1
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Wang X, Xu N, Zhu L, Yang H, Li C, Tian H, Xu W. Structural Antagonism-Aided Conformational Regulation Enables an Aptamer-Loop G-Quadruplex Modular Sensor of β-Lactoglobulin. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307995. [PMID: 38212277 DOI: 10.1002/smll.202307995] [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: 09/12/2023] [Revised: 12/13/2023] [Indexed: 01/13/2024]
Abstract
A simple, reliable method for identifying β-lactoglobulin (β-LG) in dairy products is needed to protect those with β-LG allergies. A common, practical strategy for target detection is designing simplified nucleic acid nanodevices by integrating functional components. This work presents a label-free modular β-LG aptasensor consisting of an aptamer-loop G-quadruplex (G4), the working conformation of which is regulated by conformational antagonism to ensure respective module functionality and the related signal transduction. The polymorphic conformations of the module-fused sequence are systematically characterized, and the cause is revealed as shifting antagonistic equilibrium. Combined with conformational folding dynamics, this helped regulate functional conformations by fine-tuning the sequences. Furthermore, the principle of specific β-LG detection by parallel G4 topology is examined as binding on the G4 aptamer loop by β-LG to reinforce the G4 topology and fluorescence. Finally, a label-free, assembly-free, succinct, and turn-on fluorescent aptasensor is established, achieving excellent sensitivity across five orders of magnitude, rapidly detecting β-LG within 22-min. This study provides a generalizable approach for the conformational regulation of module-fused G4 sequences and a reference model for creating simplified sensing devices for a variety of targets.
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Affiliation(s)
- Xinxin Wang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
- College of Life Science and Engineering, Handan University, Handan, 056005, China
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Ning Xu
- School of Life Science, Tsinghua University, Beijing, 100091, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - He Yang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Chen Li
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Hongtao Tian
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
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2
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Zhang Z, Mlýnský V, Krepl M, Šponer J, Stadlbauer P. Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. J Chem Inf Model 2024; 64:3896-3911. [PMID: 38630447 PMCID: PMC11094737 DOI: 10.1021/acs.jcim.4c00227] [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: 02/08/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
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Affiliation(s)
- Zhengyue Zhang
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
- CEITEC−Central
European Institute of Technology, Masaryk
University, Kamenice
5, Brno 625 00, Czech Republic
- National
Center for Biomolecular Research,
Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Vojtěch Mlýnský
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Miroslav Krepl
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Petr Stadlbauer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
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3
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Sun JW, Zou J, Zheng Y, Yuan H, Xie YZY, Wang XN, Ou TM. Design, synthesis, and evaluation of novel quindoline derivatives with fork-shaped side chains as RNA G-quadruplex stabilizers for repressing oncogene NRAS translation. Eur J Med Chem 2024; 271:116406. [PMID: 38688064 DOI: 10.1016/j.ejmech.2024.116406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/25/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
NRAS mutation is the second most common oncogenic factor in cutaneous melanoma. Inhibiting NRAS translation by stabilizing the G-quadruplex (G4) structure with small molecules seems to be a potential strategy for cancer therapy due to the NRAS protein's lack of a druggable pocket. To enhance the effects of previously reported G4 stabilizers quindoline derivatives, we designed and synthesized a novel series of quindoline derivatives with fork-shaped side chains by introducing (alkylamino)alkoxy side chains. Panels of experimental results showed that introducing a fork-shaped (alkylamino)alkoxy side chain could enhance the stabilizing abilities of the ligands against NRAS RNA G-quadruplexes and their anti-melanoma activities. One of them, 10b, exhibited good antitumor activity in the NRAS-mutant melanoma xenograft mouse model, showing the therapeutic potential of this kind of compounds.
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Affiliation(s)
- Jia-Wei Sun
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jing Zou
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ying Zheng
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hao Yuan
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuan-Ze-Yu Xie
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiao-Na Wang
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China.
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4
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Lai R, Zeng X, Xu Q, Xu Y, Li X, Ru Y, Wang Y, Wang D, Zhou X, Shao Y. Ratiometric G-quadruplex/hemin DNAzymes with low-dosage associative substrates. Anal Chim Acta 2024; 1295:342320. [PMID: 38355221 DOI: 10.1016/j.aca.2024.342320] [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: 01/02/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND G-quadruplex (G4)/hemin DNAzymes with conversion of substrates into colorimetric readouts are well recognized as convenient biocatalysis tools in sensor development. However, the previously developed colorimetric G4/hemin DNAzymes are diffusive substrate-based DNAzymes (DSBDs). The current colorimetric DSBDs have several drawbacks including high dosage (∼mM) of diffusive substrates (DSs), colorimetric product toxicity, and single colorimetric readout without tolerance to fluctuation of experimental factors and background. In addition, the usage of high-dosage DSs can smear the G4 foldings and their discard is more harmful to environment. Therefore, exploring alternative DNAzymes with potential to overcome these drawbacks of DSBDs is urgently needed. RESULTS We herein developed associative substrate-based DNAzymes (ASBDs). Cyanine dyes were selected as associative substrates (ASs) due to their binding competency with G4/hemin DNAzymes. With respect to DSBDs, ASBDs needed only low dosage (∼10 μM) of ASs to be able to cause a rapid and visible substrate conversion. In addition, since cyanine dyes are NIR dyes with high extinction coefficients and their conversion products have absorption bands at shorter wavelength. Therefore, a colorimetric ratio response can be developed to follow activities of G4/hemin DNAzymes with competency to tolerate fluctuation of experimental factors and background. In particular, herein developed ASBDs can endure somewhat concentration fluctuation of H2O2. ASBDs are able to cowork with other enzymes (for example, glucose oxidase) to realize cascade sensing. SIGNIFICANCE The developed ASBDs can operate at low dosage of substrates with a colorimetric ratio response and can overcome the drawbacks met in DSBDs. We expect that, by designing ASs with fruitful color panel in the future, our work will inspire more interesting in developing environment-benign and low-carbon G4/hemin DNAzymes and desired colorful high-performance sensors.
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Affiliation(s)
- Rong Lai
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xingli Zeng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Qiuda Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Ying Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xueni Li
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yulu Ru
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yilin Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR 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, PR China.
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5
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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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6
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Yan X, Yang P, Qiu D, Chen D, Pan J, Zhang X, Ju H, Zhou J. Ligation-Based High-Performance Mimetic Enzyme Sensing Platform for Nucleic Acid Detection. Anal Chem 2024; 96:388-393. [PMID: 38153911 DOI: 10.1021/acs.analchem.3c04417] [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: 12/30/2023]
Abstract
G-quadruplex (G4)/hemin DNAzyme is a promising candidate to substitute horseradish peroxidase in biosensing systems, especially for the detection of nucleic acids. However, the relatively suboptimal catalytic capacity limits its potential applications. This makes it imperative to develop an ideal signal for the construction of highly sensitive biosensing platforms. Herein, we integrated a novel chimeric peptide-DNAzyme (CPDzyme) with the ligase chain reaction (LCR) for the cost-efficient and highly sensitive detection of nucleic acids. By employing microRNA (miRNA) and single-nucleotide polymorphism detection as the model, we designed a G4-forming sequence on the LCR probe with a terminally labeled amino group. Subsequently, asymmetric hemin with carboxylic arms allowed assembly with the LCR products and peptide to form CPDzyme, followed by the magnetic separation of the extraneous components and chemiluminescence detection. Compared with the conventional G4/hemin signaling-based method, the LCR-CPDzyme system demonstrated 3 orders of magnitude improved sensitivity, with accurate quantification of as low as 25 aM miRNA and differentiation of 0.1% of mutant DNA from the pool containing a large amount of wild-type DNA. The proposed LCR-CPDzyme strategy is a potentially powerful method for in vitro diagnostics and serves as a reference for the development of other ligation- or hybridization-based nucleic acid amplification assays.
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Affiliation(s)
- Xinrong Yan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P.R. China
| | - Peiru Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P.R. China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P.R. China
| | - Desheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P.R. China
| | - Jianbin Pan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P.R. China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P.R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P.R. China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P.R. China
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7
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Luo Y, Granzhan A, Marquevielle J, Cucchiarini A, Lacroix L, Amrane S, Verga D, Mergny JL. Guidelines for G-quadruplexes: I. In vitro characterization. Biochimie 2023; 214:5-23. [PMID: 36596406 DOI: 10.1016/j.biochi.2022.12.019] [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: 10/29/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Besides the well-known DNA double-helix, non-canonical nucleic acid structures regulate crucial biological activities. Among these oddities, guanine-rich DNA sequences can form unusual four-stranded secondary structures called G-quadruplexes (G4s). G4-prone sequences have been found in the genomes of most species, and G4s play important roles in essential processes such as transcription, replication, genome integrity and epigenetic regulation. Here, we present a short overview of G-quadruplexes followed by a detailed description of the biophysical and biochemical methods used to characterize G4s in vitro. The principles, experimental details and possible shortcomings of each method are discussed to provide a comprehensive view of the techniques used to study these structures. We aim to provide a set of guidelines for standardizing research on G-quadruplexes; these guidelines are not meant to be a dogmatic set of rules, but should rather provide useful information on the methods currently used to study these fascinating motifs.
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Affiliation(s)
- Yu Luo
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
| | - Julien Marquevielle
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Anne Cucchiarini
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Laurent Lacroix
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Samir Amrane
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France.
| | - Jean-Louis Mergny
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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8
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D'Anna L, Miclot T, Bignon E, Perricone U, Barone G, Monari A, Terenzi A. Resolving a guanine-quadruplex structure in the SARS-CoV-2 genome through circular dichroism and multiscale molecular modeling. Chem Sci 2023; 14:11332-11339. [PMID: 37886086 PMCID: PMC10599604 DOI: 10.1039/d3sc04004f] [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: 08/01/2023] [Accepted: 09/08/2023] [Indexed: 10/28/2023] Open
Abstract
The genome of SARS-CoV-2 coronavirus is made up of a single-stranded RNA fragment that can assume a specific secondary structure, whose stability can influence the virus's ability to reproduce. Recent studies have identified putative guanine quadruplex sequences in SARS-CoV-2 genome fragments that are involved in coding for both structural and non-structural proteins. In this contribution, we focus on a specific G-rich sequence referred to as RG-2, which codes for the non-structural protein 10 (Nsp10) and assumes a guanine-quadruplex (G4) arrangement. We provide the secondary structure of RG-2 G4 at atomistic resolution by molecular modeling and simulation, validated by the superposition of experimental and calculated electronic circular dichroism spectra. Through both experimental and simulation approaches, we have demonstrated that pyridostatin (PDS), a widely recognized G4 binder, can bind to and stabilize RG-2 G4 more strongly than RG-1, another G4 forming sequence that was previously proposed as a potential target for antiviral drug candidates. Overall, this study highlights RG-2 as a valuable target to inhibit the translation and replication of SARS-CoV-2, paving the way towards original therapeutic approaches against emerging RNA viruses.
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Affiliation(s)
- Luisa D'Anna
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo Viale delle Scienze, Ed. 17 90128 Palermo Italy
| | - Tom Miclot
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo Viale delle Scienze, Ed. 17 90128 Palermo Italy
- Université de Lorraine and CNRS UMR 7019 LPCT F-54000 Nancy France
| | | | - Ugo Perricone
- Fondazione Ri.MED Via Filippo Marini 14 90128 Palermo Italy
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo Viale delle Scienze, Ed. 17 90128 Palermo Italy
| | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS F-75006 Paris France
| | - Alessio Terenzi
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo Viale delle Scienze, Ed. 17 90128 Palermo Italy
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9
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Vianney YM, Schröder N, Jana J, Chojetzki G, Weisz K. Showcasing Different G-Quadruplex Folds of a G-Rich Sequence: Between Rule-Based Prediction and Butterfly Effect. J Am Chem Soc 2023; 145:22194-22205. [PMID: 37751488 DOI: 10.1021/jacs.3c08336] [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: 09/28/2023]
Abstract
In better understanding the interactions of G-quadruplexes in a cellular or noncellular environment, a reliable sequence-based prediction of their three-dimensional fold would be extremely useful, yet is often limited by their remarkable structural diversity. A G-rich sequence related to a promoter sequence of the PDGFR-β nuclease hypersensitivity element (NHE) comprises a G3-G3-G2-G4-G3 pattern of five G-runs with two to four G residues. Although the predominant formation of three-layered canonical G-quadruplexes with uninterrupted G-columns can be expected, minimal base substitutions in a non-G-tract domain were shown to guide folding into either a basket-type antiparallel quadruplex, a parallel-stranded quadruplex with an interrupted G-column, a quadruplex with a V-shaped loop, or a (3+1) hybrid quadruplex. A 3D NMR structure for each of the different folds was determined. Supported by thermodynamic profiling on additional sequence variants, formed topologies were rationalized by the identification and assessment of specific critical interactions of loop and overhang residues, giving valuable insights into their contribution to favor a particular conformer. The variability of such tertiary interactions, together with only small differences in quadruplex free energies, emphasizes current limits for a reliable sequence-dependent prediction of favored topologies from sequences with multiple irregularly positioned G-tracts.
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Affiliation(s)
- Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Nina Schröder
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Jagannath Jana
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Gregor Chojetzki
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, D-17489 Greifswald, Germany
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10
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Monsen RC. Higher-order G-quadruplexes in promoters are untapped drug targets. Front Chem 2023; 11:1211512. [PMID: 37351517 PMCID: PMC10282141 DOI: 10.3389/fchem.2023.1211512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid secondary structures that form within guanine-rich regions of chromatin. G4 motifs are abundant in the genome, with a sizable proportion (∼40%) existing within gene promoter regions. G4s are proven epigenetic features that decorate the promoter landscape as binding centers for transcription factors. Stabilizing or disrupting promoter G4s can directly influence adjacent gene transcription, making G4s attractive as indirect drug targets for hard-to-target proteins, particularly in cancer. However, no G4 ligands have progressed through clinical trials, mostly owing to off targeting effects. A major hurdle in G4 drug discovery is the lack of distinctiveness of the small monomeric G4 structures currently used as receptors. This mini review describes and contrasts monomeric and higher-order G-quadruplex structure and function and provides a rationale for switching focus to the higher-order forms as selective molecular targets. The human telomerase reverse transcriptase (hTERT) core promoter G-quadruplex is then used as a case study that highlights the potential for higher-order G4s as selective indirect inhibitors of hard-to-target proteins in cancer.
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11
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Zhang L, Wu H, Chen Y, Zhang S, Song M, Liu C, Li J, Cheng W, Ding S. Target response controlled enzyme activity switch for multimodal biosensing detection. J Nanobiotechnology 2023; 21:122. [PMID: 37031177 PMCID: PMC10082497 DOI: 10.1186/s12951-023-01860-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/16/2023] [Indexed: 04/10/2023] Open
Abstract
How to achieve delicate regulation of enzyme activity and empower it with more roles is the peak in the field of enzyme catalysis research. Traditional proteases or novel nano-enzymes are unable to achieve stimulus-responsive activity modulation due to their own structural limitations. Here, we propose a novel Controllable Enzyme Activity Switch, CEAS, based on hemin aggregation regulation, to deeply explore its regulatory mechanism and develop multimodal biosensing applications. The core of CEAS relies on the dimerizable inactivation of catalytically active center hemin and utilizes a DNA template to orderly guide the G4-Hemin DNAzyme to tightly bind to DNA-Hemin, thereby shutting down the catalytic ability. By customizing the design of the guide template, different target stimulus responses lead to hemin dimerization dissociation and restore the synergistic catalysis of G4-Hemin and DNA-Hemin, thus achieving a target-regulated enzymatic activity switch. Moreover, the programmability of CEAS allowed it easy to couple with a variety of DNA recognition and amplification techniques, thus developing a series of visual protein detection systems and highly sensitive fluorescent detection systems with excellent bioanalytical performance. Therefore, the construction of CEAS is expected to break the limitation of conventional enzymes that cannot be targetable regulated, thus enabling customizable enzymatic reaction systems and providing a new paradigm for controllable enzyme activities.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Yirong Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Songzhi Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Mingxuan Song
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Changjin Liu
- Department of Laboratory Medicine, The Fifth People's Hospital of Chongqing, Chongqing, 400062, China
| | - Jia Li
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People's Republic of China.
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
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12
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Bai D, Shan SW, Zhang X, Li Y, Xie J, Wu WQ. Comprehensive insights into the structures and dynamics of plant telomeric G-quadruplexes. Int J Biol Macromol 2023; 231:123281. [PMID: 36657543 DOI: 10.1016/j.ijbiomac.2023.123281] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/30/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Telomeres, which are located at the ends of eukaryotic chromosomes, are crucial for genomic maintenance. Most telomeric DNA is composed of tandemly repeated guanine (G)-rich sequences, which form G-quadruplexes (G4s). The structures and dynamics of telomeric G4s are essential for telomere functioning and helpful for G4-based biosensing. However, they are far from being understood, especially for plants. In this contribution, the folding, environment-induced G4 dynamics, and protein-catalyzed unfolding of plant telomeric G4s were comprehensively studied. It was found that diverse plant telomeric sequences from land plants to green algae could fold into G4 structures. In addition, 5'-proximal ssDNA but not 3'-proximal ssDNA drove conversion of anti-parallel G4 structures to parallel structures, and both 5' and 3' ssDNA decreased the stability of G4s in dilute solution. Furthermore, molecular crowding promoted the formation of parallel structures for three-layer but not for two-layer G4s, and increased the stability of all selected G4s. Finally, AtRecQ2 helicase resolved the stable parallel structure of typical plant telomeric G4 in crowded solution, but ssDNA binding protein AtRPA did not. Furthermore, AtRecQ2 unwound the structure more efficiently in the presence of AtRPA. The results may expand our understanding on the structures and dynamics of plant telomeric G4s.
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Affiliation(s)
- Di Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Song-Wang Shan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yan Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jie Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Wen-Qiang Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Henan University, Kaifeng 475004, China.
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13
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Kristoffersen E, Coletta A, Lund L, Schiøtt B, Birkedal V. Inhibited complete folding of consecutive human telomeric G-quadruplexes. Nucleic Acids Res 2023; 51:1571-1582. [PMID: 36715345 PMCID: PMC9976873 DOI: 10.1093/nar/gkad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 12/24/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Noncanonical DNA structures, termed G-quadruplexes, are present in human genomic DNA and are important elements in many DNA metabolic processes. Multiple sites in the human genome have G-rich DNA stretches able to support formation of several consecutive G-quadruplexes. One of those sites is the telomeric overhang region that has multiple repeats of TTAGGG and is tightly associated with both cancer and aging. We investigated the folding of consecutive G-quadruplexes in both potassium- and sodium-containing solutions using single-molecule FRET spectroscopy, circular dichroism, thermal melting and molecular dynamics simulations. Our observations show coexistence of partially and fully folded DNA, the latter consisting of consecutive G-quadruplexes. Following the folding process over hours in sodium-containing buffers revealed fast G-quadruplex folding but slow establishment of thermodynamic equilibrium. We find that full consecutive G-quadruplex formation is inhibited by the many DNA structures randomly nucleating on the DNA, some of which are off-path conformations that need to unfold to allow full folding. Our study allows describing consecutive G-quadruplex formation in both nonequilibrium and equilibrium conditions by a unified picture, where, due to the many possible DNA conformations, full folding with consecutive G-quadruplexes as beads on a string is not necessarily achieved.
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Affiliation(s)
- Emil Laust Kristoffersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Andrea Coletta
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Line Mørkholt Lund
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Birgit Schiøtt
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
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14
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Kotkowiak W, Roxo C, Pasternak A. Physicochemical and antiproliferative characteristics of RNA and DNA sequence-related G-quadruplexes. ACS Med Chem Lett 2023; 14:35-40. [PMID: 36655120 PMCID: PMC9841586 DOI: 10.1021/acsmedchemlett.2c00361] [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: 08/04/2022] [Accepted: 10/03/2022] [Indexed: 01/21/2023] Open
Abstract
In this article the physicochemical and biological properties of sequence-related G-quadruplex forming oligonucleotides in RNA and DNA series are analyzed and compared. The intermolecular G-quadruplexes vary in loop length, number of G-tetrads and homogeneity of the core. Our studies show that even slight variations in sequence initiate certain changes of G-quadruplex properties. DNA G-quadruplexes are less thermally stable than their RNA counterparts, more topologically diversified and are better candidates as inhibitors of cancer cells proliferation. The most efficient antiproliferative activity within the studied group of molecules was observed for two DNA G-quadruplexes with unperturbed core and lower content of thymidine residues within the loops leading to reduction of cells viability up to 65% and 33% for HeLa and MCF-7 cell lines, respectively.
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Affiliation(s)
- Weronika Kotkowiak
- Department of Nucleic Acids
Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Carolina Roxo
- Department of Nucleic Acids
Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Pasternak
- Department of Nucleic Acids
Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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15
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Structural insight into the bulge-containing KRAS oncogene promoter G-quadruplex bound to berberine and coptisine. Nat Commun 2022; 13:6016. [PMID: 36224201 PMCID: PMC9556435 DOI: 10.1038/s41467-022-33761-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/30/2022] [Indexed: 12/08/2022] Open
Abstract
KRAS is one of the most highly mutated oncoproteins, which is overexpressed in various human cancers and implicated in poor survival. The G-quadruplex formed in KRAS oncogene promoter (KRAS-G4) is a transcriptional modulator and amenable to small molecule targeting. However, no available KRAS-G4-ligand complex structure has yet been determined, which seriously hinders the structure-based rational design of KRAS-G4 targeting drugs. In this study, we report the NMR solution structures of a bulge-containing KRAS-G4 bound to berberine and coptisine, respectively. The determined complex structure shows a 2:1 binding stoichiometry with each compound recruiting the adjacent flacking adenine residue to form a "quasi-triad plane" that stacks over the two external G-tetrads. The binding involves both π-stacking and electrostatic interactions. Moreover, berberine and coptisine significantly lowered the KRAS mRNA levels in cancer cells. Our study thus provides molecular details of ligand interactions with KRAS-G4 and is beneficial for the design of specific KRAS-G4-interactive drugs.
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16
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Xu Q, Yang M, Chang Y, Peng S, Wang D, Zhou X, Shao Y. Switching G-quadruplex to parallel duplex by molecular rotor clustering. Nucleic Acids Res 2022; 50:10249-10263. [PMID: 36130267 PMCID: PMC9561263 DOI: 10.1093/nar/gkac811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/31/2022] [Accepted: 09/10/2022] [Indexed: 11/12/2022] Open
Abstract
Switching of G-quadruplex (G4) structures between variant types of folding has been proved to be a versatile tool for regulation of genomic expression and development of nucleic acid-based constructs. Various specific ligands have been developed to target G4s in K+ solution with therapeutic prospects. Although G4 structures have been reported to be converted by sequence modification or a unimolecular ligand binding event in K+-deficient conditions, switching G4s towards non-G4 folding continues to be a great challenge due to the stability of G4 in physiological K+ conditions. Herein, we first observed the G4 switching towards parallel-stranded duplex (psDNA) by multimolecular ligand binding (namely ligand clustering) to overcome the switching barrier in K+. Purine-rich sequences (e.g. those from the KRAS promoter region) can be converted from G4 structures to dimeric psDNAs using molecular rotors (e.g. thioflavin T and thiazole orange) as initiators. The formed psDNAs provided multiple binding sites for molecular rotor clustering to favor subsequent structures with stability higher than the corresponding G4 folding. Our finding provides a clue to designing ligands with the competency of molecular rotor clustering to implement an efficient G4 switching.
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Affiliation(s)
- Qiuda Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Mujing Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Yun Chang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Shuzhen Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
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17
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Dobrovolná M, Bohálová N, Peška V, Wang J, Luo Y, Bartas M, Volná A, Mergny JL, Brázda V. The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation. Int J Mol Sci 2022; 23:8482. [PMID: 35955617 PMCID: PMC9369095 DOI: 10.3390/ijms23158482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022] Open
Abstract
G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional relevance in bacteria and animals, including humans, their importance has been recently demonstrated in evolutionarily distinct plant species. In this study, we analyzed the genome of Pisum sativum (garden pea, or the so-called green pea), a unique member of the Fabaceae family. Our results showed that this genome contained putative G4 sequences (PQSs). Interestingly, these PQSs were located nonrandomly in the nuclear genome. We also found PQSs in mitochondrial (mt) and chloroplast (cp) DNA, and we experimentally confirmed G4 formation for sequences found in these two organelles. The frequency of PQSs for nuclear DNA was 0.42 PQSs per thousand base pairs (kbp), in the same range as for cpDNA (0.53/kbp), but significantly lower than what was found for mitochondrial DNA (1.58/kbp). In the nuclear genome, PQSs were mainly associated with regulatory regions, including 5'UTRs, and upstream of the rRNA region. In contrast to genomic DNA, PQSs were located around RNA genes in cpDNA and mtDNA. Interestingly, PQSs were also associated with specific transposable elements such as TIR and LTR and around them, pointing to their role in their spreading in nuclear DNA. The nonrandom localization of PQSs uncovered their evolutionary and functional significance in the Pisum sativum genome.
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Affiliation(s)
- Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Vratislav Peška
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
| | - Jiawei Wang
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Yu Luo
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, CEDEX, 91405 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
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18
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Jana J, Vianney YM, Schröder N, Weisz K. Guiding the folding of G-quadruplexes through loop residue interactions. Nucleic Acids Res 2022; 50:7161-7175. [PMID: 35758626 PMCID: PMC9262619 DOI: 10.1093/nar/gkac549] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/25/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
A G-rich sequence was designed to allow folding into either a stable parallel or hybrid-type topology. With the parent sequence featuring coexisting species, various related sequences with single and double mutations and with a shortened central propeller loop affected the topological equilibrium. Two simple modifications, likewise introduced separately to all sequences, were employed to lock folds into one of the topologies without noticeable structural alterations. The unique combination of sequence mutations, high-resolution NMR structural information, and the thermodynamic stability for both topological competitors identified critical loop residue interactions. In contrast to first loop residues, which are mostly disordered and exposed to solvent in both propeller and lateral loops bridging a narrow groove, the last loop residue in a lateral three-nucleotide loop is engaged in stabilizing stacking interactions. The propensity of single-nucleotide loops to favor all-parallel topologies by enforcing a propeller-like conformation of an additional longer loop is shown to result from their preference in linking two outer tetrads of the same tetrad polarity. Taken together, the present studies contribute to a better structural and thermodynamic understanding of delicate loop interactions in genomic and artificially designed quadruplexes, e.g. when employed as therapeutics or in other biotechnological applications.
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Affiliation(s)
- Jagannath Jana
- Institute of Biochemistry, Universität Greifswald, D-17489 Greifswald, Germany
| | | | - Nina Schröder
- Institute of Biochemistry, Universität Greifswald, D-17489 Greifswald, Germany
| | - Klaus Weisz
- To whom correspondence should be addressed. Tel: +49 3834 420 4426; Fax: +49 3834 420 4427;
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19
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Xiong K, Ouyang C, Liu J, Karges J, Lin X, Chen X, Chen Y, Wan J, Ji L, Chao H. Chiral RuII‐PtII Complexes Inducing Telomere Dysfunction against Cisplatin‐Resistant Cancer Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kai Xiong
- Sun Yat-Sen University School of Chemistry CHINA
| | - Cheng Ouyang
- Sun Yat-Sen University School of Chemistry CHINA
| | - Jiaqi Liu
- Central China Normal University College of Chemistry CHINA
| | | | - Xinlin Lin
- Sun Yat-Sen University School of Chemistry CHINA
| | - Xiang Chen
- Sun Yat-Sen University School of Chemistry CHINA
| | - Yu Chen
- Sun Yat-Sen University School of Chemistry CHINA
| | - Jian Wan
- Central China Normal University College of Chemistry CHINA
| | - Liangnian Ji
- Sun Yat-Sen University School of Chemistry CHINA
| | - Hui Chao
- Sun Yat-Sen University Chemistry Xingang Xilu 135# 510275 Guangzhou CHINA
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20
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Xiong K, Ouyang C, Liu J, Karges J, Lin X, Chen X, Chen Y, Wan J, Ji L, Chao H. Chiral Ru II -Pt II Complexes Inducing Telomere Dysfunction against Cisplatin-Resistant Cancer Cells. Angew Chem Int Ed Engl 2022; 61:e202204866. [PMID: 35736788 DOI: 10.1002/anie.202204866] [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: 04/02/2022] [Indexed: 11/06/2022]
Abstract
The application of G-quadruplex stabilizers presents a promising anticancer strategy. However, the molecular crowding conditions within cells diminish the potency of current G-quadruplex stabilizers. Herein, chiral RuII -PtII dinuclear complexes were developed as highly potent G-quadruplex stabilizers even under challenging molecular crowding conditions. The compounds were encapsulated with biotin-functionalized DNA cages to enhance sub-cellular localization and provide cancer selectivity. The nanoparticles were able to efficiently inhibit the endogenous activities of telomerase in cisplatin-resistant cancer cells and cause cell death by apoptosis. The nanomaterials demonstrated high antitumor activity towards cisplatin-resistant tumor cells as well as tumor-bearing mice. To the best of our knowledge, this study presents the first example of a RuII -PtII dinuclear complex as a G-quadruplex stabilizer with an anti-cancer effect towards drug-resistant tumors inside an animal model.
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Affiliation(s)
- Kai Xiong
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Cheng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Jiaqi Liu
- College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Johannes Karges
- Department of Chemistry and, Biochemistry University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Xinlin Lin
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Xiang Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Yu Chen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Jian Wan
- College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Liangnian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China
| | - Hui Chao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510006, P. R. China.,MOE Key Laboratory of Theoretical Organic Chemistry and Functional Molecule, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 400201, P. R. China
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21
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Qin S, Chen X, Xu Z, Li T, Zhao S, Hu R, Zhu J, Li Y, Yang Y, Liu M. Telomere G-triplex lights up Thioflavin T for RNA detection: new wine in an old bottle. Anal Bioanal Chem 2022; 414:6149-6156. [PMID: 35725832 PMCID: PMC9208972 DOI: 10.1007/s00216-022-04180-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 02/07/2023]
Abstract
Few reports are found working on the features and functions of the human telomere G-triplex (ht-G3) though the telomere G-quadruplex has been intensely studied and widely implemented to develop various biosensors. We herein report that ht-G3 lights up Thioflavin T (ThT) and establish a sensitive biosensing platform for RNA detection by introducing a target recycling strategy. An optimal condition was selected out for ht-G3 to promote ThT to generate a strong fluorescence. Accordingly, an ht-G3-based molecular beacon was successfully designed against the corresponding RNA sequence of the SARS-CoV-2 N-gene. The sensitivity for the non-amplified RNA target achieves 0.01 nM, improved 100 times over the conventional ThT–based method. We believe this ht-G3/ThT–based label-free strategy could be widely applied for RNA detection.
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Affiliation(s)
- Shanshan Qin
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xuliang Chen
- Department of Cardiovascular Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zhichen Xu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Tao Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Shuhong Zhao
- University of Chinese Academy of Sciences, Beijing, 10049, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China.
- University of Chinese Academy of Sciences, Beijing, 10049, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China.
- University of Chinese Academy of Sciences, Beijing, 10049, China.
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
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22
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Monsen RC, DeLeeuw LW, Dean W, Gray R, Chakravarthy S, Hopkins J, Chaires J, Trent J. Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc, k-Ras and c-Kit promoter sequences. Nucleic Acids Res 2022; 50:4127-4147. [PMID: 35325198 PMCID: PMC9023277 DOI: 10.1093/nar/gkac182] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022] Open
Abstract
We report on higher-order G-quadruplex structures adopted by long promoter sequences obtained by an iterative integrated structural biology approach. Our approach uses quantitative biophysical tools (analytical ultracentrifugation, small-angle X-ray scattering, and circular dichroism spectroscopy) combined with modeling and molecular dynamics simulations, to derive self-consistent structural models. The formal resolution of our approach is 18 angstroms, but in some cases structural features of only a few nucleotides can be discerned. We report here five structures of long (34-70 nt) wild-type sequences selected from three cancer-related promoters: c-Myc, c-Kit and k-Ras. Each sequence studied has a unique structure. Three sequences form structures with two contiguous, stacked, G-quadruplex units. One longer sequence from c-Myc forms a structure with three contiguous stacked quadruplexes. A longer c-Kit sequence forms a quadruplex-hairpin structure. Each structure exhibits interfacial regions between stacked quadruplexes or novel loop geometries that are possible druggable targets. We also report methodological advances in our integrated structural biology approach, which now includes quantitative CD for counting stacked G-tetrads, DNaseI cleavage for hairpin detection and SAXS model refinement. Our results suggest that higher-order quadruplex assemblies may be a common feature within the genome, rather than simple single quadruplex structures.
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Affiliation(s)
- Robert C Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Lynn W DeLeeuw
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - William L Dean
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Robert D Gray
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jonathan B Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
| | - John O Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
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23
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Meier-Stephenson V. G4-quadruplex-binding proteins: review and insights into selectivity. Biophys Rev 2022; 14:635-654. [PMID: 35791380 PMCID: PMC9250568 DOI: 10.1007/s12551-022-00952-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found largely in promoter regions, telomeres, and other regions of high regulation. Growing evidence links their presence to functionality in various cellular processes, where cellular proteins interact with them, either stabilizing and/or anchoring upon them, or unwinding them to allow a process to proceed. Interest in understanding and manipulating the plethora of processes regulated by these G4Qs has spawned a new area of small-molecule binder development, with attempts to mimic and block the associated G4-binding protein (G4BP). Despite the growing interest and focus on these G4Qs, there is limited data (in particular, high-resolution structural information), on the nature of these G4Q-G4BP interactions and what makes a G4BP selective to certain G4Qs, if in fact they are at all. This review summarizes the current literature on G4BPs with regards to their interactions with G4Qs, providing groupings for binding mode, drawing conclusions around commonalities and highlighting information on specific interactions where available.
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Affiliation(s)
- Vanessa Meier-Stephenson
- Department of Medicine, Division of Infectious Diseases, University of Alberta, Edmonton, AB Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB Canada
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24
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Ngo KH, Liew CW, Lattmann S, Winnerdy FR, Phan AT. Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A•G•G•G•G pentad in an interlocked G-quadruplex. Biochem Biophys Res Commun 2022; 613:153-158. [DOI: 10.1016/j.bbrc.2022.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 11/27/2022]
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25
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to have devastating consequences worldwide. Recently, great efforts have been made to identify SARS-CoV-2 host factors, but the regulatory mechanisms of these host molecules, as well as the virus per se, remain elusive. Here we report a role of RNA G-quadruplex (RG4) in SARS-CoV-2 infection. Combining bioinformatics, biochemical and biophysical assays, we demonstrate the presence of RG4s in both SARS-CoV-2 genome and host factors. The biological and pathological importance of these RG4s is then exemplified by a canonical 3-quartet RG4 within Tmprss2, which can inhibit Tmprss2 translation and prevent SARS-CoV-2 entry. Intriguingly, G-quadruplex (G4)-specific stabilizers attenuate SARS-CoV-2 infection in pseudovirus cell systems and mouse models. Consistently, the protein level of TMPRSS2 is increased in lungs of COVID-19 patients. Our findings reveal a previously unknown mechanism underlying SARS-CoV-2 infection and suggest RG4 as a potential target for COVID-19 prevention and treatment. Understanding the mechanisms of SARS-CoV-2 infection is important to control the pandemic. Here the authors show the biological and pathological role of RNA G-quadruplex structure in both SARS-CoV-2 genome and host factors, particularly TMPRSS2.
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26
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Li J, Wu H, Yan Y, Yuan T, Shu Y, Gao X, Zhang L, Li S, Ding S, Cheng W. Zippered G-quadruplex/hemin DNAzyme: exceptional catalyst for universal bioanalytical applications. Nucleic Acids Res 2021; 49:13031-13044. [PMID: 34878146 PMCID: PMC8682752 DOI: 10.1093/nar/gkab1178] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/09/2021] [Accepted: 11/17/2021] [Indexed: 12/04/2022] Open
Abstract
G-quadruplex (G4)/hemin DNAzyme is promising horseradish peroxidase (HRP)-mimic candidate in the biological field. However, its relatively unsatisfactory catalytic capacity limits the potential applications. Inspired by nature protease, we conducted a proximity-enhanced cofactor assembly strategy (PECA) to form an exceptional HRP mimic, namely zippered G4/hemin DNAzyme (Z-G4/H). The hybridization of short oligonucleotides induced proximity assembly of the DNA-grafted hemin (DGH) with the complementary G4 sequences (cG4s), mimicking the tight configuration of protease cofactor and apoenzyme. The detailed investigations of catalytic efficiency and mechanism verified the higher activity, more rapid catalytic rate and high environmental tolerance of the Z-G4/H than the classical G4/hemin DNAzymes (C-G4/H). Furthermore, a proximity recognition transducer has been developed based on the PECA for sensitive detection of gene rearrangement and imaging human epidermal growth factor receptor 2 protein (HER2) dimerization on cell surfaces. Our studies demonstrate the high efficiency of Z-G4/H and its universal application potential in clinical diagnostics and biomolecule interaction research. It also may offer significant opportunities and inspiration for the engineering of the protease-free mimic enzyme.
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Affiliation(s)
- Jia Li
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China.,Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Taixian Yuan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yue Shu
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xin Gao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Lu Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Siqiao Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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