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Liu X, Qi Q, Xiong W, Shen W, Zhang K, Fan R, Zhang Y, Zhao Y, Xu X, Li M, Zhou E, Tian T, Zhou X. Unveiling a Potent Small Molecule Disruptor for RNA G-Quadruplexes Tougher Than DNA G-Quadruplex Disruption. ACS Chem Biol 2024. [PMID: 39225324 DOI: 10.1021/acschembio.4c00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
This research presents a unique small molecule characterized by its ability to effectively disrupt RNA G-quadruplexes (G4s), which are notably more stable than their DNA counterparts. We conducted a comprehensive series of in vitro experiments to thoroughly assess the disruptive capabilities of this molecule on RNA G4s. These experiments included comparisons with established G4 stabilizers and DNA G4 disruptors, providing a multifaceted evaluation of the molecule's efficacy. Our extensive in vitro analyses demonstrated that this molecule effectively alters G4 structures and interactions with the BG4 protein, a well-recognized G4-specific antibody. These findings underscore the molecule's potential to modulate G4-protein interactions, indicating promising applications for manipulating cellular functions associated with G4 dynamics in future research.
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Affiliation(s)
- Xingyu Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Qianqian Qi
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Wei Xiong
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Wei Shen
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Kaisong Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Ruochen Fan
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Yuanyuan Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Yunting Zhao
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Xinyan Xu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Ming Li
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Enyi Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Tian Tian
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
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Liu X, Xiong W, Qi Q, Zhang Y, Ji H, Cui S, An J, Sun X, Yin H, Tian T, Zhou X. Rational guide RNA engineering for small-molecule control of CRISPR/Cas9 and gene editing. Nucleic Acids Res 2022; 50:4769-4783. [PMID: 35446403 PMCID: PMC9071477 DOI: 10.1093/nar/gkac255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 12/24/2022] Open
Abstract
It is important to control CRISPR/Cas9 when sufficient editing is obtained. In the current study, rational engineering of guide RNAs (gRNAs) is performed to develop small-molecule-responsive CRISPR/Cas9. For our purpose, the sequence of gRNAs are modified to introduce ligand binding sites based on the rational design of ligand-RNA pairs. Using short target sequences, we demonstrate that the engineered RNA provides an excellent scaffold for binding small molecule ligands. Although the 'stem-loop 1' variants of gRNA induced variable cleavage activity for different target sequences, all 'stem-loop 3' variants are well tolerated for CRISPR/Cas9. We further demonstrate that this specific ligand-RNA interaction can be utilized for functional control of CRISPR/Cas9 in vitro and in human cells. Moreover, chemogenetic control of gene editing in human cells transfected with all-in-one plasmids encoding Cas9 and designer gRNAs is demonstrated. The strategy may become a general approach for generating switchable RNA or DNA for controlling other biological processes.
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Affiliation(s)
- Xingyu Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Wei Xiong
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Qianqian Qi
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Yutong Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Huimin Ji
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Shuangyu Cui
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Jing An
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, Hubei, China
| | - Xiaoming Sun
- Department of Human Anatomy, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Hao Yin
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, Hubei, China
| | - Tian Tian
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
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Zhang L, Gu J, Luo X, Tang Z, Qu Y, Zhang C, Liu H, Liu J, Xie C, Wu Z. Photoregulative phase change biomaterials showing thermodynamic and mchanical stabilities. NANOSCALE 2022; 14:976-983. [PMID: 34989736 DOI: 10.1039/d1nr06000g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Azobenzenes are great photochromic molecules for switching the physical properties of various materials via trans-cis isomerization. However, the UV light resulted cis-azobenzene is metastable and thermodynamically gets back to trans-azobenzene after ceasing UV irradiation, which causes an unwanted property change of azobenzene-containing materials. Additionally, thermal and mechanical conditions would accelerate this process dramatically. In this present work, a new type of azobenzene-containing surfactant is designed for the fabrication of photoresponsive phase change biomaterials. With a "locked" cis-azobenzene conformation, the resulting biomaterials could maintain their disordered state after ceasing UV light, which exhibit great resistance to thermal and piezo conditions. Interestingly, the "locked" cis-azobenzene could be unlocked by Vis light in high efficiency, which opens a new way for the design of phase change materials only responding to light. By showing stable cis-azobenzene maintained physical state, the newly fabricated biomaterials provide new potential for the construction of advanced materials, like self-healing materials, with less use of long time UV irradiation for maintaining their disordered states.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Jingjing Gu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Zhenyu Tang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Yang Qu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Chenghao Zhang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Han Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Jishuai Liu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Congxia Xie
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Zhongtao Wu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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Simeth NA, Kobayashi S, Kobauri P, Crespi S, Szymanski W, Nakatani K, Dohno C, Feringa BL. Rational design of a photoswitchable DNA glue enabling high regulatory function and supramolecular chirality transfer. Chem Sci 2021; 12:9207-9220. [PMID: 34276952 PMCID: PMC8261765 DOI: 10.1039/d1sc02194j] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/22/2021] [Indexed: 01/02/2023] Open
Abstract
Short, complementary DNA single strands with mismatched base pairs cannot undergo spontaneous formation of duplex DNA (dsDNA). Mismatch binding ligands (MBLs) can compensate this effect, inducing the formation of the double helix and thereby acting as a molecular glue. Here, we present the rational design of photoswitchable MBLs that allow for reversible dsDNA assembly by light. Careful choice of the azobenzene core structure results in excellent band separation of the E and Z isomers of the involved chromophores. This effect allows for efficient use of light as an external control element for duplex DNA formation and for an in-depth study of the DNA-ligand interaction by UV-Vis, SPR, and CD spectroscopy, revealing a tight mutual interaction and complementarity between the photoswitchable ligand and the mismatched DNA. We also show that the configuration of the switch reversibly dictates the conformation of the DNA strands, while the dsDNA serves as a chiral clamp and translates its chiral information onto the ligand inducing a preference in helical chirality of the Z isomer of the MBLs.
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Affiliation(s)
- Nadja A Simeth
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Shotaro Kobayashi
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Piermichele Kobauri
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Stefano Crespi
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- Department of Radiology, Medical Imaging Center, University of Groningen, University Medical Centre Groningen Hanzeplein 1 9713 GZ Groningen The Netherlands
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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Wu Q, Liao S, Yu G, Wu J, Mei W. High-order self-assembly of G-quadruplex DNA: Nano-network formation under the guidance of arene ruthenium(II) complexes. J Inorg Biochem 2018; 189:81-90. [PMID: 30243121 DOI: 10.1016/j.jinorgbio.2018.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Qiong Wu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Siyan Liao
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 510180, China
| | - Gengnan Yu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jian Wu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wenjie Mei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China.
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Kotera N, Guillot R, Teulade-Fichou MP, Granzhan A. Copper(II)-Controlled Molecular Glue for Mismatched DNA. Chembiochem 2017; 18:618-622. [PMID: 28106332 DOI: 10.1002/cbic.201600675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Indexed: 01/20/2023]
Abstract
Isothermal hybridization of two DNA strands bearing three thymine-thymine (T:T) mismatches can be brought about in the presence of a stoichiometric amount of a bis-naphthalene macrocycle, 2,7-BisNP-NH. This process can be reverted by addition of a CuII salt due to formation of a dinuclear metal complex which does not bind to DNA. Subsequent sequestration of CuII releases the macrocycle and restores the hybridization state of DNA strands, thus allowing implementation of a fast fluorescent two-state DNA switch.
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Affiliation(s)
- Naoko Kotera
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS UMR8182, Université Paris Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, 91405, Orsay, France
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Granzhan A, Kotera N, Teulade-Fichou MP. Finding needles in a basestack: recognition of mismatched base pairs in DNA by small molecules. Chem Soc Rev 2014; 43:3630-65. [DOI: 10.1039/c3cs60455a] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Goulet-Hanssens A, Barrett CJ. Photo-control of biological systems with azobenzene polymers. ACTA ACUST UNITED AC 2013. [DOI: 10.1002/pola.26735] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alexis Goulet-Hanssens
- Department of Chemistry; McGill University; 801 Sherbrooke Street West Montreal Quebec Canada H3A 0B8
| | - Christopher J. Barrett
- Department of Chemistry; McGill University; 801 Sherbrooke Street West Montreal Quebec Canada H3A 0B8
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Irvoas J, Noirot A, Chouini-Lalanne N, Reynes O, Sartor V. DNA three-way junction–ruthenium complex assemblies. NEW J CHEM 2013. [DOI: 10.1039/c3nj00288h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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