Conjugates that add volume are attached to a given AA type, this biases the set of inequalities toward the volume of the conjugated AA, from this biased set the position of occurrence of every residue of the AA type in the whole sequence is extracted. By applying this step separately to each of the 20 standard AAs the full sequence can be obtained. The procedure is illustrated with a protein in the human proteome (Uniprot id UP000005640_9606).
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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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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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8
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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9
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Wu Y, Gooding JJ. The application of single molecule nanopore sensing for quantitative analysis. Chem Soc Rev 2022; 51:3862-3885. [PMID: 35506519 DOI: 10.1039/d1cs00988e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.
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Affiliation(s)
- Yanfang Wu
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
| | - J Justin Gooding
- School of Chemistry and Australian Centre for NanoMedicine, The University of New South Wales, Sydney, New South Wales 2052, Australia.
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10
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Abstract
Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and out of cells, contributing to maintaining most of the fundamental processes that sustain living organisms. As in several other occasions, we have borrowed from the natural properties of these biological systems to push technology forward and have been able to hijack these nano-scale proteinaceous pores to learn about the physical and chemical features of molecules passing through them. Today, a large repertoire of biological pores is exploited as molecular sensors for characterizing biomolecules that are relevant for the advancement of life sciences and application to medicine. Although the technology has quickly matured to enable nucleic acid sensing with transformative implications for genomics, biological pores stand as some of the most promising candidates to drive the next developments in single-molecule proteomics.
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Affiliation(s)
- Simon Finn Mayer
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Chan Cao
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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11
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Li F, Luo Y, Xi G, Fu J, Tu J. Single-Molecule Analysis of DNA structures using nanopore sensors. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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Millar DP. Conformational Dynamics of DNA Polymerases Revealed at the Single-Molecule Level. Front Mol Biosci 2022; 9:826593. [PMID: 35281261 PMCID: PMC8913937 DOI: 10.3389/fmolb.2022.826593] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/20/2022] [Indexed: 12/25/2022] Open
Abstract
DNA polymerases are intrinsically dynamic macromolecular machines. The purpose of this review is to describe the single-molecule Förster resonance energy transfer (smFRET) methods that are used to probe the conformational dynamics of DNA polymerases, focusing on E. coli DNA polymerase I. The studies reviewed here reveal the conformational dynamics underpinning the nucleotide selection, proofreading and 5′ nuclease activities of Pol I. Moreover, the mechanisms revealed for Pol I are likely employed across the DNA polymerase family. smFRET methods have also been used to examine other aspects of DNA polymerase activity.
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13
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Zhang M, Chen C, Zhang Y, Geng J. Biological nanopores for sensing applications. Proteins 2022; 90:1786-1799. [PMID: 35092317 DOI: 10.1002/prot.26308] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/27/2021] [Accepted: 01/27/2022] [Indexed: 02/05/2023]
Abstract
Biological nanopores are proteins with transmembrane pore that can be embedded in lipid bilayer. With the development of single-channel current measurement technologies, biological nanopores have been reconstituted into planar lipid bilayer and used for single-molecule sensing of various analytes and events such as single-molecule DNA sensing and sequencing. To improve the sensitivity for specific analytes, various engineered nanopore proteins and strategies are deployed. Here, we introduce the origin and principle of nanopore sensing technology as well as the structure and associated properties of frequently used protein nanopores. Furthermore, sensing strategies for different applications are reviewed, with focus on the alteration of buffer condition, protein engineering, and deployment of accessory proteins and adapter-assisted sensing. Finally, outlooks for de novo design of nanopore and nanopore beyond sensing are discussed.
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Affiliation(s)
- Ming Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Chen Chen
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Yanjing Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Jia Geng
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
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14
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Singh A, Patel SS. Quantitative methods to study helicase, DNA polymerase, and exonuclease coupling during DNA replication. Methods Enzymol 2022; 672:75-102. [PMID: 35934486 PMCID: PMC9933136 DOI: 10.1016/bs.mie.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Genome replication is accomplished by highly regulated activities of enzymes in a multi-protein complex called the replisome. Two major enzymes, DNA polymerase and helicase, catalyze continuous DNA synthesis on the leading strand of the parental DNA duplex while the lagging strand is synthesized discontinuously. The helicase and DNA polymerase on their own are catalytically inefficient and weak motors for unwinding/replicating double-stranded DNA. However, when a helicase and DNA polymerase are functionally and physically coupled, they catalyze fast and highly processive leading strand DNA synthesis. DNA polymerase has a 3'-5' exonuclease activity, which removes nucleotides misincorporated in the nascent DNA. DNA synthesis kinetics, processivity, and accuracy are governed by the interplay of the helicase, DNA polymerase, and exonuclease activities within the replisome. This chapter describes quantitative biochemical and biophysical methods to study the coupling of these three critical activities during DNA replication. The methods include real-time quantitation of kinetics of DNA unwinding-synthesis by a coupled helicase-DNA polymerase complex, a 2-aminopurine fluorescence-based assay to map the precise positions of helicase and DNA polymerase with respect to the replication fork junction, and a radiometric assay to study the coupling of DNA polymerase, exonuclease, and helicase activities during processive leading strand DNA synthesis. These methods are presented here with bacteriophage T7 replication proteins as an example but can be applied to other systems with appropriate modifications.
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15
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Lv P, Yang Y, Li S, Tan CS, Ming D. Biological nanopore approach for single‐molecule analysis of nucleobase modifications. ELECTROCHEMICAL SCIENCE ADVANCES 2021. [DOI: 10.1002/elsa.202100119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Pengrui Lv
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Yongyi Yang
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Shuang Li
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Cherie S. Tan
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Dong Ming
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
- Department of Biomedical Engineering College of Precision Instruments and Optoelectronics Engineering Tianjin University Tianjin China
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16
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Xie S, Leung AWS, Zheng Z, Zhang D, Xiao C, Luo R, Luo M, Zhang S. Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era. Innovation (N Y) 2021; 2:100153. [PMID: 34901902 PMCID: PMC8640597 DOI: 10.1016/j.xinn.2021.100153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
The Human Genome Project opened an era of (epi)genomic research, and also provided a platform for the development of new sequencing technologies. During and after the project, several sequencing technologies continue to dominate nucleic acid sequencing markets. Currently, Illumina (short-read), PacBio (long-read), and Oxford Nanopore (long-read) are the most popular sequencing technologies. Unlike PacBio or the popular short-read sequencers before it, which, as examples of the second or so-called Next-Generation Sequencing platforms, need to synthesize when sequencing, nanopore technology directly sequences native DNA and RNA molecules. Nanopore sequencing, therefore, avoids converting mRNA into cDNA molecules, which not only allows for the sequencing of extremely long native DNA and full-length RNA molecules but also document modifications that have been made to those native DNA or RNA bases. In this review on direct DNA sequencing and direct RNA sequencing using Oxford Nanopore technology, we focus on their development and application achievements, discussing their challenges and future perspective. We also address the problems researchers may encounter applying these approaches in their research topics, and how to resolve them.
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Affiliation(s)
- Shangqian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou 570228, China
| | - Amy Wing-Sze Leung
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Zhenxian Zheng
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Dake Zhang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangzhou 510060, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China
| | - Ming Luo
- Agriculture and Biotechnology Research Center, Guangdong Provincial Key Laboratory of Applied Botany, Center of Economic Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shoudong Zhang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
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17
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Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021; 39:1348-1365. [PMID: 34750572 PMCID: PMC8988251 DOI: 10.1038/s41587-021-01108-x] [Citation(s) in RCA: 486] [Impact Index Per Article: 162.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.
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Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yue Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA
| | - Audrey Bollas
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yuru Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA.
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18
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Thomas NK, Poodari VC, Jain M, Olsen HE, Akeson M, Abu-Shumays RL. Direct Nanopore Sequencing of Individual Full Length tRNA Strands. ACS NANO 2021; 15:16642-16653. [PMID: 34618430 PMCID: PMC10189790 DOI: 10.1021/acsnano.1c06488] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual transfer RNA (tRNA) molecules at subnanometer precision. A second advance is a nanopore sequencing pipeline optimized for tRNA. We tested this method using purified E. coli tRNAfMet, tRNALys, and tRNAPhe samples. 76-92% of individual aligned tRNA sequence reads were full length. As a proof of concept, we showed that nanopore sequencing detected all 43 expected isoacceptors in total E. coli MRE600 tRNA as well as isodecoders that further define that tRNA population. Alignment-based comparisons between the three purified tRNAs and their synthetic controls revealed systematic nucleotide miscalls that were diagnostic of known modifications. Systematic miscalls were also observed proximal to known modifications in total E. coli tRNA alignments, including a highly conserved pseudouridine in the T loop. This work highlights the potential of nanopore direct tRNA sequencing as well as improvements needed to implement tRNA sequencing for human healthcare applications.
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19
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Thomas NK, Poodari VC, Jain M, Olsen HE, Akeson M, Abu-Shumays RL. Direct Nanopore Sequencing of Individual Full Length tRNA Strands. ACS NANO 2021; 15:16642-16653. [PMID: 34618430 DOI: 10.1101/2021.1104.1126.441285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual transfer RNA (tRNA) molecules at subnanometer precision. A second advance is a nanopore sequencing pipeline optimized for tRNA. We tested this method using purified E. coli tRNAfMet, tRNALys, and tRNAPhe samples. 76-92% of individual aligned tRNA sequence reads were full length. As a proof of concept, we showed that nanopore sequencing detected all 43 expected isoacceptors in total E. coli MRE600 tRNA as well as isodecoders that further define that tRNA population. Alignment-based comparisons between the three purified tRNAs and their synthetic controls revealed systematic nucleotide miscalls that were diagnostic of known modifications. Systematic miscalls were also observed proximal to known modifications in total E. coli tRNA alignments, including a highly conserved pseudouridine in the T loop. This work highlights the potential of nanopore direct tRNA sequencing as well as improvements needed to implement tRNA sequencing for human healthcare applications.
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Affiliation(s)
- Niki K Thomas
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
| | - Vinay C Poodari
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
| | - Miten Jain
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
| | - Hugh E Olsen
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
| | - Mark Akeson
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
| | - Robin L Abu-Shumays
- Biomolecular Engineering Department, Genomics Institute, and Center for Molecular Biology of RNA University of California, Santa Cruz, California 95064, United States
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20
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Abstract
This paper provides a perspective on potential applications of a new single-molecule technique, viz., the nanopore electro-osmotic trap (NEOtrap). This solid-state nanopore-based method uses locally induced electro-osmosis to form a hydrodynamic trap for single molecules. Ionic current recordings allow one to study an unlabeled protein or nanoparticle of arbitrary charge that can be held in the nanopore's most sensitive region for very long times. After motivating the need for improved single-molecule technologies, we sketch various possible technical extensions and combinations of the NEOtrap. We lay out diverse applications in biosensing, enzymology, protein folding, protein dynamics, fingerprinting of proteins, detecting post-translational modifications, and all that at the level of single proteins - illustrating the unique versatility and potential of the NEOtrap.
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Affiliation(s)
- Sonja Schmid
- Nanodynamics Lab, Laboratory of Biophysics, Wageningen University, Stippeneng 4, 6708WE Wageningen, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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21
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Robertson JW, Ghimire M, Reiner JE. Nanopore sensing: A physical-chemical approach. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183644. [PMID: 33989531 PMCID: PMC9793329 DOI: 10.1016/j.bbamem.2021.183644] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/30/2022]
Abstract
Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.
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Affiliation(s)
- Joseph W.F. Robertson
- Biophysical and Biomedical Measurement Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg MD. 20899, correspondence to:
| | - Madhav Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, VA
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA
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22
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Ma F, Yan S, Zhang J, Wang Y, Wang L, Wang Y, Zhang S, Du X, Zhang P, Chen HY, Huang S. Nanopore Sequencing Accurately Identifies the Cisplatin Adduct on DNA. ACS Sens 2021; 6:3082-3092. [PMID: 34319692 DOI: 10.1021/acssensors.1c01212] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cisplatin, which selectively binds to N7 atoms of purines to inhibit normal replication and transcription, is a widely applied chemotherapeutic drug in the treatment of cancer. Though direct identification of cisplatin lesions on DNA is of great significance, existing sequencing methods have issues such as complications of preamplification or enrichment-induced false-positive reports. Direct identification of cisplatin lesions by nanopore sequencing (NPS) is in principle feasible. However, relevant investigations have never been reported. By constructing model sequences (83 nucleotides in length) containing a sole cisplatin lesion, identification of corresponding lesions by NPS is achieved with <10 ng of input sequencing library. Moreover, characteristic high-frequency noises caused by cisplatin lesions are consistently observed during NPS, clearly identifiable in corresponding high-pass filtered traces. This feature is, however, never observed in any other combinations of natural DNA bases and could be taken as a reference to identify cisplatin lesions on DNA. Further investigations demonstrate that cisplatin stalls the replication of phi29 DNA polymerase, which appears as a ∼5 pA level fluctuation in the single-molecule resolution. These results have confirmed the feasibility of NPS to identify cisplatin lesions at the genomic level and may provide new insights into understanding the molecular mechanism of platinum-based drugs.
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Affiliation(s)
- Fubo Ma
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Jinyue Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Yu Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
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23
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Sarkar A, Gasperi W, Begley U, Nevins S, Huber SM, Dedon PC, Begley TJ. Detecting the epitranscriptome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1663. [PMID: 33987958 DOI: 10.1002/wrna.1663] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 11/09/2022]
Abstract
RNA modifications and their corresponding epitranscriptomic writer and eraser enzymes regulate gene expression. Altered RNA modification levels, dysregulated writers, and sequence changes that disrupt epitranscriptomic marks have been linked to mitochondrial and neurological diseases, cancer, and multifactorial disorders. The detection of epitranscriptomics marks is challenging, but different next generation sequencing (NGS)-based and mass spectrometry-based approaches have been used to identify and quantitate the levels of individual and groups of RNA modifications. NGS and mass spectrometry-based approaches have been coupled with chemical, antibody or enzymatic methodologies to identify modifications in most RNA species, mapped sequence contexts and demonstrated the dynamics of specific RNA modifications, as well as the collective epitranscriptome. While epitranscriptomic analysis is currently limited to basic research applications, specific approaches for the detection of individual RNA modifications and the epitranscriptome have potential biomarker applications in detecting human conditions and diseases. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Processing > tRNA Processing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anwesha Sarkar
- Department of Biological Sciences, University at Albany, Albany, New York, USA.,The RNA Institute, University at Albany, Albany, New York, USA
| | - William Gasperi
- Department of Biological Sciences, University at Albany, Albany, New York, USA.,The RNA Institute, University at Albany, Albany, New York, USA
| | - Ulrike Begley
- Department of Biological Sciences, University at Albany, Albany, New York, USA.,The RNA Institute, University at Albany, Albany, New York, USA
| | - Steven Nevins
- Nanoscale Science Constellation, SUNY Polytechnic Institute, Albany, New York, USA
| | | | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, Albany, New York, USA.,The RNA Institute, University at Albany, Albany, New York, USA
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24
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Bocanegra R, Ismael Plaza GA, Pulido CR, Ibarra B. DNA replication machinery: Insights from in vitro single-molecule approaches. Comput Struct Biotechnol J 2021; 19:2057-2069. [PMID: 33995902 PMCID: PMC8085672 DOI: 10.1016/j.csbj.2021.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/03/2021] [Accepted: 04/03/2021] [Indexed: 11/16/2022] Open
Abstract
The replisome is the multiprotein molecular machinery that replicates DNA. The replisome components work in precise coordination to unwind the double helix of the DNA and replicate the two strands simultaneously. The study of DNA replication using in vitro single-molecule approaches provides a novel quantitative understanding of the dynamics and mechanical principles that govern the operation of the replisome and its components. ‘Classical’ ensemble-averaging methods cannot obtain this information. Here we describe the main findings obtained with in vitro single-molecule methods on the performance of individual replisome components and reconstituted prokaryotic and eukaryotic replisomes. The emerging picture from these studies is that of stochastic, versatile and highly dynamic replisome machinery in which transient protein-protein and protein-DNA associations are responsible for robust DNA replication.
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Affiliation(s)
- Rebeca Bocanegra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - G A Ismael Plaza
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Carlos R Pulido
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Borja Ibarra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
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25
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Athapattu US, Amarasekara CA, Immel JR, Bloom S, Barany F, Nagel AC, Soper SA. Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing. Nucleic Acids Res 2021; 49:e41. [PMID: 33511416 PMCID: PMC8053086 DOI: 10.1093/nar/gkab001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 01/29/2023] Open
Abstract
Modifications in RNA are numerous (∼170) and in higher numbers compared to DNA (∼5) making the ability to sequence an RNA molecule to identify these modifications highly tenuous using next generation sequencing (NGS). The ability to immobilize an exoribonuclease enzyme, such as XRN1, to a solid support while maintaining its activity and capability to cleave both the canonical and modified ribonucleotides from an intact RNA molecule can be a viable approach for single-molecule RNA sequencing. In this study, we report an enzymatic reactor consisting of covalently attached XRN1 to a solid support as the groundwork for a novel RNA exosequencing technique. The covalent attachment of XRN1 to a plastic solid support was achieved using EDC/NHS coupling chemistry. Studies showed that the solid-phase digestion efficiency of model RNAs was 87.6 ± 2.8%, while the XRN1 solution-phase digestion for the same model was 78.3 ± 4.4%. The ability of immobilized XRN1 to digest methylated RNA containing m6A and m5C ribonucleotides was also demonstrated. The processivity and clipping rate of immobilized XRN1 secured using single-molecule fluorescence measurements of a single RNA transcript demonstrated a clipping rate of 26 ± 5 nt s-1 and a processivity of >10.5 kb at 25°C.
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Affiliation(s)
| | | | - Jacob R Immel
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Steven Bloom
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | | | | | - Steven A Soper
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
- Sunflower Genomics, Inc., Lawrence, KS 66047, USA
- Department of Mechanical Engineering and Bioengineering, University of Kansas, Lawrence, KS 66045, USA
- Department of Cancer Biology and KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
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26
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Nanopores: a versatile tool to study protein dynamics. Essays Biochem 2021; 65:93-107. [PMID: 33296461 DOI: 10.1042/ebc20200020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022]
Abstract
Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now readily available, observing the functional cycle of proteins - involving conformational changes and interactions - remains very challenging, e.g., due to ensemble averaging. However, time-resolved information is crucial to gain a mechanistic understanding of protein function. Single-molecule techniques such as FRET and force spectroscopies provide answers but can be limited by the required labelling, a narrow time bandwidth, and more. Here, we describe electrical nanopore detection as a tool for probing protein dynamics. With a time bandwidth ranging from microseconds to hours, nanopore experiments cover an exceptionally wide range of timescales that is very relevant for protein function. First, we discuss the working principle of label-free nanopore experiments, various pore designs, instrumentation, and the characteristics of nanopore signals. In the second part, we review a few nanopore experiments that solved research questions in protein science, and we compare nanopores to other single-molecule techniques. We hope to make electrical nanopore sensing more accessible to the biochemical community, and to inspire new creative solutions to resolve a variety of protein dynamics - one molecule at a time.
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27
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Piguet F, Ensslen T, Bakshloo MA, Talarimoghari M, Ouldali H, Baaken G, Zaitseva E, Pastoriza-Gallego M, Behrends JC, Oukhaled A. Pore-forming toxins as tools for polymer analytics: From sizing to sequencing. Methods Enzymol 2021; 649:587-634. [PMID: 33712201 DOI: 10.1016/bs.mie.2021.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We report here on the nanopore resistive pulse sensing (Np-RPS) method, involving pore-forming toxins as tools for polymer analytics at single molecule level. Np-RPS is an electrical method for the label-free detection of single molecules. A molecule interacting with the pore causes a change of the electrical resistance of the pore, called a resistive pulse, associated with a measurable transient current blockade. The features of the blockades, in particular their depth and duration, contain information on the molecular properties of the analyte. We first revisit the history of Np-RPS, then we discuss the effect of the configuration of the molecule/nanopore interaction on the molecular information that can be extracted from the signal, illustrated in two different regimes that either favor molecular sequencing or molecular sizing. Specifically, we focus on the sizing regime and on the use of two different pore-forming toxins, staphylococcal α-hemolysin (αHL) and aerolysin (AeL) nanopores, for the characterization of water-soluble polymers (poly-(ethylene glycol), (PEG)), homopeptides, and heteropeptides. We discuss how nanopore sizing of polymers could be envisioned as a new approach for peptide/protein sequencing.
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Affiliation(s)
- Fabien Piguet
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Tobias Ensslen
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mazdak A Bakshloo
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Monasadat Talarimoghari
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hadjer Ouldali
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | | | | | - Manuela Pastoriza-Gallego
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France
| | - Jan C Behrends
- Laboratory for Membrane Physiology and Technology, Department of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Freiburg Centre for Interactive Materials and Bioinspired Technologies (FIT), Freiburg, Germany; Freiburg Centre for Materials Research, Freiburg, Germany.
| | - Abdelghani Oukhaled
- CY Cergy Paris Université, CNRS, LAMBE, Cergy, France; Université Paris-Saclay, Univ Evry, CNRS, LAMBE, Evry-Courcouronnes, France.
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Amarasekara CA, Rathnayaka C, Athapattu US, Zhang L, Choi J, Park S, Nagel AC, Soper SA. Electrokinetic identification of ribonucleotide monophosphates (rNMPs) using thermoplastic nanochannels. J Chromatogr A 2021; 1638:461892. [PMID: 33477027 PMCID: PMC8107831 DOI: 10.1016/j.chroma.2021.461892] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/11/2022]
Abstract
With advances in the design and fabrication of nanofluidic devices during the last decade, there have been a few reports on nucleic acid analysis using nanoscale electrophoresis. The attractive nature of nanofluidics is the unique phenomena associated with this length scale that are not observed using microchip electrophoresis. Many of these effects are surface-related and include electrostatics, surface roughness, van der Waals interactions, hydrogen bonding, and the electric double layer. The majority of reports related to nanoscale electrophoresis have utilized glass-based devices, which are not suitable for broad dissemination into the separation community because of the sophisticated, time consuming, and high-cost fabrication methods required to produce the relevant devices. In this study, we report the use of thermoplastic nanochannels (110 nm x 110 nm, depth x width) for the free solution electrokinetic analysis of ribonucleotide monophosphates (rNMPs). Thermoplastic devices with micro- and nanofluidic networks were fabricated using nanoimprint lithography (NIL) with the structures enclosed via thermal fusion bonding of a cover plate to the fluidic substrate. Unique to this report is that we fabricated devices in cyclic olefin copolymer (COC) that was thermally fusion bonded to a COC cover plate. Results using COC/COC devices were compared to poly(methyl methacrylate), PMMA, devices with a COC cover plate. Our results indicated that at pH = 7.9, the electrophoresis in free solution resulted in an average resolution of the rNMPs >4 (COC/COC device range = 1.94 - 8.88; PMMA/COC device range = 1.4 - 7.8) with some of the rNMPs showing field-dependent electrophoretic mobilities. Baseline separation of the rNMPs was not possible using PMMA- or COC-based microchip electrophoresis. We also found that COC/COC devices could be assembled and UV/O3 activated after device assembly with the dose of the UV/O3 affecting the magnitude of the electroosmotic flow, EOF. In addition, the bond strength between the substrate and cover plate of unmodified COC/COC devices was higher compared to PMMA/COC devices. The large differences in the electrophoretic mobilities of the rNMPs afforded by nanoscale electrophoresis will enable a new single-molecule sequencing platform we envision, which uses molecular-dependent electrophoretic mobilities to identify the constituent rNMPs generated from an intact RNA molecule using a processive exonuclease. With optimized nanoscale electrophoresis, the rNMPs could be identified via mobility matching at an accuracy >99% in both COC/COC and PMMA/COC devices.
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Affiliation(s)
- Charuni A Amarasekara
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045; Center of Biomodular Multiscale Systems for Precision Medicine
| | - Chathurika Rathnayaka
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045; Center of Biomodular Multiscale Systems for Precision Medicine
| | - Uditha S Athapattu
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045; Center of Biomodular Multiscale Systems for Precision Medicine
| | - Lulu Zhang
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045; Center of Biomodular Multiscale Systems for Precision Medicine
| | - Junseo Choi
- Center of Biomodular Multiscale Systems for Precision Medicine; Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803
| | - Sunggook Park
- Center of Biomodular Multiscale Systems for Precision Medicine; Department of Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803
| | | | - Steven A Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045; Center of Biomodular Multiscale Systems for Precision Medicine; Sunflower Genomics, Inc. Lawrence, KS 66047; Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045; Bioengineering Program, The University of Kansas, Lawrence, KS 66045; KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160.
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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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30
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Willems K, Ruić D, L R Lucas F, Barman U, Verellen N, Hofkens J, Maglia G, Van Dorpe P. Accurate modeling of a biological nanopore with an extended continuum framework. NANOSCALE 2020; 12:16775-16795. [PMID: 32780087 DOI: 10.1039/d0nr03114c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Despite the broad success of biological nanopores as powerful instruments for the analysis of proteins and nucleic acids at the single-molecule level, a fast simulation methodology to accurately model their nanofluidic properties is currently unavailable. This limits the rational engineering of nanopore traits and makes the unambiguous interpretation of experimental results challenging. Here, we present a continuum approach that can faithfully reproduce the experimentally measured ionic conductance of the biological nanopore Cytolysin A (ClyA) over a wide range of ionic strengths and bias potentials. Our model consists of the extended Poisson-Nernst-Planck and Navier-Stokes (ePNP-NS) equations and a computationally efficient 2D-axisymmetric representation for the geometry and charge distribution of the nanopore. Importantly, the ePNP-NS equations achieve this accuracy by self-consistently considering the finite size of the ions and the influence of both the ionic strength and the nanoscopic scale of the pore on the local properties of the electrolyte. These comprise the mobility and diffusivity of the ions, and the density, viscosity and relative permittivity of the solvent. Crucially, by applying our methodology to ClyA, a biological nanopore used for single-molecule enzymology studies, we could directly quantify several nanofluidic characteristics difficult to determine experimentally. These include the ion selectivity, the ion concentration distributions, the electrostatic potential landscape, the magnitude of the electro-osmotic flow field, and the internal pressure distribution. Hence, this work provides a means to obtain fundamental new insights into the nanofluidic properties of biological nanopores and paves the way towards their rational engineering.
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Affiliation(s)
- Kherim Willems
- KU Leuven, Department of Chemistry, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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31
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Shankla M, Aksimentiev A. Molecular Transport across the Ionic Liquid-Aqueous Electrolyte Interface in a MoS 2 Nanopore. ACS APPLIED MATERIALS & INTERFACES 2020; 12:26624-26634. [PMID: 32393017 PMCID: PMC7292782 DOI: 10.1021/acsami.0c04523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanopore sequencing of DNA has been enabled by the use of a biological enzyme to thread DNA through an engineered biological nanopore while recording the ionic current flowing through the nanopore. Efforts to realize a similar concept using a solid-state nanopore have been met with several technical challenges, one of which is the high speed of DNA translocation and the other the low ionic current contrast among individual nucleotides. A promising avenue to addressing both problems is using an ionic liquid to slow DNA translocation and a tiny nanopore in the MoS2 membrane to distinguish individual nucleotides. The physical mechanisms enabling these technical advances have remained elusive. Here, we characterize the ion and DNA transport through the ionic liquid/aqueous electrolyte interface, with and without a MoS2 nanopore, using the all-atom molecular dynamics method. We find that the partial miscibility of the ionic liquid and the aqueous electrolyte considerably alters the physics of the nanopore translocation process. Thus, the interface of the two phases generates a contact potential of 600 mV, the ionic current is dominated by the motion of ionic liquid molecules through the aqueous solution phase, and the DNA nucleotides exhibit preferential partitioning into the aqueous electrolyte, which leads to spontaneous transport of DNA polymers from the ionic liquid to the aqueous solution compartment in the absence of external voltage bias. The complex physics of the two-phase nanopore system offers a multitude of opportunities for extending the functionality of nanopore-sensing platforms.
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Affiliation(s)
- Manish Shankla
- Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801, United States
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32
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Sheng Y, Zhang S, Liu L, Wu H. Measuring Enzymatic Activities with Nanopores. Chembiochem 2020; 21:2089-2097. [DOI: 10.1002/cbic.202000079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/21/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Yingying Sheng
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Shouwen Zhang
- Neurophysiology Department Beijing ChaoYang Emergency Medical Center Beijing 100122 China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety Institute of High Energy Physics Chinese Academy of Sciences Beijing 100049 China
| | - Hai‐Chen Wu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
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33
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Matern BM, Olieslagers TI, Groeneweg M, Duygu B, Wieten L, Tilanus MGJ, Voorter CEM. Long-Read Nanopore Sequencing Validated for Human Leukocyte Antigen Class I Typing in Routine Diagnostics. J Mol Diagn 2020; 22:912-919. [PMID: 32302780 DOI: 10.1016/j.jmoldx.2020.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/03/2020] [Accepted: 04/02/2020] [Indexed: 01/23/2023] Open
Abstract
Matching of human leukocyte antigen (HLA) gene polymorphisms by high-resolution DNA sequence analysis is the gold standard for determining compatibility between patient and donor for hematopoietic stem cell transplantation. Single-molecule sequencing (PacBio or MinION) is a newest (third) generation sequencing approach. MinION is a nanopore sequencing platform, which provides long targeted DNA sequences. The long reads provide unambiguous phasing, but the initial high error profile prevented its use in high-impact applications, such as HLA typing for HLA matching of donor and recipient in the transplantation setting. Ongoing developments on instrumentation and basecalling software have improved the per-base accuracy of 1D2 nanopore reads tremendously. In the current study, two validation panels of samples covering 70 of the 71 known HLA class I allele groups were used to compare third field sequences obtained by MinION, with Sanger sequence-based typing showing a 100% concordance between both data sets. In addition, the first validation panel was used to set the acceptance criteria for the use of MinION in a routine setting. The acceptance criteria were subsequently confirmed with the second validation panel. In summary, the present study describes validation and implementation of nanopore sequencing HLA class I typing method and illustrates that nanopore sequencing technology has advanced to a point where it can be used in routine diagnostics with high accuracy.
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Affiliation(s)
- Benedict M Matern
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Timo I Olieslagers
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Mathijs Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Burcu Duygu
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Lotte Wieten
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Marcel G J Tilanus
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Christina E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands.
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34
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Directional conformer exchange in dihydrofolate reductase revealed by single-molecule nanopore recordings. Nat Chem 2020; 12:481-488. [DOI: 10.1038/s41557-020-0437-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/10/2020] [Indexed: 12/18/2022]
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Ding T, Yang J, Pan V, Zhao N, Lu Z, Ke Y, Zhang C. DNA nanotechnology assisted nanopore-based analysis. Nucleic Acids Res 2020; 48:2791-2806. [PMID: 32083656 PMCID: PMC7102975 DOI: 10.1093/nar/gkaa095] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/29/2020] [Accepted: 02/17/2020] [Indexed: 12/30/2022] Open
Abstract
Nanopore technology is a promising label-free detection method. However, challenges exist for its further application in sequencing, clinical diagnostics and ultra-sensitive single molecule detection. The development of DNA nanotechnology nonetheless provides possible solutions to current obstacles hindering nanopore sensing technologies. In this review, we summarize recent relevant research contributing to efforts for developing nanopore methods associated with DNA nanotechnology. For example, DNA carriers can capture specific targets at pre-designed sites and escort them from nanopores at suitable speeds, thereby greatly enhancing capability and resolution for the detection of specific target molecules. In addition, DNA origami structures can be constructed to fulfill various design specifications and one-pot assembly reactions, thus serving as functional nanopores. Moreover, based on DNA strand displacement, nanopores can also be utilized to characterize the outputs of DNA computing and to develop programmable smart diagnostic nanodevices. In summary, DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis.
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Affiliation(s)
- Taoli Ding
- Department of Computer Science and Technology, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
- Department of Biomedical Engineering, College of engineering, Peking University, Beijing 100871, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Nan Zhao
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Zuhong Lu
- Department of Biomedical Engineering, College of engineering, Peking University, Beijing 100871, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Cheng Zhang
- Department of Computer Science and Technology, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
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36
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Ying YL, Wang J, Leach AR, Jiang Y, Gao R, Xu C, Edwards MA, Pendergast AD, Ren H, Weatherly CKT, Wang W, Actis P, Mao L, White HS, Long YT. Single-entity electrochemistry at confined sensing interfaces. Sci China Chem 2020. [DOI: 10.1007/s11426-020-9716-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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37
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Rosen CB, Bayley H, Rodriguez-Larrea D. Free-energy landscapes of membrane co-translocational protein unfolding. Commun Biol 2020; 3:160. [PMID: 32246057 PMCID: PMC7125183 DOI: 10.1038/s42003-020-0841-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/20/2020] [Indexed: 11/09/2022] Open
Abstract
Protein post-translational translocation is found at the plasma membrane of prokaryotes and protein import into organellae. Translocon structures are becoming available, however the dynamics of proteins during membrane translocation remain largely obscure. Here we study, at the single-molecule level, the folding landscape of a model protein while forced to translocate a transmembrane pore. We use a DNA tag to drive the protein into the α-hemolysin pore under a quantifiable force produced by an applied electric potential. Using a voltage-quench approach we find that the protein fluctuates between the native state and an intermediate in the translocation process at estimated forces as low as 1.9 pN. The fluctuation kinetics provide the free energy landscape as a function of force. We show that our stable, ≈15 kBT, substrate can be unfolded and translocated with physiological membrane potentials and that selective divalent cation binding may have a profound effect on the translocation kinetics.
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Affiliation(s)
- Christian Bech Rosen
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Novozymes A/S, Biologiens Vej 2, 2800, Kgs. Lyngby, Denmark
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - David Rodriguez-Larrea
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology (UPV/EHU) Barrio Sarriena s/n, Leioa, 48940, Spain.
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38
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Single-molecule analysis of nucleic acid biomarkers - A review. Anal Chim Acta 2020; 1115:61-85. [PMID: 32370870 DOI: 10.1016/j.aca.2020.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are important biomarkers for disease detection, monitoring, and treatment. Advances in technologies for nucleic acid analysis have enabled discovery and clinical implementation of nucleic acid biomarkers. However, challenges remain with technologies for nucleic acid analysis, thereby limiting the use of nucleic acid biomarkers in certain contexts. Here, we review single-molecule technologies for nucleic acid analysis that can be used to overcome these challenges. We first discuss the various types of nucleic acid biomarkers important for clinical applications and conventional technologies for nucleic acid analysis. We then discuss technologies for single-molecule in vitro and in situ analysis of nucleic acid biomarkers. Finally, we discuss other ultra-sensitive techniques for nucleic acid biomarker detection.
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39
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Niedzwiecki DJ, Chou YC, Xia Z, Thei F, Drndić M. Detection of single analyte and environmental samples with silicon nitride nanopores: Antarctic dirt particulates and DNA in artificial seawater. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:031301. [PMID: 32259993 DOI: 10.1063/1.5138210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/18/2020] [Indexed: 06/11/2023]
Abstract
Nanopore sensing is a powerful tool for the detection of biomolecules. Solid-state nanopores act as single-molecule sensors that can function in harsh conditions. Their resilient nature makes them attractive candidates for taking this technology into the field to measure environmental samples for life detection in space and water quality monitoring. Here, we discuss the fabrication of silicon nitride pores from ∼1.6 to 20 nm in diameter in 20-nm-thick silicon nitride membranes suspended on glass chips and their performance. We detect pure laboratory samples containing a single analyte including DNA, BSA, microRNA, TAT, and poly-D-lys-hydrobromide. We also measured an environmental (mixed-analyte) sample, containing Antarctic dirt provided by NASA Ames. For DNA measurements, in addition to using KCl and NaCl solutions, we used the artificial (synthetic) seawater, which is a mixture of different salts mimicking the composition of natural seawater. These samples were spiked with double-stranded DNA (dsDNA) fragments at different concentrations to establish the limits of nanopore sensitivity in candidate environment conditions. Nanopore chips were cleaned and reused for successive measurements. A stand-alone, 1-MHz-bandwidth Chimera amplifier was used to determine the DNA concentration in artificial seawater that we can detect in a practical time scale of a few minutes. We also designed and developed a new compact nanopore reader, a portable read-out device with miniaturized fluidic cells, which can obtain translocation data at bandwidths up to 100 kHz. Using this new instrument, we record translocations of 400 bp, 1000 bp, and 15000 bp dsDNA fragments and show discrimination by analysis of current amplitude and event duration histograms.
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Affiliation(s)
- David J Niedzwiecki
- Goeppert LLC, Pennovation Works, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, USA
| | - Yung-Chien Chou
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 S. 33rd Street, Philadelphia, Pennsylvania 19103, USA
| | - Zehui Xia
- Goeppert LLC, Pennovation Works, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, USA
| | - Federico Thei
- Elements, SRL, Viale G. Marconi 438, Cesena 47521, Italy
| | - Marija Drndić
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 S. 33rd Street, Philadelphia, Pennsylvania 19103, USA
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40
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Bentin J, Balme S, Picaud F. Polynucleotide differentiation using hybrid solid-state nanopore functionalizing with α-hemolysin. SOFT MATTER 2020; 16:1002-1010. [PMID: 31853534 DOI: 10.1039/c9sm01833f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report results from full atomistic molecular dynamics simulations on the properties of biomimetic nanopores. This latter result was obtained through the direct insertion of an α-hemolysin protein inside a hydrophobic solid-state nanopore. Upon translocation of different DNA strands, we demonstrate here that the theoretical system presents the same discrimination properties as the experimental one obtained previously. This opens an interesting way to promote the stability of a specific protein inside a solid nanopore to develop further biomimetic applications for DNA or protein sequencing.
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Affiliation(s)
- Jérémy Bentin
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA 4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France.
| | - Sébastien Balme
- Institut Européen des Membranes, UMR5635 UM ENSCM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Fabien Picaud
- Laboratoire de Nanomédecine, Imagerie et Thérapeutique, EA 4662, Université Bourgogne-Franche-Comté (UFR Sciences et Techniques), Centre Hospitalier Universitaire de Besançon, 16 route de Gray, 25030 Besançon, France.
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41
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Wang J, Li MY, Yang J, Wang YQ, Wu XY, Huang J, Ying YL, Long YT. Direct Quantification of Damaged Nucleotides in Oligonucleotides Using an Aerolysin Single Molecule Interface. ACS CENTRAL SCIENCE 2020; 6:76-82. [PMID: 31989027 PMCID: PMC6978832 DOI: 10.1021/acscentsci.9b01129] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 05/06/2023]
Abstract
DNA lesions such as metholcytosine(mC), 8-OXO-guanine (OG), inosine (I), etc. could cause genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remains a challenge due to massive varieties and less distinguishable readouts for structural variations at the molecular level. Moreover, standard amplification and labeling hardly work in DNA lesion detection. Herein, we designed a single molecule interface from the mutant aerolysin (K238Q), whose sensing region shows high compatibility to capture and then directly convert a minor lesion into distinguishable electrochemical readouts. Compared with previous single molecule sensing interfaces, the temporal resolution of the K238Q aerolysin nanopore is enhanced by two orders, which has the best sensing performance in all reported aerolysin nanopores. In this work, the novel K238Q could discriminate directly at least three types of lesions (mC, OG, I) without labeling and quantify modification sites under the mixed heterocomposition conditions of the oligonucleotide. Such a nanopore electrochemistry approach could be further applied to diagnose genetic diseases at high sensitivity.
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Affiliation(s)
- Jiajun Wang
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Meng-Yin Li
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
| | - Jie Yang
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Ya-Qian Wang
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Xue-Yuan Wu
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
- School
of Chemistry and Molecular Engineering, East China University of Science and Technology, 200237, Shanghai, China
| | - Jin Huang
- School
of Pharmacy, East China University of Science
and Technology, 200237, Shanghai, China
| | - Yi-Lun Ying
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
| | - Yi-Tao Long
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, 210023, Nanjing, China
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42
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Gas Biosensor Arrays Based on Single-Stranded DNA-Functionalized Single-Walled Carbon Nanotubes for the Detection of Volatile Organic Compound Biomarkers Released by Huanglongbing Disease-Infected Citrus Trees. SENSORS 2019; 19:s19214795. [PMID: 31689974 PMCID: PMC6865013 DOI: 10.3390/s19214795] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 02/02/2023]
Abstract
Volatile organic compounds (VOCs) released by plants are closely associated with plant metabolism and can serve as biomarkers for disease diagnosis. Huanglongbing (HLB), also known as citrus greening or yellow shoot disease, is a lethal threat to the multi-billion-dollar citrus industry. Early detection of HLB is vital for removal of susceptible citrus trees and containment of the disease. Gas sensors are applied to monitor the air quality or toxic gases owing to their low-cost fabrication, smooth operation, and possible miniaturization. Here, we report on the development, characterization, and application of electrical biosensor arrays based on single-walled carbon nanotubes (SWNTs) decorated with single-stranded DNA (ssDNA) for the detection of four VOCs-ethylhexanol, linalool, tetradecene, and phenylacetaldehyde-that serve as secondary biomarkers for detection of infected citrus trees during the asymptomatic stage. SWNTs were noncovalently functionalized with ssDNA using π-π interaction between the nucleotide and sidewall of SWNTs. The resulting ssDNA-SWNT hybrid structure and device properties were investigated using Raman spectroscopy, ultraviolet (UV) spectroscopy, and electrical measurements. To monitor changes in the four VOCs, gas biosensor arrays consisting of bare SWNTs before and after being decorated with different ssDNA were employed to determine the different concentrations of the four VOCs. The data was processed using principal component analysis (PCA) and neural net fitting (NNF).
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Ding T, Chen AK, Lu Z. The applications of nanopores in studies of proteins. Sci Bull (Beijing) 2019; 64:1456-1467. [PMID: 36659703 DOI: 10.1016/j.scib.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/07/2019] [Accepted: 05/28/2019] [Indexed: 01/21/2023]
Abstract
Nanopores are a label-free platform with the ability to detect subtle changes in the activities of individual biomolecules under physiological conditions. Here, we comprehensively review the technological development of nanopores, focusing on their applications in studying the physicochemical properties and dynamic conformations of peptides, individual proteins, protein-protein complexes and protein-DNA complexes. This is followed by a brief discussion of the potential challenges that need to be overcome before the technology can be widely accepted by the scientific community. We believe that with continued refinement of the technology, significant understanding can be gained to help clarify the role of protein activities in the regulation of cellular physiology and pathogenesis.
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Affiliation(s)
- Taoli Ding
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.
| | - Zuhong Lu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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Willems K, Ruić D, Biesemans A, Galenkamp NS, Van Dorpe P, Maglia G. Engineering and Modeling the Electrophoretic Trapping of a Single Protein Inside a Nanopore. ACS NANO 2019; 13:9980-9992. [PMID: 31403770 PMCID: PMC6764111 DOI: 10.1021/acsnano.8b09137] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The ability to confine and to study single molecules has enabled important advances in natural and applied sciences. Recently, we have shown that unlabeled proteins can be confined inside the biological nanopore Cytolysin A (ClyA) and conformational changes monitored by ionic current recordings. However, trapping small proteins remains a challenge. Here, we describe a system where steric, electrostatic, electrophoretic, and electro-osmotic forces are exploited to immobilize a small protein, dihydrofolate reductase (DHFR), inside ClyA. Assisted by electrostatic simulations, we show that the dwell time of DHFR inside ClyA can be increased by orders of magnitude (from milliseconds to seconds) by manipulation of the DHFR charge distribution. Further, we describe a physical model that includes a double energy barrier and the main electrophoretic components for trapping DHFR inside the nanopore. Simultaneous fits to the voltage dependence of the dwell times allowed direct estimates of the cis and trans translocation probabilities, the mean dwell time, and the force exerted by the electro-osmotic flow on the protein (≅9 pN at -50 mV) to be retrieved. The observed binding of NADPH to the trapped DHFR molecules suggested that the engineered proteins remained folded and functional inside ClyA. Contact-free confinement of single proteins inside nanopores can be employed for the manipulation and localized delivery of individual proteins and will have further applications in single-molecule analyte sensing and enzymology studies.
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Affiliation(s)
- Kherim Willems
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
- imec, Kapeldreef 75, B-3001 Leuven, Belgium
| | - Dino Ruić
- imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department
of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | - Annemie Biesemans
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Nicole Stéphanie Galenkamp
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Pol Van Dorpe
- imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department
of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
- E-mail:
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45
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Ying YL, Long YT. Nanopore-Based Single-Biomolecule Interfaces: From Information to Knowledge. J Am Chem Soc 2019; 141:15720-15729. [DOI: 10.1021/jacs.8b11970] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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46
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Katkar HH, Muthukumar M. Conformational fluctuations of a DNA electrophoretically translocating through a nanopore under the action of a motor protein. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:67. [PMID: 31129744 PMCID: PMC8475728 DOI: 10.1140/epje/i2019-11830-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
Single-file single-molecule electrophoresis through a nanopore has emerged as one of the successful methods in DNA sequencing. In gaining sufficient accuracy in the readout of the sequence, it is essential to position every nucleotide of the sequence with great accuracy and precision at the interrogation point of the nanopore. A combination of a ratcheting enzyme and a threaded DNA across a protein pore under an electric field is experimentally shown to be a viable method for DNA sequencing within the single-molecule electrophoresis technique. Using coarse-grained models of the enzyme and the protein nanopore, and Langevin dynamics simulations, we have characterized the conformational fluctuations of the DNA inside the nanopore. We show that the conformational fluctuations of DNA are significant for slowly operating enzymes such as phi29 DNA polymerase. Our results imply that there is considerable uncertainty in precisely positioning a nucleotide at the interrogation point of the nanopore. The discrepancy between the results of coarse-grained simulations and the experimentally successful accurate sequencing suggests that additional features of the experiments, such as explicit treatment of electrolyte ions and hydrodynamics, must be incorporated in the simulations to accurately model experimental constructs.
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Affiliation(s)
- Harshwardhan H Katkar
- Department of Chemistry, The University of Chicago, 60637, Chicago, IL, USA
- Department of Polymer Science and Engineering, University of Massachusetts, 01003, Amherst, MA, USA
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, 01003, Amherst, MA, USA.
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47
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Smith AM, Jain M, Mulroney L, Garalde DR, Akeson M. Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing. PLoS One 2019; 14:e0216709. [PMID: 31095620 PMCID: PMC6522004 DOI: 10.1371/journal.pone.0216709] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/27/2019] [Indexed: 11/19/2022] Open
Abstract
The ribosome small subunit is expressed in all living cells. It performs numerous essential functions during translation, including formation of the initiation complex and proofreading of base-pairs between mRNA codons and tRNA anticodons. The core constituent of the small ribosomal subunit is a ~1.5 kb RNA strand in prokaryotes (16S rRNA) and a homologous ~1.8 kb RNA strand in eukaryotes (18S rRNA). Traditional sequencing-by-synthesis (SBS) of rRNA genes or rRNA cDNA copies has achieved wide use as a 'molecular chronometer' for phylogenetic studies, and as a tool for identifying infectious organisms in the clinic. However, epigenetic modifications on rRNA are erased by SBS methods. Here we describe direct MinION nanopore sequencing of individual, full-length 16S rRNA absent reverse transcription or amplification. As little as 5 picograms (~10 attomole) of purified E. coli 16S rRNA was detected in 4.5 micrograms of total human RNA. Nanopore ionic current traces that deviated from canonical patterns revealed conserved E. coli 16S rRNA 7-methylguanosine and pseudouridine modifications, and a 7-methylguanosine modification that confers aminoglycoside resistance to some pathological E. coli strains.
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Affiliation(s)
- Andrew M. Smith
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Miten Jain
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Logan Mulroney
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | | | - Mark Akeson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
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48
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Ultrasensitive detection of microRNA using an array of Au nanowires deposited within the channels of a porous anodized alumina membrane. Electrochem commun 2019. [DOI: 10.1016/j.elecom.2019.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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49
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Huang G, Voet A, Maglia G. FraC nanopores with adjustable diameter identify the mass of opposite-charge peptides with 44 dalton resolution. Nat Commun 2019; 10:835. [PMID: 30783102 PMCID: PMC6381162 DOI: 10.1038/s41467-019-08761-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/29/2019] [Indexed: 12/26/2022] Open
Abstract
A high throughput single-molecule method for identifying peptides and sequencing proteins based on nanopores could reduce costs and increase speeds of sequencing, allow the fabrication of portable home-diagnostic devices, and permit the characterization of low abundance proteins and heterogeneity in post-translational modifications. Here we engineer the size of Fragaceatoxin C (FraC) biological nanopore to allow the analysis of a wide range of peptide lengths. Ionic blockades through engineered nanopores distinguish a variety of peptides, including two peptides differing only by the substitution of alanine with glutamate. We also find that at pH 3.8 the depth of the peptide current blockades scales with the mass of the peptides irrespectively of the chemical composition of the analyte. Hence, this work shows that FraC nanopores allow direct readout of the mass of single peptide in solution, which is a crucial step towards the developing of a real-time and single-molecule protein sequencing device.
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Affiliation(s)
- Gang Huang
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Arnout Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G, 3001, Heverlee, Belgium
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
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50
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Harrington L, Alexander LT, Knapp S, Bayley H. Single-Molecule Protein Phosphorylation and Dephosphorylation by Nanopore Enzymology. ACS NANO 2019; 13:633-641. [PMID: 30588793 DOI: 10.1021/acsnano.8b07697] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Reversible protein phosphorylation plays a crucial and ubiquitous role in the control of almost all cellular processes. The interplay of protein kinases and phosphatases acting in opposition ensures tight dynamic control of protein phosphorylation states within the cell. Previously, engineered α-hemolysin pores bearing kinase substrate peptides have been developed as single-molecule stochastic sensors for protein kinases. Here, we have used these pores to observe, label-free, the phosphorylation and dephosphorylation of a single substrate molecule. Further, we investigated the effect of Mg2+ and Mn2+ upon substrate and product binding and found that Mn2+ relaxes active-site specificity toward nucleotides and enhances product binding. In doing so, we demonstrate the power and versatility of nanopore enzymology to scrutinize a critical post-translational modification.
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Affiliation(s)
- Leon Harrington
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Leila T Alexander
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute , University of Oxford , Oxford OX3 7DQ , United Kingdom
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute , University of Oxford , Oxford OX3 7DQ , United Kingdom
| | - Hagan Bayley
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
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