1
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Zhan X, Deng L, Lian Y, Shu Z, Xu Y, Mai X, Krishna MS, Lu R, Wang A, Bai S, Zhou F, Xiong C, Xu Y, Ni J, Vandana JJ, Wang Z, Li Y, Sun D, Huang S, Liu J, Cheng GJ, Wu S, Chiang YC, Stjepanovic G, Jiang C, Shao Y, Chen G. Enhanced Recognition of a Herbal Compound Epiberberine by a DNA Quadruplex-Duplex Structure. Anal Chem 2024. [PMID: 39093925 DOI: 10.1021/acs.analchem.4c02054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The small molecule epiberberine (EPI) is a natural alkaloid with versatile bioactivities against several diseases including cancer and bacterial infection. EPI can induce the formation of a unique binding pocket at the 5' side of a human telomeric G-quadruplex (HTG) sequence with four telomeric repeats (Q4), resulting in a nanomolar binding affinity (KD approximately 26 nM) with significant fluorescence enhancement upon binding. It is important to understand (1) how EPI binding affects HTG structural stability and (2) how enhanced EPI binding may be achieved through the engineering of the DNA binding pocket. In this work, the EPI-binding-induced HTG structure stabilization effect was probed by a peptide nucleic acid (PNA) invasion assay in combination with a series of biophysical techniques. We show that the PNA invasion-based method may be useful for the characterization of compounds binding to DNA (and RNA) structures under physiological conditions without the need to vary the solution temperature or buffer components, which are typically needed for structural stability characterization. Importantly, the combination of theoretical modeling and experimental quantification allows us to successfully engineer Q4 derivative Q4-ds-A by a simple extension of a duplex structure to Q4 at the 5' end. Q4-ds-A is an excellent EPI binder with a KD of 8 nM, with the binding enhancement achieved through the preformation of a binding pocket and a reduced dissociation rate. The tight binding of Q4 and Q4-ds-A with EPI allows us to develop a novel magnetic bead-based affinity purification system to effectively extract EPI from Rhizoma coptidis (Huang Lian) extracts.
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Affiliation(s)
- Xuan Zhan
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Liping Deng
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Yun Lian
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Zhiyu Shu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Yunong Xu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Xinyi Mai
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Rongguang Lu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Anni Wang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Shiyao Bai
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Fangyu Zhou
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Chi Xiong
- MinJiang Collaborative Center for Theoretical Physics, College of Physics and Electronic Information Engineering, Minjiang University, Fuzhou 350108, Fujian, P. R. China
| | - Yingyi Xu
- LightEdge Technologies Ltd., Zhongshan 528400, Guangdong, P. R. China
| | - Jie Ni
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - J Jeya Vandana
- Department of Surgery, Weill Cornell Medicine, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, Memorial Sloan Kettering Cancer Center, The Rockefeller University, New York, New York 10065, United States
| | - Zi Wang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Yuqing Li
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen 518111, Guangdong, P. R. China
| | - Dongmei Sun
- Guangdong Yifang Pharmaceutical, Foshan 528244, Guangdong, P. R. China
| | - Shaohui Huang
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 101499, P. R. China
| | - Jingyan Liu
- School of Medicine, The Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen 518172, Guangdong, P. R. China
| | - Gui-Juan Cheng
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Song Wu
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen 518111, Guangdong, P. R. China
| | - Ying-Chih Chiang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Goran Stjepanovic
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Cheng Jiang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua 321004, Zhejiang, P. R. China
| | - Gang Chen
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
- Shenzhen Key Laboratory of Innovative Drug Synthesis, The Chinese University of Hong Kong, Shenzhen 518172, P. R. China
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2
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Wang R, Hu MH. Development of a fluorescent ligand that specifically binds to the c-MYC G-quadruplex by migrating the benzene group on a carbazole-benzothiazolium scaffold. Bioorg Chem 2024; 151:107690. [PMID: 39098087 DOI: 10.1016/j.bioorg.2024.107690] [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: 05/19/2024] [Revised: 07/16/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024]
Abstract
c-MYC is one of the most important oncogenes, which is overexpressed in many cancers, and is highly related to development, metastasis, and drug resistance of cancers. The G4 structure in the promoter of c-MYC oncogene contributes a lot to the gene transcriptional mechanism. Small-molecule ligands binding to the c-MYC G4 appear to be a new class of anticancer agents. However, selective ligands for the c-MYC G4 over other G4s have been rarely reported. In this study, we reported a novel fluorescent ligand by migrating the benzene group on a carbazole-benzothiazolium scaffold, which was demonstrated to exhibit considerable specificity to the c-MYC G4, which was distinguished from other small-molecule ligands. The further cellular experiments suggested that this ligand may indeed target the promoter G4 and cause apparent transcriptional inhibition of the c-MYC oncogene instead of other G4-mediated oncogenes, which thereby resulted in cancer cell growth inhibition. Collectively, this study provided a good example for developing specific c-MYC G4 ligands, which may further develop into an effective anticancer agent that inhibit the c-MYC expression.
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Affiliation(s)
- Rui Wang
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China
| | - Ming-Hao Hu
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China.
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3
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Joo SY, Sung K, Lee H. Balancing act: BRCA2's elaborate management of telomere replication through control of G-quadruplex dynamicity. Bioessays 2024; 46:e2300229. [PMID: 38922965 DOI: 10.1002/bies.202300229] [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: 11/29/2023] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
In billion years of evolution, eukaryotes preserved the chromosome ends with arrays of guanine repeats surrounded by thymines and adenines, which can form stacks of four-stranded planar structure known as G-quadruplex (G4). The rationale behind the evolutionary conservation of the G4 structure at the telomere remained elusive. Our recent study has shed light on this matter by revealing that telomere G4 undergoes oscillation between at least two distinct folded conformations. Additionally, tumor suppressor BRCA2 exhibits a unique mode of interaction with telomere G4. To elaborate, BRCA2 directly interacts with G-triplex (G3)-derived intermediates that form during the interconversion of the two different G4 states. In doing so, BRCA2 remodels the G4, facilitating the restart of stalled replication forks. In this review, we succinctly summarize the findings regarding the dynamicity of telomeric G4, emphasize its importance in maintaining telomere replication homeostasis, and the physiological consequences of losing G4 dynamicity at the telomere.
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Affiliation(s)
- So Young Joo
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, Seoul, South Korea
| | - Keewon Sung
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, South Korea
| | - Hyunsook Lee
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, Seoul, South Korea
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4
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Moura NMM, Guedes S, Salvador D, Oliveira H, Alves MQ, Paradis N, Wu C, Neves MGPMS, Ramos CIV. Oncogenic and telomeric G-quadruplexes: Targets for porphyrin-triphenylphosphonium conjugates. Int J Biol Macromol 2024:134126. [PMID: 39097044 DOI: 10.1016/j.ijbiomac.2024.134126] [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: 04/17/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/05/2024]
Abstract
DNA chains with sequential guanine (G) repeats can lead to the formation of G-quadruplexes (G4), which are found in functional DNA and RNA regions like telomeres and oncogene promoters. The development of molecules with adequate structural features to selectively stabilize G4 structures can counteract cell immortality, highly described for cancer cells, and also downregulate transcription events underlying cell apoptosis and/or senescence processes. We describe here, the efficiency of four highly charged porphyrins-phosphonium conjugates to act as G4 stabilizing agents. The spectrophotometric results allowed to select the conjugates P2-PPh3 and P3-PPh3 as the most promising ones to stabilize selectively G4 structures. Molecular dynamics simulation experiments were performed and support the preferential binding of P2-PPh3 namely to MYC and of P3-PPh3 to KRAS. The ability of both ligands to block the activity of Taq polymerase was confirmed and also their higher cytotoxicity against the two melanoma cell lines A375 and SK-MEL-28 than to immortalized skin keratinocytes. Both ligands present efficient cellular uptake, nuclear co-localization and high ability to generate 1O2 namely when interacting with G4 structure. The obtained data points the synthesized porphyrins as promising ligands to be used in a dual approach that can combine G4 stabilization and Photodynamic therapy (PDT).
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Affiliation(s)
- Nuno M M Moura
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Sofia Guedes
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Diana Salvador
- CESAM-Centre for Environmental and Marine Studies, Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; CICECO, Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Helena Oliveira
- CESAM-Centre for Environmental and Marine Studies, Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Mariana Q Alves
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Nicholas Paradis
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, United States of America
| | - Chun Wu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, United States of America
| | - M Graça P M S Neves
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Catarina I V Ramos
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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5
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Liu W, Zhu BC, Liu LY, Xia XY, Jang J, Dickerhoff J, Yang D, Mao ZW. Solution structures and effects of a platinum compound successively bound MYC G-quadruplex. Nucleic Acids Res 2024:gkae649. [PMID: 39077944 DOI: 10.1093/nar/gkae649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 07/08/2024] [Accepted: 07/24/2024] [Indexed: 07/31/2024] Open
Abstract
G-quadruplex (G4) structures play integral roles in modulating biological functions and can be regulated by small molecules. The MYC gene is critical during tumor initiation and malignant progression, in which G4 acts as an important modulation motif. Herein, we reported the MYC promoter G4 recognized by a platinum(II) compound Pt-phen. Two Pt-phen-MYC G4 complex structures in 5 mM K+ were determined by NMR. The Pt-phen first strongly binds the 3'-end of MYC G4 to form a 1:1 3'-end binding complex and then binds 5'-end to form a 2:1 complex with more Pt-phen. In the complexes, the Pt-phen molecules are well-defined and stack over four bases at the G-tetrad for a highly extensive π-π interaction, with the Pt atom aligning with the center of the G-tetrad. The flanking residues were observed to rearrange and cover on top of Pt-phen to stabilize the whole complex. We further demonstrated that Pt-phen targets G4 DNA in living cells and represses MYC gene expression in cancer cells. Our work elucidated the structural basis of ligand binding to MYC promoter G4. The platinum compound bound G4 includes multiple complexes formation, providing insights into the design of metal ligands targeting oncogene G4 DNA.
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Affiliation(s)
- Wenting Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, State Key Laboratory of Anti-Infective Drug Discovery and Development, IGCME, GBRCE for Functional Molecular Engineering, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bo-Chen Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, State Key Laboratory of Anti-Infective Drug Discovery and Development, IGCME, GBRCE for Functional Molecular Engineering, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Liu-Yi Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, State Key Laboratory of Anti-Infective Drug Discovery and Development, IGCME, GBRCE for Functional Molecular Engineering, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiao-Yu Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, State Key Laboratory of Anti-Infective Drug Discovery and Development, IGCME, GBRCE for Functional Molecular Engineering, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jinho Jang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Department of Chemistry, and Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Jonathan Dickerhoff
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Department of Chemistry, and Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Department of Chemistry, and Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, State Key Laboratory of Anti-Infective Drug Discovery and Development, IGCME, GBRCE for Functional Molecular Engineering, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
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6
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Assadawi N, Ferderer M, Kusi-Appauh N, Yu H, Dillon CT, Sluyter R, Richardson C, Ralph SF. Effect of substituents on the ability of nickel Schiff base complexes with four pendant groups to bind to G-quadruplexes. Dalton Trans 2024; 53:12720-12739. [PMID: 39017709 DOI: 10.1039/d4dt00448e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The synthesis of eleven new nickel Schiff base complexes each bearing four pendant groups is reported. The structures of the complexes differ in the identity of the pendant groups and/or diamine moiety. All complexes were characterised by microanalysis, Nuclear Magnetic Resonance (NMR) spectroscopy and Electrospray Ionisation Mass Spectrometry (ESI-MS), while the solid-state structures of two of the molecules were also determined using X-ray crystallographic methods. The DNA binding properties of the nickel complexes with double stranded DNA and a range of G-quadruplex DNA structures was explored using different spectroscopic methods as well as computational techniques. Results from ESI-MS experiments and Fluorescent Indicator Displacement (FID) assays were consistent with each other and indicated that varying the diamine moiety had less influence on DNA affinity than changing the pendant groups. These conclusions were also generally supported by results obtained from UV melting experiments and Fluorescence Resonance Energy Transfer (FRET) assays. The cytotoxicity of selected examples of the new complexes, and close analogues reported recently, towards V79 Chinese hamster lung cancer cells and THP-1 human leukemia cells was measured. All were found to display modest cytotoxicity, with flow cytometry experiments suggesting an apoptotic pathway was the most likely mechanism of cell death.
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Affiliation(s)
- Nawal Assadawi
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong 2522, Australia.
| | - Myles Ferderer
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong 2522, Australia.
| | - Nicholas Kusi-Appauh
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong 2522, Australia.
| | - Haibo Yu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong 2522, Australia.
| | - Carolyn T Dillon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong 2522, Australia.
| | - Ronald Sluyter
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong 2522, Australia.
| | - Christopher Richardson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong 2522, Australia.
| | - Stephen F Ralph
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong 2522, Australia.
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7
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Mazzini S, Borgonovo G, Princiotto S, Artali R, Musso L, Aviñó A, Eritja R, Gargallo R, Dallavalle S. Quadruplex-duplex junction in LTR-III: A molecular insight into the complexes with BMH-21, namitecan and doxorubicin. PLoS One 2024; 19:e0306239. [PMID: 39046961 PMCID: PMC11268700 DOI: 10.1371/journal.pone.0306239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024] Open
Abstract
Quadruplex-Duplex (Q-D) junctions are unique structural motifs garnering increasing interest as drug targets, due to their frequent occurrence in genomic sequences. The viral HIV LTR-III sequence was chosen as a Q-D junction model to study the affinity of the selected compounds BMH-21, namitecan (ST-1968), and doxorubicin (DOXO), all containing a planar polycyclic aromatic moiety, linked to either one short aminoalkyl or an aminoglycosyl group. A multidisciplinary approach that combines NMR spectroscopy, molecular modelling, circular dichroism (CD) and fluorescence spectroscopy was employed. The studied ligands induced moderate but clear stabilization to the Q-D junction by interacting with the interfacial tetrad. DOXO was found to be the best Q-D junction binder. Interestingly, the removal of the aminoglycosyl group significantly changed the pattern of the interactions, indicating that highly polar substituents have a stronger affinity with the exposed regions of the Q-D junction, particularly at the level of the interfacial tetrad.
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Affiliation(s)
- Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Gigliola Borgonovo
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Salvatore Princiotto
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Roberto Artali
- Scientia Advice di Roberto Artali, Cesano Maderno (MB), Italy
| | - Loana Musso
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), ISCIII, Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), ISCIII, Barcelona, Spain
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
- National Institute of Fundamental Studies, Kandy, Sri Lanka
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8
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Kaur S, Kundu N, Sharma T, Shankaraswamy J, Singh S, Saxena S. Structural analysis of peptide identified from the 2KRR domain of the nucleolin protein with a c-Myc G4 structure using biophysical and biochemical methods. RSC Adv 2024; 14:22801-22808. [PMID: 39035713 PMCID: PMC11258614 DOI: 10.1039/d4ra02785j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/02/2024] [Indexed: 07/23/2024] Open
Abstract
For the first time, the c-Myc G4 structure is reported to be stabilized by binding of the peptide (derived from the 2KRR domain of the nucleolin protein called the Nu peptide) in the loop region of the G-quadruplex structure by stacking interactions. CD results showed the formation of parallel G4 structure in the presence of 100 mM Na+ or 100 mM K+ with the appearance of two isodichroic points at 229 nm, 254 nm and 252 nm in the presence of 100 mM Na+ or 100 mM K+, respectively. In addition, in UV thermal and CD melting studies, we observed drastic changes with an increase in the hyperchromicity at a DNA : peptide ratio of 1 : 50. On titrating the Nu peptide with c-Myc G4, we calculated the value of binding constant (K a) by plotting fluorescence intensity and DNA concentration as 0.1369 ± 0.008 μM and 0.1277 ± 0.073 μM in Na+ and K+, respectively, which confirms the strong association of Nu peptide with c-Myc G4. The Nu peptide showed preferential cytotoxicity against MDA-MB-231 cells with IC50 values of 5.020 μM and 5.501 μM after 72 and 96 hours. This approach suggests a novel strategy to target G4 structure using natural key peptide segments derived from G4 stabilizing protein.
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Affiliation(s)
- Sarvpreet Kaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida 201313 India +91 120-4735600
| | - Nikita Kundu
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida 201313 India +91 120-4735600
| | - Taniya Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida 201313 India +91 120-4735600
| | - J Shankaraswamy
- Department of Fruit Science, College of Horticulture, Mojerla, Sri Konda Laxman Telangana State Horticultural University 509382 Telangana India
| | - Sweta Singh
- Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO Brig. S. K. Mazumdar Marg Delhi-110054 India
| | - Sarika Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Noida 201313 India +91 120-4735600
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9
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Hong Z, Byrd AK, Gao J, Das P, Tan VQ, Malone EG, Osei B, Marecki JC, Protacio RU, Wahls WP, Raney KD, Song H. Eukaryotic Pif1 helicase unwinds G-quadruplex and dsDNA using a conserved wedge. Nat Commun 2024; 15:6104. [PMID: 39030241 PMCID: PMC11275212 DOI: 10.1038/s41467-024-50575-8] [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: 12/11/2023] [Accepted: 07/16/2024] [Indexed: 07/21/2024] Open
Abstract
G-quadruplexes (G4s) formed by guanine-rich nucleic acids induce genome instability through impeding DNA replication fork progression. G4s are stable DNA structures, the unfolding of which require the functions of DNA helicases. Pif1 helicase binds preferentially to G4 DNA and plays multiple roles in maintaining genome stability, but the mechanism by which Pif1 unfolds G4s is poorly understood. Here we report the co-crystal structure of Saccharomyces cerevisiae Pif1 (ScPif1) bound to a G4 DNA with a 5' single-stranded DNA (ssDNA) segment. Unlike the Thermus oshimai Pif1-G4 structure, in which the 1B and 2B domains confer G4 recognition, ScPif1 recognizes G4 mainly through the wedge region in the 1A domain that contacts the 5' most G-tetrad directly. A conserved Arg residue in the wedge is required for Okazaki fragment processing but not for mitochondrial function or for suppression of gross chromosomal rearrangements. Multiple substitutions at this position have similar effects on resolution of DNA duplexes and G4s, suggesting that ScPif1 may use the same wedge to unwind G4 and dsDNA. Our results reveal the mechanism governing dsDNA unwinding and G4 unfolding by ScPif1 helicase that can potentially be generalized to other eukaryotic Pif1 helicases and beyond.
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Affiliation(s)
- Zebin Hong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore, Republic of Singapore
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Poulomi Das
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore, Republic of Singapore
| | - Vanessa Qianmin Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore, Republic of Singapore
| | - Emory G Malone
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Bertha Osei
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - John C Marecki
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Reine U Protacio
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Wayne P Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Haiwei Song
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore, Republic of Singapore.
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10
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Adámik M, Soldánová Z, Drotárová M, Brečková K, Petr M, Helma R, Jenner LP, Vorlíčková M, Sýkorová E, Brázdová M. Human ARMC6 binds in vitro to both cancer genes and telomeric RNA, favoring G-quadruplex structure recognition. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195050. [PMID: 39029558 DOI: 10.1016/j.bbagrm.2024.195050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 06/25/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
Abstract
Armadillo repeat-containing proteins (ARMCs) are a large family found throughout eukaryotes, which play prominent roles in cell adhesion, signaling and cytoskeletal regulation. The ARMC6 protein is highly conserved in primates, including humans, but to date does not have a clear function beyond initial hints of a link to cancer and telomerase activity. We report here in vitro experiments showing ARMC6 binding to DNA promoter sequences from several cancer-related genes (e.g., EGFR, VEGF and c-MYC), and also to the telomeric RNA repeat (TERRA). ARMC6 binding activity appears to recognize G-quadruplex motifs, which are being increasingly implicated as structure-based protein binding sites in chromosome maintenance and repair. In vivo investigation of ARMC6 function revealed that when this protein is overexpressed in human cell lines, there is different expression of genes connected with oncogenic pathways and those implicated in downstream non-canonical telomerase pathways (e.g., VEGF, hTERT, c-MYC, ESM1, MMP3). ARMC6 is already known to interact with human shelterin protein TRF2 and telomerase. The protein binds G-quadruplex structures and does so preferentially to RNA over DNA. As such, this protein may be an example of how a non-canonical nucleic acid structural motif allows mediation between gene regulation and telomeric chromatin rearrangement pathways.
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Affiliation(s)
- Matej Adámik
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Zuzana Soldánová
- Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého 1/3, 612 42 Brno, Czech Republic
| | - Magdaléna Drotárová
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Katarína Brečková
- Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého 1/3, 612 42 Brno, Czech Republic
| | - Marek Petr
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Robert Helma
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Leon P Jenner
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Marie Brázdová
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic; Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého 1/3, 612 42 Brno, Czech Republic.
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11
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Cameron DP, Sornkom J, Alsahafi S, Drygin D, Poortinga G, McArthur GA, Hein N, Hannan R, Panov KI. CX-5461 Preferentially Induces Top2α-Dependent DNA Breaks at Ribosomal DNA Loci. Biomedicines 2024; 12:1514. [PMID: 39062087 PMCID: PMC11275095 DOI: 10.3390/biomedicines12071514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 07/28/2024] Open
Abstract
While genotoxic chemotherapeutic agents are among the most effective tools to combat cancer, they are often associated with severe adverse effects caused by indiscriminate DNA damage in non-tumor tissue as well as increased risk of secondary carcinogenesis. This study builds on our previous work demonstrating that the RNA Polymerase I (Pol I) transcription inhibitor CX-5461 elicits a non-canonical DNA damage response and our discovery of a critical role for Topoisomerase 2α (Top2α) in the initiation of Pol I-dependent transcription. Here, we identify Top2α as a mediator of CX-5461 response in the murine Eµ-Myc B lymphoma model whereby sensitivity to CX-5461 is dependent on cellular Top2α expression/activity. Most strikingly, and in contrast to canonical Top2α poisons, we found that the Top2α-dependent DNA damage induced by CX-5461 is preferentially localized at the ribosomal DNA (rDNA) promoter region, thereby highlighting CX-5461 as a loci-specific DNA damaging agent. This mechanism underpins the efficacy of CX-5461 against certain types of cancer and can be used to develop effective non-genotoxic anticancer drugs.
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Affiliation(s)
- Donald P. Cameron
- ACRF Department of Cancer Biology and Therapeutics, Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The College of Health and Medicine, The Australian National University, Canberra, ACT 2601, Australia; (D.P.C.); (N.H.)
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.); (G.P.)
| | - Jirawas Sornkom
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.); (G.P.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Sameerh Alsahafi
- School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK;
| | - Denis Drygin
- Pimera Therapeutics, 7875 Highland Village Place, Suite 412, San Diego, CA 92129, USA;
| | - Gretchen Poortinga
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.); (G.P.)
| | - Grant A. McArthur
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Nadine Hein
- ACRF Department of Cancer Biology and Therapeutics, Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The College of Health and Medicine, The Australian National University, Canberra, ACT 2601, Australia; (D.P.C.); (N.H.)
| | - Ross Hannan
- ACRF Department of Cancer Biology and Therapeutics, Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The College of Health and Medicine, The Australian National University, Canberra, ACT 2601, Australia; (D.P.C.); (N.H.)
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.); (G.P.)
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3053, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- School of Biomedical Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Konstantin I. Panov
- School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK;
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
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12
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Liu W, He X, Zhu Y, Li Y, Wang Z, Li P, Pan J, Wang J, Chu B, Yang G, Zhang M, He Q, Li Y, Li W, Zhang C. Identification of a conserved G-quadruplex within the E165R of African swine fever virus (ASFV) as a potential antiviral target. J Biol Chem 2024; 300:107453. [PMID: 38852886 PMCID: PMC11261444 DOI: 10.1016/j.jbc.2024.107453] [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: 11/29/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/11/2024] Open
Abstract
Identification of a conserved G-quadruplex in E165R of ASFVAfrican swine fever virus (ASFV) is a double-stranded DNA arbovirus with high transmissibility and mortality rates. It has caused immense economic losses to the global pig industry. Currently, no effective vaccines or medications are to combat ASFV infection. G-quadruplex (G4) structures have attracted increasing interest because of their regulatory role in vital biological processes. In this study, we identified a conserved G-rich sequence within the E165R gene of ASFV. Subsequently, using various methods, we verified that this sequence could fold into a parallel G4. In addition, the G4-stabilizers pyridostatin and 5,10,15,20-tetrakis-(N-methyl-4-pyridyl) porphin (TMPyP4) can bind and stabilize this G4 structure, thereby inhibiting E165R gene expression, and the inhibitory effect is associated with G4 formation. Moreover, the G4 ligand pyridostatin substantially impeded ASFV proliferation in Vero cells by reducing gene copy number and viral protein expression. These compelling findings suggest that G4 structures may represent a promising and novel antiviral target against ASFV.
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Affiliation(s)
- Wenhao Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Xinglin He
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Yance Zhu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Yaqin Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Zhihao Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Pengfei Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Jiajia Pan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Jiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Beibei Chu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Guoyu Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Mengjia Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Qigai He
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Yongtao Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Wentao Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China.
| | - Chao Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China.
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13
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Qin G, Liu Z, Yang J, Liao X, Zhao C, Ren J, Qu X. Targeting specific DNA G-quadruplexes with CRISPR-guided G-quadruplex-binding proteins and ligands. Nat Cell Biol 2024; 26:1212-1224. [PMID: 38961283 DOI: 10.1038/s41556-024-01448-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
Despite the demonstrated importance of DNA G-quadruplexes (G4s) in health and disease, technologies to readily manipulate specific G4 folding for functional analysis and therapeutic purposes are lacking. Here we employ G4-stabilizing protein/ligand in conjunction with CRISPR to selectively facilitate single or multiple targeted G4 folding within specific genomic loci. We demonstrate that fusion of nucleolin with a catalytically inactive Cas9 can specifically stabilize G4s in the promoter of oncogene MYC and muscle-associated gene Itga7 as well as telomere G4s, leading to cell proliferation arrest, inhibition of myoblast differentiation and cell senescence, respectively. Furthermore, CRISPR can confer intra-G4 selectivity to G4-binding compounds pyridodicarboxamide and pyridostatin. Compared with traditional G4 ligands, CRISPR-guided biotin-conjugated pyridodicarboxamide enables a more precise investigation into the biological functionality of de novo G4s. Our study provides insights that will enhance understanding of G4 functions and therapeutic interventions.
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Affiliation(s)
- Geng Qin
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Zhenqi Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Jie Yang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Xiaofeng Liao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
- University of Science and Technology of China, Hefei, P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China.
- University of Science and Technology of China, Hefei, P. R. China.
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14
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Peng H, Zhang Y, Luo Q, Wang X, You H. Unfolding rates of 1:1 and 2:1 complex of CX-5461 and c- MYC promoter G-quadruplexes revealed by single-molecule force spectroscopy. BIOPHYSICS REPORTS 2024; 10:180-189. [PMID: 39027314 PMCID: PMC11252239 DOI: 10.52601/bpr.2024.240018] [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: 04/10/2024] [Accepted: 05/22/2024] [Indexed: 07/20/2024] Open
Abstract
CX-5461, also known as pidnarulex, is a strong G4 stabilizer and has received FDA fast-track designation for BRCA1- and BRCA2- mutated cancers. However, quantitative measurements of the unfolding rates of CX-5461-G4 complexes which are important for the regulation function of G4s, remain lacking. Here, we employ single-molecule magnetic tweezers to measure the unfolding force distributions of c-MYC G4s in the presence of different concentrations of CX-5461. The unfolding force distributions exhibit three discrete levels of unfolding force peaks, corresponding to three binding modes. In combination with a fluorescent quenching assay and molecular docking to previously reported ligand-c-MYC G4 structure, we assigned the ~69 pN peak corresponding to the 1:1 (ligand:G4) complex where CX-5461 binds at the G4's 5'-end. The ~84 pN peak is attributed to the 2:1 complex where CX-5461 occupies both the 5' and 3'. Furthermore, using the Bell-Arrhenius model to fit the unfolding force distributions, we determined the zero-force unfolding rates of 1:1, and 2:1 complexes to be (2.4 ± 0.9) × 10-8 s-1 and (1.4 ± 1.0) × 10-9 s-1 respectively. These findings provide valuable insights for the development of G4-targeted ligands to combat c-MYC-driven cancers.
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Affiliation(s)
- Hui Peng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yashuo Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qun Luo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xinyu Wang
- College of Physics Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Huijuan You
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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15
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Ma TZ, Liu LY, Zeng YL, Ding K, Zhang H, Liu W, Cao Q, Xia W, Xiong X, Wu C, Mao ZW. G-quadruplex-guided cisplatin triggers multiple pathways in targeted chemotherapy and immunotherapy. Chem Sci 2024; 15:9756-9774. [PMID: 38939132 PMCID: PMC11206235 DOI: 10.1039/d4sc00643g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/09/2024] [Indexed: 06/29/2024] Open
Abstract
G-quadruplexes (G4s) are atypical nucleic acid structures involved in basic human biological processes and are regulated by small molecules. To date, pyridostatin and its derivatives [e.g., PyPDS (4-(2-aminoethoxy)-N 2,N 6-bis(4-(2-(pyrrolidin-1-yl) ethoxy) quinolin-2-yl) pyridine-2,6-dicarboxamide)] are the most widely used G4-binding small molecules and considered to have the best G4 specificity, which provides a new option for the development of cisplatin-binding DNA. By combining PyPDS with cisplatin and its analogs, we synthesize three platinum complexes, named PyPDSplatins. We found that cisplatin with PyPDS (CP) exhibits stronger specificity for covalent binding to G4 domains even in the presence of large amounts of dsDNA compared with PyPDS either extracellularly or intracellularly. Multiomics analysis reveals that CP can effectively regulate G4 functions, directly damage G4 structures, activate multiple antitumor signaling pathways, including the typical cGAS-STING pathway and AIM2-ASC pathway, trigger a strong immune response and lead to potent antitumor effects. These findings reflect that cisplatin-conjugated specific G4 targeting groups have antitumor mechanisms different from those of classic cisplatin and provide new strategies for the antitumor immunity of metals.
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Affiliation(s)
- Tian-Zhu Ma
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Liu-Yi Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - You-Liang Zeng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Ke Ding
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine Hangzhou 311121 P. R. China
| | - Hang Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Wenting Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Qian Cao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Wei Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Xushen Xiong
- The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine Hangzhou 311121 P. R. China
| | - Chao Wu
- Department of Neurology, The First Affiliated Hospital, Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Sun Yat-sen University Guangzhou 510080 P. R. China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, IGCME, GBRCE for Functional Molecular Engineering, Sun Yat-Sen University Guangzhou 510275 P. R. China
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16
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Lu-Nguyen N, Snowden S, Popplewell L, Malerba A. Systemic Pharmacotherapeutic Treatment of the ACTA1-MCM/FLExDUX4 Preclinical Mouse Model of FSHD. Int J Mol Sci 2024; 25:6994. [PMID: 39000102 PMCID: PMC11241187 DOI: 10.3390/ijms25136994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/18/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
Aberrant expression of the double homeobox 4 (DUX4) gene in skeletal muscle predominantly drives the pathogenesis of facioscapulohumeral muscular dystrophy (FSHD). We recently demonstrated that berberine, an herbal extract known for its ability to stabilize guanine-quadruplex structures, effectively downregulates DUX4 expression in FSHD patient-derived myoblasts and in mice overexpressing exogenous DUX4 after viral vector-based treatment. Here, we sought to confirm berberine's inhibitory efficacy on DUX4 in the widely used FSHD-like transgenic mouse model, ACTA1-MCM/FLExDUX4, where DUX4 is induced at pathogenic levels using tamoxifen. Animals repeatedly treated with berberine via intraperitoneal injections for 4 weeks exhibited significant reductions in both mRNA and protein levels of DUX4, and in mRNA expression of murine DUX4-related genes. This inhibition translated into improved forelimb muscle strength and positive alterations in important FSHD-relevant cellular pathways, although its impact on muscle mass and histopathology was less pronounced. Collectively, our data confirm the efficacy of berberine in downregulating DUX4 expression in the most relevant FSHD mouse model. However, further optimization of dosing regimens and new studies to enhance the bioavailability of berberine in skeletal muscle are warranted to fully leverage its therapeutic potential for FSHD treatment.
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Affiliation(s)
- Ngoc Lu-Nguyen
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Stuart Snowden
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Linda Popplewell
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
- National Horizons Centre, Teesside University, Darlington DL1 1HG, UK
| | - Alberto Malerba
- Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
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17
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Paul R, Dutta D, Mukhopadhyay TK, Müller D, Lala B, Datta A, Schwalbe H, Dash J. A non-B DNA binding peptidomimetic channel alters cellular functions. Nat Commun 2024; 15:5275. [PMID: 38902227 PMCID: PMC11190219 DOI: 10.1038/s41467-024-49534-0] [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: 08/08/2022] [Accepted: 06/07/2024] [Indexed: 06/22/2024] Open
Abstract
DNA binding transcription factors possess the ability to interact with lipid membranes to construct ion-permeable pathways. Herein, we present a thiazole-based DNA binding peptide mimic TBP2, which forms transmembrane ion channels, impacting cellular ion concentration and consequently stabilizing G-quadruplex DNA structures. TBP2 self-assembles into nanostructures, e.g., vesicles and nanofibers and facilitates the transportation of Na+ and K+ across lipid membranes with high conductance (~0.6 nS). Moreover, TBP2 exhibits increased fluorescence when incorporated into the membrane or in cellular nuclei. Monomeric TBP2 can enter the lipid membrane and localize to the nuclei of cancer cells. The coordinated process of time-dependent membrane or nuclear localization of TBP2, combined with elevated intracellular cation levels and direct G-quadruplex (G4) interaction, synergistically promotes formation and stability of G4 structures, triggering cancer cell death. This study introduces a platform to mimic and control intricate biological functions, leading to the discovery of innovative therapeutic approaches.
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Affiliation(s)
- Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Titas Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Diana Müller
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe, University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Binayak Lala
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe, University Frankfurt, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India.
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18
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Zhao L, Cheng L, Yang Y, Wang P, Tian P, Yang T, Nian H, Cao L. Biomimetic Hydrogen-Bonded G ⋅ C ⋅ G ⋅ C Quadruplex within a Tetraphenylethene-Based Octacationic Spirobicycle in Water. Angew Chem Int Ed Engl 2024; 63:e202405150. [PMID: 38591857 DOI: 10.1002/anie.202405150] [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: 03/15/2024] [Revised: 04/01/2024] [Accepted: 04/09/2024] [Indexed: 04/10/2024]
Abstract
In biological systems, nucleotide quadruplexes (such as G-quadruplexes) in DNA and RNA that are held together by multiple hydrogen bonds play a crucial functional role. The biomimetic formation of these hydrogen-bonded quadruplexes captured by artificial systems in water poses a significant challenge but can offer valuable insights into these complex functional structures. Herein, we report the formation of biomimetic hydrogen-bonded G ⋅ C ⋅ G ⋅ C quadruplex captured by a tetraphenylethene (TPE) based octacationic spirobicycle (1). The spirobicyclic compound possesses a three-dimensional (3D) crossing dual-cavity structure, which enables the encapsulation of four d(GpC) dinucleotide molecules, thereby realizing 1 : 4 host-guest complexation in water. The X-ray structure reveals that four d(GpC) molecules further form a two-layer G ⋅ C ⋅ G ⋅ C quadruplex with Watson-Crick hydrogen bonds, which are stabilized within the dual hydrophobic cavities of 1 through the cooperative non-covalent interactions of hydrogen bonds, CH⋅⋅⋅π interactions, and hydrophobic effect. Due to the dynamically-rotational propeller chirality of TPE units, 1 with adaptive chirality can further serve as a chiroptical sensor to exhibit opposite Cotton effects with mirror-image CD spectra for the pH-dependent hydrogen-bonded assemblies of d(GpC) including the Watson-Crick G ⋅ C ⋅ G ⋅ C (pH 9.22) and Hoogsteen G ⋅ C+ ⋅ G ⋅ C+ (pH 5.74) quartets through the host-guest chirality transfer in water.
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Affiliation(s)
- Lingyu Zhao
- College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, P. R. China)
| | - Lin Cheng
- College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, P. R. China)
| | - Yanxia Yang
- College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, P. R. China)
| | - Pingxia Wang
- College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, P. R. China)
| | - Ping Tian
- College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, P. R. China)
| | - Ting Yang
- College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, P. R. China)
| | - Hao Nian
- College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, P. R. China)
| | - Liping Cao
- College of Chemistry and Materials Science, Northwest University, Xi'an, 710069, P. R. China)
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19
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Ciaco S, Aronne R, Fiabane M, Mori M. The Rise of Bacterial G-Quadruplexes in Current Antimicrobial Discovery. ACS OMEGA 2024; 9:24163-24180. [PMID: 38882119 PMCID: PMC11170735 DOI: 10.1021/acsomega.4c01731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024]
Abstract
Antimicrobial resistance (AMR) is a silent critical issue that poses several challenges to health systems. While the discovery of novel antibiotics is currently stalled and prevalently focused on chemical variations of the scaffolds of available drugs, novel targets and innovative strategies are urgently needed to face this global threat. In this context, bacterial G-quadruplexes (G4s) are emerging as timely and profitable targets for the design and development of antimicrobial agents. Indeed, they are expressed in regulatory regions of bacterial genomes, and their modulation has been observed to provide antimicrobial effects with translational perspectives in the context of AMR. In this work, we review the current knowledge of bacterial G4s as well as their modulation by small molecules, including tools and techniques suitable for these investigations. Finally, we critically analyze the needs and future directions in the field, with a focus on the development of small molecules as bacterial G4s modulators endowed with remarkable drug-likeness.
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Affiliation(s)
- Stefano Ciaco
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Rossella Aronne
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Martina Fiabane
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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20
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Gorb L, Voiteshenko I, Hurmach V, Zarudnaya M, Nyporko A, Shyryna T, Platonov M, Roszak S, Rasulev B. From RNA sequence to its three-dimensional structure: geometrical structure, stability and dynamics of selected fragments of SARS-CoV-2 RNA. NAR Genom Bioinform 2024; 6:lqae062. [PMID: 38835951 PMCID: PMC11148665 DOI: 10.1093/nargab/lqae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
In this computational study, we explore the folding of a particular sequence using various computational tools to produce two-dimensional structures, which are then transformed into three-dimensional structures. We then study the geometry, energetics and dynamics of these structures using full electron quantum-chemical and classical molecular dynamics calculations. Our study focuses on the SARS-CoV-2 RNA fragment GGaGGaGGuguugcaGG and its various structures, including a G-quadruplex and five different hairpins. We examine the impact of two types of counterions (K+ and Na+) and flanking nucleotides on their geometrical characteristics, relative stability and dynamic properties. Our results show that the G-quadruplex structure is the most stable among the constructed hairpins. We confirm its topological stability through molecular dynamics simulations. Furthermore, we observe that the nucleotide loop consisting of seven nucleotides is the most flexible part of the RNA fragment. Additionally, we find that RNA networks of intermolecular hydrogen bonds are highly sensitive to the surrounding environment. Our findings reveal the loss of 79 old hydrogen bonds and the formation of 91 new ones in the case when the G-quadruplex containing flanking nucleotides is additionally stabilized by Na+ counterions.
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Affiliation(s)
- Leonid Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Ivan Voiteshenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv01033, Ukraine
| | - Vasyl Hurmach
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Margarita Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Alex Nyporko
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv01033, Ukraine
| | - Tetiana Shyryna
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Maksym Platonov
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Szczepan Roszak
- Faculty of Chemistry, University of Wrocław, 50-370Wrocław, Poland
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymer Materials, North Dakota State University, NDSU Department 2760, PO Box 6050, Fargo, ND 58108, USA
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21
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Miranda A, Cucchiarini A, Esnault C, Andrau JC, Oliveira PA, Mergny JL, Cruz C. G-quadruplex forming motifs in the promoter region of the B-MYB proto-oncogene. Int J Biol Macromol 2024; 270:132244. [PMID: 38729459 DOI: 10.1016/j.ijbiomac.2024.132244] [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: 01/26/2024] [Revised: 04/10/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
To combat cancer, a comprehensive understanding of the molecular mechanisms and behaviors involved in carcinogenesis is crucial, as tumorigenesis is a complex process influenced by various genetic events and disease hallmarks. The B-MYB gene encodes a transcription factor involved in cell cycle regulation, survival, and differentiation in normal cells. B-MYB can be transformed into an oncogene through mutations, and abnormal expression of B-MYB has been identified in various cancers, including lung cancer, and is associated with poor prognosis. Targeting this oncogene is a promising approach for anti-cancer drug design. B-MYB has been deemed undruggable in previous reports, necessitating the search for novel therapeutic options. In this study, we found that the B-MYB gene promoter contains several G/C rich motifs compatible with G-quadruplex (G4) formation. We investigated and validated the existence of G4 structures in the promoter region of B-MYB, first in vitro using a combination of bioinformatics, biophysical, and biochemical methods, then in cell with the recently developed G4access method.
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Affiliation(s)
- André Miranda
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal; Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Inov4Agro, University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Cyril Esnault
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR, 5535 Montpellier, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR, 5535 Montpellier, France
| | - Paula A Oliveira
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Inov4Agro, University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France.
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal; Departamento de Química, Universidade da Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal.
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22
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Ellenbroek BD, Kahler JP, Evers SR, Pomplun SJ. Synthetic Peptides: Promising Modalities for the Targeting of Disease-Related Nucleic Acids. Angew Chem Int Ed Engl 2024; 63:e202401704. [PMID: 38456368 DOI: 10.1002/anie.202401704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
Abstract
DNA and RNA play pivotal roles in life processes by storing and transferring genetic information, modulating gene expression, and contributing to essential cellular machinery such as ribosomes. Dysregulation and mutations in nucleic acid-related processes are implicated in numerous diseases. Despite the critical impact on health of nucleic acid mutations or dysregulation, therapeutic compounds addressing these biomolecules remain limited. Peptides have emerged as a promising class of molecules for biomedical research, offering potential solutions for challenging drug targets. This review focuses on the use of synthetic peptides to target disease-related nucleic acids. We discuss examples of peptides targeting double-stranded DNA, including the clinical candidate Omomyc, and compounds designed for regulatory G-quadruplexes. Further, we provide insights into both library-based screenings and the rational design of peptides to target regulatory human RNA scaffolds and viral RNAs, emphasizing the potential of peptides in addressing nucleic acid-related diseases.
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Affiliation(s)
| | | | - Sophie R Evers
- Leiden University, 2333 CC, Leiden, The Netherlands
- Present address, Department of Chemistry, University of Zurich, Wintherthurerstrasse 190, 8057, Zurich, Switzerland
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23
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Han Y, Buric A, Chintareddy V, DeMoss M, Chen L, Dickerhoff J, De Dios R, Chand P, Riggs R, Yang D, Cushman M. Design, Synthesis, and Investigation of the Pharmacokinetics and Anticancer Activities of Indenoisoquinoline Derivatives That Stabilize the G-Quadruplex in the MYC Promoter and Inhibit Topoisomerase I. J Med Chem 2024; 67:7006-7032. [PMID: 38668707 PMCID: PMC11134171 DOI: 10.1021/acs.jmedchem.3c02303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
G-quadruplexes are noncanonical four-stranded DNA secondary structures. MYC is a master oncogene and the G-quadruplex formed in the MYC promoter functions as a transcriptional silencer and can be stabilized by small molecules. We have previously revealed a novel mechanism of action for indenoisoquinoline anticancer drugs, dual-downregulation of MYC and inhibition of topoisomerase I. Herein, we report the design and synthesis of novel 7-aza-8,9-methylenedioxyindenoisoquinolines based on desirable substituents and π-π stacking interactions. These compounds stabilize the MYC promoter G-quadruplex, significantly lower MYC levels in cancer cells, and inhibit topoisomerase I. MYC targeting was demonstrated by differential activities in Raji vs CA-46 cells and cytotoxicity in MYC-dependent cell lines. Cytotoxicities in the NCI-60 panel of human cancer cell lines were investigated. Favorable pharmacokinetics were established, and in vivo anticancer activities were demonstrated in xenograft mouse models. Furthermore, favorable brain penetration, brain pharmacokinetics, and anticancer activity in an orthotopic glioblastoma mouse model were demonstrated.
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Affiliation(s)
- Yichen Han
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Adam Buric
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Venkat Chintareddy
- Therachem Research Medilab LLC, 100 Jade Park, Chelsea, Alabama 35043, United States
| | - Mercedes DeMoss
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Luying Chen
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jonathan Dickerhoff
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Robyn De Dios
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Pooran Chand
- Therachem Research Medilab LLC, 100 Jade Park, Chelsea, Alabama 35043, United States
| | - Randall Riggs
- Gibson Oncology, 7772 Fisher Island Drive, Miami, Florida 33109, United States
| | - Danzhou Yang
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mark Cushman
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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24
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Amato J, Randazzo A, Pagano B. Chemistry and Biology of Noncanonical Nucleic Acid Structures: From Physicochemical Properties to Therapeutic Applications. Int J Mol Sci 2024; 25:4952. [PMID: 38732170 PMCID: PMC11084433 DOI: 10.3390/ijms25094952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
The aim of this Special Issue is to highlight significant and new aspects concerning the chemistry and biology of noncanonical nucleic acid structures, with emphasis on their structure, stability, and conformational equilibria, as well as on the biological relevance of their interactions with proteins and ligands [...].
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Affiliation(s)
| | | | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (J.A.); (A.R.)
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25
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Ji J, Sharma A, Pokhrel P, Karna D, Pandey S, Zheng YR, Mao H. Dynamic Structures and Fast Transition Kinetics of Oxidized G-Quadruplexes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2400485. [PMID: 38678502 DOI: 10.1002/smll.202400485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/04/2024] [Indexed: 05/01/2024]
Abstract
8-oxoguanines (8-oxoG) in cells form compromised G-quadruplexes (GQs), which may vary GQ mediated gene regulations. By mimicking molecularly crowded cellular environment using 40% DMSO or sucrose, here it is found that oxidized human telomeric GQs have stabilities close to the wild-type (WT) GQs. Surprisingly, while WT GQs show negative formation cooperativity between a Pt(II) binder and molecularly crowded environment, positive cooperativity is observed for oxidized GQ formation. Single-molecule mechanical unfolding reveals that 8-oxoG sequence formed more diverse and flexible structures with faster folding/unfolding transition kinetics, which facilitates the Pt(II) ligand to bind the best-fit structures with positive cooperativity. These findings offer new understanding on structures and properties of oxidized G-rich species in crowded environments. They also provide insights into the design of better ligands to target oxidized G-rich structures formed under oxidative cell stress.
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Affiliation(s)
- Jiahao Ji
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Arpit Sharma
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Pravin Pokhrel
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Deepak Karna
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Shankar Pandey
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Yao-Rong Zheng
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
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26
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Zhang X, Hu MH. Development of a fluorescent ligand that can illuminate nuclear G-quadruplexes and modulate oncogene expression. Bioorg Med Chem 2024; 104:117713. [PMID: 38574409 DOI: 10.1016/j.bmc.2024.117713] [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: 03/05/2024] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
In this study, we developed a promising dual-function fluorescent ligand termed KS-1 by a slight structural modification on a reported carbazole-based scaffold. KS-1 was then found to mainly bind and illuminate the nuclear DNA G-quadruplexes (G4s) in a sandwich-like interacting mode, and also effectively modulate the oncogene expression through a G4-mediated manner. Furthermore, KS-1 was proved to inhibit cancer cell growth either in 2D monolayer cells or 3D multicellular tumor spheroids. To be noted, this ligand could overcome the shortcomings of other reported dual-function ligands that appeared to accumulate in the lysosomes or mitochondria, and may be used as a theranostic agent in the future.
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Affiliation(s)
- Xiao Zhang
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China
| | - Ming-Hao Hu
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China.
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27
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Wang XD, Liu YS, Chen MD, Hu MH. Discovery of a triphenylamine-based ligand that targets mitochondrial DNA G-quadruplexes and activates the cGAS-STING immunomodulatory pathway. Eur J Med Chem 2024; 269:116361. [PMID: 38547736 DOI: 10.1016/j.ejmech.2024.116361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024]
Abstract
Stabilization of G-quadruplex (G4) structures in mitochondria leads to the damage of mitochondrial DNA (mtDNA), making mtDNA G4s a promising target in the field of cancer therapy in recent years. Damaged mtDNA released into the cytosol can stimulate cytosolic DNA-sensing pathways, and cGAS-STING pathway is a typical one with potent immunostimulatory effects. A few small molecule ligands of mtDNA G4s are identified with antitumor efficacy, but little is known about their results and mechanisms on immunomodulation. In this study, we engineered a series of triphenylamine-based analogues targeting mtDNA G4s, and A6 was determined as the most promising compound. Cellular studies indicated that A6 caused severe mtDNA damage. Then, damaged mtDNA stimulated cGAS-STING pathway, resulting in the following cytokine production of tumor cells and the maturation of DCs. In vivo experiments certified that A6 exerted suppressive influences on tumor growth and metastasis in 4T1 cell-bearing mice by the regulation of TME, including the remodeling of macrophages and the activation of T cells. To our knowledge, it is the first time to report a ligand targeting mtDNA G4s to activate the cGAS-STING immunomodulatory pathway, providing a novel strategy for the future development of mtDNA G4-based antitumor agents.
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Affiliation(s)
- Xiao-Dong Wang
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen, 518060, China
| | - Yong-Si Liu
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen, 518060, China
| | - Meng-Die Chen
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen, 518060, China
| | - Ming-Hao Hu
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen, 518060, China.
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Granger SL, Sharma R, Kaushik V, Razzaghi M, Honda M, Gaur P, Bhat DS, Labenz SM, Heinen JE, Williams BA, Tabei SMA, Wlodarski MW, Antony E, Spies M. Human hnRNPA1 reorganizes telomere-bound Replication Protein A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.09.540056. [PMID: 37214874 PMCID: PMC10197631 DOI: 10.1101/2023.05.09.540056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Human replication protein A (RPA) is a heterotrimeric ssDNA binding protein responsible for many aspects of cellular DNA metabolism. Dynamic interactions of the four RPA DNA binding domains (DBDs) with DNA control replacement of RPA by downstream proteins in various cellular metabolic pathways. RPA plays several important functions at telomeres where it binds to and melts telomeric G-quadruplexes, non-canonical DNA structures formed at the G-rich telomeric ssDNA overhangs. Here, we combine single-molecule total internal reflection fluorescence microscopy (smTIRFM) and mass photometry (MP) with biophysical and biochemical analyses to demonstrate that heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) specifically remodels RPA bound to telomeric ssDNA by dampening the RPA configurational dynamics and forming a ternary complex. Uniquely, among hnRNPA1 target RNAs, telomeric repeat-containing RNA (TERRA) is selectively capable of releasing hnRNPA1 from the RPA-telomeric DNA complex. We speculate that this telomere specific RPA-DNA-hnRNPA1 complex is an important structure in telomere protection. One Sentence Summary At the single-stranded ends of human telomeres, the heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) binds to and modulates conformational dynamics of the ssDNA binding protein RPA forming a ternary complex which is controlled by telomeric repeat-containing RNA (TERRA).
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29
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Bisoi A, Sarkar S, Singh PC. Loop nucleobases-dependent folding of G-quadruplex in normal and cancer cell-mimicking KCl microenvironments. Int J Biol Macromol 2024; 265:131050. [PMID: 38522708 DOI: 10.1016/j.ijbiomac.2024.131050] [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: 12/01/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
In this study, the folding of G-quadruplex (G4) from the telomeric DNA sequences having loop nucleobases of different chemical natures, numbers, and arrangements in 10 mM and 100 mM KCl salt conditions mimicking the cancerous and normal KCl salt microenvironments have been investigated. The data suggest that the structure and stability of the G4 are highly dependent on the KCl salt concentration. In general, the conformational flexibility of the folded G4 is higher in KCl salt relevant to cancer than in the normal case for any loop arrangements with the same number of nucleobases. The stability of the G4 decreases with the increase in the number of loop nucleobases for both salt conditions. However, the decrease in the stability of G4 having adenine in the loop region is significantly higher than the case of thymine, particularly more prominent in the KCl salt relevant to the cancer. The topology of the folded G4 and its stability also depend delicately on the permutation of the nucleobases in the loop and the salt concentrations for a particular sequence. The findings indicate that the structure and stability of G4 are noticeably different in KCl salt relevant to physiological and cancer conditions.
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Affiliation(s)
- Asim Bisoi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
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30
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Akdeniz Y, Kesimci TG. Chemical Composition and Biocontrol Activity of Different Essential Oils against Soil-Borne Fungal Pathogens. THE PLANT PATHOLOGY JOURNAL 2024; 40:192-204. [PMID: 38606448 PMCID: PMC11016558 DOI: 10.5423/ppj.oa.01.2024.0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/19/2024] [Accepted: 03/03/2024] [Indexed: 04/13/2024]
Abstract
In this study, the efficacy of the essential oil of Mentha longifolia, Achillea arabica and Artemisia absinthium plants were evaluated against important soil-borne fungal pathogens as Verticillium dahliae, Rhizoctonia solani, and Fusarium oxysporum. Essential oils were obtained from plants by hydrodistillation method and the chemical components of essential oils were determined by analyzing by gas chromatography-mass spectrometry. The main components found as piperitone oxide (13.61%), piperitenone oxide (15.55%), pulegone (12.47%), 1-menthone (5.75%), and camphor (5.75%) in M. longifolia, á-selinene 13.38%, camphor 13.34%, L-4-terpineneol 8.40%, (-)-á-Elemene 7.01%, 1,8-cineole 4.71%, and (-)-spathulenol 3.84% in A. arabica, and á-thujone (34.64%), 1,8-cineole (19.54%), pulegone (7.86%), camphene (5.31%), sabinene (4.86%), and germacrene-d (3.67%) in A. absinthium. The antifungal activities of the oils were investigated 0.05, 0.1, 0.25, 0.5, 1.00, and 2.00 μl/ml concentrations with the contact effect method. M. longifolia oil (1.00 and 2.00 μl/ml) has displayed remarkable antifungal effect and provided 100% inhibition on mycelial growth of V. dahliae, R. solani and F. oxysporum. The results obtained from this study may contribute to the development of new alternative and safe methods against soil-borne fungal pathogens.
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Affiliation(s)
- Yusuf Akdeniz
- Department of Plant Protection, Faculty of Agriculture, Iğdır University, Iğdır 76002, Türkiye
| | - Tuba Genç Kesimci
- Department of Plant Protection, Faculty of Agriculture, Iğdır University, Iğdır 76002, Türkiye
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31
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Huynh M, Vinck R, Gibert B, Gasser G. Strategies for the Nuclear Delivery of Metal Complexes to Cancer Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311437. [PMID: 38174785 DOI: 10.1002/adma.202311437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/20/2023] [Indexed: 01/05/2024]
Abstract
The nucleus is an essential organelle for the function of cells. It holds most of the genetic material and plays a crucial role in the regulation of cell growth and proliferation. Since many antitumoral therapies target nucleic acids to induce cell death, tumor-specific nuclear drug delivery could potentiate therapeutic effects and prevent potential off-target side effects on healthy tissue. Due to their great structural variety, good biocompatibility, and unique physico-chemical properties, organometallic complexes and other metal-based compounds have sparked great interest as promising anticancer agents. In this review, strategies for specific nuclear delivery of metal complexes are summarized and discussed to highlight crucial parameters to consider for the design of new metal complexes as anticancer drug candidates. Moreover, the existing opportunities and challenges of tumor-specific, nucleus-targeting metal complexes are emphasized to outline some new perspectives and help in the design of new cancer treatments.
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Affiliation(s)
- Marie Huynh
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry of Life and Health Sciences, Laboratory for Inorganic Chemistry, Paris, F-75005, France
- Gastroenterology and technologies for Health, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, Lyon, 69008, France
| | - Robin Vinck
- Orano, 125 avenue de Paris, Châtillon, 92320, France
| | - Benjamin Gibert
- Gastroenterology and technologies for Health, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, Lyon, 69008, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry of Life and Health Sciences, Laboratory for Inorganic Chemistry, Paris, F-75005, France
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32
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Chaudhuri R, Prasanth T, Biswas D, Mandal S, Dash J. Combating multidrug-resistance in S. pneumoniae: a G-quadruplex binding inhibitor of efflux pump and its bio-orthogonal assembly. NAR MOLECULAR MEDICINE 2024; 1:ugae005. [PMID: 38694210 PMCID: PMC11059089 DOI: 10.1093/narmme/ugae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024]
Abstract
Antibiotic resistance poses a significant global health threat, necessitating innovative strategies to combat multidrug-resistant bacterial infections. Streptococcus pneumoniae, a pathogen responsible for various infections, harbors highly conserved DNA quadruplexes in genes linked to its pathogenesis. In this study, we introduce a novel approach to counter antibiotic resistance by stabilizing G-quadruplex structures within the open reading frames of key resistance-associated genes (pmrA, recD and hsdS). We synthesized An4, a bis-anthracene derivative, using Cu(I)-catalyzed azide-alkyne cycloaddition, which exhibited remarkable binding and stabilization of the G-quadruplex in the pmrA gene responsible for drug efflux. An4 effectively permeated multidrug-resistant S. pneumoniae strains, leading to a substantial 12.5-fold reduction in ciprofloxacin resistance. Furthermore, An4 downregulated pmrA gene expression, enhancing drug retention within bacterial cells. Remarkably, the pmrA G-quadruplex cloned into the pET28a(+) plasmid transformed into Escherichia coli BL21 cells can template Cu-free bio-orthogonal synthesis of An4 from its corresponding alkyne and azide fragments. This study presents a pioneering strategy to combat antibiotic resistance by genetically reducing drug efflux pump expression through G-quadruplex stabilization, offering promising avenues for addressing antibiotic resistance.
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Affiliation(s)
- Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West-Bengal 700032, India
| | - Thumpati Prasanth
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West-Bengal 700032, India
| | - Debasmita Biswas
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West-Bengal 700032, India
| | - Subhranshu Mandal
- Laboratory Medicine, Chittaranjan National Cancer Institute, Kolkata, West Bengal 700156, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, West-Bengal 700032, India
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Tateishi-Karimata H, Kawauchi K, Takahashi S, Sugimoto N. Development of a Pseudocellular System to Quantify Specific Interactions Determining the G-Quadruplex Function in Cells. J Am Chem Soc 2024; 146:8005-8015. [PMID: 38498910 DOI: 10.1021/jacs.3c11160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Intracellular chemical microenvironments, including ion concentrations and molecular crowding, play pivotal roles in cell behaviors, such as proliferation, differentiation, and cell death via regulation of gene expression. However, there is no method for quantitative analysis of intracellular environments due to their complexity. Here, we have developed a system for highlighting the environment inside of the cell (SHELL). SHELL is a pseudocellular system, wherein small molecules are removed from the cell and a crowded intracellular environment is maintained. SHELL offers two prominent advantages: (1) It allows for precise quantitative biochemical analysis of a specific factor, and (2) it enables the study of any cell, thereby facilitating the study of target molecule effects in various cellular environments. Here, we used SHELL to study G-quadruplex formation, an event that implicated cancer. We show that G-quadruplexes are more stable in SHELL compared with in vitro conditions. Although malignant transformation perturbs cellular K+ concentrations, environments in SHELL act as buffers against G-quadruplex destabilization at lower K+ concentrations. Notably, the buffering effect was most pronounced in SHELL derived from nonaggressive cancer cells. Stable G-quadruplexes form due to the binding of the G-quadruplex with K+ in different cancer cells. Furthermore, the observed pattern of G-quadruplex-induced transcriptional inhibition in SHELL is consistent with that in living cells at different cancer stages. Our results indicate that ion binding to G-quadruplexes regulates gene expression during pathogenesis.
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Affiliation(s)
- Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Keiko Kawauchi
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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Giraud G, Rodà M, Huchon P, Michelet M, Maadadi S, Jutzi D, Montserret R, Ruepp MD, Parent R, Combet C, Zoulim F, Testoni B. G-quadruplexes control hepatitis B virus replication by promoting cccDNA transcription and phase separation in hepatocytes. Nucleic Acids Res 2024; 52:2290-2305. [PMID: 38113270 PMCID: PMC10954475 DOI: 10.1093/nar/gkad1200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 11/12/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Phase separation regulates fundamental processes in gene expression and is mediated by the local concentration of proteins and nucleic acids, as well as nucleic acid secondary structures such as G-quadruplexes (G4s). These structures play fundamental roles in both host gene expression and in viral replication due to their peculiar localisation in regulatory sequences. Hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) is an episomal minichromosome whose persistence is at the basis of chronic infection. Identifying the mechanisms controlling its transcriptional activity is indispensable to develop new therapeutic strategies against chronic hepatitis B. The aim of this study was to determine whether G4s are formed in cccDNA and regulate viral replication. Combining biochemistry and functional studies, we demonstrate that cccDNA indeed contains ten G4s structures. Furthermore, mutations disrupting two G4s located in the enhancer I HBV regulatory region altered cccDNA transcription and viral replication. Finally, we showed for the first time that cccDNA undergoes phase separation in a G4-dependent manner to promote its transcription in infected hepatocytes. Altogether, our data give new insight in the transcriptional regulation of the HBV minichromosome that might pave the way for the identification of novel targets to destabilize or silence cccDNA.
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Affiliation(s)
- Guillaume Giraud
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
| | - Mélanie Rodà
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
| | - Pélagie Huchon
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
- Université Claude-Bernard Lyon I, 69003 Lyon, France
| | - Maud Michelet
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
| | - Sarah Maadadi
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 lyon, france; université claude-bernard lyon i, 69003 Lyon, France
| | - Daniel Jutzi
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, WC2R 2LS London, UK
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7 Passage du Vercors 69367Lyon, France
| | - Marc-David Ruepp
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, WC2R 2LS London, UK
| | - Romain Parent
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
| | - Christophe Combet
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
| | - Fabien Zoulim
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
- Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Service, Hospices Civils de Lyon, 69004 Lyon, France
| | - Barbara Testoni
- INSERM U1052, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-5286, Cancer Research Center of Lyon, 69003 Lyon, France; Université Claude-Bernard Lyon I, 69003 Lyon, France
- Hepatology Institute of Lyon, 69004 Lyon, France
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Hoque ME, Kabir ML, Shiekh S, Balci H, Basu S. Stalling of Transcription by Putative G-quadruplex Sequences and CRISPR-dCas9. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585391. [PMID: 38559215 PMCID: PMC10979993 DOI: 10.1101/2024.03.17.585391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Putative G-quadruplex forming sequences (PQS) have been identified in promoter sequences of prominent genes that are implicated among others in cancer and neurological disorders. We explored mechanistic aspects of CRISPR-dCas9-mediated gene expression regulation, which is transient and sequence specific unlike alternative approaches that lack such specificity or create permanent mutations, using the PQS in tyrosine hydroxylase (TH) and c-Myc promoters as model systems. We performed in vitro ensemble and single molecule investigations to study whether G-quadruplex (GQ) structures or dCas9 impede T7 RNA polymerase (RNAP) elongation process and whether orientation of these factors is significant. Our results demonstrate that dCas9 is more likely to block RNAP progression when the non-template strand is targeted. While the GQ in TH promoter was effectively destabilized when the dCas9 target site partially overlapped with the PQS, the c-Myc GQ remained folded and stalled RNAP elongation. We also determined that a minimum separation between the transcription start site and the dCas9 target site is required for effective stalling of RNAP by dCas9. Our study provides significant insights about the factors that impact dCas9-mediated transcription regulation when dCas9 targets the vicinity of sequences that form secondary structures and provides practical guidelines for designing guide RNA sequences.
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Affiliation(s)
- Mohammed Enamul Hoque
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Mohammad Lutful Kabir
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
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36
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Chen Y, Simeone A, Melidis L, Cuesta SM, Tannahill D, Balasubramanian S. An Upstream G-Quadruplex DNA Structure Can Stimulate Gene Transcription. ACS Chem Biol 2024; 19:736-742. [PMID: 38417105 PMCID: PMC10949190 DOI: 10.1021/acschembio.3c00775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/01/2024]
Abstract
Four-stranded G-quadruplexes (G4s) are DNA secondary structures that can form in the human genome. G4 structures have been detected in gene promoters and are associated with transcriptionally active chromatin and the recruitment of transcription factors and chromatin remodelers. We adopted a controlled, synthetic biology approach to understand how G4s can influence transcription. We stably integrated G4-forming sequences into the promoter of a synthetic reporter gene and inserted these into the genome of human cells. The integrated G4 sequences were shown to fold into a G4 structure within a cellular genomic context. We demonstrate that G4 structure formation within a gene promoter stimulates transcription compared to the corresponding G4-negative control promoter in a way that is not dependent on primary sequence or inherent G-richness. Systematic variation in the stability of folded G4s showed that in this system, transcriptional levels increased with higher stability of the G4 structure. By creating and manipulating a chromosomally integrated synthetic promoter, we have shown that G4 structure formation in a defined gene promoter can cause gene transcription to increase, which aligns with earlier observational correlations reported in the literature linking G4s to active transcription.
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Affiliation(s)
- Yuqi Chen
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
| | - Angela Simeone
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Cambridge CB2 0RE, U.K.
| | - Larry Melidis
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Cambridge CB2 0RE, U.K.
| | - Sergio Martinez Cuesta
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Cambridge CB2 0RE, U.K.
| | - David Tannahill
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Cambridge CB2 0RE, U.K.
| | - Shankar Balasubramanian
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, U.K.
- Cancer
Research UK Cambridge Institute, University
of Cambridge, Cambridge CB2 0RE, U.K.
- School
of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, U.K.
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37
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Zhao Z, Wang J, Yu H, Wang X. Guide for phenotype-specific profiling of DNA G-quadruplex-regulated genes. STAR Protoc 2024; 5:102820. [PMID: 38198280 PMCID: PMC10820308 DOI: 10.1016/j.xpro.2023.102820] [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: 09/01/2023] [Revised: 11/06/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
DNA G-quadruplex (G4) is a non-canonical four-stranded secondary structure that has been shown to play a role in epigenetic modulation of gene expression. Here, we present a primer on phenotype-specific profiling of DNA G-quadruplex-regulated genes. We provide guidance on in silico exploration of G4-related genes and phenotypes, and in vitro and in vivo validation of the relationship between G4 and phenotype. We describe commonly utilized techniques and detail critical steps involved in determining the phenotype-specific G4-regulated genes for subsequent investigations.
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Affiliation(s)
- Zhuoyang Zhao
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong 510655, China; Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou 510080, China
| | - Jianru Wang
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou 510080, China
| | - Huichuan Yu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510655, China.
| | - Xiaolin Wang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510655, China.
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Chen Y, Li J, Niu K, Peng Y, Song Q, Feng Q. G-quadruplex is involved in the regulation of BmSGF1 expression in the Silkworm, Bombyx mori. INSECT SCIENCE 2024. [PMID: 38439572 DOI: 10.1111/1744-7917.13334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 03/06/2024]
Abstract
Advanced DNA structures, such as the G-quadruplex (G4) and the i-motif, are widely but not randomly present in the genomes of many organisms. A G4 structure was identified in the promoter of the silk gland factor-1 gene (SGF1), which is the main regulatory gene for silk production in Bombyx mori. In this study, a BmSGF1 G4-/- homozygous mutant was generated with the G4 sequence knocked out. The promoter activity of BmSGF1 was lowered in the BmSGF1 G4-/- mutant. Pyridostatin (PDS) stabilized the G4 structure and increased the promoter activity of BmSGF1, whereas anti-sense oligonucleotide (ASO) complementary to the G4 sequence suppressed the promoter activity of BmSGF1. Compared with wild-type larvae, the deletion of the BmSGF1 G4 structure decreased both the expression of BmSGF1 and the fibroin heavy chain gene BmFib-H in the posterior silk gland and the weight of the cocoons. Overall, these results suggest that the promoter G4 structure of BmSGF1 participates in the transcription regulation of the BmSGF1 gene in the silkworm.
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Affiliation(s)
- Yanfei Chen
- School of Biology and Agriculture, Shaoguan University, Shaoguan, China
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jin Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yuling Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Qisheng Song
- Division of Plant Science & Technology, University of Missouri, Columbia, Missouri, USA
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
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Cai JH, Yang DY, Zhang JJ, Tan JH, Huang ZS, Chen SB. Constructing triazole-modified quinazoline derivatives as selective c-MYC G-quadruplex ligands and potent anticancer agents through click chemistry. Bioorg Chem 2024; 144:107173. [PMID: 38335759 DOI: 10.1016/j.bioorg.2024.107173] [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: 01/04/2024] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
c-MYC is a hallmark of various cancers, playing a critical role in promoting tumorigenesis. The formation of G-quadruplex (G4) in the c-MYC promoter region significantly suppresses its expression. Therefore, developing small-molecule ligands to stabilize c-MYC G4 formation and subsequentially suppress c-MYC expression is an attractive topic for c-MYC-driven cancer therapy. However, achieving selective ligands for c-MYC G4 poses challenges. In this study, we developed a series of triazole-modified quinazoline (TMQ) derivatives as potential c-MYC G4 ligands and c-MYC transcription inhibitors from 4-anilinoquinazoline lead 7a using click chemistry. Importantly, the c-MYC G4 stabilizing ability and antiproliferation activity were well correlated among these new derivatives, particularly in the c-MYC highly expressed colorectal cancer cell line HCT116. Among them, compound A6 exhibited good selectivity in stabilizing c-MYC G4 and in suppressing c-MYC transcription better than 7a. This compound induced G4 formation, selectively inhibited G4-related c-MYC transcription and suppressed the progression of HCT116 cells. These findings identify a new c-MYC transcription inhibitor and provide new insights for optimizing c-MYC G4-targeting ligands.
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Affiliation(s)
- Jiong-Heng Cai
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Dan-Yan Yang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun-Jie Zhang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
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40
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Han X, Xu S, Wang L, Bi Z, Wang D, Bu H, Da J, Liu Y, Tan W. Artificial DNA Framework Channel Modulates Antiapoptotic Behavior in Ischemia-Stressed Cells via Destabilizing Promoter G-Quadruplex. ACS NANO 2024; 18:6147-6161. [PMID: 38372229 DOI: 10.1021/acsnano.3c06563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Regulating folding/unfolding of gene promoter G-quadruplexes (G4s) is important for understanding the topological changes in genomic DNAs and the biological effects of such changes on important cellular events. Although many G4-stabilizing ligands have been screened out, effective G4-destabilizing ligands are extremely rare, posing a great challenge for illustrating how G4 destabilization affects gene function in living cells under stress, a long-standing question in neuroscience. Herein, we report a distinct methodology able to destabilize gene promoter G4s in ischemia-stressed neural cells by mitigating the ischemia-induced accumulation of intracellular K+ with an artificial membrane-spanning DNA framework channel (DFC). We also show that ischemia-triggered K+ influx is positively correlated to anomalous stabilization of promoter G4s and downregulation of Bcl-2, an antiapoptotic gene with neuroprotective effects against ischemic injury. Intriguingly, the DFC enables rapid transmembrane transport of excessive K+ mediated by the internal G4 filter, leading to the destabilization of endogenous promoter G4 in Bcl-2 and subsequent turnover of gene expression at both transcription and translation levels under ischemia. Consequently, this work enriches our understanding of the biological roles of endogenous G4s and may offer important clues to study the cellular behaviors in response to stress.
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Affiliation(s)
- Xiaoyan Han
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Shujuan Xu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Linlin Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Zhengyan Bi
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Dan Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Huitong Bu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Jun Da
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Yanlan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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41
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Lowran K, Salib V, Cismas E, Wu CG. Advancing the study of protein-G4 interactions in DNA repair: Insights from biolayer interferometry. Methods Enzymol 2024; 695:89-101. [PMID: 38521592 DOI: 10.1016/bs.mie.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
Biolayer interferometry (BLI) is a powerful tool that enables direct observations of protein-G4 interactions in real-time. In this article, we discuss the crucial aspects in conducting a BLI experiment by using the TAR DNA-binding protein (TDP43) and a G4 DNA formed by (GGGGCC)4 as a sample application. We also describe the necessary precautions in designing the DNA substrate and evaluating the signal contributions arising from nonspecific binding interactions. A comprehensive guide is included that details the necessary materials and reagents, experimental procedures, and data analysis methods for researchers who are interested in using BLI for similar studies. The insights provided in this article will allow researchers to harness the potential of BLI and unravel the complexities of protein-G4 interactions with precision and confidence.
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Affiliation(s)
- Kaitlin Lowran
- Department of Chemistry, Oakland University, Rochester, MI, United States
| | - Vereena Salib
- Department of Chemistry, Oakland University, Rochester, MI, United States
| | - Emma Cismas
- Department of Chemistry, Oakland University, Rochester, MI, United States
| | - Colin G Wu
- Department of Chemistry, Oakland University, Rochester, MI, United States.
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42
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Zhang Y, Cheng Y, Luo Q, Wu T, Huo J, Yin M, Peng H, Xiao Y, Tong Q, You H. Distinguishing G-Quadruplexes Stabilizer and Chaperone for c- MYC Promoter G-Quadruplexes through Single-Molecule Manipulation. J Am Chem Soc 2024; 146:3689-3699. [PMID: 38296825 DOI: 10.1021/jacs.3c09074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
G-quadruplex (G4) selective stabilizing ligands can regulate c-MYC gene expression, but the kinetic basis remains unclear. Determining the effects of ligands on c-MYC promoter G4s' folding/unfolding kinetics is challenging due to the polymorphic nature of G4s and the high energy barrier to unfold c-MYC promoter G4s. Here, we used single-molecule magnetic tweezers to manipulate a duplex hairpin containing a c-MYC promoter sequence to mimic the transiently denatured duplex during transcription. We measured the effects of six commonly used G4s binding ligands on the competition between quadruplex and duplex structures, as well as the folding/unfolding kinetics of G4s. Our results revealed two distinct roles for G4s selective stabilization: CX-5461 is mainly acting as c-MYC G4s stabilizer, reducing the unfolding rate (ku) of c-MYC G4s, whereas PDS and 360A also act as G4s chaperone, accelerating the folding rates (kf) of c-MYC G4s. qRT-PCR results obtained from CA46 and Raji cell lines demonstrated that G4s stabilizing ligands can downregulate c-MYC expression, while G4s stabilizer CX-5461 exhibited the strongest c-MYC gene suppression. These results shed light on the potential of manipulating G4s' folding/unfolding kinetics by ligands for precise regulation of promoter G4-associated biological activities.
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Affiliation(s)
- Yashuo Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuanlei Cheng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Qun Luo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tongbo Wu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Junfeng Huo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Meng Yin
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hui Peng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yang Xiao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qingyi Tong
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huijuan You
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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43
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Esain-Garcia I, Kirchner A, Melidis L, Tavares RDCA, Dhir S, Simeone A, Yu Z, Madden SK, Hermann R, Tannahill D, Balasubramanian S. G-quadruplex DNA structure is a positive regulator of MYC transcription. Proc Natl Acad Sci U S A 2024; 121:e2320240121. [PMID: 38315865 PMCID: PMC10873556 DOI: 10.1073/pnas.2320240121] [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: 11/17/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
DNA structure can regulate genome function. Four-stranded DNA G-quadruplex (G4) structures have been implicated in transcriptional regulation; however, previous studies have not directly addressed the role of an individual G4 within its endogenous cellular context. Using CRISPR to genetically abrogate endogenous G4 structure folding, we directly interrogate the G4 found within the upstream regulatory region of the critical human MYC oncogene. G4 loss leads to suppression of MYC transcription from the P1 promoter that is mediated by the deposition of a de novo nucleosome alongside alterations in RNA polymerase recruitment. We also show that replacement of the endogenous MYC G4 with a different G4 structure from the KRAS oncogene restores G4 folding and MYC transcription. Moreover, we demonstrate that the MYC G4 structure itself, rather than its sequence, recruits transcription factors and histone modifiers. Overall, our work establishes that G4 structures are important features of transcriptional regulation that coordinate recruitment of key chromatin proteins and the transcriptional machinery through interactions with DNA secondary structure, rather than primary sequence.
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Affiliation(s)
- Isabel Esain-Garcia
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Angie Kirchner
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Larry Melidis
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | | | - Somdutta Dhir
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Angela Simeone
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Zutao Yu
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Sarah K. Madden
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Regina Hermann
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - David Tannahill
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- School of Clinical Medicine, University of Cambridge, CambridgeCB2 0SP, United Kingdom
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44
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Ahmed AA, Chen S, Roman-Escorza M, Angell R, Oxenford S, McConville M, Barton N, Sunose M, Neidle D, Haider S, Arshad T, Neidle S. Structure-activity relationships for the G-quadruplex-targeting experimental drug QN-302 and two analogues probed with comparative transcriptome profiling and molecular modeling. Sci Rep 2024; 14:3447. [PMID: 38342953 PMCID: PMC10859377 DOI: 10.1038/s41598-024-54080-2] [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: 11/21/2023] [Accepted: 02/08/2024] [Indexed: 02/13/2024] Open
Abstract
The tetrasubstituted naphthalene diimide compound QN-302 binds to G-quadruplex (G4) DNA structures. It shows high potency in pancreatic ductal adenocarcinoma (PDAC) cells and inhibits the transcription of cancer-related genes in these cells and in PDAC animal models. It is currently in Phase 1a clinical evaluation as an anticancer drug. A study of structure-activity relationships of QN-302 and two related analogues (CM03 and SOP1247) is reported here. These have been probed using comparisons of transcriptional profiles from whole-genome RNA-seq analyses, together with molecular modelling and molecular dynamics simulations. Compounds CM03 and SOP1247 differ by the presence of a methoxy substituent in the latter: these two compounds have closely similar transcriptional profiles. Whereas QN-302 (with an additional benzyl-pyrrolidine group), although also showing down-regulatory effects in the same cancer-related pathways, has effects on distinct genes, for example in the hedgehog pathway. This distinctive pattern of genes affected by QN-302 is hypothesized to contribute to its superior potency compared to CM03 and SOP1247. Its enhanced ability to stabilize G4 structures has been attributed to its benzyl-pyrrolidine substituent fitting into and filling most of the space in a G4 groove compared to the hydrogen atom in CM03 or the methoxy group substituent in SOP1247.
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Affiliation(s)
- Ahmed Abdullah Ahmed
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
- Now at Guy's Cancer Centre, Guy's Hospital, London, SE1 9RT, UK
| | - Shuang Chen
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | | | - Richard Angell
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
- Now at Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - Sally Oxenford
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
- Now at Artios Ltd, Cambridge, CB22 3FH, UK
| | | | | | - Mihiro Sunose
- Sygnature Discovery Ltd, BioCity, Nottingham, NG1 1GR, UK
| | - Dan Neidle
- Tax Policy Associates, London, EC1R 0ET, UK
| | - Shozeb Haider
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Tariq Arshad
- Qualigen Therapeutics Inc, Carlsbad, CA, 92011, USA
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK.
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45
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Andreasson M, Donzel M, Abrahamsson A, Berner A, Doimo M, Quiroga A, Eriksson A, Chao YK, Overman J, Pemberton N, Wanrooij S, Chorell E. Exploring the Dispersion and Electrostatic Components in Arene-Arene Interactions between Ligands and G4 DNA to Develop G4-Ligands. J Med Chem 2024; 67:2202-2219. [PMID: 38241609 PMCID: PMC10860144 DOI: 10.1021/acs.jmedchem.3c02127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024]
Abstract
G-Quadruplex (G4) DNA structures are important regulatory elements in central biological processes. Small molecules that selectively bind and stabilize G4 structures have therapeutic potential, and there are currently >1000 known G4 ligands. Despite this, only two G4 ligands ever made it to clinical trials. In this work, we synthesized several heterocyclic G4 ligands and studied their interactions with G4s (e.g., G4s from the c-MYC, c-KIT, and BCL-2 promoters) using biochemical assays. We further studied the effect of selected compounds on cell viability, the effect on the number of G4s in cells, and their pharmacokinetic properties. This identified potent G4 ligands with suitable properties and further revealed that the dispersion component in arene-arene interactions in combination with electron-deficient electrostatics is central for the ligand to bind with the G4 efficiently. The presented design strategy can be applied in the further development of G4-ligands with suitable properties to explore G4s as therapeutic targets.
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Affiliation(s)
- Måns Andreasson
- Chemical
Biology Consortium Sweden, Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Maxime Donzel
- Chemical
Biology Consortium Sweden, Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Alva Abrahamsson
- Chemical
Biology Consortium Sweden, Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Andreas Berner
- Departments
of Medical Biochemistry and Biophysics, Umeå University, Umeå 90736, Sweden
| | - Mara Doimo
- Departments
of Medical Biochemistry and Biophysics, Umeå University, Umeå 90736, Sweden
- Clinical
Genetics Unit, Department of Women and Children’s Health, Padua University, 35128 Padua, Italy
| | - Anna Quiroga
- Departments
of Medical Biochemistry and Biophysics, Umeå University, Umeå 90736, Sweden
| | - Anna Eriksson
- Chemical
Biology Consortium Sweden, Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Yu-Kai Chao
- Mechanistic
and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
| | - Jeroen Overman
- Mechanistic
and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
| | - Nils Pemberton
- Medicinal
Chemistry, Research and Early Development, Respiratory and Immunology
(R&I), Bio Pharmaceuticals R&D, AstraZeneca, Gothenburg SE-43183, Sweden
| | - Sjoerd Wanrooij
- Departments
of Medical Biochemistry and Biophysics, Umeå University, Umeå 90736, Sweden
| | - Erik Chorell
- Chemical
Biology Consortium Sweden, Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
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46
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Bowleg JL, Mikek CG, Gwaltney SR. Computed interactions of berenil with restricted foldamers of c-MYC DNA G-quadruplexes. J Biomol Struct Dyn 2024; 42:2162-2169. [PMID: 37286380 DOI: 10.1080/07391102.2023.2217913] [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: 11/12/2022] [Accepted: 04/16/2023] [Indexed: 06/09/2023]
Abstract
G-quadruplexes (G4s) are secondary four-stranded DNA helical structures made up of guanine-rich nucleic acids that can assemble in the promoter regions of multiple genes under the appropriate conditions. Stabilization of G4 structures by small molecules can regulate transcription in non-telomeric regions, including in proto-oncogenes and promoter regions, contributing to anti-proliferative and anti-tumor activities. Because G4s are detectable in cancer cells but not in normal cells, they make excellent drug discovery targets. Diminazene, DMZ (or berenil), has been shown to be an efficient G-quadruplex binder. Due to the stability of the folding topology, G-quadruplex structures are frequently found in the promotor regions of oncogenes and may play a regulatory role in gene activation. Using molecular docking and molecular dynamics simulations on several different binding poses, we have studied DMZ binding toward multiple G4 topologies of the c-MYC G-quadruplex. DMZ binds preferentially to G4s that have extended loops and flanking bases. This preference arises from its interactions with the loops and the flanking nucleotides, which were not found in the structure lacking extended regions. The binding to the G4s with no extended regions instead occurred mostly through end stacking. All binding sites for DMZ were confirmed by 100 ns molecular dynamics simulations and through binding enthalpies calculated using the MM-PBSA method. The primary driving forces were electrostatic, as the cationic DMZ interacts with the anionic phosphate backbone, and through van der Waals interactions, which primarily contributed in end stacking interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jerrano L Bowleg
- Department of Chemistry, Mississippi State University, College Town, MS, USA
| | - Clinton G Mikek
- Department of Chemistry, Mississippi State University, College Town, MS, USA
| | - Steven R Gwaltney
- Department of Chemistry, Mississippi State University, College Town, MS, USA
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47
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Gumina JM, Richardson AE, Shojiv MH, Chambers AE, Sandwith SN, Reisinger MA, Karns TJ, Osborne TL, Alashi HN, Anderson QT, Sharlow ME, Seiler DC, Rogers EM, Bartosik AR, Smaldino MA, Vaughn JP, Wang YH, Smaldino PJ, Haney RA. Differential Gene Expression following DHX36/ G4R1 Knockout Is Associated with G-Quadruplex Content and Cancer. Int J Mol Sci 2024; 25:1753. [PMID: 38339029 PMCID: PMC10855491 DOI: 10.3390/ijms25031753] [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: 11/27/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
G-quadruplexes (G4s) are secondary DNA and RNA structures stabilized by positive cations in a central channel formed by stacked tetrads of Hoogsteen base-paired guanines. G4s form from G-rich sequences across the genome, whose biased distribution in regulatory regions points towards a gene-regulatory role. G4s can themselves be regulated by helicases, such as DHX36 (aliases: G4R1 and RHAU), which possess the necessary activity to resolve these stable structures. G4s have been shown to both positively and negatively regulate gene expression when stabilized by ligands, or through the loss of helicase activity. Using DHX36 knockout Jurkat cell lines, we identified widespread, although often subtle, effects on gene expression that are associated with the presence or number of observed G-quadruplexes in promoters or gene regions. Genes that significantly change their expression, particularly those that show a significant increase in RNA abundance under DHX36 knockout, are associated with a range of cellular functions and processes, including numerous transcription factors and oncogenes, and are linked to several cancers. Our work highlights the direct and indirect role of DHX36 in the transcriptome of T-lymphocyte leukemia cells and the potential for DHX36 dysregulation in cancer.
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Affiliation(s)
- Joseph M. Gumina
- Department of Biology, Ball State University, Muncie, IN 47306, USA
| | | | | | | | | | | | - Taylor J. Karns
- Department of Biology, Ball State University, Muncie, IN 47306, USA
| | - Tyler L. Osborne
- Department of Biology, Ball State University, Muncie, IN 47306, USA
| | - Hasna N. Alashi
- Department of Biology, Ball State University, Muncie, IN 47306, USA
| | | | | | - Dylan C. Seiler
- Department of Biology, Ball State University, Muncie, IN 47306, USA
| | - Evan M. Rogers
- Department of Biology, Ball State University, Muncie, IN 47306, USA
| | - Anna R. Bartosik
- School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | | | | | - Yuh-Hwa Wang
- School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | | | - Robert A. Haney
- Department of Biology, Ball State University, Muncie, IN 47306, USA
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48
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Majumder P, Shukla C, Arya A, Sharma S, Datta B. G-quadruplexes in MTOR and induction of autophagy. Sci Rep 2024; 14:2525. [PMID: 38291093 PMCID: PMC10827794 DOI: 10.1038/s41598-024-52561-y] [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: 11/02/2023] [Accepted: 01/20/2024] [Indexed: 02/01/2024] Open
Abstract
G-quadruplex (G4) structures have emerged as singular therapeutic targets for cancer and neurodegeneration. Autophagy, a crucial homeostatic mechanism of the cell, is often dysregulated in neurodegenerative diseases and cancers. We used QGRS mapper to identify 470 G4 sequences in MTOR, a key negative regulator of autophagy. We sought to identify a functional context by leveraging the effect of G4-targeting ligands on MTOR G4 sequences. The effect of Bis-4,3, a G4 selective dimeric carbocyanine dye, was compared with the known G4-stabilizing activity of the porphyrin, TMPyP4 in HeLa and SHSY-5Y cells. Our results show that treatment with G4-selective ligands downregulates MTOR RNA and mTOR protein expression levels. This is the first report describing G4 motifs in MTOR. This study indicates a possible role of G4 stabilizing ligands in induction of autophagy by downregulation of mTOR levels, albeit not precluding MTOR independent pathways.
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Affiliation(s)
- Piyali Majumder
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Chinmayee Shukla
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Arjun Arya
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Shubham Sharma
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India
| | - Bhaskar Datta
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India.
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, 382355, India.
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49
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Valle-Orero J, Rieu M, Allemand JF, Bujaa D, Joubert A, Tran PLT, Croquette V, Boulé JB. Observing G4 formation and its resolution by Pif1 in real time by manipulation under magnetic tweezers. Methods Enzymol 2024; 695:119-158. [PMID: 38521583 DOI: 10.1016/bs.mie.2023.12.012] [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: 03/25/2024]
Abstract
G-quadruplexes (G4s) are nucleic acids secondary structures that may form in guanine-rich sequences, either intra or inter-molecularly. Ability of a primary sequence to form a G4 can be predicted computationally with an improving accuracy as well as tested in bulk using biophysical measurements. As a result, G4 density maps have been devised for a large number of genomes from all life kingdoms. Experimental validation of the formation of G4s in vivo however remains indirect and relies on their stabilization with small molecules, antibodies or proteins, or mutational studies, in order to measure downstream effects on gene expression or genome stability for example. Although numerous techniques exist to observe spontaneous formation of G4s in single-stranded DNA, observing G4 formation in double-stranded DNA (dsDNA) is more challenging. However, it is particularly relevant to understand if a given G4 sequence forms stably in a dsDNA context, if it is stable enough to dock proteins or pose a challenge to molecular motors such as helicases or polymerases. In essence, G4s can be a threat to genomic stability but carry as well as the potential to be elements of a structural language in the non-replicating genome. To study quantitatively the formation dynamics and stability of single intramolecular G4s embedded in dsDNA, we have adapted techniques of DNA manipulation under magnetic tweezers. This technique also allows to study encounters of molecular motors with G4 at a single molecule resolution, in order to gain insight into the specificity of G4 resolution by molecular motors, and its efficiency. The procedures described here include the design of the G4 substrate, the study of G4 formation probability and lifetime in dsDNA, as well as procedures to characterize the encounter between the Pif1 helicase and a G4 until G4 resolution. The procedures that we described here can easily be extended to the study of other G4s or molecular motors.
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Affiliation(s)
- Jessica Valle-Orero
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; Department of Computer Science, Mathematics and Environmental Sciences, The American University of Paris, Paris, France.
| | - Martin Rieu
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Jean-François Allemand
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France
| | - Dulamkhuu Bujaa
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France
| | - Alexandra Joubert
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France
| | - Phong Lan Thao Tran
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France; Depixus SAS, 3-5 impasse Reille, Paris, France
| | - Vincent Croquette
- Physics Laboratory of the École Normale Supérieure, CNRS, ENS, PSL University, Sorbonne University, Paris-Cité University, Paris, France; Biology Institute of the École Normale Supérieure (IBENS), ENS, CNRS, INSERM, PSL University, Paris, France; ESPCI Paris, PSL University, Paris, France.
| | - Jean-Baptiste Boulé
- Genome Structure and Instability Laboratory, National Museum of Natural History, CNRS, INSERM, Sorbonne University Alliance, Paris, France.
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Zheng YY, Dartawan R, Wu Y, Wu C, Zhang H, Lu J, Hu A, Vangaveti S, Sheng J. Structural effects of inosine substitution in telomeric DNA quadruplex. Front Chem 2024; 12:1330378. [PMID: 38312345 PMCID: PMC10834636 DOI: 10.3389/fchem.2024.1330378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
The telomeric DNA, a distal region of eukaryotic chromosome containing guanine-rich repetitive sequence of (TTAGGG)n, has been shown to adopt higher-order structures, specifically G-quadruplexes (G4s). Previous studies have demonstrated the implication of G4 in tumor inhibition through chromosome maintenance and manipulation of oncogene expression featuring their G-rich promoter regions. Besides higher order structures, several regulatory roles are attributed to DNA epigenetic markers. In this work, we investigated how the structural dynamics of a G-quadruplex, formed by the telomeric sequence, is affected by inosine, a prevalent modified nucleotide. We used the standard (TTAGGG)n telomere repeats with guanosine mutated to inosine at each G position. Sequences (GGG)4, (IGG)4, (GIG)4, (GGI)4, (IGI)4, (IIG)4, (GII)4, and (III)4, bridged by TTA linker, are studied using biophysical experiments and molecular modeling. The effects of metal cations in quadruplex folding were explored in both Na+ and K+ containing buffers using CD and UV-melting studies. Our results show that antiparallel quadruplex topology forms with the native sequence (GGG)4 and the terminal modified DNAs (IGG)4 and (GGI)4 in both Na+ and K+ containing buffers. Specifically, quadruplex hybrid was observed for (GGG)4 in K+ buffer. Among the other modified sequences, (GIG)4, (IGI)4 and (GII)4 show parallel features, while (IIG)4 and (III)4 show no detectable conformation in the presence of either Na+ or K+. Our studies indicate that terminal lesions (IGG)4 and (GGI)4 may induce certain unknown conformations. The folding dynamics become undetectable in the presence of more than one inosine substitution except (IGI)4 in both buffer ions. In addition, both UV melting and CD melting studies implied that in most cases the K+ cation confers more thermodynamic stability compared to Na+. Collectively, our conformational studies revealed the diverse structural polymorphisms of G4 with position dependent G-to-I mutations in different ion conditions.
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Affiliation(s)
- Ya Ying Zheng
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Ricky Dartawan
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Yuhan Wu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Chengze Wu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Hope Zhang
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Jeanne Lu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Ashley Hu
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
| | - Jia Sheng
- Department of Chemistry, Albany, NY, United States
- The RNA Institute, University at Albany, State University of New York, Albany, NY, United States
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