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Yang D, Sun Y, Chang F, Tian H, Liu C, Li Z. Highly specific quantification of mRNA mutation in single cells based on RNase H cleavage-assisted reverse transcription (RT)-PCR. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.09.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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2
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Han S, Lei Y, Pannecouque C, De Clercq E, Zhuang C, Chen F. Fragment-based discovery of sulfur-containing diarylbenzopyrimidines as novel nonnucleoside reverse transcriptase inhibitors. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.11.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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3
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Wang R, Jin X, Kong D, Chen Z, Liu J, Liu L, Cheng L. Visible‐Light Facilitated Fluorescence “Switch‐On” Labelling of 5‐Formylpyrimidine RNA. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201901032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Rui‐Li Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
| | - Xiao‐Yang Jin
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - De‐Long Kong
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
| | - Zhi‐Gang Chen
- BNLMS, State Key Laboratory of Polymer Physics and Chemistry, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
| | - Ji Liu
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 China
- Key Lab of Functional Molecular Engineering of Guangdong ProvinceSouth China University of Technology Guangzhou 510640 China
- University of Chinese Academy of Sciences Beijing 100049 China
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Jin X, Wang R, Xie L, Kong D, Liu L, Cheng L. A Chemical Photo‐Oxidation of 5‐Methyl Cytidines. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900811] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xiao‐Yang Jin
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Rui‐Li Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Li‐Jun Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - De‐Long Kong
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of ChemistryChinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
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Song J, Ni J, Wang Q, Chen H, Gao F, Lin Z, Wang Q. A planar and uncharged copper(II)-picolinic acid chelate: Its intercalation to duplex DNA by experimental and theoretical studies and electrochemical sensing application. Biosens Bioelectron 2019; 141:111405. [PMID: 31195198 DOI: 10.1016/j.bios.2019.111405] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 05/30/2019] [Accepted: 06/01/2019] [Indexed: 11/28/2022]
Abstract
Using an external redox-active molecule as a DNA hybridization indicator is still a popular strategy in electrochemical DNA biosensors because it is label-free and the multi-site binding can enhance the response signal. A planar and uncharged transition metal complex, Cu(PA)2 (PA = picolinic acid) with excellent electrochemical activity has been synthesized and its interaction with double-stranded DNA (dsDNA) is studied by experimental electrochemical methods and theoretical molecular docking technology. The experimental results reveal that the copper complex interacts with dsDNA via specific intercalation, which is verified by the molecular docking result. The surface-based voltammetric analysis demonstrates that the planar Cu(PA)2 can effectively accumulate within the electrode-confined hybridized duplex DNA rather than the single-stranded probe DNA. Based on this phenomenon, the Cu(PA)2 is utilized as an electrochemical hybridization indicator for the detection of oligonucleotides. The sensing assays show that upon incubation in Cu(PA)2 solution, the probe electrode does not display any Faraday signal, but the hybridized one has a pair of strong redox peaks corresponding to the electrochemistry of Cu(PA)2, showing excellent hybridization indicating function of Cu(PA)2 without background interference. The signal intensity of Cu(PA)2 is dependent on the concentrations of the target oligonucleotide ranging from 1 fM to 100 nM with an experimental detection limit of 1.0 fM. Due to the specific intercalation of Cu(PA)2 with dsDNA, the biosensor also exhibits good ability to recognize oligonucleotide with different base mismatching degree.
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Affiliation(s)
- Juan Song
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China
| | - Jiancong Ni
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China; Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, 350116, China
| | - Qinghua Wang
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China
| | - Huangcan Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Feng Gao
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China
| | - Zhenyu Lin
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China; Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, 350116, China
| | - Qingxiang Wang
- Department of Chemistry and Environment Science, Fujian Province University Key Laboratory of Analytical Science, Minnan Normal University, Zhangzhou, 363000, PR China.
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6
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Wicks SL, Hargrove AE. Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA. Methods 2019; 167:3-14. [PMID: 31051253 DOI: 10.1016/j.ymeth.2019.04.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 01/15/2023] Open
Abstract
Fluorescent indicator displacement (FID) assays are an advantageous approach to convert receptors into optical sensors that can detect binding of various ligands. In particular, the identification of ligands that bind to RNA receptors has become of increasing interest as the roles of RNA in cellular processes and disease pathogenesis continue to be discovered. Small molecules have been validated as tools to elucidate unknown RNA functions, underscoring the critical need to rapidly identify and quantitatively characterize RNA:small molecule interactions for the development of chemical probes. The successful application of FID assays to evaluate interactions between diverse RNA receptors and small molecules has been facilitated by the characterization of distinct fluorescent indicators that reversibly bind RNA and modulate the fluorescence signal. The utility of RNA-based FID assays to both academia and industry has been demonstrated through numerous uses in high-throughput screening efforts, structure-activity relationship studies, and in vitro target engagement studies. Furthermore, the development, optimization, and validation of a variety of RNA-based FID assays has led to general guidelines that can be utilized for facile implementation of the method with new or underexplored RNA receptors. Altogether, the use of RNA-based FID assays as a general analysis tool has provided valuable insights into small molecule affinity and selectivity, furthering the fundamental understanding of RNA:small molecule recognition. In this review, we will summarize efforts to employ FID assays using RNA receptors and describe the significant contributions of the method towards the development of chemical probes to reveal unknown RNA functions.
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Affiliation(s)
- Sarah L Wicks
- Duke University, Department of Chemistry, Durham, NC 27705, United States
| | - Amanda E Hargrove
- Duke University, Department of Chemistry, Durham, NC 27705, United States.
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Li XD, Liu L, Cheng L. Identification of thienopyridine carboxamides as selective binders of HIV-1 trans Activation Response (TAR) and Rev Response Element (RRE) RNAs. Org Biomol Chem 2019; 16:9191-9196. [PMID: 30465585 DOI: 10.1039/c8ob02753f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Small organic molecules that can selectively bind to RNA with specificity are relatively rare. Here we report the synthesis, biochemical and structural studies of thienopyridine carboxamide derivatives with the capacity of selectively recognizing and binding with HIV-1 TAR and RRE RNAs that are essential elements for viral replication.
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Affiliation(s)
- Xue-Dong Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
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8
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Identification of Flavin Mononucleotide as a Cell‐Active Artificial
N
6
‐Methyladenosine RNA Demethylase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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9
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Xie LJ, Yang XT, Wang RL, Cheng HP, Li ZY, Liu L, Mao L, Wang M, Cheng L. Identification of Flavin Mononucleotide as a Cell-Active Artificial N 6 -Methyladenosine RNA Demethylase. Angew Chem Int Ed Engl 2019; 58:5028-5032. [PMID: 30756480 DOI: 10.1002/anie.201900901] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Indexed: 01/05/2023]
Abstract
N6 -Methyladenosine (m6 A) represents a common and highly dynamic modification in eukaryotic RNA that affects various cellular pathways. Natural dioxygenases such as FTO and ALKBH5 are enzymes that demethylate m6 A residues in mRNA. Herein, the first identification of a small-molecule modulator that functions as an artificial m6 A demethylase is reported. Flavin mononucleotide (FMN), the metabolite produced by riboflavin kinase, mediates substantial photochemical demethylation of m6 A residues of RNA in live cells. This study provides a new perspective to the understanding of demethylation of m6 A residues in mRNA and sheds light on the development of powerful small molecules as RNA demethylases and new probes for use in RNA biology.
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Affiliation(s)
- Li-Jun Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Ti Yang
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui-Li Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hou-Ping Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Yan Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lanqun Mao
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Wang
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,Key Lab of Functional Molecular Engineering of Guangdong Province, South China University of Technology), Guangzhou, 510640, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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