1
|
Chen HW, Cao HW, Li JZ, Chen YS, Li LY, Li ZK, Wang HJ, Wang MQ. D-π-A type fluorescent dyes: Effect of π-bridge units on optical and G4 DNA binding properties. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 323:124901. [PMID: 39094268 DOI: 10.1016/j.saa.2024.124901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/15/2024] [Accepted: 07/28/2024] [Indexed: 08/04/2024]
Abstract
Fluorescent solvatochromic dyes that are sensitive to the nature of local microenvironmental, have been explored as probes in applications ranging from the imaging biomolecules to understanding of basic biomolecule functions. To expand the scope of fluorescent solvatochromic dyes for G-quadruplex (G4) DNA structures, and to illustrate the relationship between structure and properties, three newly designed D-π-A type fluorescent dyes were synthesized by introducing diarylimidazole to carbazole skeleton linked to benzene, furan or thiophene π-conjugated bridge and connected with pyridinium acceptor, respectively. Their structural characteristics, optical properties, and G4 DNA binding properties were discussed in detail. In general, the incorporation of furan and thiophene as π-conjugated bridges leads the better conjugation and molecular coplanarity with more efficient intramolecular charge transfer (ICT) effect compared with benzene bridge. The fluorescence intensities induced upon interaction were found that TP-6 with thiophene π-conjugated bridge had the strongest response toward G4 DNAs. In addition, the application of this dye as a fluorescent agent for living cell imaging was also demonstrated.
Collapse
Affiliation(s)
- Hai-Wen Chen
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
| | - Hao-Wen Cao
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
| | - Jing-Zhi Li
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
| | - Yan-Song Chen
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
| | - Lu-Yu Li
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
| | - Ze-Kai Li
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
| | - Hai-Jiao Wang
- The Key Laboratory of Biomedical Material, School of Life Science and Technology, Xinxiang Medical University, Xinxiang 453003, PR China.
| | - Ming-Qi Wang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China.
| |
Collapse
|
2
|
Libera V, Fasolato C, Ripanti F, Catalini S, Bertini L, Petrillo C, Schirò G, D'Amico F, Rossi B, Paciaroni A, Comez L. Molecular mechanisms behind BRACO19 and human telomeric G-quadruplex interaction. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124684. [PMID: 38981290 DOI: 10.1016/j.saa.2024.124684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024]
Abstract
Human telomeres (HTs) can form DNA G-quadruplex (G4), an attractive target for anticancer and antiviral drugs. HT-G4s exhibit inherent structural polymorphism, posing challenges for understanding their specific recognition by ligands. Here, we aim to explore the impact of different topologies within a small segment of the HT (Tel22) on its interaction with BRACO19, a rationally designed G4 ligand with high quadruplex affinity, already employed in in-vivo treatments. Our multi-technique approach is based on the combined use of a set of contactless spectroscopic tools. Circular dichroism and UV resonance Raman spectroscopy probe ligand-induced conformational changes in the G4 sequence, while UV-visible absorption, coupled with steady-state fluorescence spectroscopy, provides further insights into the electronic features of the complex, exploiting the photoresponsive properties of BRACO19. Overall, we find that modifying the topology of the unbound Tel22 through cations (K+ or Na+), serves as a critical determinant for ligand interactions and binding modes, thus influencing the HT-G4's assembly capabilities. Furthermore, we show how fluorescence serves as a valuable probe for recognizing cation-driven multimeric structures, which may be present in living organisms, giving rise to pathological forms.
Collapse
Affiliation(s)
- Valeria Libera
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy.
| | - Claudia Fasolato
- Institute for Complex System, National Research Council (ISC-CNR), Piazzale Aldo Moro, 5, 00185, Roma, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Sara Catalini
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy; European Laboratory for Non-Linear Spectroscopy (LENS), via Nello Carrara 1, 50019, Sesto Fiorentino (FI), Italy; National Research Council-National Institute of Optics (CNR-INO), Largo Fermi 6, 50125, Florence, Italy
| | - Luca Bertini
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Francesco D'Amico
- Elettra - Sincrotrone Trieste S.C.p.A, s.s. 14 km 163, 500 in Area Science Park, 34149, Trieste, Italy
| | - Barbara Rossi
- Elettra - Sincrotrone Trieste S.C.p.A, s.s. 14 km 163, 500 in Area Science Park, 34149, Trieste, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Lucia Comez
- CNR-IOM - Istituto Officina dei Materiali, Via Alessandro Pascoli, 06123, Perugia, Italy.
| |
Collapse
|
3
|
Nocentini A, Di Porzio A, Bonardi A, Bazzicalupi C, Petreni A, Biver T, Bua S, Marzano S, Amato J, Pagano B, Iaccarino N, De Tito S, Amente S, Supuran CT, Randazzo A, Gratteri P. Development of a multi-targeted chemotherapeutic approach based on G-quadruplex stabilisation and carbonic anhydrase inhibition. J Enzyme Inhib Med Chem 2024; 39:2366236. [PMID: 38905127 PMCID: PMC11195807 DOI: 10.1080/14756366.2024.2366236] [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: 02/23/2024] [Accepted: 06/02/2024] [Indexed: 06/23/2024] Open
Abstract
A novel class of compounds designed to hit two anti-tumour targets, G-quadruplex structures and human carbonic anhydrases (hCAs) IX and XII is proposed. The induction/stabilisation of G-quadruplex structures by small molecules has emerged as an anticancer strategy, disrupting telomere maintenance and reducing oncogene expression. hCAs IX and XII are well-established anti-tumour targets, upregulated in many hypoxic tumours and contributing to metastasis. The ligands reported feature a berberine G-quadruplex stabiliser scaffold connected to a moiety inhibiting hCAs IX and XII. In vitro experiments showed that our compounds selectively stabilise G-quadruplex structures and inhibit hCAs IX and XII. The crystal structure of a telomeric G-quadruplex in complex with one of these ligands was obtained, shedding light on the ligand/target interaction mode. The most promising ligands showed significant cytotoxicity against CA IX-positive HeLa cancer cells in hypoxia, and the ability to stabilise G-quadruplexes within tumour cells.
Collapse
Affiliation(s)
- Alessio Nocentini
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Alessandro Bonardi
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Carla Bazzicalupi
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Andrea Petreni
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Silvia Bua
- Research Institute of the University of Bucharest (ICUB), Bucharest, Romania
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Stefano De Tito
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Claudiu T. Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Paola Gratteri
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| |
Collapse
|
4
|
Shi K, Chen K, Lu S, Luo Q, Xu Q. G-quadruplex structures in FGFR3 promoter negatively regulate its gene expression and DNA replication. Biochem Biophys Res Commun 2024; 730:150384. [PMID: 39003866 DOI: 10.1016/j.bbrc.2024.150384] [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: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 07/16/2024]
Abstract
FGFR3 activating mutations and abnormal expression are linked to tumor development. However, the current state of research on FGFR3 gene expression regulation is relatively insufficient. In this study, we have reported that the FGFR3 promoter's positive strand contains several G-tracts and most likely forms a G-quadruplex (G4) structure. Circular dichroism investigations revealed that oligonucleotides from this region exhibit G-quadruplex-like molar ellipticity. We further validated the G4 structure of the FGFR3 promoter using biochemical and cellular molecular biology techniques. The G-quadruplex mutation enhanced the transcriptional activity of the FGFR3 promoter and DNA replication, suggesting that the G4 structure inhibits its expression. Furthermore, we conducted a preliminary screen for helicases associated with FGFR3 expression and explored their regulatory effects on FGFR3 gene transcription. Subsequently, we investigated the effect of curcumin on the stability of the G4 structure of the FGFR3 promoter and its regulatory effect on FGFR3 expression.
Collapse
Affiliation(s)
- Ke Shi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Kuida Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Shipeng Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Qiong Luo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China; Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine in Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China.
| |
Collapse
|
5
|
Huang HY, Chen CH, Cheng FJ, Wang BW, Tu CY, Chen YJ, He YH, Yao CH, Huang WC. Incense-burning smoke ingredient Auramine enhances lincRNA-p21 expression for chemosensitization in p53-mutated non-small cell lung cancer. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135105. [PMID: 39047551 DOI: 10.1016/j.jhazmat.2024.135105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/21/2024] [Accepted: 07/03/2024] [Indexed: 07/27/2024]
Abstract
Incense-burning smoke is a deleterious air pollutant that initiates cytotoxic effects by inducing apoptosis in lung epithelial cells and also acts as a risk factor for lung cancers. Auramine, an ingredient of incense smoke, has been implicated in tumor progression and cellular sensitivity in non-small cell lung cancer (NSCLC) towards anti-cancer agents through unclear mechanisms. Tumor protein p53 (TP53)-activated long intergenic non-coding RNA-p21 (lincRNA-p21) undertakes a pivotal role in regulating cell apoptosis and chemosensitivity. TP53 mutations prevalent in 50% of NSCLC, contribute to diminished therapeutic efficacy. However, the influence of auramine on chemotherapy-induced lincRNA-p21 expression and apoptosis in NSCLC with different TP53 genetic statuses remains unexplored. This study disclosed that both wild-type p53 (wtp53) and mutant p53 (mutp53) mediate lincRNA-p21 expression, albeit through distinct promoter enhancers, p53-response element (p53RE) and non-B DNA structure G-quadruplex (GQ), respectively. Intriguingly, auramine functions as an effective stabilizer of the GQ structure, augmenting mutp53-mediated lincRNA-p21 expression and enhancing apoptosis and cellular sensitivity to chemotherapy in mutp53-expressing NSCLC cells. These findings suggest a mechanism by which mutp53, in the presence of auramine, is endowed with tumor-suppressing function akin to wtp53, thereby aiding in combating chemoresistance in NSCLC cells harboring TP53 mutations.
Collapse
Affiliation(s)
- Hsuan-Yu Huang
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Chia-Hung Chen
- School of Medicine, China Medical University, Taichung 404, Taiwan; Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, China Medical University Hospital, Taichung 404, Taiwan; Department of Respiratory Therapy, China Medical University, Taichung 404, Taiwan
| | - Fang-Ju Cheng
- School of Medicine, China Medical University, Taichung 404, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan; Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan
| | - Bo-Wei Wang
- Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan; Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan
| | - Chih-Yen Tu
- School of Medicine, China Medical University, Taichung 404, Taiwan; Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, China Medical University Hospital, Taichung 404, Taiwan; Department of Respiratory Therapy, China Medical University, Taichung 404, Taiwan
| | - Yun-Ju Chen
- School of Medicine for International Students, I-Shou University, Kaohsiung 824, Taiwan; Department of Medical Research, E-Da Hospital, Kaohsiung 824, Taiwan
| | - Yu-Hao He
- Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan; Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung 404, Taiwan.
| | - Chun-Hsu Yao
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung 404, Taiwan; Biomaterials Translational Research Center, China Medical University Hospital, Taichung 404, Taiwan; Department of Bioinformatics and Medical Engineering, Asia University, Taichung 413, Taiwan.
| | - Wei-Chien Huang
- Center for Molecular Medicine, China Medical University Hospital, Taichung 404, Taiwan; Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404, Taiwan; Drug Development Center, China Medical University, Taichung 404, Taiwan; Department of Medical Research, China Medical University Hsinchu Hospital, Hsinchu 302, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 413, Taiwan.
| |
Collapse
|
6
|
Odahara Y, Momotake A, Syokaku Y, Yamamoto Y. Catalytic and Selective Red Light-Triggered Photodegradation of a G-Quadruplex DNA by a Zinc (II) Phthalocyanine. Chembiochem 2024; 25:e202400197. [PMID: 38940417 DOI: 10.1002/cbic.202400197] [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: 03/02/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024]
Abstract
Water-soluble phthalocyanine (Pc) derivatives have been regarded as potential G-quadruplex (G4) nucleic acid-targeting ligands for anticancer therapy and have been extensively studied as effective photosensitizers for photodynamic therapy (PDT). Understanding how photosensitizers interact with nucleic acids and the subsequent photolytic reactions is essential for deciphering the initial steps of PDT, thereby aiding in the development of new photosensitizing agents. In this study, we found that red-light irradiation of a mixture of a Zn(II) Pc derivative and an all-parallel G4 DNA leads to catalytic and selective photodegradation of the DNA by reactive oxygen species (ROS) generated from the Zn(II) Pc derivative bound to DNA through a reaction mechanism similar to that of an enzyme reaction. This finding provides a novel insight into the molecular design of a photosensitizer to enhance its PDT efficacy.
Collapse
Affiliation(s)
- Yusuke Odahara
- Department of Chemistry, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Yuri Syokaku
- Department of Chemistry, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| |
Collapse
|
7
|
Zhang Q, Wei Y, Liu L. GraphPro: An interpretable graph neural network-based model for identifying promoters in multiple species. Comput Biol Med 2024; 180:108974. [PMID: 39096613 DOI: 10.1016/j.compbiomed.2024.108974] [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: 02/24/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024]
Abstract
Promoters are DNA sequences that bind with RNA polymerase to initiate transcription, regulating this process through interactions with transcription factors. Accurate identification of promoters is crucial for understanding gene expression regulation mechanisms and developing therapeutic approaches for various diseases. However, experimental techniques for promoter identification are often expensive, time-consuming, and inefficient, necessitating the development of accurate and efficient computational models for this task. Enhancing the model's ability to recognize promoters across multiple species and improving its interpretability pose significant challenges. In this study, we introduce a novel interpretable model based on graph neural networks, named GraphPro, for multi-species promoter identification. Initially, we encode the sequences using k-tuple nucleotide frequency pattern, dinucleotide physicochemical properties, and dna2vec. Subsequently, we construct two feature extraction modules based on convolutional neural networks and graph neural networks. These modules aim to extract specific motifs from the promoters, learn their dependencies, and capture the underlying structural features of the promoters, providing a more comprehensive representation. Finally, a fully connected neural network predicts whether the input sequence is a promoter. We conducted extensive experiments on promoter datasets from eight species, including Human, Mouse, and Escherichia coli. The experimental results show that the average Sn, Sp, Acc and MCC values of GraphPro are 0.9123, 0.9482, 0.8840 and 0.7984, respectively. Compared with previous promoter identification methods, GraphPro not only achieves better recognition accuracy on multiple species, but also outperforms all previous methods in cross-species prediction ability. Furthermore, by visualizing GraphPro's decision process and analyzing the sequences matching the transcription factor binding motifs captured by the model, we validate its significant advantages in biological interpretability. The source code for GraphPro is available at https://github.com/liuliwei1980/GraphPro.
Collapse
Affiliation(s)
- Qi Zhang
- College of Science, Dalian Jiaotong University, Dalian, 116028, China
| | - Yuxiao Wei
- College of Software, Dalian Jiaotong University, Dalian, 116028, China
| | - Liwei Liu
- College of Science, Dalian Jiaotong University, Dalian, 116028, China.
| |
Collapse
|
8
|
Peña Martinez CD, Zeraati M, Rouet R, Mazigi O, Henry JY, Gloss B, Kretzmann JA, Evans CW, Ruggiero E, Zanin I, Marušič M, Plavec J, Richter SN, Bryan TM, Smith NM, Dinger ME, Kummerfeld S, Christ D. Human genomic DNA is widely interspersed with i-motif structures. EMBO J 2024:10.1038/s44318-024-00210-5. [PMID: 39210146 DOI: 10.1038/s44318-024-00210-5] [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: 03/07/2024] [Revised: 08/05/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
DNA i-motif structures are formed in the nuclei of human cells and are believed to provide critical genomic regulation. While the existence, abundance, and distribution of i-motif structures in human cells has been demonstrated and studied by immunofluorescent staining, and more recently NMR and CUT&Tag, the abundance and distribution of such structures in human genomic DNA have remained unclear. Here we utilise high-affinity i-motif immunoprecipitation followed by sequencing to map i-motifs in the purified genomic DNA of human MCF7, U2OS and HEK293T cells. Validated by biolayer interferometry and circular dichroism spectroscopy, our approach aimed to identify DNA sequences capable of i-motif formation on a genome-wide scale, revealing that such sequences are widely distributed throughout the human genome and are common in genes upregulated in G0/G1 cell cycle phases. Our findings provide experimental evidence for the widespread formation of i-motif structures in human genomic DNA and a foundational resource for future studies of their genomic, structural, and molecular roles.
Collapse
Affiliation(s)
- Cristian David Peña Martinez
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia
| | - Mahdi Zeraati
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia
| | - Romain Rouet
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia
| | - Ohan Mazigi
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia
| | - Jake Y Henry
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia
| | - Brian Gloss
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia
| | - Jessica A Kretzmann
- School of Molecular Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Cameron W Evans
- School of Molecular Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Emanuela Ruggiero
- Department of Molecular Medicine, University of Padua, 35121, Padua, Italy
| | - Irene Zanin
- Department of Molecular Medicine, University of Padua, 35121, Padua, Italy
| | - Maja Marušič
- Slovenian NMR Centre, National Institute of Chemistry, SI-1000, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, SI-1000, Ljubljana, Slovenia
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, 35121, Padua, Italy
| | - Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2145, Australia
| | - Nicole M Smith
- School of Molecular Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia
- Faculty of Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Sarah Kummerfeld
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW, 2010, Australia.
| |
Collapse
|
9
|
Park D, Chung WC, Gong S, Ravichandran S, Lee GM, Han M, Kim KK, Ahn JH. G-quadruplex as an essential structural element in cytomegalovirus replication origin. Nat Commun 2024; 15:7353. [PMID: 39191758 PMCID: PMC11350156 DOI: 10.1038/s41467-024-51797-6] [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: 02/22/2024] [Accepted: 08/16/2024] [Indexed: 08/29/2024] Open
Abstract
G-quadruplex (G4) structures are found in eukaryotic cell replication origins, but their role in origin function remains unclear. In this study G4 motifs are found in the lytic DNA replication origin (oriLyt) of human cytomegalovirus (HCMV) and recombinant viruses show that a G4 motif in oriLyt essential region I (ER-I) is necessary for viral growth. Replication assays of oriLyt-containing plasmids and biochemical/biophysical analyses show that G4 formation in ER-I is crucial for viral DNA replication. G4 pull-down analysis identifies viral DNA replication factors, such as IE2, UL84, and UL44, as G4-binding proteins. In enzyme-linked immunosorbent assays, specific G4-binding ligands inhibit G4 binding by the viral proteins. The Epstein-Barr virus oriLyt core element also forms a stable G4 that could substitute for the oriLyt ER-I G4 in HCMV. These results demonstrate that viral G4s in replication origins represent an essential structural element in recruiting replication factors and might be a therapeutic target against viral infections.
Collapse
Affiliation(s)
- Daegyu Park
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Woo-Chang Chung
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Shuang Gong
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | | | - Gwang Myeong Lee
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Minji Han
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
- Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jin-Hyun Ahn
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea.
- Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea.
| |
Collapse
|
10
|
Shukla C, Datta B. G-quadruplexes in long non-coding RNAs and their interactions with proteins. Int J Biol Macromol 2024; 278:134946. [PMID: 39187110 DOI: 10.1016/j.ijbiomac.2024.134946] [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: 06/07/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as crucial regulators of cellular processes, with their dysregulation linked to various disease states. Among the structural motifs in lncRNAs, RNA G-quadruplexes (rG4s) have gained increasing attention due to their diverse roles in cellular function and disease pathogenesis. This review provides an updated and comprehensive overview of rG4s in lncRNAs, elucidating their formation, interaction with proteins, and distinctive roles in cellular processes. We discuss current methodologies for experimentally probing RNA G4s, including the use of specific small molecules, biomolecular ligands and fluorescent probes. The commonly found RNA G4-interacting protein domains are summarised along with potential strategies for disrupting lncRNA G4-protein interactions from a therapeutic perspective.
Collapse
Affiliation(s)
- Chinmayee Shukla
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India
| | - Bhaskar Datta
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India; Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, Gujarat, India.
| |
Collapse
|
11
|
Fallah A, Havaei SA, Sedighian H, Kachuei R, Fooladi AAI. Prediction of aptamer affinity using an artificial intelligence approach. J Mater Chem B 2024. [PMID: 39158322 DOI: 10.1039/d4tb00909f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Aptamers are oligonucleotide sequences that can connect to particular target molecules, similar to monoclonal antibodies. They can be chosen by systematic evolution of ligands by exponential enrichment (SELEX), and are modifiable and can be synthesized. Even if the SELEX approach has been improved a lot, it is frequently challenging and time-consuming to identify aptamers experimentally. In particular, structure-based methods are the most used in computer-aided design and development of aptamers. For this purpose, numerous web-based platforms have been suggested for the purpose of forecasting the secondary structure and 3D configurations of RNAs and DNAs. Also, molecular docking and molecular dynamics (MD), which are commonly utilized in protein compound selection by structural information, are suitable for aptamer selection. On the other hand, from a large number of sequences, artificial intelligence (AI) may be able to quickly discover the possible aptamer candidates. Conversely, sophisticated machine and deep-learning (DL) models have demonstrated efficacy in forecasting the binding properties between ligands and targets during drug discovery; as such, they may provide a reliable and precise method for forecasting the binding of aptamers to targets. This research looks at advancements in AI pipelines and strategies for aptamer binding ability prediction, such as machine and deep learning, as well as structure-based approaches, molecular dynamics and molecular docking simulation methods.
Collapse
Affiliation(s)
- Arezoo Fallah
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Asghar Havaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Hamid Sedighian
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Reza Kachuei
- Molecular Biology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
12
|
Wang JX, Wang XD, Hu MH. Novel quinoxaline analogs as telomeric G-quadruplex ligands exert antitumor effects related to enhanced immunomodulation. Eur J Med Chem 2024; 274:116536. [PMID: 38805936 DOI: 10.1016/j.ejmech.2024.116536] [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: 04/12/2024] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 05/30/2024]
Abstract
G-quadruplexes (G4s) are commonly formed in the G-rich strand of telomeric DNA. Ligands targeting telomeric G4 induce DNA damage and telomere dysfunction, which makes them potential antitumor drugs. New telomeric G4 ligands with drug-likeness are still needed to be exploited, especially with their antitumor mechanisms thoroughly discussed. In this study, a novel series of quinoxaline analogs were rationally designed and synthesized. Among them, R1 was the most promising ligand for its cytotoxic effects on tumor cells and stabilizing ability with telomeric G4. Cellular assays illustrated that R1 stabilized G4 and induced R-loop accumulation in the telomeric regions, subsequently triggering DNA damage responses, cell cycle arrest in G2/M phase, apoptosis and antiproliferation. Moreover, R1 evoked immunogenic cell death (ICD) in tumor cells, which promoted the maturation of bone marrow derived dendritic cells (BMDCs). In breast cancer mouse model, R1 exhibited a significant decrease in tumor burden through the immunomodulatory effects, including the increase of CD4+ and CD8+ T cells in tumors and cytokine levels in sera. Our research provides a new idea that targeting telomeric G4 induces DNA damage responses, causing antitumor effects both in vitro and in vivo, partially due to the enhancement of immunomodulation.
Collapse
Affiliation(s)
- Jia-Xin Wang
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen, 518060, China
| | - 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
| | - 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.
| |
Collapse
|
13
|
Stoianova D, Grozeva S, Golub NV, Anokhin BA, Kuznetsova VG. The First FISH-Confirmed Non-Canonical Telomeric Motif in Heteroptera: Cimex lectularius Linnaeus, 1758 and C. hemipterus (Fabricius, 1803) (Hemiptera, Cimicidae) Have a 10 bp Motif (TTAGGGATGG) n. Genes (Basel) 2024; 15:1026. [PMID: 39202386 PMCID: PMC11354137 DOI: 10.3390/genes15081026] [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: 07/09/2024] [Revised: 07/26/2024] [Accepted: 08/01/2024] [Indexed: 09/03/2024] Open
Abstract
Fluorescence in situ hybridization (FISH) with two different probes, the canonical insect telomeric sequence (TTAGG)n and the sequence (TTAGGGATGG)n, was performed on meiotic chromosomes of two members of the true bug family Cimicidae (Cimicomorpha), the common bed bug Cimex lectularius Linnaeus, 1758 and the tropical bed bug C. hemipterus (Fabricius, 1803), whose telomeric motifs were not known. In both species, there were no hybridization signals with the first probe, but strong signals at chromosomal ends were observed with the second probe, indicating the presence of a telomeric motif (TTAGGGATGG)n. This study represents the first FISH confirmation of the presence of a non-canonical telomeric motif not only for the infraorder Cimicomorpha but also for the suborder Heteroptera (Hemiptera) as a whole. The present finding is of key significance for unraveling the evolutionary shifts in the telomeric sequences in this suborder.
Collapse
Affiliation(s)
- Desislava Stoianova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria;
| | - Snejana Grozeva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria;
| | - Natalia V. Golub
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (N.V.G.); (B.A.A.)
| | - Boris A. Anokhin
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (N.V.G.); (B.A.A.)
| | - Valentina G. Kuznetsova
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia; (N.V.G.); (B.A.A.)
| |
Collapse
|
14
|
Liu S, Xu W, Zheng J, Ngocho K, Chen H, Wang K, Xiong S, He X, Liu J. G-quadruplex-Based Artificial Transmembrane Channels Induce Cancer Cell Apoptosis by Perturbing Potassium Ion Homeostasis. Adv Healthc Mater 2024:e2402023. [PMID: 39092635 DOI: 10.1002/adhm.202402023] [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: 06/03/2024] [Revised: 07/25/2024] [Indexed: 08/04/2024]
Abstract
Transmembrane ion transport modality has received a widespread attention due to its apoptotic activation toward anticancer cell activities. In this study, G-quadruplex-based potassium-specific transmembrane channels have been developed to facilitate the intracellular K+ efflux, which perturbs the cellular ion homeostasis thereby inducing cancer cell apoptosis. Cholesterol-tag, a lipophilic anchor moiety, serves as a rudiment for the G-quadruplex immobilization onto the membrane, while G-quadruplex channel structure as a transport module permits ion binding and migration along the channels. A c-Myc sequence tagged with two-cholesterol is designed as a representative lipophilic G-quadruplex, which forms intramolecular parallel G-quadruplex with three stacks of G-quartets (Ch2-Para3). Fluorescence transport assay demonstrates Ch2-Para3 a high transport activity (EC50 = 10.9 × 10-6 m) and an ion selectivity (K+/Na+ selectivity ratio of 84). Ch2-Para3 mediated K+ efflux in cancer cells is revealed to purge cancer cells through K+ efflux-mediated cell apoptosis, which is confirmed by monitoring the changes in membrane potential of mitochondria, leakage of cytochrome c, reactive oxygen species yield, as well as activation of a family of caspases. The lipophilic G-quadruplex exhibits obvious antitumor activity in vivo without systemic toxicity. This study provides a functional scheme aimed at generating DNA-based selective artificial membrane channels for the purpose of regulating cellular processes and inducing cell apoptosis, which shows a great promising for anticancer therapy in the future.
Collapse
Affiliation(s)
- Shuangna Liu
- College of Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, P. R. China
| | - Wanyu Xu
- College of Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, P. R. China
| | - Jing Zheng
- College of Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, P. R. China
| | - Kleins Ngocho
- College of Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, P. R. China
| | - Hui Chen
- College of Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, P. R. China
| | - Kemin Wang
- College of Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, P. R. China
| | - Siqi Xiong
- Eye Center of Xiangya Hospital, Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, 410008, P. R. China
| | - Xiaoxiao He
- College of Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, P. R. China
| | - Jianbo Liu
- College of Biology, College of Chemistry and Chemical Engineering, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, P. R. China
| |
Collapse
|
15
|
He Z, Wang Z, Lu L, Wang X, Guo G. Enhanced recognition of G-quadruplex DNA oxidative damage based on DNA-mediated charge transfer. Bioelectrochemistry 2024; 158:108714. [PMID: 38653106 DOI: 10.1016/j.bioelechem.2024.108714] [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: 02/13/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 04/25/2024]
Abstract
G-quadruplex (G4) DNA is present in human telomere oligonucleotide sequences. Oxidative damage to telomeric DNA accelerates telomere shortening, which is strongly associated with aging and cancer. Most of the current analyses on oxidative DNA damage are based on ds-DNA. Here, we developed a electrochemiluminescence (ECL) probe for enhanced recognition of oxidative damage in G4-DNA based on DNA-mediated charge transfer (CT), which could specifically recognize damaged sites depending on the position of 8-oxoguanine (8-oxoG). First, a uniform G4-DNA monolayer interface was fabricated; the G4-DNA mediated CT properties were examined using an iridium(III) complex [Ir(ppy)2(pip)]PF6 stacked with G4-DNA as an indicator. The results showed that G4-DNA with 8-oxoG attenuated DNA CT. The topological effects of oxidative damage at different sites of G4-DNA and their effects on DNA CT were revealed. The sensing platform was also used for the sensitive and quantitative detection of 8-oxoG in G4-DNA, with a detection limit of 28.9 fmol. Overall, these findings present a sensitive platform to study G4-DNA structural and stability changes caused by oxidative damage as well as the specific and quantitative detection of oxidation sites. The different damage sites in the G-quadruplex could provide detailed clues for understanding the function of G4-associated telomere functional enzymes.
Collapse
Affiliation(s)
- Zhangjin He
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China
| | - Ziqi Wang
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China
| | - Liping Lu
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, PR China; Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China.
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China
| | - Guangsheng Guo
- Center of Excellence for Environmental Safety and Biological Effects, Beijing University of Technology, Beijing 100124, PR China
| |
Collapse
|
16
|
Qiu D, He F, Liu Y, Zhou Z, Yang Y, Long Z, Chen Q, Chen D, Wei S, Mao X, Zhang X, Mergny J, Monchaud D, Ju H, Zhou J. A Cost-Effective Hemin-Based Artificial Enzyme Allows for Practical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402237. [PMID: 38924304 PMCID: PMC11348135 DOI: 10.1002/advs.202402237] [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: 03/01/2024] [Revised: 05/24/2024] [Indexed: 06/28/2024]
Abstract
Nanomaterials excel in mimicking the structure and function of natural enzymes while being far more interesting in terms of structural stability, functional versatility, recyclability, and large-scale preparation. Herein, the story assembles hemin, histidine analogs, and G-quadruplex DNA in a catalytically competent supramolecular assembly referred to as assembly-activated hemin enzyme (AA-heminzyme). The catalytic properties of AA-heminzyme are investigated both in silico (by molecular docking and quantum chemical calculations) and in vitro (notably through a systematic comparison with its natural counterpart horseradish peroxidase, HRP). It is found that this artificial system is not only as efficient as HRP to oxidize various substrates (with a turnover number kcat of 115 s-1) but also more practically convenient (displaying better thermal stability, recoverability, and editability) and more economically viable, with a catalytic cost amounting to <10% of that of HRP. The strategic interest of AA-heminzyme is further demonstrated for both industrial wastewater remediation and biomarker detection (notably glutathione, for which the cost is decreased by 98% as compared to commercial kits).
Collapse
Affiliation(s)
- Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Fangni He
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Yuan Liu
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Zhaoxi Zhou
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Yuqin Yang
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Zhongwen Long
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Qianqian Chen
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Desheng Chen
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Shijiong Wei
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Xuanxiang Mao
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Jean‐Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
- Laboratoire d'Optique et Biosciences (LOB)Ecole PolytechniqueCNRSINSERMInstitut Polytechnique de ParisPalaiseau91120France
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFCDijon21078France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China
| |
Collapse
|
17
|
Neidle S. A Phenotypic Approach to the Discovery of Potent G-Quadruplex Targeted Drugs. Molecules 2024; 29:3653. [PMID: 39125057 PMCID: PMC11314571 DOI: 10.3390/molecules29153653] [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: 07/17/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
G-quadruplex (G4) sequences, which can fold into higher-order G4 structures, are abundant in the human genome and are over-represented in the promoter regions of many genes involved in human cancer initiation, progression, and metastasis. They are plausible targets for G4-binding small molecules, which would, in the case of promoter G4s, result in the transcriptional downregulation of these genes. However, structural information is currently available on only a very small number of G4s and their ligand complexes. This limitation, coupled with the currently restricted information on the G4-containing genes involved in most complex human cancers, has led to the development of a phenotypic-led approach to G4 ligand drug discovery. This approach was illustrated by the discovery of several generations of tri- and tetra-substituted naphthalene diimide (ND) ligands that were found to show potent growth inhibition in pancreatic cancer cell lines and are active in in vivo models for this hard-to-treat disease. The cycles of discovery have culminated in a highly potent tetra-substituted ND derivative, QN-302, which is currently being evaluated in a Phase 1 clinical trial. The major genes whose expression has been down-regulated by QN-302 are presented here: all contain G4 propensity and have been found to be up-regulated in human pancreatic cancer. Some of these genes are also upregulated in other human cancers, supporting the hypothesis that QN-302 is a pan-G4 drug of potential utility beyond pancreatic cancer.
Collapse
Affiliation(s)
- Stephen Neidle
- The School of Pharmacy, University College London, London WC1N 1AX, UK
| |
Collapse
|
18
|
Cui X, Zhang C, Fu C, Hu J, Li T, Li L. YY1 is involved in homologous recombination inhibition at guanine quadruplex sites in human cells. Nucleic Acids Res 2024; 52:7401-7413. [PMID: 38869071 PMCID: PMC11260479 DOI: 10.1093/nar/gkae502] [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: 09/25/2023] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Homologous recombination (HR) is a key process for repairing DNA double strand breaks and for promoting genetic diversity. However, HR occurs unevenly across the genome, and certain genomic features can influence its activity. One such feature is the presence of guanine quadruplexes (G4s), stable secondary structures widely distributed throughout the genome. These G4s play essential roles in gene transcription and genome stability regulation. Especially, elevated G4 levels in cells deficient in the Bloom syndrome helicase (BLM) significantly enhance HR at G4 sites, potentially threatening genome stability. Here, we investigated the role of G4-binding protein Yin Yang-1 (YY1) in modulating HR at G4 sites in human cells. Our results show that YY1's binding to G4 structures suppresses sister chromatid exchange after BLM knockdown, and YY1's chromatin occupancy negatively correlates with the overall HR rate observed across the genome. By limiting RAD51 homolog 1 (RAD51) access, YY1 preferentially binds to essential genomic regions, shielding them from excessive HR. Our findings unveil a novel role of YY1-G4 interaction, revealing novel insights into cellular mechanisms involved in HR regulation.
Collapse
Affiliation(s)
- Xinyu Cui
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chengwen Zhang
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunqing Fu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinglei Hu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tengjiao Li
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Li
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Michael Sabo T, Trent JO, Chaires JB, Monsen RC. Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination. Methods 2024; 230:9-20. [PMID: 39032720 DOI: 10.1016/j.ymeth.2024.07.004] [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: 04/05/2024] [Revised: 06/22/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024] Open
Abstract
Guanine-rich nucleic acids can form intramolecularly folded four-stranded structures known as G-quadruplexes (G4s). Traditionally, G4 research has focused on short, highly modified DNA or RNA sequences that form well-defined homogeneous compact structures. However, the existence of longer sequences with multiple G4 repeats, from proto-oncogene promoters to telomeres, suggests the potential for more complex higher-order structures with multiple G4 units that might offer selective drug-targeting sites for therapeutic development. These larger structures present significant challenges for structural characterization by traditional high-resolution methods like multi-dimensional NMR and X-ray crystallography due to their molecular complexity. To address this current challenge, we have developed an integrated structural biology (ISB) platform, combining experimental and computational methods to determine self-consistent molecular models of higher-order G4s (xG4s). Here we outline our ISB method using two recent examples from our lab, an extended c-Myc promoter and long human telomere G4 repeats, that highlights the utility and generality of our approach to characterizing biologically relevant xG4s.
Collapse
Affiliation(s)
- T Michael Sabo
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - John O Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - Jonathan B Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - Robert C Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States.
| |
Collapse
|
21
|
Hegedus L, Toth A, Harami GM, Palinkas J, Karatayeva N, Sajben-Nagy E, Bene S, Afzali Jaktajdinani S, Kovacs M, Juhasz S, Burkovics P. Werner helicase interacting protein 1 contributes to G-quadruplex processing in human cells. Sci Rep 2024; 14:15740. [PMID: 38977862 PMCID: PMC11231340 DOI: 10.1038/s41598-024-66425-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: 04/25/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
Genome replication is frequently impeded by highly stable DNA secondary structures, including G-quadruplex (G4) DNA, that can hinder the progression of the replication fork. Human WRNIP1 (Werner helicase Interacting Protein 1) associates with various components of the replication machinery and plays a crucial role in genome maintenance processes. However, its detailed function is still not fully understood. Here we show that human WRNIP1 interacts with G4 structures and provide evidence for its contribution to G4 processing. The absence of WRNIP1 results in elevated levels of G4 structures, DNA damage and chromosome aberrations following treatment with PhenDC3, a G4-stabilizing ligand. Additionally, we establish a functional and physical relationship between WRNIP1 and the PIF1 helicase in G4 processing. In summary, our results suggest that WRNIP1 aids genome replication and maintenance by regulating G4 processing and this activity relies on Pif1 DNA helicase.
Collapse
Affiliation(s)
- Lili Hegedus
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
| | - Agnes Toth
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Gabor M Harami
- ELTE-MTA Momentum Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Janos Palinkas
- ELTE-MTA Momentum Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Nargis Karatayeva
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Eniko Sajben-Nagy
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
| | - Szabolcs Bene
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
| | - Sara Afzali Jaktajdinani
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Mihaly Kovacs
- ELTE-MTA Momentum Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- HUN-REN-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Szilvia Juhasz
- HCEMM Cancer Microbiome Core Group, Szeged, Hungary.
- Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary.
| | - Peter Burkovics
- Institute of Genetics, Biological Research Centre, HUN-REN Szeged, Szeged, Hungary.
| |
Collapse
|
22
|
Nageshan RK, Krogan N, Cooper JP. Parallel genetic screens identify nuclear envelope homeostasis as a key determinant of telomere entanglement resolution in fission yeast. G3 (BETHESDA, MD.) 2024; 14:jkae078. [PMID: 38657142 PMCID: PMC11228871 DOI: 10.1093/g3journal/jkae078] [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: 12/26/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
In fission yeast lacking the telomere binding protein, Taz1, replication forks stall at telomeres, triggering deleterious downstream events. Strand invasion from one taz1Δ telomeric stalled fork to another on a separate (nonsister) chromosome leads to telomere entanglements, which are resolved in mitosis at 32°C; however, entanglement resolution fails at ≤20°C, leading to cold-specific lethality. Previously, we found that loss of the mitotic function of Rif1, a conserved DNA replication and repair factor, suppresses cold sensitivity by promoting resolution of entanglements without affecting entanglement formation. To understand the underlying pathways of mitotic entanglement resolution, we performed a series of genome-wide synthetic genetic array screens to generate a comprehensive list of genetic interactors of taz1Δ and rif1Δ. We modified a previously described screening method to ensure that the queried cells were kept in log phase growth. In addition to recapitulating previously identified genetic interactions, we find that loss of genes encoding components of the nuclear pore complex (NPC) promotes telomere disentanglement and suppresses taz1Δ cold sensitivity. We attribute this to more rapid anaphase midregion nuclear envelope (NE) breakdown in the absence of these NPC components. Loss of genes involved in lipid metabolism reverses the ability of rif1+ deletion to suppress taz1Δ cold sensitivity, again pinpointing NE modulation. A rif1+ separation-of-function mutant that specifically loses Rif1's mitotic functions yields similar genetic interactions. Genes promoting membrane fluidity were enriched in a parallel taz1+ synthetic lethal screen at permissive temperature, cementing the idea that the cold specificity of taz1Δ lethality stems from altered NE homeostasis.
Collapse
Affiliation(s)
- Rishi Kumar Nageshan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave, Aurora, CO 80045, USA
- Former address: Telomere Biology Laboratory, Laboratory of Biochemistry and Molecular Biology, NCI, NIH, Bethesda, MD 20892, USA
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, 308D, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Julia Promisel Cooper
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave, Aurora, CO 80045, USA
- Former address: Telomere Biology Laboratory, Laboratory of Biochemistry and Molecular Biology, NCI, NIH, Bethesda, MD 20892, USA
| |
Collapse
|
23
|
Wu Y, Wang GA, Yang Q, Li F. Native Characterization of Noncanonical Nucleic Acid Thermodynamics via Programmable Dynamic DNA Chemistry. J Am Chem Soc 2024; 146:18041-18049. [PMID: 38899479 DOI: 10.1021/jacs.4c04721] [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: 06/21/2024]
Abstract
Folding thermodynamics, quantitatively described using parameters such as ΔGfold°, ΔHfold°, and ΔSfold°, is essential for characterizing the stability and functionality of noncanonical nucleic acid structures but remains difficult to measure at the molecular level. Leveraging the programmability of dynamic deoxyribonucleic acid (DNA) chemistry, we introduce a DNA-based molecular tool capable of performing a free energy shift assay (FESA) that directly characterizes the thermodynamics of noncanonical DNA structures in their native environments. FESA operates by the rational design of a reference DNA probe that is energetically equivalent to a target noncanonical nucleic acid structure in a series of toehold-exchange reactions, yet is structurally incapable of folding. As a result, a free energy shift (ΔΔGrxn°) is observed when plotting the reaction yield against the free energy of each toehold-exchange. We mathematically demonstrated that ΔGfold°, ΔHfold°, and ΔSfold° of the analyte can be calculated based on ΔΔGrxn°. After validating FESA using six DNA hairpins by comparing the measured ΔGfold°, ΔHfold°, and ΔSfold° values against predictions made by NUPACK software, we adapted FESA to characterize noncanonical nucleic acid structures, encompassing DNA triplexes, G-quadruplexes, and aptamers. This adaptation enabled the successful characterization of the folding thermodynamics for these complex structures under various experimental conditions. The successful development of FESA marks a paradigm shift and a technical advancement in characterizing the thermodynamics of noncanonical DNA structures through molecular tools. It also opens new avenues for probing fundamental chemical and biophysical questions through the lens of molecular engineering and dynamic DNA chemistry.
Collapse
Affiliation(s)
- Yuqin Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Guan Alex Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Qianfan Yang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| |
Collapse
|
24
|
Teng X, Hu D, Dai Y, Jing H, Hu W, Zhang Q, Zhang N, Li J. Discovery of A G-Quadruplex Unwinder That Unleashes the Translation of G-Quadruplex-Containing mRNA without Inducing DNA Damage. Angew Chem Int Ed Engl 2024:e202407353. [PMID: 38953247 DOI: 10.1002/anie.202407353] [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: 04/17/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/03/2024]
Abstract
To explore the mechanisms and therapeutic strategies for G-quadruplex (G4) mediated diseases, it is crucial to manipulate and intervene in intracellular G4 structures using small molecular tools. While hundreds of G4 stabilizers have been developed, there is a significant gap in the availability of G4 unwinding agents. Here, we propose a strategy to disrupt G-quadruplexes by forming G-C hydrogen bonds with chemically modified cytidine trimers. We validated a good G4 unwinder, the 2'-F cytidine trimer (2'-F C3). 2'-F C3 does not inhibit cell growth nor cause severe DNA damage at a concentration below 10 μM. Moreover, 2'-F C3 does not affect gene transcription nor RNA splicing, while it significantly enhances the translation of G4-containing mRNA and upregulates RNA splicing, RNA processing and cell cycle pathways. The discovery of this G4 unwinder provides a functional tool for the chemical modulation of G4s in living cells.
Collapse
Affiliation(s)
- Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- New Cornerstone Science Laboratory, Shenzhen, 518054, China
- Beijing Life Science Academy, Beijing, 102209, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Difei Hu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yicong Dai
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Wenxuan Hu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Qiushuang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Na Zhang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- New Cornerstone Science Laboratory, Shenzhen, 518054, China
- Beijing Life Science Academy, Beijing, 102209, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, 230026, China
| |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
Ibrahim N, Gan KB, Mohd Yusof NY, Goh CT, Krupa B N, Tan LL. Electrochemical genosensor based on RNA-responsive human telomeric G-quadruplex DNA: A proof-of-concept with SARS-CoV-2 RNA. Talanta 2024; 274:125916. [PMID: 38547835 DOI: 10.1016/j.talanta.2024.125916] [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: 09/10/2023] [Revised: 01/07/2024] [Accepted: 03/11/2024] [Indexed: 05/04/2024]
Abstract
In this report, a facile and label-free electrochemical RNA biosensor is developed by exploiting methylene blue (MB) as an electroactive positive ligand of G-quadruplex. The electrochemical response mechanism of the nucleic acid assay was based on the change in differential pulse voltammetry (DPV) signal of adsorbed MB on the immobilized human telomeric G-quadruplex DNA with a loop that is complementary to the target RNA. Hybridization between synthetic positive control RNA and G-quadruplex DNA probe on the transducer platform rendered a conformational change of G-quadruplex to double-stranded DNA (dsDNA), and increased the redox current of cationic MB π planar ligand at the sensing interface, thereby the electrochemical signal of the MB-adsorbed duplex is proportional to the concentration of target RNA, with SARS-CoV-2 (COVID-19) RNA as the model. Under optimal conditions, the target RNA can be detected in a linear range from 1 zM to 1 μM with a limit of detection (LOD) obtained at 0.59 zM for synthetic target RNA and as low as 1.4 copy number for positive control plasmid. This genosensor exhibited high selectivity towards SARS-CoV-2 RNA over other RNA nucleotides, such as SARS-CoV and MERS-CoV. The electrochemical RNA biosensor showed DPV signal, which was proportional to the 2019-nCoV_N_positive control plasmid from 2 to 200000 copies (R2 = 0.978). A good correlation between the genosensor and qRT-PCR gold standard was attained for the detection of SARS-CoV-2 RNA in terms of viral copy number in clinical samples from upper respiratory specimens.
Collapse
Affiliation(s)
- Nadiah Ibrahim
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor Darul Ehsan, Malaysia.
| | - Kok Beng Gan
- Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor Darul Ehsan, Malaysia.
| | - Nurul Yuziana Mohd Yusof
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor Darul Ehsan, Malaysia.
| | - Choo Ta Goh
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor Darul Ehsan, Malaysia.
| | - Niranjana Krupa B
- Department of Electronics and Communication Engineering, PES University, Bengaluru-85, Karnataka, India.
| | - Ling Ling Tan
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor Darul Ehsan, Malaysia.
| |
Collapse
|
27
|
Juribašić Kulcsár M, Gabelica V, Plavec J. Solution-State Structure of a Long-Loop G-Quadruplex Formed Within Promoters of Plasmodium falciparum B var Genes. Chemistry 2024; 30:e202401190. [PMID: 38647110 DOI: 10.1002/chem.202401190] [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: 03/25/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
We report the high-resolution NMR solution-state structure of an intramolecular G-quadruplex with a diagonal loop of ten nucleotides. The G-quadruplex is formed by a 34-nt DNA sequence, d[CAG3T2A2G3TATA2CT3AG4T2AG3T2], named UpsB-Q-1. This sequence is found within promoters of the var genes of Plasmodium falciparum, which play a key role in malaria pathogenesis and evasion of the immune system. The [3+1]-hybrid G-quadruplex formed under physiologically relevant conditions exhibits a unique equilibrium between two structures, both stabilized by base stacking and non-canonical hydrogen bonding. Unique equilibrium of the two closely related 3D structures originates from a North-South repuckering of deoxyribose moiety of residue T27 in the lateral loop. Besides the 12 guanines involved in three G-quartets, most residues in loop regions are involved in interactions at both G-quartet-loop interfaces.
Collapse
Affiliation(s)
- Marina Juribašić Kulcsár
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Valérie Gabelica
- School of Pharmaceutical Sciences, University of Geneva, 1 rue Michel-Servet, CH-1211, Geneva 4, Switzerland
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Trg OF 13, SI-1000, Ljubljana, Slovenia
| |
Collapse
|
28
|
Pham P, Wood EA, Dunbar EL, Cox M, Goodman M. Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements. Nucleic Acids Res 2024; 52:6392-6405. [PMID: 38676944 PMCID: PMC11194060 DOI: 10.1093/nar/gkae320] [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: 10/17/2023] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Sequences or RRS, are each 650 kb from the terminus sequence dif and flank the Ter macrodomain. RRS sequence and positioning is highly conserved in enterobacteria. At least one RRS appears to be essential unless a 200 kb region encompassing one of them is amplified. The RRS contain a G-quadruplex on the lagging strand which impedes DNA polymerase extension producing lagging strand ssDNA gaps, $ \le$2000 bp long, upon replisome passage. Deletion of both RRS elements has substantial effects on global genome structure and topology. We hypothesize that RRS elements serve as topological relief valves during chromosome replication and segregation. There have been no screens for genomic sequences that trigger transient gap formation. Functional analogs of RRS could be widespread, possibly including some enigmatic G-quadruplexes in eukaryotes.
Collapse
Affiliation(s)
- Phuong Pham
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910, USA
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Emma L Dunbar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Myron F Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910, USA
| |
Collapse
|
29
|
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.
Collapse
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.
| |
Collapse
|
30
|
Dore MD, Rafique MG, Yang TP, Zorman M, Platnich CM, Xu P, Trinh T, Rizzuto FJ, Cosa G, Li J, Guarné A, Sleiman HF. Heat-activated growth of metastable and length-defined DNA fibers expands traditional polymer assembly. Nat Commun 2024; 15:4384. [PMID: 38782917 PMCID: PMC11116425 DOI: 10.1038/s41467-024-48722-2] [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: 11/03/2022] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Biopolymers such as nucleic acids and proteins exhibit dynamic backbone folding, wherein site-specific intramolecular interactions determine overall structure. Proteins then hierarchically assemble into supramolecular polymers such as microtubules, that are robust yet dynamic, constantly growing or shortening to adjust to cellular needs. The combination of dynamic, energy-driven folding and growth with structural stiffness and length control is difficult to achieve in synthetic polymer self-assembly. Here we show that highly charged, monodisperse DNA-oligomers assemble via seeded growth into length-controlled supramolecular fibers during heating; when the temperature is lowered, these metastable fibers slowly disassemble. Furthermore, the specific molecular structures of oligomers that promote fiber formation contradict the typical theory of block copolymer self-assembly. Efficient curling and packing of the oligomers - or 'curlamers' - determine morphology, rather than hydrophobic to hydrophilic ratio. Addition of a small molecule stabilises the DNA fibers, enabling temporal control of polymer lifetime and underscoring their potential use in nucleic-acid delivery, stimuli-responsive biomaterials, and soft robotics.
Collapse
Affiliation(s)
- Michael D Dore
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | | | - Tianxiao Peter Yang
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Marlo Zorman
- Department of Chemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Casey M Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Pengfei Xu
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Tuan Trinh
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Felix J Rizzuto
- School of Chemistry, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Jianing Li
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47906, USA
| | - Alba Guarné
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada.
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada.
| |
Collapse
|
31
|
Lee YW, Weissbein U, Blum R, Lee JT. G-quadruplex folding in Xist RNA antagonizes PRC2 activity for stepwise regulation of X chromosome inactivation. Mol Cell 2024; 84:1870-1885.e9. [PMID: 38759625 DOI: 10.1016/j.molcel.2024.04.015] [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: 05/31/2023] [Revised: 11/25/2023] [Accepted: 04/19/2024] [Indexed: 05/19/2024]
Abstract
How Polycomb repressive complex 2 (PRC2) is regulated by RNA remains an unsolved problem. Although PRC2 binds G-tracts with the potential to form RNA G-quadruplexes (rG4s), whether rG4s fold extensively in vivo and whether PRC2 binds folded or unfolded rG4 are unknown. Using the X-inactivation model in mouse embryonic stem cells, here we identify multiple folded rG4s in Xist RNA and demonstrate that PRC2 preferentially binds folded rG4s. High-affinity rG4 binding inhibits PRC2's histone methyltransferase activity, and stabilizing rG4 in vivo antagonizes H3 at lysine 27 (H3K27me3) enrichment on the inactive X chromosome. Surprisingly, mutagenizing the rG4 does not affect PRC2 recruitment but promotes its release and catalytic activation on chromatin. H3K27me3 marks are misplaced, however, and gene silencing is compromised. Xist-PRC2 complexes become entrapped in the S1 chromosome compartment, precluding the required translocation into the S2 compartment. Thus, Xist rG4 folding controls PRC2 activity, H3K27me3 enrichment, and the stepwise regulation of chromosome-wide gene silencing.
Collapse
Affiliation(s)
- Yong Woo Lee
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Uri Weissbein
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Roy Blum
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
| |
Collapse
|
32
|
Han J, Qin R, Zheng S, Hou X, Wang X, An H, Li Z, Li Y, Zhang H, Zhai D, Liu H, Meng J, Sun T. MSC microvesicles loaded G-quadruplex-enhanced circular single-stranded DNA-9 inhibits tumor growth by targeting MDSCs. J Nanobiotechnology 2024; 22:237. [PMID: 38735920 PMCID: PMC11089713 DOI: 10.1186/s12951-024-02504-6] [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: 07/02/2023] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Myeloid-derived suppressor cells (MDSCs) promote tumor growth, metastasis, and lead to immunotherapy resistance. Studies revealed that miRNAs are also expressed in MDSCs and promote the immunosuppressive function of MDSCs. Currently, few studies have been reported on inducible cellular microvesicle delivery of nucleic acid drugs targeting miRNA in MDSCs for the treatment of malignant tumors. RESULTS AND CONCLUSION In this study, we designed an artificial DNA named G-quadruplex-enhanced circular single-stranded DNA-9 (G4-CSSD9), that specifically adsorbs the miR-9 sequence. Its advanced DNA folding structure, rich in tandem repeat guanine (G-quadruplex), also provides good stability. Mesenchymal stem cells (MSCs) were prepared into nanostructured vesicles by membrane extrusion. The MSC microvesicles-encapsulated G4-CSSD9 (MVs@G4-CSSD9) was delivered into MDSCs, which affected the downstream transcription and translation process, and reduced the immunosuppressive function of MDSCs, so as to achieve the purpose of treating melanoma. In particular, it provides an idea for the malignant tumor treatment.
Collapse
Affiliation(s)
- Jingxia Han
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Rong Qin
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Shaoting Zheng
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Xiaohui Hou
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Xiaorui Wang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huihui An
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Zhongwei Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Yinan Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Heng Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China
| | - Denghui Zhai
- College of Life Sciences, Nankai University, Tianjin, China
| | - Huijuan Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China.
| | - Jing Meng
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China.
| | - Tao Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China.
| |
Collapse
|
33
|
Zheng BX, Long W, Zheng W, Zeng Y, Guo XC, Chan KH, She MT, Leung ASL, Lu YJ, Wong WL. Mitochondria-Selective Dicationic Small-Molecule Ligand Targeting G-Quadruplex Structures for Human Colorectal Cancer Therapy. J Med Chem 2024; 67:6292-6312. [PMID: 38624086 DOI: 10.1021/acs.jmedchem.3c02240] [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: 04/17/2024]
Abstract
Mitochondria are important drug targets for anticancer and other disease therapies. Certain human mitochondrial DNA sequences capable of forming G-quadruplex structures (G4s) are emerging drug targets of small molecules. Despite some mitochondria-selective ligands being reported for drug delivery against cancers, the ligand design is mostly limited to the triphenylphosphonium scaffold. The ligand designed with lipophilic small-sized scaffolds bearing multipositive charges targeting the unique feature of high mitochondrial membrane potential (MMP) is lacking and most mitochondria-selective ligands are not G4-targeting. Herein, we report a new small-sized dicationic lipophilic ligand to target MMP and mitochondrial DNA G4s to enhance drug delivery for anticancer. The ligand showed marked alteration of mitochondrial gene expression and substantial induction of ROS production, mitochondrial dysfunction, DNA damage, cellular senescence, and apoptosis. The ligand also exhibited high anticancer activity against HCT116 cancer cells (IC50, 3.4 μM) and high antitumor efficacy in the HCT116 tumor xenograft mouse model (∼70% tumor weight reduction).
Collapse
Affiliation(s)
- Bo-Xin Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Wei Long
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Wende Zheng
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| | - Yaoxun Zeng
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| | - Xiao-Chun Guo
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Ka-Hin Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Meng-Ting She
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| | - Alan Siu-Lun Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Yu-Jing Lu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| |
Collapse
|
34
|
Gong P, Zhang R, Xiao K, Shu H, Li X, Fan H, Sun X. DNA G-Quadruplex in NRP1 Promoter Facilitates SARS-CoV-2 Infection. Int J Mol Sci 2024; 25:4422. [PMID: 38674009 PMCID: PMC11050221 DOI: 10.3390/ijms25084422] [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: 03/24/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to raise concerns worldwide. Numerous host factors involved in SARS-CoV-2 infection have been identified, but the regulatory mechanisms of these host factor remain unclear. Here, we report the role of G-quadruplexes (G4s) located in the host factor promoter region in SARS-CoV-2 infection. Using bioinformatics, biochemical, and biological assays, we provide evidence for the presence of G4 structures in the promoter regions of SARS-CoV-2 host factors NRP1. Specifically, we focus on two representative G4s in the NRP1 promoter and highlight its importance in SARS-CoV-2 pathogenesis. The presence of the G4 structure greatly increases NRP1 expression, facilitating SARS-CoV-2 entry into cells. Utilizing published single-cell RNA sequencing data obtained from simulated SARS-CoV-2 infection in human bronchial epithelial cells (HBECs), we found that ciliated cells with high levels of NRP1 are prominently targeted by the virus during infection. Furthermore, our study identifies E2F1 act as a transcription factor that binds to G4s. These findings uncover a previously unknown mechanism underlying SARS-CoV-2 infection and suggest that targeting G4 structures could be a potential strategy for COVID-19 prevention and treatment.
Collapse
Affiliation(s)
- Pihai Gong
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 211189, China
| | - Rongxin Zhang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 211189, China
| | - Ke Xiao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 211189, China
| | - Huiling Shu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 211189, China
| | - Xinxiu Li
- Department of Medical Genetics and Developmental Biology, School of Medicine, Southeast University, 87 Dingjiaqiao Road, Nanjing 210009, China;
| | - Hong Fan
- Department of Medical Genetics and Developmental Biology, School of Medicine, Southeast University, 87 Dingjiaqiao Road, Nanjing 210009, China;
| | - Xiao Sun
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 211189, China
| |
Collapse
|
35
|
Brown A, Brill J, Amini R, Nurmi C, Li Y. Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications. Angew Chem Int Ed Engl 2024; 63:e202318665. [PMID: 38253971 DOI: 10.1002/anie.202318665] [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: 12/05/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are short single-stranded oligonucleotides capable of binding to targets with high specificity and selectivity through structural recognition. While aptamers offer advantages over other molecular recognition elements such as their ease of production, smaller size, extended shelf-life, and lower immunogenicity, they have yet to show significant success in real-world applications. By analyzing the importance of structured library designs, reviewing different SELEX methodologies, and the effects of chemical modifications, we provide a comprehensive overview on the production of aptamers for applications in drug delivery systems, therapeutics, diagnostics, and molecular imaging.
Collapse
Affiliation(s)
- Alex Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Jake Brill
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Connor Nurmi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| |
Collapse
|
36
|
Katrivas L, Makarovsky A, Kempinski B, Randazzo A, Improta R, Rotem D, Porath D, Kotlyar AB. Ag +-Mediated Folding of Long Polyguanine Strands to Double and Quadruple Helixes. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:663. [PMID: 38668157 PMCID: PMC11055002 DOI: 10.3390/nano14080663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/03/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024]
Abstract
Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the ions, make these structures interesting candidates in the context of using DNA in nanotechnology. Here, we report the formation and characterization of conjugates of long (kilo bases) homoguanine DNA strands with silver ions. We demonstrate using atomic force microscopy (AFM) and scanning tunneling microscope (STM) that binding of silver ions leads to folding of homoguanine DNA strands in a "hairpin" fashion to yield double-helical, left-handed molecules composed of G-G base pairs each stabilized by a silver ion. Further folding of the DNA-silver conjugate yields linear molecules in which the two halves of the double helix are twisted one against the other in a right-handed fashion. Quantum mechanical calculations on smaller molecular models support the helical twist directions obtained by the high resolution STM analysis. These long guanine-based nanostructures bearing a chain of silver ions have not been synthesized and studied before and are likely to possess conductive properties that will make them attractive candidates for nanoelectronics.
Collapse
Affiliation(s)
- Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
| | - Anna Makarovsky
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Benjamin Kempinski
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Napoli, Italy;
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy;
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Alexander B. Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
| |
Collapse
|
37
|
Pham P, Wood EA, Dunbar EL, Cox MM, Goodman MF. Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: The E. coli RRS Elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.01.560376. [PMID: 37873128 PMCID: PMC10592627 DOI: 10.1101/2023.10.01.560376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
We report that the Escherichia coli chromosome includes novel GC-rich genomic structural elements that trigger formation of post-replication gaps upon replisome passage. The two nearly perfect 222 bp repeats, designated Replication Risk Sequences or RRS, are each 650 kb from the terminus sequence dif and flank the Ter macrodomain. RRS sequence and positioning is highly conserved in enterobacteria. At least one RRS appears to be essential unless a 200 kb region encompassing one of them is amplified. The RRS contain a G-quadruplex on the lagging strand which impedes DNA polymerase extension producing lagging strand ssDNA gaps, ≤2000 bp long, upon replisome passage. Deletion of both RRS elements has substantial effects on global genome structure and topology. We hypothesize that RRS elements serve as topological relief valves during chromosome replication and segregation. There have been no screens for genomic sequences that trigger transient gap formation. Functional analogs of RRS could be widespread, possibly including some enigmatic G-quadruplexes in eukaryotes.
Collapse
Affiliation(s)
- Phuong Pham
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544
| | - Emma L. Dunbar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544
| | - Myron F. Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089-2910
| |
Collapse
|
38
|
Cathcart B, Cheedipudi SM, Rouhi L, Zhao Z, Gurha P, Marian AJ. DNA double-stranded breaks, a hallmark of aging, defined at the nucleotide resolution, are increased and associated with transcription in the cardiac myocytes in LMNA-cardiomyopathy. Cardiovasc Res 2024:cvae063. [PMID: 38577741 DOI: 10.1093/cvr/cvae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/06/2024] Open
Abstract
AIMS An intrinsic feature of gene transcription is the formation of DNA superhelices near the transcription bubble, which are resolved upon induction of transient double-stranded breaks (DSBs) by topoisomerases. Unrepaired DSBs are pathogenic as they lead to cell cycle arrest, senescence, inflammation, and organ dysfunction. We posit that DSBs would be more prevalent at the genomic sites that are associated with gene expression. The objectives were to identify and characterize genome-wide DSBs at the nucleotide resolution and determine the association of DSBs with transcription in cardiac myocytes. METHODS AND RESULTS We identified the genome-wide DSBs in ∼1 million cardiac myocytes per heart in three wild-type and three myocyte-specific LMNA-deficient (Myh6-Cre:LmnaF/F) mice by END-Sequencing. The prevalence of DSBs was 0.8% and 2.2% in the wild-type and Myh6-Cre:LmnaF/F myocytes, respectively. The END-Seq signals were enriched for 8 and 6764 DSBs in the wild-type and Myh6-Cre:LmnaF/F myocytes, respectively (q < 0.05). The DSBs were preferentially localized to the gene regions, transcription initiation sites, cardiac transcription factor motifs, and the G quadruplex forming structures. Because LMNA regulates transcription through the lamin-associated domains (LADs), we defined the LADs in cardiac myocytes by a Cleavage Under Targets & Release Using Nuclease (CUT&RUN) assay (N = 5). On average there were 818 LADs per myocyte. Constitutive LADs (cLADs), defined as LADs that were shared by at least three genomes (N = 2572), comprised about a third of the mouse cardiac myocyte genomes. Transcript levels of the protein-coding genes located at the cLADs (N = 3975) were ∼16-fold lower than those at the non-LAD regions (N = ∼17 778). The prevalence of DSBs was higher in the non-LAD as compared to the cLAD regions. Likewise, DSBs were more common in the loss-of-LAD regions, defined as the genomic regions in the Myh6-Cre:LmnaF/F that were juxtaposed to the LAD regions in the wild-type myocytes. CONCLUSION To our knowledge, this is the first identification of the DSBs, at the nucleotide resolution in the cardiovascular system. The prevalence of DSBs was higher in the genomic regions associated with transcription. Because transcription is pervasive, DSBs are expected to be common and pathogenic in various states and aging.
Collapse
Affiliation(s)
- Benjamin Cathcart
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Sirisha M Cheedipudi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Leila Rouhi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
- Center for Precision Health, School of Biomedical Informatics and School of Public Health, UTHealth, Houston, TX 77030, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| | - Ali J Marian
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center, 6770 Bertner Street, Suite C900A, Houston, TX 77030, USA
| |
Collapse
|
39
|
Yuan L, Wang K, Fang Y, Xu X, Chen Y, Zhao D, Lu K. Interaction of Cecropin A (1-7) Analogs with DNA Analyzed by Multi-spectroscopic Methods. Protein J 2024; 43:274-282. [PMID: 38265732 DOI: 10.1007/s10930-023-10177-7] [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] [Accepted: 12/12/2023] [Indexed: 01/25/2024]
Abstract
Cecropin A (1-7) is a cationic antimicrobial peptide which contain lots of basic amino acids. To understand the effect of basic amino acids on cecropin A (1-7), analogues CA2, CA3 and CA4 which have more arginine or lysine at the N-terminal or C-terminal were designed and synthesized. The interaction of cecropin A (1-7) and its analogs with DNA was studied using ultraviolet-visible spectroscopy, fluorescence spectroscopy and circular dichroism spectroscopy. Multispectral analysis showed that basic amino acids improved the interaction between the analogues and DNA. The interaction between CA4 and DNA is most pronounced. Fluorescence spectrum indicated that Ksv value of CA4 is 1.19 × 105 L mol-1 compared to original peptide cecropin A (1-7) of 3.73 × 104 L mol-1. The results of antimicrobial experiments with cecropin A (1-7) and its analogues showed that basic amino acids enhanced the antimicrobial effect of the analogues. The antimicrobial activity of CA4 against E. coli was eightfold higher than that of cecropin A (1-7). The importance of basic amino acid in peptides is revealed and provides useful information for subsequent studies of antimicrobial peptides.
Collapse
Affiliation(s)
- Libo Yuan
- College of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.
| | - Ke Wang
- College of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China
| | - Yuan Fang
- Pharmacy Department, Zhengzhou People's Hospital, Zhengzhou, 450003, People's Republic of China.
| | - Xiujuan Xu
- College of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China
| | - Yingcun Chen
- College of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China
| | - Dongxin Zhao
- College of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China
| | - Kui Lu
- College of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, 450001, People's Republic of China.
| |
Collapse
|
40
|
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.
Collapse
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.
| |
Collapse
|
41
|
Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024; 263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [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: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
The neuroscience and neurobiology of gene editing to enhance learning and memory is of paramount interest to the scientific community. The advancements of CRISPR system have created avenues to treat neurological disorders by means of versatile modalities varying from expression to suppression of genes and proteins. Neurodegenerative disorders have also been attributed to non-canonical DNA secondary structures by affecting neuron activity through controlling gene expression, nucleosome shape, transcription, translation, replication, and recombination. Changing DNA regulatory elements which could contribute to the fate and function of neurons are thoroughly discussed in this review. This study presents the ability of CRISPR system to boost learning power and memory, treat or cure genetically-based neurological disorders, and alleviate psychiatric diseases by altering the activity and the irritability of the neurons at the synaptic cleft through DNA manipulation, and also, epigenetic modifications using Cas9. We explore and examine how each different OMIC techniques can come useful when altering DNA sequences. Such insight into the underlying relationship between OMICs and cellular behaviors leads us to better neurological and psychiatric therapeutics by intelligently designing and utilizing the CRISPR/Cas9 technology.
Collapse
Affiliation(s)
- Mohammad Banazadeh
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ardavan Abiri
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT 06520, USA
| | | | - Lida Asnaashari
- Student Research Committee, Kerman Universiy of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Langarizadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran.
| |
Collapse
|
42
|
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.
Collapse
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.
| |
Collapse
|
43
|
Liang HT, Yan JY, Yao HJ, Zhang XN, Xing ZM, Liu L, Chen YQ, Li GR, Huang J, He YD, Zheng KW. G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity. Nucleic Acids Res 2024; 52:2142-2156. [PMID: 38340342 PMCID: PMC10954455 DOI: 10.1093/nar/gkae073] [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: 10/21/2023] [Revised: 01/03/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Human DNA topoisomerase 1 (Top1) is a crucial enzyme responsible for alleviating torsional stress on DNA during transcription and replication, thereby maintaining genome stability. Previous researches had found that non-working Top1 interacted extensively with chromosomal DNA in human cells. However, the reason for its retention on chromosomal DNA remained unclear. In this study, we discovered a close association between Top1 and chromosomal DNA, specifically linked to the presence of G-quadruplex (G4) structures. G4 structures, formed during transcription, trap Top1 and hinder its ability to relax neighboring DNAs. Disruption of the Top1-G4 interaction using G4 ligand relieved the inhibitory effect of G4 on Top1 activity, resulting in a further reduction of R-loop levels in cells. Additionally, the activation of Top1 through the use of a G4 ligand enhanced the toxicity of Top1 inhibitors towards cancer cells. Our study uncovers a negative regulation mechanism of human Top1 and highlights a novel pathway for activating Top1.
Collapse
Affiliation(s)
- Hui-ting Liang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Jiang-yu Yan
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Hao-jun Yao
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Xue-nan Zhang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Zhi-ming Xing
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Lin Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yao-qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Guo-rui Li
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Jing Huang
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Yi-de He
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Ke-wei Zheng
- School of Biomedical Sciences, Hunan University, Changsha 410082, China
| |
Collapse
|
44
|
Wang Y, Wang J, Yan Z, Hou J, Wan L, Yang Y, Liu Y, Yi J, Guo P, Han D. Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS. Nucleic Acids Res 2024; 52:2698-2710. [PMID: 38266156 PMCID: PMC10954463 DOI: 10.1093/nar/gkae032] [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: 11/10/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
An expansion of AAGGG pentanucleotide repeats in the replication factor C subunit 1 (RFC1) gene is the genetic cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS), and it also links to several other neurodegenerative diseases including the Parkinson's disease. However, the pathogenic mechanism of RFC1 AAGGG repeat expansion remains enigmatic. Here, we report that the pathogenic RFC1 AAGGG repeats form DNA and RNA parallel G-quadruplex (G4) structures that play a role in impairing biological processes. We determine the first high-resolution nuclear magnetic resonance (NMR) structure of a bimolecular parallel G4 formed by d(AAGGG)2AA and reveal how AAGGG repeats fold into a higher-order structure composed of three G-tetrad layers, and further demonstrate the formation of intramolecular G4s in longer DNA and RNA repeats. The pathogenic AAGGG repeats, but not the nonpathogenic AAAAG repeats, form G4 structures to stall DNA replication and reduce gene expression via impairing the translation process in a repeat-length-dependent manner. Our results provide an unprecedented structural basis for understanding the pathogenic mechanism of AAGGG repeat expansion associated with CANVAS. In addition, the high-resolution structures resolved in this study will facilitate rational design of small-molecule ligands and helicases targeting G4s formed by AAGGG repeats for therapeutic interventions.
Collapse
Affiliation(s)
- Yang Wang
- School of Materials Science and Engineering, Tianjin University, Tianjin 300350, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Junyan Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zhenzhen Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Jianing Hou
- Institute of Molecular Medicine (IMM) Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liqi Wan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yingquan Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yu Liu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jie Yi
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Da Han
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine (IMM) Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| |
Collapse
|
45
|
Kligfeld H, Han I, Abraham A, Shukla V. Alternative DNA structures in hematopoiesis and adaptive immunity. Adv Immunol 2024; 161:109-126. [PMID: 38763699 DOI: 10.1016/bs.ai.2024.03.002] [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] [Indexed: 05/21/2024]
Abstract
Besides the canonical B-form, DNA also adopts alternative non-B form conformations which are highly conserved in all domains of life. While extensive research over decades has centered on the genomic functions of B-form DNA, understanding how non-B-form conformations influence functional genomic states remains a fundamental and open question. Recent studies have ascribed alternative DNA conformations such as G-quadruplexes and R-loops as important functional features in eukaryotic genomes. This review delves into the biological importance of alternative DNA structures, with a specific focus on hematopoiesis and adaptive immunity. We discuss the emerging roles of G-quadruplex and R-loop structures, the two most well-studied alternative DNA conformations, in the hematopoietic compartment and present evidence for their functional roles in normal cellular physiology and associated pathologies.
Collapse
Affiliation(s)
- Heather Kligfeld
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Isabella Han
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States
| | - Ajay Abraham
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Center for Human Immunobiology, Northwestern University, Chicago, IL, United States
| | - Vipul Shukla
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Center for Human Immunobiology, Northwestern University, Chicago, IL, United States; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, United States.
| |
Collapse
|
46
|
Datta S, Patel M, Sathyaseelan C, Ghosh C, Mudgal A, Patel D, Rathinavelan T, Singh U. G-quadruplex landscape and its regulation revealed by a new antibody capture method. Oncotarget 2024; 15:175-198. [PMID: 38484151 PMCID: PMC10939474 DOI: 10.18632/oncotarget.28564] [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: 10/27/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
Our understanding of DNA G-quadruplexes (G4s) from in vitro studies has been complemented by genome-wide G4 landscapes from cultured cells. Conventionally, the formation of G4s is accepted to depend on G-repeats such that they form tetrads. However, genome-wide G4s characterized through high-throughput sequencing suggest that these structures form at a large number of regions with no such canonical G4-forming signatures. Many G4-binding proteins have been described with no evidence for any protein that binds to and stabilizes G4s. It remains unknown what fraction of G4s formed in human cells are protein-bound. The G4-chromatin immunoprecipitation (G4-ChIP) method hitherto employed to describe G4 landscapes preferentially reports G4s that get crosslinked to proteins in their proximity. Our current understanding of the G4 landscape is biased against representation of G4s which escape crosslinking as they are not stabilized by protein-binding and presumably transient. We report a protocol that captures G4s from the cells efficiently without any bias as well as eliminates the detection of G4s formed artifactually on crosslinked sheared chromatin post-fixation. We discover that G4s form sparingly at SINEs. An application of this method shows that depletion of a repeat-binding protein CGGBP1 enhances net G4 capture at CGGBP1-dependent CTCF-binding sites and regions of sharp interstrand G/C-skew transitions. Thus, we present an improved method for G4 landscape determination and by applying it we show that sequence property-specific constraints of the nuclear environment mitigate G4 formation.
Collapse
Affiliation(s)
- Subhamoy Datta
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| | - Manthan Patel
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Chakkarai Sathyaseelan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi Campus, Telangana 502285, India
| | - Chandrama Ghosh
- Azrieli Faculty of Medicine, Bar-Ilan University, Henrietta Szold 8A, Safed 1311502, Israel
| | - Akanksha Mudgal
- Department of Biopharmacy, Medical University of Lublin, Lublin 20059, Poland
| | - Divyesh Patel
- Research Programs Unit, Applied Tumor Genomics Program, Faculty of Medicine, University of Helsinki, Biomedicum, Helsinki 00290, Finland
| | | | - Umashankar Singh
- HoMeCell Lab, Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat 382355, India
| |
Collapse
|
47
|
Geng Y, Liu C, Xu N, Shi X, Suen MC, Zhou B, Yan B, Wu C, Li H, Song Y, Chen X, Wang Z, Cai Q, Zhu G. The N-terminal region of Cdc6 specifically recognizes human DNA G-quadruplex. Int J Biol Macromol 2024; 260:129487. [PMID: 38237821 DOI: 10.1016/j.ijbiomac.2024.129487] [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: 10/12/2023] [Revised: 12/28/2023] [Accepted: 01/11/2024] [Indexed: 01/22/2024]
Abstract
Guanine (G)-rich nucleic acid sequences can form diverse G-quadruplex structures located in functionally significant genome regions, exerting regulatory control over essential biological processes, including DNA replication in vivo. During the initiation of DNA replication, Cdc6 is recruited by the origin recognition complex (ORC) to target specific chromosomal DNA sequences. This study reveals that human Cdc6 interacts with G-quadruplex structure through a distinct region within the N-terminal intrinsically disordered region (IDR), encompassing residues 7-20. The binding region assumes a hook-type conformation, as elucidated by the NMR solution structure in complex with htel21T18. Significantly, mutagenesis and in vivo investigations confirm the highly specific nature of Cdc6's recognition of G-quadruplex. This research enhances our understanding of the fundamental mechanism governing the interaction between G-quadruplex and the N-terminal IDR region of Cdc6, shedding light on the intricate regulation of DNA replication processes.
Collapse
Affiliation(s)
- Yanyan Geng
- Clinical Research Institute of the First Affiliated Hospital of Xiamen University, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China; Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Changdong Liu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Naining Xu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xiao Shi
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Monica Ching Suen
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Bo Zhou
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Bing Yan
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Caiming Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hui Li
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yuanjian Song
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xueqin Chen
- Clinical Research Institute of the First Affiliated Hospital of Xiamen University, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Zhanxiang Wang
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Qixu Cai
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, Xiamen, Fujian, China.
| | - Guang Zhu
- Institute for Advanced Study and State Key Laboratory of Molecular Neuroscience, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| |
Collapse
|
48
|
Pokorná P, Mlýnský V, Bussi G, Šponer J, Stadlbauer P. Molecular dynamics simulations reveal the parallel stranded d(GGGA) 3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble. Int J Biol Macromol 2024; 261:129712. [PMID: 38286387 DOI: 10.1016/j.ijbiomac.2024.129712] [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: 09/21/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/31/2024]
Abstract
G-quadruplexes (G4s) are non-canonical nucleic acid structures that fold through complex processes. Characterization of the G4 folding landscape may help to elucidate biological roles of G4s but is challenging both experimentally and computationally. Here, we achieved complete folding of a three-quartet parallel DNA G4 with (GGGA)3GGG sequence using all-atom explicit-solvent enhanced-sampling molecular dynamics (MD) simulations. The simulations suggested early formation of guanine stacks in the G-tracts, which behave as semi-rigid blocks in the folding process. The folding continues via the formation of a collapsed compact coil-like ensemble. Structuring of the G4 from the coil then proceeds via various cross-like, hairpin, slip-stranded and two-quartet ensembles and can bypass the G-triplex structure. Folding of the parallel G4 does not appear to involve any salient intermediates and is a multi-pathway process. We also carried out an extended set of simulations of parallel G-hairpins. While parallel G-hairpins are extremely unstable when isolated, they are more stable inside the coil structure. On the methodology side, we show that the AMBER DNA force field predicts the folded G4 to be less stable than the unfolded ensemble, uncovering substantial force-field issues. Overall, we provide unique atomistic insights into the folding landscape of parallel-stranded G4 but also reveal limitations of current state-of-the-art MD techniques.
Collapse
Affiliation(s)
- Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste 34136, Italy
| | - 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.
| |
Collapse
|
49
|
Guo L, Bao Y, Zhao Y, Ren Z, Bi L, Zhang X, Liu C, Hou X, Wang MD, Sun B. Joint Efforts of Replicative Helicase and SSB Ensure Inherent Replicative Tolerance of G-Quadruplex. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307696. [PMID: 38126671 PMCID: PMC10916570 DOI: 10.1002/advs.202307696] [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: 10/13/2023] [Revised: 11/28/2023] [Indexed: 12/23/2023]
Abstract
G-quadruplex (G4) is a four-stranded noncanonical DNA structure that has long been recognized as a potential hindrance to DNA replication. However, how replisomes effectively deal with G4s to avoid replication failure is still obscure. Here, using single-molecule and ensemble approaches, the consequence of the collision between bacteriophage T7 replisome and an intramolecular G4 located on either the leading or lagging strand is examined. It is found that the adjacent fork junctions induced by G4 formation incur the binding of T7 DNA polymerase (DNAP). In addition to G4, these inactive DNAPs present insuperable obstacles, impeding the progression of DNA synthesis. Nevertheless, T7 helicase can dismantle them and resolve lagging-strand G4s, paving the way for the advancement of the replication fork. Moreover, with the assistance of the single-stranded DNA binding protein (SSB) gp2.5, T7 helicase is also capable of maintaining a leading-strand G4 structure in an unfolded state, allowing for a fraction of T7 DNAPs to synthesize through without collapse. These findings broaden the functional repertoire of a replicative helicase and underscore the inherent G4 tolerance of a replisome.
Collapse
Affiliation(s)
- Lijuan Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Yanling Bao
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Yilin Zhao
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Zhiyun Ren
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Lulu Bi
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xia Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai201210China
| | - Xi‐Miao Hou
- College of Life SciencesNorthwest A&F UniversityYanglingShaanxi712100China
| | - Michelle D. Wang
- Department of Physics, Laboratory of Atomic and Solid State PhysicsCornell UniversityIthacaNY14853USA
- Howard Hughes Medical InstituteCornell UniversityIthacaNY14853USA
| | - Bo Sun
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| |
Collapse
|
50
|
Varon M, Dovrat D, Heuzé J, Tsirkas I, Singh SP, Pasero P, Galletto R, Aharoni A. Rrm3 and Pif1 division of labor during replication through leading and lagging strand G-quadruplex. Nucleic Acids Res 2024; 52:1753-1762. [PMID: 38117984 PMCID: PMC10899776 DOI: 10.1093/nar/gkad1205] [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: 01/17/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023] Open
Abstract
Members of the conserved Pif1 family of 5'-3' DNA helicases can unwind G4s and mitigate their negative impact on genome stability. In Saccharomyces cerevisiae, two Pif1 family members, Pif1 and Rrm3, contribute to the suppression of genomic instability at diverse regions including telomeres, centromeres and tRNA genes. While Pif1 can resolve lagging strand G4s in vivo, little is known regarding Rrm3 function at G4s and its cooperation with Pif1 for G4 replication. Here, we monitored replication through G4 sequences in real time to show that Rrm3 is essential for efficient replisome progression through G4s located on the leading strand template, but not on the lagging strand. We found that Rrm3 importance for replication through G4s is dependent on its catalytic activity and its N-terminal unstructured region. Overall, we show that Rrm3 and Pif1 exhibit a division of labor that enables robust replication fork progression through leading and lagging strand G4s, respectively.
Collapse
Affiliation(s)
- Mor Varon
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Daniel Dovrat
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Jonathan Heuzé
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396 Montpellier, France
| | - Ioannis Tsirkas
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Saurabh P Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, 34396 Montpellier, France
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amir Aharoni
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| |
Collapse
|