1
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Li Y, Yang Y, Zhong C, Xiao D, Zhou C. Highly Sensitive Detection of T790 M with a Three-Level Characteristic Current by Thymine-Hg(II)-Thymine in the α-Hemolysin Nanopore. Anal Chem 2024; 96:3587-3592. [PMID: 38372205 DOI: 10.1021/acs.analchem.3c05571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Sensitive detection of resistance mutation T790 M is of great significance for early diagnosis and prognostic monitoring of non-small-cell lung cancer (NSCLC). In this paper, we showed a highly sensitive detection strategy for T790 M using a three-level characteristic current signal pattern in an α-hemolysin nanopore. A probe was designed that formed a C-T mismatched base pair with wild-type/P and a T-T mismatched with the T790M/P. The T790M/P produced a unique three-level characteristic current signal in the presence of mercury ions(II): first, T790M-Hg2+-P entering the vestibule of α-HL under the transmembrane potential and overhang of probe occupying the β-barrel, then probe unzipping from the T790M/P, T790 M temporally residing inside the nanocavity due to the interaction with Hg(II), and finally T790 M passing through the β-barrel. The blocking current distribution was concentrated with a small relative standard deviation of about 3%, and the signal peaks of T790 M and wild-type can be completely separated with a high separation resolution of more than 2.5, which achieved the highly sensitive detection of T790 M down to 0.001 pM (confidence level P 95%) with a linear range from 0.001 pM to 1 nM in human serum samples. This highly sensitive recognition strategy enables the detection of low abundance T790 M and provides a method for prognostic monitoring in NSCLC patients.
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Affiliation(s)
- Yaping Li
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Yongqi Yang
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Chunmeng Zhong
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Dan Xiao
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
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2
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Hussein EA, Rice B, White RJ. Recent advances in ion-channel probes for nanopore sensing: Insights into the probe architectures. Anal Chim Acta 2022; 1224:340162. [DOI: 10.1016/j.aca.2022.340162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 11/01/2022]
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3
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Denuga S, Whelan DE, O'Neill SP, Johnson RP. Capture and analysis of double‐stranded DNA with the α‐hemolysin nanopore: Fundamentals and applications. ELECTROCHEMICAL SCIENCE ADVANCES 2022. [DOI: 10.1002/elsa.202200001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
| | | | | | - Robert P. Johnson
- School of Chemistry University College Dublin Ireland
- UCD‐Centre for Food Safety University College Dublin Dublin Ireland
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4
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Wang Y, Sun W, Wang J, Wang X, Xu Y, Guo Y, Wang Y, Zhang M, Jiang L, Liu S, Huang J. Ultrasensitive Uracil-DNA Glycosylase Activity Assay and Its Inhibitor Screening Based on Primer Remodeling Jointly via Repair Enzyme and Polymerase. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3868-3875. [PMID: 35298179 DOI: 10.1021/acs.langmuir.2c00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The development of isothermal nucleic acid amplification techniques has great significance for highly sensitive biosensing in modern biology and biomedicine. A facile and robust exponential rolling circle amplification (RCA) strategy is proposed based on primer-remodeling amplification jointly via a repair enzyme and polymerase, and uracil-DNA glycosylase (UDG) is selected as a model analyte. Two kinds of complexes, complex I and complex II, are preprepared by hybridizing a circular template (CT) with a uracil-containing hairpin probe and tetrahydrofuran abasic site mimic (AP site)-embedded fluorescence-quenched probe (AFP), respectively. The target UDG specifically binds to complex I, resulting in the generation of an AP site, followed by cleavage via endonuclease IV (Endo IV) and the successive trimming of unmatched 3' terminus via phi29 DNA polymerase, thus producing a useable primer-CT complex that actuates the primary RCA. Then, numerous complex II anneal with the first-generation RCA product (RP), generating a complex II-RP assembly containing AP sites within the DNA duplex. With the aid of Endo IV and phi29, AFP, as a pre-primer in complex II, is converted into a mature primer to initiate additional rounds of RCA. So, countless AFPs are cleaved, releasing remarkably strong fluorescent signals. The biosensor is demonstrated to enable rapid and accurate detection of the UDG activity with an improved detection limit as low as 4.7 × 10-5 U·mL-1. Moreover, this biosensor is successfully applied for UDG inhibitor screening and complicated biological samples analysis. Compared to the previous exponential RCA methods, our proposed strategy offers additional advantages, including excellent stability, optional design of CT, and simplified operating steps. Therefore, this proposed strategy may create a useful and practical platform for ultrasensitive detection of low levels of analytes in clinical diagnosis and fundamental biomedicine research.
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Affiliation(s)
- Yu Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Wenyu Sun
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Jingfeng Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xu Wang
- Shandong Institute of Metrology and Science, Jinan 250014, P. R. China
| | - Yicheng Xu
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Yuanzhen Guo
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Yeru Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Manru Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Long Jiang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Su Liu
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Jiadong Huang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
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5
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Zhong W, Yang Q, Fang K, Xiao D, Zhou C. Current Simultaneous Discrimination of Mismatched MicroRNAs Using Base-Flipping within the α-Hemolysin Latch. ACS Sens 2021; 6:4482-4488. [PMID: 34793139 DOI: 10.1021/acssensors.1c02005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The simultaneous discrimination of let-7 microRNAs (miRNAs) would greatly facilitate the early diagnosis and prognosis monitoring of diseases. In this work, a molecular beacon DNA probe was designed to be able to flip out its mismatched cytosine base within the α-hemolysin (α-HL) latch and generate completely separated blocking currents to identify the single-base difference. As a result, the characteristic blocking current of fully matched MB/let-7a and single-base mismatched MB/let-7f was 84.30 ± 0.92 and 87.05 ± 0.86% (confidence level P 95%), respectively. Let-7 miRNA family let-7a and let-7f were completely simultaneously discriminated, which could be attributed to the following strengths. (1) The statistic distribution of blocking current is extremely concentrated with a small relative standard deviation (RSD) of less than 1% and a narrow distribution range. (2) Complete separation is achieved with a high separation resolution of 1.54. (3) The cytosine base flipping out within the α-HL latch provides a universal labeling-free strategy to simultaneously discriminate the single-base mismatch. Overall, the target let-7f sequences were detected with a linear range from 0.001 to 10 pM in human serum samples containing 200 nM let-7a. Great potential has been demonstrated for precise detection, early diagnosis, and prognosis monitoring of diseases related to single-base difference.
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Affiliation(s)
- Wenjun Zhong
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Qiufang Yang
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Kerui Fang
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Dan Xiao
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
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6
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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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7
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Liu T, Li Z, Chen M, Zhao H, Zheng Z, Cui L, Zhang X. Sensitive electrochemical biosensor for Uracil-DNA glycosylase detection based on self-linkable hollow Mn/Ni layered doubled hydroxides as oxidase-like nanozyme for cascade signal amplification. Biosens Bioelectron 2021; 194:113607. [PMID: 34507096 DOI: 10.1016/j.bios.2021.113607] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/11/2021] [Accepted: 08/29/2021] [Indexed: 02/06/2023]
Abstract
Nanozymes have been widely used in biosensors instead of natural enzymes because of low cost, high stability and ease of storage. However, few works use oxidase-like nanozymes to fabricate electrochemical biosensors. Herein, we proposed a sensitive electrochemical biosensor to detect uracil-DNA glycosylase (UDG) based on the hollow Mn/Ni layered doubled hydroxides (h-Mn/Ni LDHs) as oxidase-like nanozyme. Briefly, the h-Mn/Ni LDHs, which was prepared by a facile hydrothermal method, exhibited excellent oxidase-like activity because the hollow structure provided rich active sites and high specific surface area. Then, the signal probes were constructed by assembling the hairpin DNA (hDNA), single DNA1 and DNA2 on the h-Mn/Ni LDHs, respectively. In the presence of UDG, the uracil bases in the stem of hDNA were specifically excised, generating apyrimidinic (AP) sites and inducing the unwinding of the hDNA. Afterwards, the h-Mn/Ni LDHs@Au-hDNA/DNA1 was connected on the electrode via hybridization between unwinded hDNA and capture DNA (cDNA). Subsequently, the self-linking process allowed the retention of numerous h-Mn/Ni LDHs through simple DNA hybridization to amplify the signal of o-phenylenediamine (o-PD). Unlike many peroxidase-like nanozyme-based electrochemical biosensors, there is no need to add H2O2 during the experimental process, which effectively reduced the background signal as well as improved the stability of the biosensor. As expected, the biosensor exhibited excellent performance with a wide linear range and a low detection limit. This work highlights an appealing opportunity to develop a no H2O2 platform based on h-Mn/Ni LDHs for future application in biological analysis and clinical diagnosis.
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Affiliation(s)
- Tingting Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Zhiwen Li
- School of Chemistry and Pharmaceutical Engineering, Shandong First Medical University & Shandong Academy of Medical Science, Taian, 271016, PR China
| | - Mohan Chen
- Jinan Foreign Language School, Jinan, Shandong Province, 250353, China
| | - Huijuan Zhao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Zekun Zheng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Lin Cui
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong, 250014, China.
| | - Xiaomei Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China.
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8
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Ren H, Edwards MA. Stochasticity in Single-Entity Electrochemistry. CURRENT OPINION IN ELECTROCHEMISTRY 2021; 25:100632. [PMID: 33102927 PMCID: PMC7584144 DOI: 10.1016/j.coelec.2020.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Most electrochemical processes are stochastic and discrete in nature. Yet experimental observables, e.g., i vs E, are typically smooth and deterministic, due to many events/processes, e.g., electron transfers, being averaged together. However, when the number of entities measured approaches a few or even one, stochasticity frequently emerges. Yet all is not lost! Probabilistic and statistical interpretation can generate insights matching or superseding those from macroscale/ensemble measurements, revealing phenomena that were hitherto averaged over. Herein, we review recent literature examples of stochastic processes in single-entity electrochemistry, highlighting strategies for interpreting stochasticity, contrasting them with macroscale measurements, and describing the insights generated.
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Affiliation(s)
- Hang Ren
- Department of Chemistry & Biochemistry, Miami University, Oxford, OH 45056
| | - Martin A Edwards
- Department of Chemistry & Biochemistry, University of Arkansas, Fayetteville, AR 72701
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9
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Zhao H, Hu W, Jing J, Zhang X. One-step G-quadruplex-based fluorescence resonance energy transfer sensing method for ratiometric detection of uracil-DNA glycosylase activity. Talanta 2020; 221:121609. [PMID: 33076139 DOI: 10.1016/j.talanta.2020.121609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 10/23/2022]
Abstract
Uracil-DNA glycosylase (UDG) is a crucial enzyme in base excision repair (BER) pathway. It can repair the uracil-induced DNA lesions and maintain the integrity of genome. In this paper, we developed a facile and ratiometric strategy for UDG activity detection using fluorescence resonance energy transfer (FRET). One double-stranded DNA (dsDNA) substrate consisting of strand 1 (dual-fluorescent dye-modified G-quadruplex sequence single-stranded DNA (ssDNA)), carboxyfluorescein (FAM) acted as donor and tetramethylrhodamine (TAMRA) as acceptor) and strand 2 (the complementary sequence of strand 1 containing three mismatched bases and three uracil bases) was introduced. When the UDG-catalyzed uracil is removed from dsDNA, the thermo-stability of dsDNA is decreased and the dual-fluorescent dye-modified G-quadruplex sequence ssDNA is released. Then, the ssDNA transforms into a G-quadruplex comformation, which brings the labeled FAM and TAMRA into close proximity, resulting in a strong FRET signal. In the absence of UDG, the relatively stable dsDNA separates the labeled FAM and TAMRA, giving a weak FRET signal. Thus, by measuring the system fluorescence intensity and exploiting FRET signal difference, UDG activity can be detected in a simple process. The detection limit is 0.087 U/mL without requiring additional signal amplification process. Besides, our developed strategy can also be used for screening the UDG inhibitors in a ratiometric fluorescence detection way.
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Affiliation(s)
- Hengzhi Zhao
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Wei Hu
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Jing Jing
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Xiaoling Zhang
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China.
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10
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Ferenc G, Váradi Z, Kupihár Z, Paragi G, Kovács L. Analytical and Structural Studies for the Investigation of Oxidative Stress in Guanine Oligonucleotides. Int J Mol Sci 2020; 21:E4981. [PMID: 32679695 PMCID: PMC7404036 DOI: 10.3390/ijms21144981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 11/16/2022] Open
Abstract
DNA damage plays a decisive role in epigenetic effects. The detection and analysis of DNA damages, like the most common change of guanine (G) to 8-oxo-7,8-dihydroguanine (OG), is a key factor in cancer research. It is especially true for G quadruplex structure (GQ), which is one of the best-known examples of a non-canonical DNA arrangement. In the present work, we provided an overview on analytical methods in connection with the detection of OG in oligonucleotides with GQ-forming capacity. Focusing on the last five years, novel electrochemical tools, like dedicated electrodes, were overviewed, as well as different optical methods (fluorometric assays, resonance light scattering or UV radiation) along with hyphenated detection and structural analysis methods (CD, NMR, melting temperature analysis and nanopore detection) were also applied for OG detection. Additionally, GQ-related computational simulations were also summarized. All these results emphasize that OG detection and the analysis of the effect of its presence in higher ordered structures like GQ is still a state-of-the-art research line with continuously increasing interest.
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Affiliation(s)
- Györgyi Ferenc
- Nucleic Acid Synthesis Laboratory, Biological Research Centre, Temesvári krt. 62, H-6726 Szeged, Hungary;
| | - Zoltán Váradi
- Nucleic Acids Laboratory, Department of Medicinal Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (Z.V.); (Z.K.)
| | - Zoltán Kupihár
- Nucleic Acids Laboratory, Department of Medicinal Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (Z.V.); (Z.K.)
| | - Gábor Paragi
- MTA-SZTE Biomimetic Systems Research Group, Dóm tér 8, 6720 Szeged, Hungary
- Institute of Physics, University of Pécs, Ifjúság útja 6, 7624 Pécs, Hungary
| | - Lajos Kovács
- Nucleic Acids Laboratory, Department of Medicinal Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (Z.V.); (Z.K.)
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11
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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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12
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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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13
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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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14
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Tang Z, Choi G, Nouri R, Guan W. Loop-Mediated Isothermal Amplification-Coupled Glass Nanopore Counting Toward Sensitive and Specific Nucleic Acid Testing. NANO LETTERS 2019; 19:7927-7934. [PMID: 31657939 DOI: 10.1021/acs.nanolett.9b03040] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Solid-state nanopores have shown great promise and achieved tremendous success in label-free single-molecule analysis. However, there are three common challenges in solid-state nanopore sensors, including the nanopore size variations from batch to batch that makes the interpretation of the sensing results difficult, the incorporation of sensor specificity, and the impractical analysis time at low analyte concentration due to diffusion-limited mass transport. Here, we demonstrate a novel loop-mediated isothermal amplification (LAMP)-coupled glass nanopore counting strategy that could effectively address these challenges. By using the glass nanopore in the counting mode (versus the sizing mode), the device fabrication challenge is considerably eased since it allows a certain degree of pore size variations and no surface functionalization is needed. The specific molecule replication effectively breaks the diffusion-limited mass transport thanks to the exponential growth of the target molecules. We show the LAMP-coupled glass nanopore counting has the potential to be used in a qualitative test as well as in a quantitative nucleic acid test. This approach lends itself to most amplification strategies as long as the target template is specifically replicated in numbers. The highly sensitive and specific sensing strategy would open a new avenue for solid-state nanopore sensors toward a new form of compact, rapid, low-cost nucleic acid testing at the point of care.
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Affiliation(s)
- Zifan Tang
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Gihoon Choi
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Reza Nouri
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Weihua Guan
- Department of Electrical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Department of Biomedical Engineering , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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15
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Sultan M, Kanavarioti A. Nanopore device-based fingerprinting of RNA oligos and microRNAs enhanced with an Osmium tag. Sci Rep 2019; 9:14180. [PMID: 31578367 PMCID: PMC6775150 DOI: 10.1038/s41598-019-50459-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/12/2019] [Indexed: 12/19/2022] Open
Abstract
Protein and solid-state nanopores are used for DNA/RNA sequencing as well as for single molecule analysis. We proposed that selective labeling/tagging may improve base-to-base resolution of nucleic acids via nanopores. We have explored one specific tag, the Osmium tetroxide 2,2'-bipyridine (OsBp), which conjugates to pyrimidines and leaves purines intact. Earlier reports using OsBp-tagged oligodeoxyribonucleotides demonstrated proof-of-principle during unassisted voltage-driven translocation via either alpha-Hemolysin or a solid-state nanopore. Here we extend this work to RNA oligos and a third nanopore by employing the MinION, a commercially available device from Oxford Nanopore Technologies (ONT). Conductance measurements demonstrate that the MinION visibly discriminates oligoriboadenylates with sequence A15PyA15, where Py is an OsBp-tagged pyrimidine. Such resolution rivals traditional chromatography, suggesting that nanopore devices could be exploited for the characterization of RNA oligos and microRNAs enhanced by selective labeling. The data also reveal marked discrimination between a single pyrimidine and two consecutive pyrimidines in OsBp-tagged AnPyAn and AnPyPyAn. This observation leads to the conjecture that the MinION/OsBp platform senses a 2-nucleotide sequence, in contrast to the reported 5-nucleotide sequence with native nucleic acids. Such improvement in sensing, enabled by the presence of OsBp, may enhance base-calling accuracy in enzyme-assisted DNA/RNA sequencing.
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Affiliation(s)
- Madiha Sultan
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA
| | - Anastassia Kanavarioti
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA.
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16
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Thakur AK, Movileanu L. Single-Molecule Protein Detection in a Biofluid Using a Quantitative Nanopore Sensor. ACS Sens 2019; 4:2320-2326. [PMID: 31397162 DOI: 10.1021/acssensors.9b00848] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein detection in complex biological fluids has wide-ranging significance across proteomics and molecular medicine. Existing detectors cannot readily distinguish between specific and nonspecific interactions in a heterogeneous solution. Here, we show that this daunting shortcoming can be overcome by using a protein bait-containing biological nanopore in mammalian serum. The capture and release events of a protein analyte by the tethered protein bait occur outside the nanopore and are accompanied by uniform current openings. Conversely, nonspecific pore penetrations by nontarget components of serum, which take place inside the nanopore, are featured by irregular current blockades. As a result of this unique peculiarity of the readout between specific protein captures and nonspecific pore penetration events, our selective sensor can quantitatively sample proteins at single-molecule precision in a manner distinctive from those employed by prevailing methods. Because our sensor can be integrated into nanofluidic devices and coupled with high-throughput technologies, our approach will have a transformative impact in protein identification and quantification in clinical isolates for disease prognostics and diagnostics.
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Affiliation(s)
- Avinash Kumar Thakur
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, United States
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
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17
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Edwards MA, Robinson DA, Ren H, Cheyne CG, Tan CS, White HS. Nanoscale electrochemical kinetics & dynamics: the challenges and opportunities of single-entity measurements. Faraday Discuss 2019; 210:9-28. [PMID: 30264833 DOI: 10.1039/c8fd00134k] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The development of nanoscale electrochemistry since the mid-1980s has been predominately coupled with steady-state voltammetric (i-E) methods. This research has been driven by the desire to understand the mechanisms of very fast electrochemical reactions, by electroanalytical measurements in small volumes and unusual media, including in vivo measurements, and by research on correlating electrocatalytic activity, e.g., O2 reduction reaction, with nanoparticle size and structure. Exploration of the behavior of nanoelectrochemical structures (nanoelectrodes, nanoparticles, nanogap cells, etc.) of a characteristic dimension λ using steady-state i-E methods generally relies on the well-known relationship, λ2 ∼ Dt, which relates diffusional lengths to time, t, through the coefficient, D. Decreasing λ, by performing measurements at a nanometric length scales, results in a decrease in the effective timescale of the measurement, and provides a direct means to probe the kinetics of steps associated with very rapid electrochemical reactions. For instance, steady-state voltammetry using a nanogap twin-electrode cell of characteristic width, λ ∼ 10 nm, allows investigations of events occurring at timescales on the order of ∼100 ns. Among many other advantages, decreasing λ also increases spatial resolution in electrochemical imaging, e.g., in scanning electrochemical microscopy, and allows probing of the electric double layer. This Introductory Lecture traces the evolution and driving forces behind the "λ2 ∼ Dt" steady-state approach to nanoscale electrochemistry, beginning in the late 1950s with the introduction of the rotating ring-disk electrode and twin-electrode thin-layer cells, and evolving to current-day investigations using nanoelectrodes, scanning nanocells for imaging, nanopores, and nanoparticles. The recent focus on so-called "single-entity" electrochemistry, in which individual and very short redox events are probed, is a significant departure from the steady-state approach, but provides new opportunities to probe reaction dynamics. The stochastic nature of very fast single-entity events challenges current electrochemical methods and modern electronics, as illustrated using recent experiments from the authors' laboratory.
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Affiliation(s)
- M A Edwards
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA.
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18
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Liu L, You Y, Zhou K, Guo B, Cao Z, Zhao Y, Wu H. A Dual‐Response DNA Probe for Simultaneously Monitoring Enzymatic Activity and Environmental pH Using a Nanopore. Angew Chem Int Ed Engl 2019; 58:14929-14934. [DOI: 10.1002/anie.201907816] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Lei Liu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- Key Laboratory for Biomedical Effects of Nanomaterials &, Nanosafety Institute of High Energy Physics Chinese Academy of Sciences Beijing 100049 China
| | - Yi You
- Collaborative Innovation Center of Micro/nano Bio-sensing, and Food Safety Inspection Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation School of Chemistry and Biological Engineering Changsha University of Science and Technology Changsha 410114 China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Bingyuan Guo
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Zhong Cao
- Collaborative Innovation Center of Micro/nano Bio-sensing, and Food Safety Inspection Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation School of Chemistry and Biological Engineering Changsha University of Science and Technology Changsha 410114 China
| | - Yuliang Zhao
- 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
- University of Chinese Academy of Sciences Beijing 100049 China
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19
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Liu L, You Y, Zhou K, Guo B, Cao Z, Zhao Y, Wu H. A Dual‐Response DNA Probe for Simultaneously Monitoring Enzymatic Activity and Environmental pH Using a Nanopore. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Lei Liu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- Key Laboratory for Biomedical Effects of Nanomaterials &, Nanosafety Institute of High Energy Physics Chinese Academy of Sciences Beijing 100049 China
| | - Yi You
- Collaborative Innovation Center of Micro/nano Bio-sensing, and Food Safety Inspection Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation School of Chemistry and Biological Engineering Changsha University of Science and Technology Changsha 410114 China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Bingyuan Guo
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Zhong Cao
- Collaborative Innovation Center of Micro/nano Bio-sensing, and Food Safety Inspection Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation School of Chemistry and Biological Engineering Changsha University of Science and Technology Changsha 410114 China
| | - Yuliang Zhao
- 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
- University of Chinese Academy of Sciences Beijing 100049 China
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20
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Gao R, Lin Y, Ying YL, Long YT. Nanopore-based sensing interface for single molecule electrochemistry. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9509-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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21
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Wang J, Wang Y, Liu S, Wang H, Zhang X, Song X, Huang J. Base excision repair initiated rolling circle amplification-based fluorescent assay for screening uracil-DNA glycosylase activity using Endo IV-assisted cleavage of AP probes. Analyst 2019; 143:3951-3958. [PMID: 29999513 DOI: 10.1039/c8an00716k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Uracil-DNA glycosylase (UDG) is a crucial damage repair enzyme that initiates the cellular base excision repair pathway that maintains the integrity of the genome. Abnormal UDG activity may induce the malfunction of uracil excision repair that is directly related to a range of diseases including cancers, genotypic diseases, and human immunodeficiencies. In this work, a simple, robust and cost effective biosensing platform for the ultrasensitive detection of UDG activity is established based on the combination of base excision repair-initiated primer generation for rolling circular amplification (RCA) with Endo IV-assisted signal amplification. In the presence of target UDG, UDG can catalyze the removal of uracil on a hairpin probe (HP) leaving an apurinic/apyrimidinic (AP site) which can be cleaved by Endo IV to generate a primer for triggering the RCA reaction. Subsequently, numerous AP site-embedded signal probes, acting as fluorescence-quenched probes, combine with the RCA products to perform signal transduction and quadradic signal amplification through an Endo IV-catalyzed cleavage reaction, thus significantly enhancing the fluorescence signal, which can be used for UDG activity screening. Under optimum conditions, this biosensor exhibits improved sensitivity toward target UDG with a detection limit of as low as 9.3 × 10-5 U mL-1 and a wide detection range across 5 orders of magnitude. Additionally, our biosensor demonstrates high selectivity toward UDG for simple, rapid, and low-cost detection. Furthermore, by redesigning the modification of HP and using of suitable endonuclease enzymes, this RCA coupled with Endo IV-assisted signal amplification strategy might be applied for the detection of various other targets, such as thymine DNA glycosylase, 8-oxoguanine DNA glycosylase, DNA methyltransferase, and so on. Hence, the proposed strategy provides a useful and versatile biosensing platform for the ultrasensitive detection of UDG activity and related fundamental biomedicine research and clinical diagnosis.
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Affiliation(s)
- Jingfeng Wang
- College of Biological Sciences and Technology, University of Jinan, Jinan 250022, P.R. China.
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22
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Wang J, Yang J, Ying YL, Long YT. Nanopore-Based Confined Spaces for Single-Molecular Analysis. Chem Asian J 2019; 14:389-397. [PMID: 30548206 DOI: 10.1002/asia.201801648] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/09/2018] [Indexed: 11/07/2022]
Abstract
The field of nanopore sensing at the single-molecular level is in a "boom" period. Such nanopores, which are either composed of biological materials or are fabricated from solid-state substrates, offer a unique confined space that is compatible with the single-molecular scale. Under the influence of an electrical field, such single-biomolecular interfaces can read single-molecular information and, if appropriately fine-tuned, each molecule plays its individual ionic rhythm to compose a "molecular symphony". Over the past few decades, many research groups have worked on nanopore-based single-molecular sensors for a range of thrilling chemical and clinical applications. Furthermore, for the past decade, we have also focused on nanopore-based sensors. In this Minireview, we summarize the recent developments in fundamental research and applications in this area, along with data algorithms and advances in hardware, which act as infrastructure for the electrochemical analysis.
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Affiliation(s)
- Jiajun Wang
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jie Yang
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
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23
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Tan CS, Fleming AM, Ren H, Burrows CJ, White HS. γ-Hemolysin Nanopore Is Sensitive to Guanine-to-Inosine Substitutions in Double-Stranded DNA at the Single-Molecule Level. J Am Chem Soc 2018; 140:14224-14234. [PMID: 30269492 DOI: 10.1021/jacs.8b08153] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biological nanopores provide a unique single-molecule sensing platform to detect target molecules based on their specific electrical signatures. The γ-hemolysin (γ-HL) protein produced by Staphylococcus aureus is able to assemble into an octamer nanopore with a ∼2.3 nm diameter β-barrel. Herein, we demonstrate the first application of γ-HL nanopore for DNA structural analysis. To optimize conditions for ion-channel recording, the properties of the γ-HL pore (e.g., conductance, voltage-dependent gating, and ion-selectivity) were characterized at different pH, temperature, and electrolyte concentrations. The optimal condition for DNA analysis using γ-HL corresponds to 3 M KCl, pH 5, and T = 20 °C. The γ-HL protein nanopore is able to translocate dsDNA at about ∼20 bp/ms, and the unique current-signature of captured dsDNA can directly distinguish guanine-to-inosine substitutions at the single-molecule level with ∼99% accuracy. The slow dsDNA threading and translocation processes indicate this wild-type γ-HL channel has potential to detect other base modifications in dsDNA.
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Affiliation(s)
- Cherie S Tan
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Hang Ren
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
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24
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Johnson RP, Perera RT, Fleming AM, Burrows CJ, White HS. Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin. Faraday Discuss 2018; 193:471-485. [PMID: 27711888 DOI: 10.1039/c6fd00058d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Unique, two-state modulating current signatures are observed when a cytosine-cytosine mismatch pair is confined at the 2.4 nm latch constriction of the α-hemolysin (αHL) nanopore. We have previously speculated that the modulation is due to base flipping at the mismatch site. Base flipping is a biologically significant mechanism in which a single base is rotated out of the DNA helical stack by 180°. It is the mechanism by which enzymes are able to access bases for repair operations without disturbing the global structure of the helix. Here, temperature dependent ion channel recordings of individual double-stranded DNA duplexes inside αHL are used to derive thermodynamic (ΔH, ΔS) and kinetic (EA) parameters for base flipping of a cytosine at an unstable cytosine-cytosine mismatch site. The measured activation energy for flipping a cytosine located at the latch of αHL out of the helix (18 ± 1 kcal mol-1) is comparable to that previously reported for base flipping at mismatch sites from NMR measurements and potential mean force calculations. We propose that the αHL nanopore is a useful tool for measuring conformational changes in dsDNA at the single molecule level.
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Affiliation(s)
- Robert P Johnson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Rukshan T Perera
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Henry S White
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850, USA.
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25
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Mapping the sensing spots of aerolysin for single oligonucleotides analysis. Nat Commun 2018; 9:2823. [PMID: 30026547 PMCID: PMC6053387 DOI: 10.1038/s41467-018-05108-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/05/2018] [Indexed: 12/05/2022] Open
Abstract
Nanopore sensing is a powerful single-molecule method for DNA and protein sequencing. Recent studies have demonstrated that aerolysin exhibits a high sensitivity for single-molecule detection. However, the lack of the atomic resolution structure of aerolysin pore has hindered the understanding of its sensing capabilities. Herein, we integrate nanopore experimental results and molecular simulations based on a recent pore structural model to precisely map the sensing spots of this toxin for ssDNA translocation. Rationally probing ssDNA length and composition upon pore translocation provides new important insights for molecular determinants of the aerolysin nanopore. Computational and experimental results reveal two critical sensing spots (R220, K238) generating two constriction points along the pore lumen. Taking advantage of the sensing spots, all four nucleobases, cytosine methylation and oxidation of guanine can be clearly identified in a mixture sample. The results provide evidence for the potential of aerolysin as a nanosensor for DNA sequencing. Nanopores are an emerging powerful single-molecule method of DNA sequencing. Here the authors map the structure of aerolysin for use as a nanopore and show detection of modified and unmodified nucleobases.
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26
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Ren H, Cheyne CG, Fleming AM, Burrows CJ, White HS. Single-Molecule Titration in a Protein Nanoreactor Reveals the Protonation/Deprotonation Mechanism of a C:C Mismatch in DNA. J Am Chem Soc 2018; 140:5153-5160. [PMID: 29562130 DOI: 10.1021/jacs.8b00593] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Measurement of single-molecule reactions can elucidate microscopic mechanisms that are often hidden from ensemble analysis. Herein, we report the acid-base titration of a single DNA duplex confined within the wild-type α-hemolysin (α-HL) nanopore for up to 3 h, while monitoring the ionic current through the nanopore. Modulation between two states in the current-time trace for duplexes containing the C:C mismatch in proximity to the latch constriction of α-HL is attributed to the base flipping of the C:C mismatch. As the pH is lowered, the rate for the C:C mismatch to flip from the intra-helical state to the extra-helical state ( kintra-extra) decreases, while the rate for base flipping from the extra-helical state to the intra-helical state ( kextra-intra) remains unchanged. Both kintra-extra and kextra-intra are on the order of 1 × 10-2 s-1 to 1 × 10-1 s-1 and remain stable over the time scale of the measurement (several hours). Analysis of the pH-dependent kinetics of base flipping using a hidden Markov kinetic model demonstrates that protonation/deprotonation occurs while the base pair is in the intra-helical state. We also demonstrate that the rate of protonation is limited by transport of H+ into the α-HL nanopore. Single-molecule kinetic isotope experiments exhibit a large kinetic isotope effect (KIE) for kintra-extra ( kH/ kD ≈ 5) but a limited KIE for kextra-intra ( kH/ kD ≈ 1.3), supporting our model. Our experiments correspond to the longest single-molecule measurements performed using a nanopore, and demonstrate its application in interrogating mechanisms of single-molecule reactions in confined geometries.
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Affiliation(s)
- Hang Ren
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Cameron G Cheyne
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
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27
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Zeng T, Fleming AM, Ding Y, Ren H, White HS, Burrows CJ. Nanopore Analysis of the 5-Guanidinohydantoin to Iminoallantoin Isomerization in Duplex DNA. J Org Chem 2018; 83:3973-3978. [PMID: 29490132 DOI: 10.1021/acs.joc.8b00317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In DNA, guanine oxidation yields diastereomers of 5-guanidinohydantoin (Gh) as one of the major products. In nucleosides and single-stranded DNA, Gh is in a pH-dependent equilibrium with its constitutional isomer iminoallantoin (Ia). Herein, the isomerization reaction between Gh and Ia was monitored in duplex DNA using a protein nanopore by measuring the ionic current when duplex DNA interacts with the pore under an electrophoretic force. Monitoring current levels in this single-molecule method proved to be superior for analysis of population distributions in an equilibrating mixture of four isomers in duplex DNA as a function of pH. The results identified Gh as a major isomer observed when base paired with A, C, or G at pH 6.4-8.4, and Ia was a minor isomer of the reaction mixture that was only observed when the pH was >7.4 in the duplex DNA context. The present results suggest that Gh will be the dominant isomer in duplex DNA under physiological conditions regardless of the base-pairing partner in the duplex.
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Affiliation(s)
- Tao Zeng
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Yun Ding
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Hang Ren
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
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28
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Cao C, Long YT. Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis. Acc Chem Res 2018; 51:331-341. [PMID: 29364650 DOI: 10.1021/acs.accounts.7b00143] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis, we develop an integrated current measurement system and an accurate data processing method for nanopore sensing. The unique geometric structure of a biological nanopore offers a distinct advantage as a nanosensor for single-molecule sensing. The construction of the pore entrance is responsible for capturing the target molecule, while the lumen region determines the translocation process of the single molecule. Since the capture of the target molecule is predominantly diffusion-limited, it is expected that the capture ability of the nanopore toward the target analyte could be effectively enhanced by site-directed mutations of key amino acids with desirable groups. Additionally, changing the side chains inside the wall of the biological nanopore could optimize the geometry of the pore and realize an optimal interaction between the single-molecule interface and the analyte. These improvements would allow for high spatial and current resolution of nanopore sensors, which would ensure the possibility of dynamic study of single biomolecules, including their metastable conformations, charge distributions, and interactions. In the future, data analysis with powerful algorithms will make it possible to automatically and statistically extract detailed information while an analyte translocates through the pore. We conclude that these improvements could have tremendous potential applications for nanopore sensing in the near future.
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Affiliation(s)
- Chan Cao
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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29
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Wang L, Yao F, Kang XF. Nanopore Single-Molecule Analysis of Metal Ion–Chelator Chemical Reaction. Anal Chem 2017; 89:7958-7965. [DOI: 10.1021/acs.analchem.7b01119] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Linlin Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Fujun Yao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Xiao-feng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi’an 710069, P. R. China
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30
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Zeng T, Fleming AM, Ding Y, White HS, Burrows CJ. Interrogation of Base Pairing of the Spiroiminodihydantoin Diastereomers Using the α-Hemolysin Latch. Biochemistry 2017; 56:1596-1603. [PMID: 28230976 DOI: 10.1021/acs.biochem.6b01175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Spiroiminodihydantoin (Sp) is a hyperoxidized form of guanine (G) resulting from oxidation by reactive oxygen species. The lesion is highly mutagenic, and the stereocenter renders the two isomers with distinct behaviors in chemical, spectroscopic, enzymatic, and computational studies. In this work, the α-hemolysin (αHL) latch sensing zone was employed to investigate the base pairing properties of the Sp diastereomers embedded in a double-stranded DNA. Duplexes containing (S)-Sp consistently gave deeper current blockage, and a baseline resolution of ∼0.8 pA was achieved between (S)-Sp:G and (R)-Sp:G base pairs. Ion fluxes were generally more hindered when Sp was placed opposite pyrimidines. Analysis of the current noise of blockade events further provided dynamics information about the Sp-containing base pairs. In general, base pairs comprised of (S)-Sp generated current fluctuations larger than those of their (R)-Sp counterparts, suggesting enhanced base pairing dynamics. The current noise was also substantially affected by the identity of the base opposite Sp, increasing in the following order: A < G < T < C. This report provides information about the dynamic structure of Sp in the DNA duplex and therefore has implications for the enzymatic repair of the Sp diastereomers.
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Affiliation(s)
- Tao Zeng
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Yun Ding
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Henry S White
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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Johnson RP, Fleming AM, Perera RT, Burrows CJ, White HS. Dynamics of a DNA Mismatch Site Held in Confinement Discriminate Epigenetic Modifications of Cytosine. J Am Chem Soc 2017; 139:2750-2756. [PMID: 28125225 DOI: 10.1021/jacs.6b12284] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The identification and discrimination of four epigenetic modifications to cytosine in the proposed active demethylation cycle is demonstrated at the single-molecule level, without the need for chemical pretreatment or labeling. The wild-type protein nanopore α-hemolysin is used to capture individual DNA duplexes containing a single cytosine-cytosine mismatch. The mismatch is held at the latch constriction of α-hemolysin, which is used to monitor the kinetics of base-flipping at the mismatch site. Base-flipping and the subsequent interactions between the DNA and the protein are dramatically altered when one of the cytosine bases is replaced with methyl-, hydroxymethyl-, formyl-, or carboxylcytosine. As well as providing a route to single-molecule analysis of important epigenetic markers in DNA, our results provide important insights into how the introduction of biologically relevant, but poorly understood, modifications to cytosine affect the local conformational dynamics of a DNA duplex in a confined environment.
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Affiliation(s)
- Robert P Johnson
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Rukshan T Perera
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Henry S White
- Department of Chemistry, University of Utah , 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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32
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Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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33
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Tan CS, Riedl J, Fleming AM, Burrows CJ, White HS. Kinetics of T3-DNA Ligase-Catalyzed Phosphodiester Bond Formation Measured Using the α-Hemolysin Nanopore. ACS NANO 2016; 10:11127-11135. [PMID: 28024377 PMCID: PMC5302010 DOI: 10.1021/acsnano.6b05995] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The latch region of the wild-type α-hemolysin (α-HL) protein channel can be used to distinguish single base modifications in double-stranded DNA (dsDNA) via ion channel measurements upon electrophoretic capture of dsDNA in the vestibule of α-HL. Herein, we investigated the use of the latch region to detect a nick in the phosphodiester DNA backbone. The presence of a nick in the phosphodiester backbone of one strand of the duplex results in a significant increase in both the blockade current and noise level relative to the intact duplex. Differentiation between the nicked and intact duplexes based on blockade current or noise, with near baseline resolution, allows real-time monitoring of the rate of T3-DNA ligase-catalyzed phosphodiester bond formation. Under low ionic strength conditions containing divalent cations and a molecular crowding agent (75 mg mL-1 PEG), the rate of enzyme-catalyzed reaction in the bulk solution was continuously monitored by electrophoretically capturing reaction substrate or product dsDNA in the α-HL protein channel vestibule. Enzyme kinetic results obtained from the nanopore experiments match those from gel electrophoresis under the same reaction conditions, indicating the α-HL nanopore measurement provides a viable approach for monitoring enzymatic DNA repair activity.
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34
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Perera RT, Fleming AM, Peterson AM, Heemstra JM, Burrows CJ, White HS. Unzipping of A-Form DNA-RNA, A-Form DNA-PNA, and B-Form DNA-DNA in the α-Hemolysin Nanopore. Biophys J 2016; 110:306-314. [PMID: 26789754 DOI: 10.1016/j.bpj.2015.11.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/03/2015] [Accepted: 11/16/2015] [Indexed: 01/04/2023] Open
Abstract
Unzipping of double-stranded nucleic acids by an electric field applied across a wild-type α-hemolysin (αHL) nanopore provides structural information about different duplex forms. In this work, comparative studies on A-form DNA-RNA duplexes and B-form DNA-DNA duplexes with a single-stranded tail identified significant differences in the blockage current and the unzipping duration between the two helical forms. We observed that the B-form duplex blocks the channel 1.9 ± 0.2 pA more and unzips ∼15-fold more slowly than an A-form duplex at 120 mV. We developed a model to describe the dependence of duplex unzipping on structure. We demonstrate that the wider A-form duplex (d = 2.4 nm) is unable to enter the vestibule opening of αHL on the cis side, leading to unzipping outside of the nanopore with higher residual current and faster unzipping times. In contrast, the smaller B-form duplexes (d = 2.0 nm) enter the vestibule of αHL, resulting in decreased current blockages and slower unzipping. We investigated the effects of varying the length of the single-stranded overhang, and studied A-form DNA-PNA duplexes to provide additional support for the proposed model. This study identifies key differences between A- and B-form duplex unzipping that will be important in the design of future probe-based methods for detecting DNA or RNA.
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Affiliation(s)
- Rukshan T Perera
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | | | | | | | - Henry S White
- Department of Chemistry, University of Utah, Salt Lake City, Utah.
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Ding Y, Kanavarioti A. Single pyrimidine discrimination during voltage-driven translocation of osmylated oligodeoxynucleotides via the α-hemolysin nanopore. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:91-101. [PMID: 26925357 PMCID: PMC4734350 DOI: 10.3762/bjnano.7.11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 01/08/2016] [Indexed: 06/05/2023]
Abstract
The influence of an electric field on an isolated channel or nanopore separating two compartments filled with electrolytes produces a constant ion flux through the pore. Nucleic acids added to one compartment traverse the pore, and modulate the current in a sequence-dependent manner. While translocation is faster than detection, the α-hemolysin nanopore (α-HL) successfully senses base modifications in ssDNA immobilized within the pore. With the assistance of a processing enzyme to slow down translocation, nanopore-based DNA sequencing is now a commercially available platform. However, accurate base calling is challenging because α-HL senses a sequence, and not a single nucleotide. Osmylated DNA was recently proposed as a surrogate for nanopore-based sequencing. Osmylation is the addition of osmium tetroxide 2,2'-bipyridine (OsBp) to the C5-C6 pyrimidine double bond. The process is simple, selective for deoxythymidine (dT) over deoxycytidine (dC), unreactive towards the purines, practically 100% effective, and strikingly independent of length, sequence, and composition. Translocation of an oligodeoxynucleotide (oligo) dA10XdA9 via α-HL is relatively slow, and exhibits distinct duration as well as distinct residual current when X = dA, dT(OsBp), or dC(OsBp). The data indicate that the α-HL constriction zone/β-barrel interacts strongly with both OsBp and the base. A 23 nucleotide long oligo with four dT(OsBp) traverses 18-times slower, and the same oligo with nine (dT+dC)(OsBp) moieties traverses 84-times slower compared to dA20, suggesting an average rate of 40 or 180 μs/base, respectively. These translocation speeds are well above detection limits, may be further optimized, and clear the way for nanopore-based sequencing using osmylated DNA.
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Affiliation(s)
- Yun Ding
- Chemistry Department, University of Utah, Salt Lake City, UT, USA
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36
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Johnson RP, Fleming AM, Beuth LR, Burrows CJ, White HS. Base Flipping within the α-Hemolysin Latch Allows Single-Molecule Identification of Mismatches in DNA. J Am Chem Soc 2016; 138:594-603. [PMID: 26704521 PMCID: PMC4828915 DOI: 10.1021/jacs.5b10710] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A method for identifying and differentiating DNA duplexes containing the mismatched base pairs CC and CA at single molecule resolution with the protein pore α-hemolysin (αHL) is presented. Unique modulating current signatures are observed for duplexes containing the CC and CA mismatches when the mismatch site in the duplex is situated in proximity to the latch constriction of αHL during DNA residence inside the pore. The frequency and current amplitude of the modulation states are dependent on the mismatch type (CC or CA) permitting easy discrimination of these mismatches from one another, and from a fully complementary duplex that exhibits no modulation. We attribute the modulating current signatures to base flipping and subsequent interaction with positively charged lysine residues at the latch constriction of αHL. Our hypothesis is supported by the extended residence times of DNA duplexes within the pore when a mismatch is in proximity to the latch constriction, and by the loss of the two-state current signature in low pH buffers (<6.3), where the protonation of one of the cytosine bases increases the stability of the intrahelical state.
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Affiliation(s)
- Robert P Johnson
- Department of Chemistry, University of Utah , 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah , 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Laura R Beuth
- Department of Chemistry, University of Utah , 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah , 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Henry S White
- Department of Chemistry, University of Utah , 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
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Basak D, Sridhar S, Bera AK, Madhavan N. Cation–halide transport through peptide pores containing aminopicolinic acid. Org Biomol Chem 2016; 14:4712-7. [DOI: 10.1039/c6ob00592f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aminopicolinic acid incorporated peptides form pores that promote cation–halide co-transport across lipid bilayers and do not show a closed state.
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Affiliation(s)
- Debajyoti Basak
- Department of Chemistry
- Indian institute of Technology
- Chennai 600036
- India
| | - Sucheta Sridhar
- Department of Biotechnology
- Indian institute of Technology
- Chennai 600036
- India
| | - Amal K. Bera
- Department of Biotechnology
- Indian institute of Technology
- Chennai 600036
- India
| | - Nandita Madhavan
- Department of Chemistry
- Indian institute of Technology
- Chennai 600036
- India
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Ding Y, Fleming AM, White HS, Burrows CJ. Differentiation of G:C vs A:T and G:C vs G:mC Base Pairs in the Latch Zone of α-Hemolysin. ACS NANO 2015; 9:11325-32. [PMID: 26506108 PMCID: PMC4876701 DOI: 10.1021/acsnano.5b05055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The α-hemolysin (α-HL) nanopore can detect DNA strands under an electrophoretic force via many regions of the channel. Our laboratories previously demonstrated that trapping duplex DNA in the vestibule of wild-type α-HL under force could distinguish the presence of an abasic site compared to a G:C base pair positioned in the latch zone at the top of the vestibule. Herein, a series of duplexes were probed in the latch zone to establish if this region can detect more subtle features of base pairs beyond the complete absence of a base. The results of these studies demonstrate that the most sensitive region of the latch can readily discriminate duplexes in which one G:C base pair is replaced by an A:T. Additional experiments determined that while neither 8-oxo-7,8-dihydroguanine nor 7-deazaguanine opposite C could be differentiated from a G:C base pair, in contrast, the epigenetic marker 5-methylcytosine, when present in both strands of the duplex, yielded new blocking currents when compared to strands with unmodified cytosine. The results are discussed with respect to experimental design for utilization of the latch zone of α-HL to probe specific regions of genomic samples.
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Affiliation(s)
| | | | - Henry S. White
- To whom correspondence should be addressed: Telephone: (801) 585-7290 or (801) 585-6256, or
| | - Cynthia J. Burrows
- To whom correspondence should be addressed: Telephone: (801) 585-7290 or (801) 585-6256, or
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Wang Y, Gu LQ. Biomedical diagnosis perspective of epigenetic detections using alpha-hemolysin nanopore. AIMS MATERIALS SCIENCE 2015; 2:448-472. [PMID: 30931380 PMCID: PMC6436813 DOI: 10.3934/matersci.2015.4.448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The α-hemolysin nanopore has been studied for applications in DNA sequencing, various single-molecule detections, biomolecular interactions, and biochips. The detection of single molecules in a clinical setting could dramatically improve cancer detection and diagnosis as well as develop personalized medicine practices for patients. This brief review shortly presents the current solid state and protein nanopore platforms and their applications like biosensing and sequencing. We then elaborate on various epigenetic detections (like microRNA, G-quadruplex, DNA damages, DNA modifications) with the most widely used alpha-hemolysin pore from a biomedical diagnosis perspective. In these detections, a nanopore electrical current signature was generated by the interaction of a target with the pore. The signature often was evidenced by the difference in the event duration, current level, or both of them. An ideal signature would provide obvious differences in the nanopore signals between the target and the background molecules. The development of cancer biomarker detection techniques and nanopore devices have the potential to advance clinical research and resolve health problems. However, several challenges arise in applying nanopore devices to clinical studies, including super low physiological concentrations of biomarkers resulting in low sensitivity, complex biological sample contents resulting in false signals, and fast translocating speed through the pore resulting in poor detections. These issues and possible solutions are discussed.
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Affiliation(s)
- Yong Wang
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Li-qun Gu
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri-Columbia, Columbia, MO 65211, USA
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Ding Y, Fleming AM, He L, Burrows CJ. Unfolding Kinetics of the Human Telomere i-Motif Under a 10 pN Force Imposed by the α-Hemolysin Nanopore Identify Transient Folded-State Lifetimes at Physiological pH. J Am Chem Soc 2015; 137:9053-60. [PMID: 26110559 PMCID: PMC4513840 DOI: 10.1021/jacs.5b03912] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Cytosine
(C)-rich DNA can adopt i-motif folds under acidic conditions,
with the human telomere i-motif providing a well-studied example.
The dimensions of this i-motif are appropriate for capture in the
nanocavity of the α-hemolysin (α-HL) protein pore under
an electrophoretic force. Interrogation of the current vs time (i–t) traces when the i-motif interacts
with α-HL identified characteristic signals that were pH dependent.
These features were evaluated from pH 5.0 to 7.2, a region surrounding
the transition pH of the i-motif (6.1). When the i-motif without polynucleotide
tails was studied at pH 5.0, the folded structure entered the nanocavity
of α-HL from either the top or bottom face to yield characteristic
current patterns. Addition of a 5′ 25-mer poly-2′-deoxyadensosine
tail allowed capture of the i-motif from the unfolded terminus, and
this was used to analyze the pH dependency of unfolding. At pH values
below the transition point, only folded strands were observed, and
when the pH was increased above the transition pH, the number of folded
events decreased, while the unfolded events increased. At pH 6.8 and
7.2 4% and 2% of the strands were still folded, respectively. The
lifetimes for the folded states at pH 6.8 and 7.2 were 21 and 9 ms,
respectively, at 160 mV electrophoretic force. These lifetimes are
sufficiently long to affect enzymes operating on DNA. Furthermore,
these transient lifetimes are readily obtained using the α-HL
nanopore, a feature that is not easily achievable by other methods.
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Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Lidong He
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S 1400 East, Salt Lake City, Utah 84112-0850, United States
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Johnson RP, Fleming AM, Jin Q, Burrows CJ, White HS. Temperature and electrolyte optimization of the α-hemolysin latch sensing zone for detection of base modification in double-stranded DNA. Biophys J 2015; 107:924-31. [PMID: 25140427 DOI: 10.1016/j.bpj.2014.07.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/16/2014] [Accepted: 07/03/2014] [Indexed: 01/24/2023] Open
Abstract
The latch region of the wild-type protein pore α-hemolysin (α-HL) constitutes a sensing zone for individual abasic sites (and furan analogs) in double-stranded DNA (dsDNA). The presence of an abasic site or furan within a DNA duplex, electrophoretically captured in the α-HL vestibule and positioned at the latch region, can be detected based on the current blockage prior to duplex unzipping. We investigated variations in blockage current as a function of temperature (12-35°C) and KCl concentration (0.15-1.0 M) to understand the origin of the current signature and to optimize conditions for identifying the base modification. In 1 M KCl solution, substitution of a furan for a cytosine base in the latch region results in an ∼ 8 kJ mol(-1) decrease in the activation energy for ion transport through the protein pore. This corresponds to a readily measured ∼ 2 pA increase in current at room temperature. Optimal resolution for detecting the presence of a furan in the latch region is achieved at lower KCl concentrations, where the noise in the measured blockage current is significantly lower. The noise associated with the blockage current also depends on the stability of the duplex (as measured from the melting temperature), where a greater noise in the measured blockage current is observed for less stable duplexes.
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Affiliation(s)
- Robert P Johnson
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | - Qian Jin
- Department of Chemistry, University of Utah, Salt Lake City, Utah
| | | | - Henry S White
- Department of Chemistry, University of Utah, Salt Lake City, Utah.
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Abstract
Planar lipid bilayers have been used to form stable bilayers into which membrane proteins are reconstituted for measurements of their function under an applied membrane potential. Recently, a lipid bilayer membrane is formed by the apposition of two monolayers that line an oil-electrolyte interface. Here, a bilayer membrane system is developed with picoliter bubbles under mechanically and chemically manipulable conditions. A water bubble lined with a phospholipid monolayer is blown from a glass pipette into an oil phase. Two blowing pipettes are manipulated, and bubbles (each with a diameter of ~ 50 μm) are held side by side to form a bilayer, which is termed a contact bubble bilayer. With the electrode implemented in the blowing pipette, currents through the bilayer are readily measured. The intra-bubble pressure is varied with the pressure-controller, leading to various sizes of the bubble and the membrane area. A rapid solution exchange system is developed by introducing additional pressure-driven injection pipettes, and the blowing pipette works as a drain. The solution is exchanged within 20 ms. Also, an asymmetric membrane with different lipid composition of each leaflet is readily formed. Example applications of this versatile method are presented to characterize the function of ion channels.
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Perera RT, Fleming AM, Johnson RP, Burrows CJ, White HS. Detection of benzo[a]pyrene-guanine adducts in single-stranded DNA using the α-hemolysin nanopore. NANOTECHNOLOGY 2015; 26:074002. [PMID: 25629967 PMCID: PMC5266612 DOI: 10.1088/0957-4484/26/7/074002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The carcinogenic precursor benzo[a]pyrene (BP), a polycyclic aromatic hydrocarbon, is released into the environment through the incomplete combustion of hydrocarbons. Metabolism of BP in the human body yields a potent alkylating agent (benzo[a]pyrene diol epoxide, BPDE) that reacts with guanine (G) in DNA to form an adduct implicated in cancer initiation. We report that the α-hemolysin (αHL) nanopore platform can be used to detect a BPDE adduct to G in synthetic oligodeoxynucleotides. Translocation of a 41-mer poly-2'-deoxycytidine strand with a centrally located BPDE adduct to G through αHL in 1 M KCl produces a unique multi-level current signature allowing the adduct to be detected. This readily distinguishable current modulation was observed when the BPDE-adducted DNA strand translocated from either the 5' or 3' directions. This study suggests that BPDE adducts and other large aromatic biomarkers can be detected with αHL, presenting opportunities for the monitoring, quantification, and sequencing of mutagenic compounds from cellular DNA samples.
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Wolna AH, Fleming AM, Burrows CJ. Single-molecule analysis of thymine dimer-containing G-quadruplexes formed from the human telomere sequence. Biochemistry 2014; 53:7484-93. [PMID: 25407781 PMCID: PMC4263424 DOI: 10.1021/bi501072m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/14/2014] [Indexed: 02/06/2023]
Abstract
The human telomere plays crucial roles in maintaining genome stability. In the presence of suitable cations, the repetitive 5'-TTAGGG-3' human telomere sequence can fold into G-quadruplexes that adopt the hybrid, basket, or propeller fold. The telomere sequence is hypersensitive to UV-induced thymine dimer (T=T) formation, yet it does not cause telomere shortening. In this work, the potential structural disruption and thermodynamic stability of the T=T-containing natural telomere sequences were studied to understand why this damage is tolerated in telomeres. First, established methods, such as thermal melting measurements, electrophoretic mobility shift assays, and circular dichroism spectroscopy, were utilized to determine the effects of the damage on these structures. Second, a single-molecule ion channel recording technique using α-hemolysin (α-HL) was employed to examine further the structural differences between the damaged sequences. It was observed that the damage caused slightly lower thermal stabilities and subtle changes in the circular dichroism spectra for hybrid and basket folds. The α-HL experiments determined that T=Ts disrupt double-chain reversal loop formation but are tolerated in edgewise and diagonal loops. The largest change was observed for the T=T-containing natural telomere sequence when the propeller fold (all double-chain reversal loops) was studied. On the basis of the α-HL experiments, it was determined that a triplexlike structure exists under conditions that favor a propeller structure. The biological significance of these observations is discussed.
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Affiliation(s)
- Anna H. Wolna
- Department of Chemistry, University of
Utah, 315 South 1400
East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M. Fleming
- Department of Chemistry, University of
Utah, 315 South 1400
East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of
Utah, 315 South 1400
East, Salt Lake City, Utah 84112-0850, United States
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Johnson R, Fleming AM, Burrows CJ, White HS. Effect of an Electrolyte Cation on Detecting DNA Damage with the Latch Constriction of α-Hemolysin. J Phys Chem Lett 2014; 5:3781-3786. [PMID: 25400876 PMCID: PMC4226304 DOI: 10.1021/jz502030e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 10/14/2014] [Indexed: 05/30/2023]
Abstract
The effect of an electrolyte cation on the unzipping of furan-containing double-stranded DNA in an α-hemolysin (αHL) nanopore is described. The current through an open αHL channel increases in proportion to the ion mobility. However, the ionic current measured during residence of a DNA duplex inside of the protein pore shows a more complex dependence on the choice of cation, indicating that the current measured during DNA residence in the pore is modulated by the specific interactions of the cations with the DNA and/or αHL. The residence time (stability) of the DNA duplex inside of the pore prior to unzipping is also highly dependent on the cation, in striking contrast to the small variation in duplex stability (as measured by the melting temperature) in bulk electrolyte solution. A missing base in DNA can be detected in the latch region of αHL with optimal current resolution in RbCl, while optimal time resolution is possible in LiCl.
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46
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Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity. Proc Natl Acad Sci U S A 2014; 111:14325-31. [PMID: 25225404 DOI: 10.1073/pnas.1415944111] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human telomeric DNA consists of tandem repeats of the sequence 5'-TTAGGG-3' that can fold into various G-quadruplexes, including the hybrid, basket, and propeller folds. In this report, we demonstrate use of the α-hemolysin ion channel to analyze these subtle topological changes at a nanometer scale by providing structure-dependent electrical signatures through DNA-protein interactions. Whereas the dimensions of hybrid and basket folds allowed them to enter the protein vestibule, the propeller fold exceeds the size of the latch region, producing only brief collisions. After attaching a 25-mer poly-2'-deoxyadenosine extension to these structures, unraveling kinetics also were evaluated. Both the locations where the unfolding processes occur and the molecular shapes of the G-quadruplexes play important roles in determining their unfolding profiles. These results provide insights into the application of α-hemolysin as a molecular sieve to differentiate nanostructures as well as the potential technical hurdles DNA secondary structures may present to nanopore technology.
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