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Yang Y, Nakayama K, Okada S, Sato K, Wada T, Sakaguchi Y, Murayama A, Suzuki T, Sakurai M. ICLAMP: a novel technique to explore adenosine deamination via inosine chemical labeling and affinity molecular purification. FEBS Lett 2024; 598:1080-1093. [PMID: 38523059 DOI: 10.1002/1873-3468.14854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024]
Abstract
Recent developments in sequencing and bioinformatics have advanced our understanding of adenosine-to-inosine (A-to-I) RNA editing. Surprisingly, recent analyses have revealed the capability of adenosine deaminase acting on RNA (ADAR) to edit DNA:RNA hybrid strands. However, edited inosines in DNA remain largely unexplored. A precise biochemical method could help uncover these potentially rare DNA editing sites. We explore maleimide as a scaffold for inosine labeling. With fluorophore-conjugated maleimide, we were able to label inosine in RNA or DNA. Moreover, with biotin-conjugated maleimide, we purified RNA and DNA containing inosine. Our novel technique of inosine chemical labeling and affinity molecular purification offers substantial advantages and provides a versatile platform for further discovery of A-to-I editing sites in RNA and DNA.
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Affiliation(s)
- Yuxi Yang
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Koki Nakayama
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Shunpei Okada
- Department of Microbiology, Faculty of Medicine, Shimane University, Izumo-shi, Japan
| | - Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Japan
| | - Ayaka Murayama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Japan
| | - Masayuki Sakurai
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
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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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Wu Q, Liu GQ, Ma JS, Li Q. The Method of Screening and Identification of Transcription Factor in Klebsiella. Methods Mol Biol 2023; 2594:13-28. [PMID: 36264485 DOI: 10.1007/978-1-0716-2815-7_2] [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] [Indexed: 06/16/2023]
Abstract
This protocol describes a method for verifying the specific transcription factor regulating glycerol dehydratase (GDH) expression in Klebsiella. DNA pull-down accompanied with mass spectrometry is used to screen and identify the transcription factor interacting with the promoter region of the key gene in Klebsiella. EMSA method is used to validate the specific binding of the transcription factor to the promoter region in vitro. In addition, the target DNA fragments are constructed by fusion PCR to prepare competent cells from Klebsiella for electrical transformation and further transformed to obtain key gene deletion strains to verify the transcription factor responsible for the target gene expression in Klebsiella.
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Affiliation(s)
- Qiang Wu
- College of Food and Chemical Engineering, Shaoyang University, Shaoyang, China.
- Hunan Provincial Key Laboratory of Forestry Biotechnology & International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, China.
- Microbial Variety Creation Center, National Laboratory of Yuelushan Seed Industry, Changsha, China.
| | - Gao-Qiang Liu
- Hunan Provincial Key Laboratory of Forestry Biotechnology & International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, China
- Microbial Variety Creation Center, National Laboratory of Yuelushan Seed Industry, Changsha, China
| | - Jiang-Shan Ma
- Hunan Provincial Key Laboratory of Forestry Biotechnology & International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, China
- Microbial Variety Creation Center, National Laboratory of Yuelushan Seed Industry, Changsha, China
| | - Qiang Li
- Hunan Provincial Key Laboratory of Forestry Biotechnology & International Cooperation Base of Science and Technology Innovation on Forest Resource Biotechnology, Central South University of Forestry and Technology, Changsha, China
- Microbial Variety Creation Center, National Laboratory of Yuelushan Seed Industry, Changsha, China
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Zhang S, Huang J, Lu J, Liu M, Li Y, Fang L, Huang H, Huang J, Mo F, Zheng J. A novel fluorescent biosensor based on dendritic DNA nanostructure in combination with ligase reaction for ultrasensitive detection of DNA methylation. J Nanobiotechnology 2019; 17:121. [PMID: 31812164 PMCID: PMC6898925 DOI: 10.1186/s12951-019-0552-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/25/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND DNA methylation detection is indispensable for the diagnosis and prognosis of various diseases including malignancies. Hence, it is crucial to develop a simple, sensitive, and specific detection strategy. METHODS A novel fluorescent biosensor was developed based on a simple dual signal amplification strategy using functional dendritic DNA nanostructure and signal-enriching polystyrene microbeads in combination with ligase detection reaction (LDR). Dendritic DNA self-assembled from Y-DNA and X-DNA through enzyme-free DNA catalysis of a hairpin structure, which was prevented from unwinding at high temperature by adding psoralen. Then dendritic DNA polymer labeled with fluorescent dye Cy5 was ligated with reporter probe into a conjugate. Avidin-labeled polystyrene microbeads were specifically bound to biotin-labeled capture probe, and hybridized with target sequence and dendritic DNA. LDR was triggered by adding Taq ligase. When methylated cytosine existed, the capture probe and reporter probe labeled with fluorescent dye perfectly matched the target sequence, forming a stable duplex to generate a fluorescence signal. However, after bisulfite treatment, unmethylated cytosine was converted into uracil, resulting in a single base mismatch. No fluorescence signal was detected due to the absence of duplex. RESULTS The obtained dendritic DNA polymer had a large volume. This method was time-saving and low-cost. Under the optimal experimental conditions using avidin-labeled polystyrene microbeads, the fluorescence signal was amplified more obviously, and DNA methylation was quantified ultrasensitively and selectively. The detection range of this sensor was 10-15 to 10-7 M, and the limit of detection reached as low as 0.4 fM. The constructed biosensor was also successfully used to analyze actual samples. CONCLUSION This strategy has ultrasensitivity and high specificity for DNA methylation quantification, without requiring complex processes such as PCR and enzymatic digestion, which is thus of great value in tumor diagnosis and biomedical research.
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Affiliation(s)
- Shu Zhang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.,Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China.,Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jian Huang
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jingrun Lu
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Min Liu
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Hui Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Jianjun Huang
- Department of Breast Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Fei Mo
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China. .,Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.
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Ivancová I, Leone DL, Hocek M. Reactive modifications of DNA nucleobases for labelling, bioconjugations, and cross-linking. Curr Opin Chem Biol 2019; 52:136-144. [DOI: 10.1016/j.cbpa.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/26/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022]
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Cui L, Hu J, Wang M, Li CC, Zhang CY. Label-Free and Immobilization-Free Electrochemical Magnetobiosensor for Sensitive Detection of 5-Hydroxymethylcytosine in Genomic DNA. Anal Chem 2018; 91:1232-1236. [PMID: 30588799 DOI: 10.1021/acs.analchem.8b04663] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
DNA 5-hydroxymethylcytosine (5-hmC) is an important epigenetic biomarker for tumorigenesis, and the loss of 5-hmC levels is associated with leukemia and melanoma cancers. However, it is a great challenge to discriminate 5-hmC from 5-methylcytosine (5-mC) using the conventional bisulfite conversion methods. Herein, we report a label-free and immobilization-free electrochemical magnetobiosensor for sensitive quantification of 5-hmC in genomic DNA based on a dual signal amplification strategy coupled with terminal deoxynucleotidyl transferase (TDT) enzymatic amplification and Ru(III) redox cycling. This screen-printed carbon electrode (SPCE)-based electrochemical magnetobiosensor shows distinct advantages of having low cost and simple fabrication and being label-free, immobilization-free, PCR-free, and radioactive-free. It exhibits high sensitivity with a detection limit of as low as 9.06 fM and a large dynamic range from 0.01 to 1000 pM. Importantly, this biosensor can discriminate 5-hmC from cytosine and 5-mC, and it can successfully detect 5-hmC in live cells.
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Affiliation(s)
- Lin Cui
- 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, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan , Shandong 250014 , PR China
| | - Juan Hu
- 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, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan , Shandong 250014 , PR China
| | - Meng Wang
- 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, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan , Shandong 250014 , PR China
| | - Chen-Chen Li
- 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, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan , Shandong 250014 , PR China
| | - 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, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan , Shandong 250014 , PR China
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Knutson SD, Ayele TM, Heemstra JM. Chemical Labeling and Affinity Capture of Inosine-Containing RNAs Using Acrylamidofluorescein. Bioconjug Chem 2018; 29:2899-2903. [PMID: 30148626 DOI: 10.1021/acs.bioconjchem.8b00541] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a widespread and conserved post-transcriptional modification, producing significant changes in cellular function and behavior. Accurately identifying, detecting, and quantifying these sites in the transcriptome is necessary to improve our understanding of editing dynamics, its broader biological roles, and connections with diseases. Chemical labeling of edited bases coupled with affinity enrichment has enabled improved characterization of several forms of RNA editing. However, there are no approaches currently available for pull-down of inosines. To address this need, we explore acrylamide as a labeling motif and report here an acrylamidofluorescein reagent that reacts with inosine and enables enrichment of inosine-containing RNA transcripts. This method provides improved sensitivity in the detection and identification of inosines toward a more comprehensive transcriptome-wide analysis of A-to-I editing. Acrylamide derivatization is also highly generalizable, providing potential for the labeling of inosine with a wide variety of probes and affinity handles.
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Affiliation(s)
- Steve D Knutson
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Tewoderos M Ayele
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Jennifer M Heemstra
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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