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He Z, Wang Z, Lu L, Wang X, Guo G. Enhanced recognition of G-quadruplex DNA oxidative damage based on DNA-mediated charge transfer. Bioelectrochemistry 2024; 158:108714. [PMID: 38653106 DOI: 10.1016/j.bioelechem.2024.108714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 04/25/2024]
Abstract
G-quadruplex (G4) DNA is present in human telomere oligonucleotide sequences. Oxidative damage to telomeric DNA accelerates telomere shortening, which is strongly associated with aging and cancer. Most of the current analyses on oxidative DNA damage are based on ds-DNA. Here, we developed a electrochemiluminescence (ECL) probe for enhanced recognition of oxidative damage in G4-DNA based on DNA-mediated charge transfer (CT), which could specifically recognize damaged sites depending on the position of 8-oxoguanine (8-oxoG). First, a uniform G4-DNA monolayer interface was fabricated; the G4-DNA mediated CT properties were examined using an iridium(III) complex [Ir(ppy)2(pip)]PF6 stacked with G4-DNA as an indicator. The results showed that G4-DNA with 8-oxoG attenuated DNA CT. The topological effects of oxidative damage at different sites of G4-DNA and their effects on DNA CT were revealed. The sensing platform was also used for the sensitive and quantitative detection of 8-oxoG in G4-DNA, with a detection limit of 28.9 fmol. Overall, these findings present a sensitive platform to study G4-DNA structural and stability changes caused by oxidative damage as well as the specific and quantitative detection of oxidation sites. The different damage sites in the G-quadruplex could provide detailed clues for understanding the function of G4-associated telomere functional enzymes.
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Affiliation(s)
- Zhangjin He
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China
| | - Ziqi Wang
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China
| | - Liping Lu
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China; Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China.
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China
| | - Guangsheng Guo
- Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China
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2
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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J. Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P. Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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3
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Möller C, Virzi J, Chang YJ, Keidel A, Chao MR, Hu CW, Cooke MS. DNA modifications: Biomarkers for the exposome? ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2024; 108:104449. [PMID: 38636743 DOI: 10.1016/j.etap.2024.104449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
The concept of the exposome is the encompassing of all the environmental exposures, both exogenous and endogenous, across the life course. Many, if not all, of these exposures can result in the generation of reactive species, and/or the modulation of cellular processes, that can lead to a breadth of modifications of DNA, the nature of which may be used to infer their origin. Because of their role in cell function, such modifications have been associated with various major human diseases, including cancer, and so their assessment is crucial. Historically, most methods have been able to only measure one or a few DNA modifications at a time, limiting the information available. With the development of DNA adductomics, which aims to determine the totality of DNA modifications, a far more comprehensive picture of the DNA adduct burden can be gained. Importantly, DNA adductomics can facilitate a "top-down" investigative approach whereby patterns of adducts may be used to trace and identify the originating exposure source. This, together with other 'omic approaches, represents a major tool for unraveling the complexities of the exposome and hence allow a better a understanding of the environmental origins of disease.
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Affiliation(s)
- Carolina Möller
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
| | - Jazmine Virzi
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Yuan-Jhe Chang
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Alexandra Keidel
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Mu-Rong Chao
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan; Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan
| | - Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA; College of Public Health, University of South Florida, Tampa, FL 33620, USA; Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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4
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Fleming AM, Zhu J, Done VK, Burrows CJ. Advantages and challenges associated with bisulfite-assisted nanopore direct RNA sequencing for modifications. RSC Chem Biol 2023; 4:952-964. [PMID: 37920399 PMCID: PMC10619145 DOI: 10.1039/d3cb00081h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/23/2023] [Indexed: 11/04/2023] Open
Abstract
Nanopore direct RNA sequencing is a technology that allows sequencing for epitranscriptomic modifications with the possibility of a quantitative assessment. In the present work, pseudouridine (Ψ) was sequenced with the nanopore before and after the pH 7 bisulfite reaction that yields stable ribose adducts at C1' of Ψ. The adducted sites produced greater base call errors in the form of deletion signatures compared to Ψ. Sequencing studies on E. coli rRNA and tmRNA before and after the pH 7 bisulfite reaction demonstrated that using chemically-assisted nanopore sequencing has distinct advantages for minimization of false positives and false negatives in the data. The rRNA from E. coli has 19 known U/C sequence variations that give similar base call signatures as Ψ, and therefore, are false positives when inspecting base call data; however, these sites are refractory to reacting with bisulfite as is easily observed in nanopore data. The E. coli tmRNA has a low occupancy Ψ in a pyrimidine-rich sequence context that is called a U representing a false negative; partial occupancy by Ψ is revealed after the bisulfite reaction. In a final study, 5-methylcytidine (m5C) in RNA can readily be observed after the pH 5 bisulfite reaction in which the parent C deaminates to U and the modified site does not react. This locates m5C when using bisulfite-assisted nanopore direct RNA sequencing, which is otherwise challenging to observe. The advantages and challenges of the overall approach are discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
| | - Judy Zhu
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
| | - Vilhelmina K Done
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
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5
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Vijayraghavan S, Saini N. Aldehyde-Associated Mutagenesis─Current State of Knowledge. Chem Res Toxicol 2023. [PMID: 37363863 DOI: 10.1021/acs.chemrestox.3c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Aldehydes are widespread in the environment, with multiple sources such as food and beverages, industrial effluents, cigarette smoke, and additives. The toxic effects of exposure to several aldehydes have been observed in numerous studies. At the molecular level, aldehydes damage DNA, cross-link DNA and proteins, lead to lipid peroxidation, and are associated with increased disease risk including cancer. People genetically predisposed to aldehyde sensitivity exhibit severe health outcomes. In various diseases such as Fanconi's anemia and Cockayne syndrome, loss of aldehyde-metabolizing pathways in conjunction with defects in DNA repair leads to widespread DNA damage. Importantly, aldehyde-associated mutagenicity is being explored in a growing number of studies, which could offer key insights into how they potentially contribute to tumorigenesis. Here, we review the genotoxic effects of various aldehydes, focusing particularly on the DNA adducts underlying the mutagenicity of environmentally derived aldehydes. We summarize the chemical structures of the aldehydes and their predominant DNA adducts, discuss various methodologies, in vitro and in vivo, commonly used in measuring aldehyde-associated mutagenesis, and highlight some recent studies looking at aldehyde-associated mutation signatures and spectra. We conclude the Review with a discussion on the challenges and future perspectives of investigating aldehyde-associated mutagenesis.
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Affiliation(s)
- Sriram Vijayraghavan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
| | - Natalie Saini
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, United States
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6
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Hong X, Hu Y, Yuan Z, Fang Z, Zhang X, Yuan Y, Guo C. Oxidatively Damaged Nucleic Acid: Linking Diabetes and Cancer. Antioxid Redox Signal 2022; 37:1153-1167. [PMID: 35946074 DOI: 10.1089/ars.2022.0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Significance: Our current knowledge of the mechanism between diabetes and cancer is limited. Oxidatively damaged nucleic acid is considered a critical factor to explore the connections between these two diseases. Recent Advances: The link between diabetes mellitus and cancer has attracted increasing attention in recent years. Emerging evidence supports that oxidatively damaged nucleic acid caused by an imbalance between reactive oxygen species generation and elimination is a bridge connecting diabetes and cancer. 8-Oxo-7,8-dihydro-2'-deoxyguanosine and 8-oxo-7,8-dihydroguanosine assume important roles as biomarkers in assessing the relationship between oxidatively damaged nucleic acid and cancer. Critical Issues: The consequences of diabetes are extensive and may lead to the occurrence of cancer by influencing a combination of factors. At present, there is no direct evidence that diabetes causes cancer by affecting a single factor. Furthermore, the difficulty in controlling variables and differences in detection methods lead to poor reliability and repeatability of results, and there are no clear cutoff values for biomarkers to indicate cancer risk. Future Directions: A better understanding of connections as well as mechanisms between diabetes and cancer is still needed. Both diabetes and cancer are currently intractable diseases. Further exploration of the specific mechanism of oxidatively damaged nucleic acid in the connection between diabetes and cancer is urgently needed. In the future, it is necessary to further take oxidatively damaged nucleic acid as an entry point to provide new ideas for the diagnosis and treatment of diabetes and cancer. Experimental drugs targeting the repair process of oxidatively generated damage require an extensive preclinical evaluation and could ultimately provide new treatment strategies for these diseases. Antioxid. Redox Signal. 37, 1153-1167.
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Affiliation(s)
- Xiujuan Hong
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiqiu Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhijun Yuan
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhihao Fang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoxiao Zhang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Yuan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Cheng Guo
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
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7
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Singh A, Maity A, Singh N. Structure and Dynamics of dsDNA in Cell-like Environments. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1587. [PMID: 36359677 PMCID: PMC9689892 DOI: 10.3390/e24111587] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 06/01/2023]
Abstract
Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA's structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.
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8
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Li W, Wang Y, Xiao Y, Li M, Liu Q, Liang L, Xie W, Wang D, Guan X, Wang L. Simultaneous Dual-Site Identification of 5 mC/8 oG in DNA Triplex Using a Nanopore Sensor. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32948-32959. [PMID: 35816657 DOI: 10.1021/acsami.2c08478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA triplex participates in delivering site-specific epigenetic modifications critical for the regulation of gene expression. Among these marks, 5mC with 8oG functions comprehensively on gene expression. Recently, few research studies have emphasized the necessity of incorporation detection of 5mC with 8oG using one DNA triplex at the same time. Herein, DNA triplex structure was designed and tailored for the site-specific identification of 5mC with 8oG by means of nanopore electroanalysis. The identification was associated with the distinguishable current modulation types caused by DNA unzipping through the nanopore in an electrical field. Results demonstrated that the epigenetic modification proximity to the latch zone or constriction area of the nanopore enables differentiation of modification series at single nucleotide resolution in one DNA triplex, at both physiological and mildly acidic environment. In addition, our nanopore method enables the kinetic and thermodynamic studies to calculate the free energy of modified DNA triplex with applied potentials. Gibbs' energy provided the direct evidence that the DNA triplex with these epigenetic modifications is more stable in acidic environment. Considering modified DNA functions significantly in gene expression, the presented method may provide future opportunities to understand incorporating epigenetic mechanisms of many dysregulated biological processes on the basis of accurate detection.
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Affiliation(s)
- Wei Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yicen Xiao
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Minghan Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wanyi Xie
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
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9
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Castillo-González C, Barbero Barcenilla B, Young PG, Hall E, Shippen DE. Quantification of 8-oxoG in Plant Telomeres. Int J Mol Sci 2022; 23:ijms23094990. [PMID: 35563379 PMCID: PMC9102096 DOI: 10.3390/ijms23094990] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/19/2022] [Accepted: 04/26/2022] [Indexed: 02/07/2023] Open
Abstract
Chemical modifications in DNA impact gene regulation and chromatin structure. DNA oxidation, for example, alters gene expression, DNA synthesis and cell cycle progression. Modification of telomeric DNA by oxidation is emerging as a marker of genotoxic damage and is associated with reduced genome integrity and changes in telomere length and telomerase activity. 8-oxoguanine (8-oxoG) is the most studied and common outcome of oxidative damage in DNA. The G-rich nature of telomeric DNA is proposed to make it a hotspot for oxidation, but because telomeres make up only a tiny fraction of the genome, it has been difficult to directly test this hypothesis by studying dynamic DNA modifications specific to this region in vivo. Here, we present a new, robust method to differentially enrich telomeric DNA in solution, coupled with downstream methods for determination of chemical modification. Specifically, we measure 8-oxoG in Arabidopsis thaliana telomeres under normal and oxidative stress conditions. We show that telomere length is unchanged in response to oxidative stress in three different wild-type accessions. Furthermore, we report that while telomeric DNA comprises only 0.02–0.07% of the total genome, telomeres contribute between 0.2 and 15% of the total 8-oxoG. That is, plant telomeres accumulate 8-oxoG at levels approximately 100-fold higher than the rest of the genome under standard growth conditions. Moreover, they are the primary targets of further damage upon oxidative stress. Interestingly, the accumulation of 8-oxoG in the chromosome body seems to be inversely proportional to telomere length. These findings support the hypothesis that telomeres are hotspots of 8-oxoG and may function as sentinels of oxidative stress in plants.
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10
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Mazzucco G, Huda A, Galli M, Zanella E, Doksani Y. Purification of mammalian telomeric DNA for single-molecule analysis. Nat Protoc 2022; 17:1444-1467. [PMID: 35396546 DOI: 10.1038/s41596-022-00684-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/10/2022] [Indexed: 11/09/2022]
Abstract
Here we provide a detailed protocol for the enrichment of telomeric repeats from mouse and human cells. The procedure consists of two successive rounds of digestion with frequently cutting restriction enzymes followed by size fractionation. Around 2 mg of genomic DNA is required, and the procedure lasts 5-6 d and yields preparations enriched >800-fold in telomeres. The purified material is suitable for single-molecule analysis of telomere structure, visualizing telomere replication and recombination intermediates by electron microscopy or performing molecular combing at telomeric repeats. No special skills are required for the enrichment procedure, while some assistance is needed in harvesting a large number of plates in a timely fashion at the beginning of the procedure. A smaller-scale version of the protocol that involves one round of digestion and purification requires 200 µg of DNA and enriches telomeres ~50-fold in 4 d is also provided. The latter can be combined with specific labeling for single-molecule analysis of replicating DNA or for long-read sequencing analysis of telomeric repeats. The procedure described here can be adapted to the enrichment of other repetitive elements, based on the use of restriction enzymes that do not cut into the repeat of interest.
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Affiliation(s)
| | - Armela Huda
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
| | - Martina Galli
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
| | - Elia Zanella
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
| | - Ylli Doksani
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy.
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11
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Li P, Wang ZY, Yueying Li, Liu LZ, Qiu JG, Zhang CY. Bsu polymerase-mediated fluorescence coding for rapid and sensitive detection of 8-oxo-7,8-dihydroguanine in telomeres of cancer cells. Talanta 2022; 243:123340. [PMID: 35272158 DOI: 10.1016/j.talanta.2022.123340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 11/16/2022]
Abstract
Guanine is the most susceptible to oxidation among all the DNA bases, and 8-oxo-7,8-dihydroguanine (OG) is one of main oxidation products that can occur in any part of chromosomal DNA. OG in the telomere sequence is associated with telomere shortening, cell aging, and dysfunction, and it may induce cancers. The accurate detection of OG in telomeres is important to early clinical diagnosis and molecular research. Herein, we develop a simple and rapid method to sensitively measure 8-oxo-7,8-dihydroguanine (OG) in telomeres of cancer cells by using Bsu polymerase-mediated fluorescence coding. This method is very simple without the requirement for any nucleic acid amplification or specific restriction enzyme recognition reaction, and Bsu polymerase can selectively incorporate Cy5-dATP into the opposite site of OG, endowing this method with good specificity. Moreover, the introduction of single-molecule detection significantly improves the sensitivity. This method can detect OG within 70 min with a limit of detection (LOD) of 2.45 × 10-18 M, and it can detect OG in genomic DNA extracted from H2O2-treated HeLa cells with a LOD of 0.0094 ng, holding great potential in disease-specific gene damage research and early clinic diagnosis.
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Affiliation(s)
- Panyue Li
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Zi-Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
| | - Yueying Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Ling-Zhi Liu
- Department of Oncology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jian-Ge Qiu
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
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12
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Wan Y, Zong C, Li X, Wang A, Li Y, Yang T, Bao Q, Dubow M, Yang M, Rodrigo LA, Mao C. New Insights for Biosensing: Lessons from Microbial Defense Systems. Chem Rev 2022; 122:8126-8180. [PMID: 35234463 DOI: 10.1021/acs.chemrev.1c01063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.
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Affiliation(s)
- Yi Wan
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Chengli Zong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, 1700 Fourth Street, Byers Hall 303C, San Francisco, California 94158, United States
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Yan Li
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Michael Dubow
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, CEA, Université Paris-Saclay, Campus C.N.R.S, Bâtiment 12, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Mingying Yang
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Ledesma-Amaro Rodrigo
- Imperial College Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.,School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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13
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Shimizu K, Mijiddorj B, Usami M, Mizoguchi I, Yoshida S, Akayama S, Hamada Y, Ohyama A, Usui K, Kawamura I, Kawano R. De novo design of a nanopore for single-molecule detection that incorporates a β-hairpin peptide. NATURE NANOTECHNOLOGY 2022; 17:67-75. [PMID: 34811552 PMCID: PMC8770118 DOI: 10.1038/s41565-021-01008-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 09/13/2021] [Indexed: 05/11/2023]
Abstract
The amino-acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide, named SV28, that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device for practical applications. The peptide forms multidispersely sized nanopore structures ranging from 1.7 to 6.3 nm in diameter and can detect DNAs. To form a monodispersely sized nanopore, we redesigned the SV28 by introducing a glycine-kink mutation. The resulting redesigned peptide forms a monodisperse pore with a diameter of 1.7 nm leading to detection of a single polypeptide chain. Such de novo design of a β-hairpin peptide has the potential to create artificial nanopores, which can be size adjusted to a target molecule.
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Affiliation(s)
- Keisuke Shimizu
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology (TUAT), Tokyo, Japan
| | - Batsaikhan Mijiddorj
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
- School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Masataka Usami
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology (TUAT), Tokyo, Japan
| | - Ikuro Mizoguchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology (TUAT), Tokyo, Japan
| | - Shuhei Yoshida
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan
| | - Shiori Akayama
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan
| | - Yoshio Hamada
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan
| | - Akifumi Ohyama
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
| | - Kenji Usui
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology (TUAT), Tokyo, Japan.
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14
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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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15
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Luchian T, Mereuta L, Park Y, Asandei A, Schiopu I. Single-molecule, hybridization-based strategies for short nucleic acids detection and recognition with nanopores. Proteomics 2021; 22:e2100046. [PMID: 34275186 DOI: 10.1002/pmic.202100046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/21/2021] [Accepted: 07/13/2021] [Indexed: 12/23/2022]
Abstract
DNA nanotechnology has seen large developments over the last 30 years through the combination of detection and discovery of DNAs, and solid phase synthesis to increase the chemical functionalities on nucleic acids, leading to the emergence of novel and sophisticated in features, nucleic acids-based biopolymers. Arguably, nanopores developed for fast and direct detection of a large variety of molecules, are part of a revolutionary technological evolution which led to cheaper, smaller and considerably easier to use devices enabling DNA detection and sequencing at the single-molecule level. Through their versatility, the nanopore-based tools proved useful biomedicine, nanoscale chemistry, biology and physics, as well as other disciplines spanning materials science to ecology and anthropology. This mini-review discusses the progress of nanopore- and hybridization-based DNA detection, and explores a range of state-of-the-art applications afforded through the combination of certain synthetically-derived polymers mimicking nucleic acids and nanopores, for the single-molecule biophysics on short DNA structures.
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Affiliation(s)
- Tudor Luchian
- Department of Physics, Alexandru I. Cuza University, Iasi, Romania
| | - Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University, Iasi, Romania
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, Gwangju, Republic of Korea
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, "Alexandru I. Cuza" University, Iasi, Romania
| | - Irina Schiopu
- Interdisciplinary Research Institute, Sciences Department, "Alexandru I. Cuza" University, Iasi, Romania
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16
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The effect of Telomere Lengthening on Genetic Diseases. JOURNAL OF CONTEMPORARY MEDICINE 2021. [DOI: 10.16899/jcm.756562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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17
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Chao MR, Evans MD, Hu CW, Ji Y, Møller P, Rossner P, Cooke MS. Biomarkers of nucleic acid oxidation - A summary state-of-the-art. Redox Biol 2021; 42:101872. [PMID: 33579665 PMCID: PMC8113048 DOI: 10.1016/j.redox.2021.101872] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
Oxidatively generated damage to DNA has been implicated in the pathogenesis of a wide variety of diseases. Increasingly, interest is also focusing upon the effects of damage to the other nucleic acids, RNA and the (2′-deoxy-)ribonucleotide pools, and evidence is growing that these too may have an important role in disease. LC-MS/MS has the ability to provide absolute quantification of specific biomarkers, such as 8-oxo-7,8-dihydro-2′-deoxyGuo (8-oxodG), in both nuclear and mitochondrial DNA, and 8-oxoGuo in RNA. However, significant quantities of tissue are needed, limiting its use in human biomonitoring studies. In contrast, the comet assay requires much less material, and as little as 5 μL of blood may be used, offering a minimally invasive means of assessing oxidative stress in vivo, but this is restricted to nuclear DNA damage only. Urine is an ideal matrix in which to non-invasively study nucleic acid-derived biomarkers of oxidative stress, and considerable progress has been made towards robustly validating these measurements, not least through the efforts of the European Standards Committee on Urinary (DNA) Lesion Analysis. For urine, LC-MS/MS is considered the gold standard approach, and although there have been improvements to the ELISA methodology, this is largely limited to 8-oxodG. Emerging DNA adductomics approaches, which either comprehensively assess the totality of adducts in DNA, or map DNA damage across the nuclear and mitochondrial genomes, offer the potential to considerably advance our understanding of the mechanistic role of oxidatively damaged nucleic acids in disease. Oxidatively damaged nucleic acids are implicated in the pathogenesis of disease. LC-MS/MS, comet assay and ELISA are often used to study oxidatively damaged DNA. Urinary oxidatively damaged nucleic acids non-invasively reflect oxidative stress. DNA adductomics will aid understanding the role of ROS damaged DNA in disease.
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Affiliation(s)
- Mu-Rong Chao
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung, 402, Taiwan; Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung, 402, Taiwan
| | - Mark D Evans
- Leicester School of Allied Health Sciences, Faculty of Health & Life Sciences, De Montfort University, The Gateway, Leicester, LE1 9BH, United Kingdom
| | - Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung, 402, Taiwan
| | - Yunhee Ji
- Department of Environmental Health Sciences, Florida International University, Miami, FL, 33199, USA
| | - Peter Møller
- Section of Environmental Health, Department of Public Health, University of Copenhagen, Øster Farimagsgade 5A, DK, 1014, Copenhagen K, Denmark
| | - Pavel Rossner
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine of the CAS, 142 20, Prague, Czech Republic
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.
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18
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Nookaew I, Jenjaroenpun P, Du H, Wang P, Wu J, Wongsurawat T, Moon SH, Huang E, Wang Y, Boysen G. Detection and Discrimination of DNA Adducts Differing in Size, Regiochemistry, and Functional Group by Nanopore Sequencing. Chem Res Toxicol 2020; 33:2944-2952. [PMID: 32799528 DOI: 10.1021/acs.chemrestox.0c00202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Chemically induced DNA adducts can lead to mutations and cancer. Unfortunately, because common analytical methods (e.g., liquid chromatography-mass spectrometry) require adducts to be digested or liberated from DNA before quantification, information about their positions within the DNA sequence is lost. Advances in nanopore sequencing technologies allow individual DNA molecules to be analyzed at single-nucleobase resolution, enabling us to study the dynamic of epigenetic modifications and exposure-induced DNA adducts in their native forms on the DNA strand. We applied and evaluated the commercially available Oxford Nanopore Technology (ONT) sequencing platform for site-specific detection of DNA adducts and for distinguishing individual alkylated DNA adducts. Using ONT and the publicly available ELIGOS software, we analyzed a library of 15 plasmids containing site-specifically inserted O6- or N2-alkyl-2'-deoxyguanosine lesions differing in sizes and regiochemistries. Positions of DNA adducts were correctly located, and individual DNA adducts were clearly distinguished from each other.
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Affiliation(s)
- Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
| | - Hua Du
- Department of Chemistry, University of California, Riverside 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Pengcheng Wang
- Department of Chemistry, University of California, Riverside 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Jun Wu
- Department of Chemistry, University of California, Riverside 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
| | - Sun Hee Moon
- Environmental and Occupational Health, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
| | - En Huang
- Environmental and Occupational Health, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside 501 Big Springs Road, Riverside, California 92521-0403, United States
| | - Gunnar Boysen
- Environmental and Occupational Health, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, Arkansas 72205, United States
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19
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Logsdon GA, Vollger MR, Eichler EE. Long-read human genome sequencing and its applications. Nat Rev Genet 2020; 21:597-614. [PMID: 32504078 PMCID: PMC7877196 DOI: 10.1038/s41576-020-0236-x] [Citation(s) in RCA: 423] [Impact Index Per Article: 105.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2020] [Indexed: 12/27/2022]
Abstract
Over the past decade, long-read, single-molecule DNA sequencing technologies have emerged as powerful players in genomics. With the ability to generate reads tens to thousands of kilobases in length with an accuracy approaching that of short-read sequencing technologies, these platforms have proven their ability to resolve some of the most challenging regions of the human genome, detect previously inaccessible structural variants and generate some of the first telomere-to-telomere assemblies of whole chromosomes. Long-read sequencing technologies will soon permit the routine assembly of diploid genomes, which will revolutionize genomics by revealing the full spectrum of human genetic variation, resolving some of the missing heritability and leading to the discovery of novel mechanisms of disease.
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Affiliation(s)
- Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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20
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Abstract
Cellular DNA is constantly chemically altered by exogenous and endogenous agents. As all processes of life depend on the transmission of the genetic information, multiple biological processes exist to ensure genome integrity. Chemically damaged DNA has been linked to cancer and aging, therefore it is of great interest to map DNA damage formation and repair to elucidate the distribution of damage on a genome-wide scale. While the low abundance and inability to enzymatically amplify DNA damage are obstacles to genome-wide sequencing, new developments in the last few years have enabled high-resolution mapping of damaged bases. Recently, a number of DNA damage sequencing library construction strategies coupled to new data analysis pipelines allowed the mapping of specific DNA damage formation and repair at high and single nucleotide resolution. Strikingly, these advancements revealed that the distribution of DNA damage is heavily influenced by chromatin states and the binding of transcription factors. In the last seven years, these novel approaches have revealed new genomic maps of DNA damage distribution in a variety of organisms as generated by diverse chemical and physical DNA insults; oxidative stress, chemotherapeutic drugs, environmental pollutants, and sun exposure. Preferred sequences for damage formation and repair have been elucidated, thus making it possible to identify persistent weak spots in the genome as locations predicted to be vulnerable for mutation. As such, sequencing DNA damage will have an immense impact on our ability to elucidate mechanisms of disease initiation, and to evaluate and predict the efficacy of chemotherapeutic drugs.
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Affiliation(s)
- Cécile Mingard
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
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21
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Zhou T, Ge J, Shi L, Liu Z, Deng Y, Peng Y, He X, Tang R, Wen L. Electrokinetic Translocation of a Deformable Nanoparticle through a Nanopore. ACS APPLIED BIO MATERIALS 2020; 3:5160-5168. [PMID: 35021692 DOI: 10.1021/acsabm.0c00606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nanopore-based biosensing technology is built up on the fluctuation of the ionic current induced by the electrokinetic translation of a particle penetrating the nanopore. It is expected that the current change of a deformable bioparticle is dissimilar from that of a rigid one. This study theoretically investigated the transient translocation process of a deformable particle through a nanopore for the first time. The mathematical model considers the Poisson equation for the electric potential, the Nernst-Planck equations for the ionic transport, the Navier-Stokes equations for the flow field, and the stress-strain equation for the dynamics of the deformable bioparticle. The arbitrary Lagrangian-Eulerian method is used for the fully coupled particle-fluid dynamic interaction. Results show that the deformation degree of the particle, the velocity deviation, and the current is different from the rigid particle. The deformation degree of the particle will reach the maximum when the particle passes a nanopore. Because of the deformation of particles, the total force applied on deformable particles is larger than that of rigid particles, resulting in larger velocity deviation and current deviation. The influences of the ratio of the nanoparticle radius to the Debye length and surface charge density of the nanopore are also studied. The research results illustrate the translocation mechanism of a deformable nanoparticle in the nanopore, which can provide theoretical guidance for the biosensing technology based on the nanopore.
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Affiliation(s)
- Teng Zhou
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Jian Ge
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Liuyong Shi
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Zhenyu Liu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
| | - Yongbo Deng
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
| | - Yinyin Peng
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Xiaohan He
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Rongnian Tang
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Liping Wen
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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22
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Li W, Sancar A. Methodologies for detecting environmentally induced DNA damage and repair. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:664-679. [PMID: 32083352 PMCID: PMC7442611 DOI: 10.1002/em.22365] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/08/2020] [Accepted: 02/16/2020] [Indexed: 05/07/2023]
Abstract
Environmental DNA damaging agents continuously challenge the integrity of the genome by introducing a variety of DNA lesions. The DNA damage caused by environmental factors will lead to mutagenesis and subsequent carcinogenesis if they are not removed efficiently by repair pathways. Methods for detection of DNA damage and repair can be applied to identify, visualize, and quantify the DNA damage formation and repair events, and they enable us to illustrate the molecular mechanisms of DNA damage formation, DNA repair pathways, mutagenesis, and carcinogenesis. Ever since the discovery of the double helical structure of DNA in 1953, a great number of methods have been developed to detect various types of DNA damage and repair. Rapid advances in sequencing technologies have facilitated the emergence of a variety of novel methods for detecting environmentally induced DNA damage and repair at the genome-wide scale during the last decade. In this review, we provide a historical overview of the development of various damage detection methods. We also highlight the current methodologies to detect DNA damage and repair, especially some next generation sequencing-based methods.
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Affiliation(s)
- Wentao Li
- Correspondence to: Wentao Li and Aziz Sancar, Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599. and
| | - Aziz Sancar
- Correspondence to: Wentao Li and Aziz Sancar, Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599. and
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23
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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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24
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Chen R, Alanis K, Welle TM, Shen M. Nanoelectrochemistry in the study of single-cell signaling. Anal Bioanal Chem 2020; 412:6121-6132. [PMID: 32424795 DOI: 10.1007/s00216-020-02655-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/02/2020] [Accepted: 04/08/2020] [Indexed: 12/28/2022]
Abstract
Label-free biosensing has been the dream of scientists and biotechnologists as reported by Vollmer and Arnold (Nat Methods 5:591-596, 2008). The ability of examining living cells is crucial to cell biology as noted by Fang (Int J Electrochem 2011:460850, 2011). Chemical measurement with electrodes is label-free and has demonstrated capability of studying living cells. In recent years, nanoelectrodes of different functionality have been developed. These nanometer-sized electrodes, coupled with scanning electrochemical microscopy (SECM), have further enabled nanometer spatial resolution study in aqueous environments. Developments in the field of nanoelectrochemistry have allowed measurement of signaling species at single cells, contributing to better understanding of cell biology. Leading studies using nanoelectrochemistry of a variety of cellular signaling molecules, including redox-active neurotransmitter (e.g., dopamine), non-redox-active neurotransmitter (e.g., acetylcholine), reactive oxygen species (ROS), and reactive nitrogen species (RNS), are reviewed here.
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Affiliation(s)
- Ran Chen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Kristen Alanis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Theresa M Welle
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Mei Shen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA.
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Matsushita M, Shoji K, Takai N, Kawano R. Biological Nanopore Probe: Probing of Viscous Solutions in a Confined Nanospace. J Phys Chem B 2020; 124:2410-2416. [PMID: 32031807 DOI: 10.1021/acs.jpcb.9b11096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This paper describes a nanospace probing system constructed with a pore-forming toxin and a hairpin DNA (hpDNA) molecule. The single hpDNA molecule can be inserted and can move in the confined nanospace of the alpha-hemolysin (αHL) pore. The molecular motion of the hpDNA can be determined based on the fluctuation of the blocking current via channel current measurements. Using this system, we investigated the effect of viscosity of the aqueous solution in the macrospace (bulk) and in the confined nanospace with a small molecule (glycerol) and a polymer (PEG600). The molecular motion of the hpDNA in the nanospace differed in glycerol and PEG600 solutions, while the viscosity remained the same in the bulk solution. The fundamental factors for the viscosity in glycerol and PEG600 solutions are hydrogen bonding and the entanglement of polymer chains, respectively. This difference in factors becomes significant in confined nanospaces, and our system allows us to observe its effect. Additionally, we constructed a spatially resolved nanopore probe integrated into a gold nanoneedle. The αHL-hpDNA nanoprobe system was constructed with the nanoneedle and can be used to monitor the nanospace with nanometer spatial resolution.
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Affiliation(s)
- Masaki Matsushita
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan
| | - Kan Shoji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan.,Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Natsumi Takai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo 184-8588, Japan
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26
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Salk JJ, Kennedy SR. Next-Generation Genotoxicology: Using Modern Sequencing Technologies to Assess Somatic Mutagenesis and Cancer Risk. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:135-151. [PMID: 31595553 PMCID: PMC7003768 DOI: 10.1002/em.22342] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 05/09/2023]
Abstract
Mutations have a profound effect on human health, particularly through an increased risk of carcinogenesis and genetic disease. The strong correlation between mutagenesis and carcinogenesis has been a driving force behind genotoxicity research for more than 50 years. The stochastic and infrequent nature of mutagenesis makes it challenging to observe and to study. Indeed, decades have been spent developing increasingly sophisticated assays and methods to study these low-frequency genetic errors, in hopes of better predicting which chemicals may be carcinogens, understanding their mode of action, and informing guidelines to prevent undue human exposure. While effective, widely used genetic selection-based technologies have a number of limitations that have hampered major advancements in the field of genotoxicity. Emerging new tools, in the form of enhanced next-generation sequencing platforms and methods, are changing this paradigm. In this review, we discuss rapidly evolving sequencing tools and technologies, such as error-corrected sequencing and single cell analysis, which we anticipate will fundamentally reshape the field. In addition, we consider a variety emerging applications for these new technologies, including the detection of DNA adducts, inference of mutational processes based on genomic site and local sequence contexts, and evaluation of genome engineering fidelity, as well as other cutting-edge challenges for the next 50 years of environmental and molecular mutagenesis research. Environ. Mol. Mutagen. 61:135-151, 2020. © 2019 The Authors. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Jesse J. Salk
- Department of Medicine, Division of Medical OncologyUniversity of Washington School of MedicineSeattleWashington
- TwinStrand BiosciencesSeattleWashington
| | - Scott R. Kennedy
- Department of PathologyUniversity of WashingtonSeattleWashington
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27
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Wang S, Liang L, Tang J, Cai Y, Zhao C, Fang S, Wang H, Weng T, Wang L, Wang D. Label-free single-molecule identification of telomere G-quadruplexes with a solid-state nanopore sensor. RSC Adv 2020; 10:27215-27224. [PMID: 35515777 PMCID: PMC9055465 DOI: 10.1039/d0ra05083k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Telomere sequences can spontaneously form G-quadruplexes (G4) in the presence of some cations. In view of their relevance to genetic processes and potential as therapeutic-targets, hitherto, a wealth of conventional techniques have been reported for interrogation of G4 conformation diversity and corresponding folding kinetics, most of which are limited in precision and sensitivity. This work introduces a label-free solid-state nanopore (SSN) approach for the determination of inter-, intra- and tandem molecular G4 with distinct base permutation in various cation buffers with a tailored aperture and meanwhile captures the single-molecule G4 folding process. SSN translocation properties elucidated that both inter- and intramolecular G4 generated higher current blockage with longer duration than flexible homopolymer nucleotide, and intramolecular G4 are structurally more stable with higher event frequency and longer blockage time than intermolecular ones; base arrangement played weak role in translocation behaviors; the same sequences with one, two and three G4 skeletons displayed an increase in current blockage and a gradual extension in dwell time with the increase of molecule size recorded in the same nanopore. We observed the conformation change of single-molecule G4 which indicated the existence of folding/unfolding equilibration in nanopore, and real-time test suggested a gradual formation of G4 with time. Our results could provide a continued and improved understanding of the underlying relevance of structural stability and G4 folding process by utilizing SSN platform which exhibits strategic potential advances over the other methods with high spatial and temporal resolution. Nanopore detection of single-molecule G-quadruplexes.![]()
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28
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Louzon M, Coeurdassier M, Gimbert F, Pauget B, de Vaufleury A. Telomere dynamic in humans and animals: Review and perspectives in environmental toxicology. ENVIRONMENT INTERNATIONAL 2019; 131:105025. [PMID: 31352262 DOI: 10.1016/j.envint.2019.105025] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/19/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Telomeres (TLs) play major roles in stabilizing the genome and are usually shortened with ageing. The maintenance of TLs is ensured by two mechanisms involving telomerase (TA) enzyme and alternative lengthening telomeres (ALT). TL shortening and/or TA inhibition have been related to health effects on organisms (leading to reduced reproductive lifespan and survival), suggesting that they could be key processes in toxicity mechanisms (at molecular and cellular levels) and relevant as an early warning of exposure and effect of chemicals on human health and animal population dynamics. Consequently, a critical analysis of knowledge about relationships between TL dynamic and environmental pollution is essential to highlight the relevance of TL measurement in environmental toxicology. The first objective of this review is to provide a survey on the basic knowledge about TL structure, roles, maintenance mechanisms and causes of shortening in both vertebrates (including humans) and invertebrates. Overall, TL length decreases with ageing but some unexpected exceptions are reported (e.g., in species with different lifespans, such as the nematode Caenorhabditis elegans or the crustacean Homarus americanus). Inconsistent results reported in various biological groups or even between species of the same genus (e.g., the microcrustacean Daphnia sp.) indicate that the relation usually proposed between TL shortening and a decrease in TA activity cannot be generalized and depends on the species, stage of development or lifespan. Although the scientific literature provides evidence of the effect of ageing on TL shortening, much less information on the relationships between shortening, maintenance of TLs, influence of other endogenous and environmental drivers, including exposure to chemical pollutants, is available, especially in invertebrates. The second objective of this review is to connect knowledge on TL dynamic and exposure to contaminants. Most of the studies published on humans rely on correlative epidemiological approaches and few in vitro experiments. They have shown TL attrition when exposed to contaminants, such as polycyclic aromatic hydrocarbons (PAH), polychlorinated biphenyls (PCB), pesticides and metallic elements (ME). In other vertebrates, the studies we found deals mainly with birds and, overall, report a disturbance of TL dynamic consecutively to exposure to chemicals, including metals and organic compounds. In invertebrates, no data are available and the potential of TL dynamic in environmental risk assessment remains to be explored. On the basis of the main gaps identified some research perspectives (e.g., impact of endogenous and environmental drivers, dose response effects, link between TL length, TA activity, longevity and ageing) are proposed to better understand the potential of TL and TA measurements in humans and animals in environmental toxicology.
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Affiliation(s)
- Maxime Louzon
- Department Chrono-Environnement, UMR UFC/CNRS 6249 USC INRA University of Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France
| | - Michael Coeurdassier
- Department Chrono-Environnement, UMR UFC/CNRS 6249 USC INRA University of Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France
| | - Frédéric Gimbert
- Department Chrono-Environnement, UMR UFC/CNRS 6249 USC INRA University of Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France
| | - Benjamin Pauget
- TESORA, Le Visium, 22 avenue Aristide Briand, 94110 Arcueil, France
| | - Annette de Vaufleury
- Department Chrono-Environnement, UMR UFC/CNRS 6249 USC INRA University of Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France.
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29
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Maity A, Singh A, Singh N. Stability of DNA passing through different geometrical pores. ACTA ACUST UNITED AC 2019. [DOI: 10.1209/0295-5075/127/28001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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An N, Fleming AM, Rosecrans NC, Liao Y, Burrows CJ. Synthesis of Site-Specific Crown Ether Adducts to DNA Abasic Sites: 8-Oxo-7,8-Dihydro-2'-Deoxyguanosine and 2'-Deoxycytidine. Methods Mol Biol 2019; 1973:15-25. [PMID: 31016693 DOI: 10.1007/978-1-4939-9216-4_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Formation of adducts to DNA is of great benefit to DNA sequencing and damage detection technology and to enzymology. Here we describe the synthesis and characterization procedures of 18-crown-6 adducts formed to abasic (AP) sites, 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG), and 2'-deoxycytidine (C) residues in DNA oligodeoxynucleotides. These crown ether adducts were used as site-specific modifications to facilitate nanopore technology. The methods described can be readily expanded to attach other suitable primary amines of interest.
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Affiliation(s)
- Na An
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | | | - Yi Liao
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.
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31
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Sasaki S. Development of Novel Functional Molecules Targeting DNA and RNA. Chem Pharm Bull (Tokyo) 2019; 67:505-518. [PMID: 31155555 DOI: 10.1248/cpb.c19-00169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleic acid therapeutics such as antisense and small interfering RNA (siRNA) have attracted increasing attention as innovative medicines that interfere with and/or modify gene expression systems. We have developed new functional oligonucleotides that can target DNA and RNA with high efficiency and selectivity. This review summarizes our achievements, including (1) the formation of non-natural triplex DNA for sequence-specific inhibition of transcription; (2) artificial receptor molecules for 8-oxidized-guanosine nucleosides; and (3) reactive oligonucleotides with a cross-linking agent or a functionality-transfer nucleoside for RNA pinpoint modification.
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Affiliation(s)
- Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University
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32
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Wang Y, Patil KM, Yan S, Zhang P, Guo W, Wang Y, Chen H, Gillingham D, Huang S. Nanopore Sequencing Accurately Identifies the Mutagenic DNA Lesion O
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‐Carboxymethyl Guanine and Reveals Its Behavior in Replication. Angew Chem Int Ed Engl 2019; 58:8432-8436. [DOI: 10.1002/anie.201902521] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Yu Wang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Kiran M. Patil
- Department of ChemistryUniversity of Basel CH-4056 Basel Switzerland
| | - Shuanghong Yan
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Panke Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Weiming Guo
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Yuqin Wang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Hong‐Yuan Chen
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Dennis Gillingham
- Department of ChemistryUniversity of Basel CH-4056 Basel Switzerland
| | - Shuo Huang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
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33
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Wang Y, Patil KM, Yan S, Zhang P, Guo W, Wang Y, Chen H, Gillingham D, Huang S. Nanopore Sequencing Accurately Identifies the Mutagenic DNA Lesion O
6
‐Carboxymethyl Guanine and Reveals Its Behavior in Replication. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yu Wang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Kiran M. Patil
- Department of ChemistryUniversity of Basel CH-4056 Basel Switzerland
| | - Shuanghong Yan
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Panke Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Weiming Guo
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Yuqin Wang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Hong‐Yuan Chen
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
| | - Dennis Gillingham
- Department of ChemistryUniversity of Basel CH-4056 Basel Switzerland
| | - Shuo Huang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life SciencesNanjing University 210023 China
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34
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Aloisi CMN, Sturla SJ, Gahlon HL. A gene-targeted polymerase-mediated strategy to identify O 6-methylguanine damage. Chem Commun (Camb) 2019; 55:3895-3898. [PMID: 30860216 DOI: 10.1039/c9cc00278b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Detecting DNA adducts in cancer genes is important for understanding cancer etiology. This study reports a strategy to identify the mutagenic DNA adduct O6-methylguanine in K-Ras. The strategy involves selective replication past a synthetic primer when placed opposite O6-methylguanine. Future work can apply this approach to other cancer-relevant genes.
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Affiliation(s)
- Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
| | - Hailey L Gahlon
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
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35
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Gunderson CG, Barlow ST, Zhang B. FIB-Milled Quartz Nanopores in a Sealed Nanopipette. J Electroanal Chem (Lausanne) 2019; 833:181-188. [PMID: 31447621 PMCID: PMC6707750 DOI: 10.1016/j.jelechem.2018.11.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We report the use of laser-pulled quartz nanopipettes as a new platform for microfabricated nanopores. A quartz nanopipette is prepared on a laser puller and sealed closed prior to focused-ion beam (FIB) milling. A quartz nanopore can then be FIB-milled into the side walls of the sealed pipette and used to analyze single nanoparticles. This method is fast, reproducible and creates nearly cylindrical nanopores in ultrathin quartz walls with controllable diameter down to 66 nm. Both pore size and wall thickness can be readily controlled in the FIB milling process by adjusting milling parameters and milling at different locations along the pipette walls. FIB-milled quartz nanopores combine the advantages of the pipette pores and silicon chip-based membrane pores into one device while avoiding many of the challenges of two popular nanopore devices. First, they can be used as a handheld probe device like a quartz pipette. Second, the use of an ultrathin quartz membrane gives them superior electric property enabling low noise recording at a higher bandwidth and a highly focused sensing zone located at a farther distance away from the highly restricted tip region. The inner and outer diameters of the resulting pore can be precisely measured using scanning electron microscopy (SEM). As an application, FIB-milled side nanopores are used to study translocation of polystyrene nanoparticles. In addition to studying the dependence of translocation time on the pore length, we demonstrate detection of nanoparticles in parallel nanopores of different lengths and use finite-element simulation to confirm the identity of the two resulting populations. Our results show that FIB-milled side nanopores are a useful platform for future analytical applications like studying nanoparticle translocation dynamics.
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Affiliation(s)
| | - Samuel T Barlow
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bo Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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36
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Zhang Y, Hua RN, Xiang D, Zhang CY. Single-molecule counting of oxidative DNA damage in telomeres from cancer cells. Chem Commun (Camb) 2019; 55:7627-7630. [DOI: 10.1039/c9cc03766g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We demonstrate for the first time the single-molecule counting of oxidative DNA damage in telomeres from cancer cells.
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Affiliation(s)
- Yan Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Ruo-nan Hua
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Dongxue Xiang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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37
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Wu J, McKeague M, Sturla SJ. Nucleotide-Resolution Genome-Wide Mapping of Oxidative DNA Damage by Click-Code-Seq. J Am Chem Soc 2018; 140:9783-9787. [PMID: 29944356 DOI: 10.1021/jacs.8b03715] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Single-nucleotide-resolution sequencing of DNA damage is required to decipher the complex causal link between the identity and location of DNA adducts and their biological impact. However, the low abundance and inability to specifically amplify DNA damage hinders single-nucleotide mapping of adducts within whole genomes. Despite the high biological relevance of guanine oxidation and seminal recent advances in sequencing bulky adducts, single-nucleotide-resolution whole genome mapping of oxidative damage is not yet realized. We coupled the specificity of repair enzymes with the efficiency of a click DNA ligation reaction to insert a biocompatible locator code, enabling high-throughput, nucleotide-resolution sequencing of oxidative DNA damage in a genome. We uncovered thousands of oxidation sites with distinct patterns related to transcription, chromatin architecture, and chemical oxidation potential. Click-code-seq overcomes barriers to DNA damage sequencing and provides a new approach for generating comprehensive, sequence-specific information about chemical modification patterns in whole genomes.
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Affiliation(s)
- Junzhou Wu
- Department of Health Sciences and Technology , ETH Zürich , Schmelzbergstrasse 9 , 8092 Zürich , Switzerland
| | - Maureen McKeague
- Department of Health Sciences and Technology , ETH Zürich , Schmelzbergstrasse 9 , 8092 Zürich , Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology , ETH Zürich , Schmelzbergstrasse 9 , 8092 Zürich , Switzerland
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38
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Sloan DB, Broz AK, Sharbrough J, Wu Z. Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods. Trends Biotechnol 2018; 36:729-740. [PMID: 29550161 PMCID: PMC6004327 DOI: 10.1016/j.tibtech.2018.02.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/16/2018] [Accepted: 02/20/2018] [Indexed: 12/18/2022]
Abstract
There is a great need in biomedical and genetic research to detect DNA damage and de novo mutations, but doing so is inherently challenging because of the rarity of these events. The enormous capacity of current DNA sequencing technologies has opened the door for quantifying sequence variants present at low frequencies in vivo, such as within cancerous tissues. However, these sequencing technologies are error prone, resulting in high noise thresholds. Most DNA sequencing methods are also generally incapable of identifying chemically modified bases arising from DNA damage. In recent years, numerous specialized modifications to sequencing methods have been developed to address these shortcomings. Here, we review this landscape of emerging techniques, highlighting their respective strengths, weaknesses, and target applications.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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39
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Gunderson CG, Peng Z, Zhang B. Collision and Coalescence of Single Attoliter Oil Droplets on a Pipet Nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2699-2707. [PMID: 29400980 DOI: 10.1021/acs.langmuir.7b04090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We describe the use of a quartz pipet nanopore to study the collision and coalescence of individual emulsion oil droplets and their subsequent nanopore translocation. Collision and coalescence of single toluene droplets at a nanopore orifice are driven primarily by electroosmosis and electrophoresis and lead to the fast growth of a trapped oil droplet. This results in a stepwise current response due to the coalesced oil droplet increasing its volume and its ability to partially block the nanopore's ionic current, allowing us to use the resistive-pulse method to resolve single droplet collisions. Further growth of the trapped oil droplet leads to a complete blockage of the nanopore and a nearly 100% current decay. The trapped oil droplet shows enormous mechanical stability at lower voltages and stays in its trapped status for hundreds of seconds. An increased voltage can be used to drive the trapped droplet into the pipet pore within several milliseconds. Simultaneous fluorescence imaging and amperometry were performed to examine droplet collision, coalescence, and translocation, further confirming the proposed mechanism of droplet-nanopore interaction. Moreover, we demonstrate the unique ability to perform fast voltammetric measurements on a nanopore-supported attoliter oil droplet and study its voltage-driven ion transfer processes.
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Affiliation(s)
- Christopher G Gunderson
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Zhuoyu Peng
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Bo Zhang
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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40
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Li Y, Aggarwal MB, Nguyen K, Ke K, Spitale RC. Assaying RNA Localization in Situ with Spatially Restricted Nucleobase Oxidation. ACS Chem Biol 2017; 12:2709-2714. [PMID: 28952711 DOI: 10.1021/acschembio.7b00519] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report herein a novel chemical-genetic method for assaying RNA localization within living cells. RNA localization is critical for normal physiology as well as the onset of cancer and neurodegenerative disorders. Despite its importance, there is a real lack of chemical methods to directly assay RNA localization with high resolution in living cells. Our novel approach relies on in situ nucleobase oxidation by singlet oxygen generated from spatially confined fluorophores. We demonstrate that our novel method can identify RNA molecules localized within specific cellular compartments. We anticipate that this platform will provide the community with a much-needed methodology for tracking RNA localization within living cells, and set the stage for systematic large scale analysis of RNA localization in living systems.
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Affiliation(s)
- Ying Li
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Mahima B. Aggarwal
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Kim Nguyen
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Ke Ke
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Robert C. Spitale
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
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Feng Y, Cai S, Xiong G, Zhang G, Wang S, Su X, Yu C. Sensitive Detection of DNA Lesions by Bulge-Enhanced Highly Specific Coamplification at Lower Denaturation Temperature Polymerase Chain Reaction. Anal Chem 2017; 89:8084-8091. [PMID: 28675037 DOI: 10.1021/acs.analchem.7b01599] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mutagenic modifications of nucleotides or DNA lesions that result from environmental stress have proven to be associated with a variety of diseases, particularly cancer. The method for accurately detecting the lesions is therefore of great importance for biomedical research and toxicity study. We develop a sensitive and low-cost bulge-enhanced coamplification at lower denaturation temperature polymerase chain reaction (COLD-PCR) method for detecting DNA lesions (uracil and 8-oxoguanine) by combining an in vitro base excision repair (BER) pathway and COLD-PCR. The modified bases are converted to bulge via the BER pathway involving converting modified bases to an apurinic/apyrimidinic (AP) site, cleavage at the AP site, and break ligation. The presence of the bulge induces a large change of the hybridization thermodynamics of double-stranded DNA, eventually enhancing the specificity of COLD-PCR. Besides, we used the free energy of hybridization as a reference to optimize the critical denaturation temperature (Tc) of COLD-PCR obtaining more specific amplification than empirical Tc. Taking advantage of the proposed bulge-enhanced COLD-PCR, we are able to identify the presence of DNA lesion-containing strands at low abundance down to 0.01%. This method also exhibits high sensitivity for glycosylase with a detection limit of 10-4 U/mL [3 S/N (signal-to-noise ratio)] that is superior than some recently reported methods. With the design of the repair guide probe, the level of oxidative damage in genomic DNA caused by chemicals and photodynamic therapy (PDT) can be evaluated, heralding more applications in clinical diagnosis and epigenetic study.
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Affiliation(s)
- Yu Feng
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
| | - Shuang Cai
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
| | - Guoliang Xiong
- Department of Nephrology, Shenzhen Affiliated Hospital, Guangzhou University of Chinese Medicine , Shenzhen 518033, Guangdong, China
| | - Guanfei Zhang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
| | - Shihui Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
| | - Xin Su
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
| | - Changyuan Yu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
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42
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Wu T, Ye M, Mao T, Lin F, Hu Y, Gan N, Shao Y. Human telomeric hybrid-2-over-hybrid-1 G-quadruplex targeting and a selective hypersaline-tolerant sensor using abasic site-engineered monomorphism. Anal Chim Acta 2017; 964:161-169. [DOI: 10.1016/j.aca.2017.01.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/13/2017] [Accepted: 01/21/2017] [Indexed: 02/02/2023]
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Abstract
Telomeres are specialized chromatin structures that protect chromosome ends from dangerous processing events. In most tissues, telomeres shorten with each round of cell division, placing a finite limit on cell growth. In rapidly dividing cells, including the majority of human cancers, cells bypass this growth limit through telomerase-catalyzed maintenance of telomere length. The dynamic properties of telomeres and telomerase render them difficult to study using ensemble biochemical and structural techniques. This review describes single-molecule approaches to studying how individual components of telomeres and telomerase contribute to function. Single-molecule methods provide a window into the complex nature of telomeres and telomerase by permitting researchers to directly visualize and manipulate the individual protein, DNA, and RNA molecules required for telomere function. The work reviewed in this article highlights how single-molecule techniques have been utilized to investigate the function of telomeres and telomerase.
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Affiliation(s)
- Joseph W Parks
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064; .,Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064; .,Center for Molecular Biology of RNA, Santa Cruz, California 95064
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Hu J, Adar S. The Cartography of UV-induced DNA Damage Formation and DNA Repair. Photochem Photobiol 2017; 93:199-206. [PMID: 27861959 DOI: 10.1111/php.12668] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/23/2016] [Indexed: 12/29/2022]
Abstract
DNA damage presents a barrier to DNA-templated biochemical processes, including gene expression and faithful DNA replication. Compromised DNA repair leads to mutations, enhancing the risk for genetic diseases and cancer development. Conventional experimental approaches to study DNA damage required a researcher to choose between measuring bulk damage over the entire genome, with little or no resolution regarding a specific location, and obtaining data specific to a locus of interest, without a global perspective. Recent advances in high-throughput genomic tools overcame these limitations and provide high-resolution measurements simultaneously across the genome. In this review, we discuss the available methods for measuring DNA damage and their repair, focusing on genomewide assays for pyrimidine photodimers, the major types of damage induced by ultraviolet irradiation. These new genomic assays will be a powerful tool in identifying key components of genome stability and carcinogenesis.
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Affiliation(s)
- Jinchuan Hu
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Sheera Adar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
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45
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Fang R, Zhang H, Yang L, Wang H, Tian Y, Zhang X, Jiang L. Supramolecular Self-Assembly Induced Adjustable Multiple Gating States of Nanofluidic Diodes. J Am Chem Soc 2016; 138:16372-16379. [DOI: 10.1021/jacs.6b09601] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ruochen Fang
- Key
Lab of Organic Optoelectronics and Molecular Engineering, Department
of Chemistry, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Huacheng Zhang
- Department
of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Liulin Yang
- Key
Lab of Organic Optoelectronics and Molecular Engineering, Department
of Chemistry, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Huanting Wang
- Department
of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Ye Tian
- Beijing National
Laboratory for Molecular Sciences, Key Laboratory
of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Xi Zhang
- Key
Lab of Organic Optoelectronics and Molecular Engineering, Department
of Chemistry, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Lei Jiang
- Key Laboratory of Bio-inspired Materials and Interfacial
Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- Department
of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
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46
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Li G, Li Z, You X, Chen J, Tang S. A novel label-free and sensitive electrochemical biosensor for Hg2+ based on ligase-mediated formation of DNAzyme. Talanta 2016; 161:138-142. [DOI: 10.1016/j.talanta.2016.08.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/31/2016] [Accepted: 08/16/2016] [Indexed: 11/28/2022]
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47
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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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Liu L, Wu HC. DNA-Based Nanopore Sensing. Angew Chem Int Ed Engl 2016; 55:15216-15222. [DOI: 10.1002/anie.201604405] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/13/2016] [Indexed: 01/09/2023]
Affiliation(s)
- 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
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics; Chinese Academy of Sciences; Beijing 100049 China
- 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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49
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Affiliation(s)
- Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety; Institute of High Energy Physics; Chinese Academy of Sciences; Peking 100049 China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety; Institute of High Energy Physics; Chinese Academy of Sciences; Peking 100049 China
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Analytical Chemistry for Living Biosystems; Institute of Chemistry; Chinese Academy of Sciences; Peking 100190 China
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50
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Liu X, Wei M, Liu Y, Lv B, Wei W, Zhang Y, Liu S. Label-Free Detection of Telomerase Activity in Urine Using Telomerase-Responsive Porous Anodic Alumina Nanochannels. Anal Chem 2016; 88:8107-14. [DOI: 10.1021/acs.analchem.6b01817] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xu Liu
- Key
Laboratory of Environmental Medicine and Engineering, Ministry of
Education, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical
Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Min Wei
- College
of Food Science and Technology, Henan University of Technology, Zhengzhou, 450001, China
| | - Yuanjian Liu
- Key
Laboratory of Environmental Medicine and Engineering, Ministry of
Education, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical
Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Bingjing Lv
- Key
Laboratory of Environmental Medicine and Engineering, Ministry of
Education, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical
Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Wei Wei
- Key
Laboratory of Environmental Medicine and Engineering, Ministry of
Education, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical
Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Yuanjian Zhang
- Key
Laboratory of Environmental Medicine and Engineering, Ministry of
Education, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical
Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Songqin Liu
- Key
Laboratory of Environmental Medicine and Engineering, Ministry of
Education, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical
Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
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