1
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Karna D, Liang L, Sharma G, Mandal S, Asamitsu S, Kawamoto Y, Hashiya K, Bando T, Sugiyama H, Mao H. Modulation of dynamic DNA G-quadruplex structures in the hTERT promoter region by ligands. Nucleic Acids Res 2024:gkae754. [PMID: 39217470 DOI: 10.1093/nar/gkae754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/09/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Small molecules can inhibit cellular processes such as replication and transcription by binding to the promoter regions that are prone to form G-quadruplexes. However, since G-quadruplexes exist throughout the human genome, the G-quadruplex binders suffer from specificity issues. To tackle this problem, a G-quadruplex binder (Pyridostatin, or PDS) is conjugated with a ligand (Polyamide, or PA) that can specifically recognize DNA sequences flanking the G-quadruplex forming region. The binding mechanism of this hybrid ligand to the hTERT promoter region (hTERT 5-12) is then elucidated using optical tweezers. During mechanical unfolding processes, different intermediate structures of hTERT 5-12 in presence of PDS, PA, or PA-PDS conjugate are observed. These intermediate structures are consistent with two folding patterns of G-quadruplexes in the hTERT 5-12 fragment. While the duplex DNA binder PA facilitates the folding of a hairpin-G-quadruplex structure, the PDS assists the formation of two tandem G-quadruplexes. Both replication stop assay in vitro and dual luciferase assay in vivo established the effectiveness of the PA-PDS conjugate for hTERT 5-12 targeting. We expect such a ligand dependent folding dynamics will provide guidelines to the development of drugs that not only target hTERT expressions, but also other oncogenes via interactions with specific G-quadruplex structures formed in their promotor regions.
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Affiliation(s)
- Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Lin Liang
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Grinsun Sharma
- School of Biomedical Science, Kent State University, Kent, OH 44242, USA
| | - Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
- School of Biomedical Science, Kent State University, Kent, OH 44242, USA
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2
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Ooga M, Sahayasheela VJ, Hirose Y, Sasaki D, Hashiya K, Bando T, Sugiyama H. A dual DNA-binding conjugate that selectively recognizes G-quadruplex structures. Chem Commun (Camb) 2024. [PMID: 39072583 DOI: 10.1039/d4cc01572j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
G-quadruplex (G4) structures play roles in various biological processes, but the challenge lies in specific targeting. To address this, we synthesized a conjugate capable of recognizing the G4 structure and its proximal duplex. Our conjugate can enable recognition of specific G4s in the human genome to understand and target those structures.
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Affiliation(s)
- Mitsuharu Ooga
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Vinodh J Sahayasheela
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Yuki Hirose
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Daisuke Sasaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan.
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3
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Roy S, Majee P, Sudhakar S, Mishra S, Kalia J, Pradeepkumar PI, Srivatsan SG. Structural elucidation of HIV-1 G-quadruplexes in a cellular environment and their ligand binding using responsive 19F-labeled nucleoside probes. Chem Sci 2024; 15:7982-7991. [PMID: 38817587 PMCID: PMC11134374 DOI: 10.1039/d4sc01755b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Understanding the structure and recognition of highly conserved regulatory segments of the integrated viral DNA genome that forms unique topologies can greatly aid in devising novel therapeutic strategies to counter chronic infections. In this study, we configured a probe system using highly environment-sensitive nucleoside analogs, 5-fluoro-2'-deoxyuridine (FdU) and 5-fluorobenzofuran-2'-deoxyuridine (FBFdU), to investigate the structural polymorphism of HIV-1 long terminal repeat (LTR) G-quadruplexes (GQs) by fluorescence and 19F NMR. FdU and FBFdU, serving as hairpin and GQ sensors, produced distinct spectral signatures for different GQ topologies adopted by LTR G-rich oligonucleotides. Importantly, systematic 19F NMR analysis in Xenopus laevis oocytes gave unprecedented information on the structure adopted by the LTR G-rich region in the cellular environment. The results indicate that it forms a unique GQ-hairpin hybrid architecture, a potent hotspot for selective targeting. Furthermore, structural models generated using MD simulations provided insights on how the probe system senses different GQs. Using the responsiveness of the probes and Taq DNA polymerase stop assay, we monitored GQ- and hairpin-specific ligand interactions and their synergistic inhibitory effect on the replication process. Our findings suggest that targeting GQ and hairpin motifs simultaneously using bimodal ligands could be a new strategy to selectively block the viral replication.
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Affiliation(s)
- Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr Homi Bhabha Road Pune 411008 India
| | - Priyasha Majee
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Satyajit Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - Jeet Kalia
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr Homi Bhabha Road Pune 411008 India
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4
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Dinh VT, Loaëc N, Quillévéré A, Le Sénéchal R, Keruzoré M, Martins RP, Granzhan A, Blondel M. The hide-and-seek game of the oncogenic Epstein-Barr virus-encoded EBNA1 protein with the immune system: An RNA G-quadruplex tale. Biochimie 2023; 214:57-68. [PMID: 37473831 DOI: 10.1016/j.biochi.2023.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023]
Abstract
The Epstein-Barr virus (EBV) is the first oncogenic virus described in human. EBV infects more than 90% of the human population worldwide, but most EBV infections are asymptomatic. After the primary infection, the virus persists lifelong in the memory B cells of the infected individuals. Under certain conditions the virus can cause several human cancers, that include lymphoproliferative disorders such as Burkitt and Hodgkin lymphomas and non-lymphoid malignancies such as 100% of nasopharyngeal carcinoma and 10% of gastric cancers. Each year, about 200,000 EBV-related cancers emerge, hence accounting for at least 1% of worldwide cancers. Like all gammaherpesviruses, EBV has evolved a strategy to escape the host immune system. This strategy is mainly based on the tight control of the expression of its Epstein-Barr nuclear antigen-1 (EBNA1) protein, the EBV-encoded genome maintenance protein. Indeed, EBNA1 is essential for viral genome replication and maintenance but, at the same time, is also highly antigenic and T cells raised against EBNA1 exist in infected individuals. For this reason, EBNA1 is considered as the Achilles heel of EBV and the virus has seemingly evolved a strategy that employs the binding of nucleolin, a host cell factor, to RNA G-quadruplex (rG4) within EBNA1 mRNA to limit its expression to the minimal level required for function while minimizing immune recognition. This review recapitulates in a historical way the knowledge accumulated on EBNA1 immune evasion and discusses how this rG4-dependent mechanism can be exploited as an intervention point to unveil EBV-related cancers to the immune system.
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Affiliation(s)
- Van-Trang Dinh
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France.
| | - Nadège Loaëc
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | - Alicia Quillévéré
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | - Ronan Le Sénéchal
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | - Marc Keruzoré
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | | | - Anton Granzhan
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Marc Blondel
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France.
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5
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Deiana M, Andrés Castán J, Josse P, Kahsay A, Sánchez D, Morice K, Gillet N, Ravindranath R, Patel A, Sengupta P, Obi I, Rodriguez-Marquez E, Khrouz L, Dumont E, Abad Galán L, Allain M, Walker B, Ahn HS, Maury O, Blanchard P, Le Bahers T, Öhlund D, von Hofsten J, Monnereau C, Cabanetos C, Sabouri N. A new G-quadruplex-specific photosensitizer inducing genome instability in cancer cells by triggering oxidative DNA damage and impeding replication fork progression. Nucleic Acids Res 2023; 51:6264-6285. [PMID: 37191066 PMCID: PMC10325911 DOI: 10.1093/nar/gkad365] [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: 11/06/2022] [Revised: 03/31/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Photodynamic therapy (PDT) ideally relies on the administration, selective accumulation and photoactivation of a photosensitizer (PS) into diseased tissues. In this context, we report a new heavy-atom-free fluorescent G-quadruplex (G4) DNA-binding PS, named DBI. We reveal by fluorescence microscopy that DBI preferentially localizes in intraluminal vesicles (ILVs), precursors of exosomes, which are key components of cancer cell proliferation. Moreover, purified exosomal DNA was recognized by a G4-specific antibody, thus highlighting the presence of such G4-forming sequences in the vesicles. Despite the absence of fluorescence signal from DBI in nuclei, light-irradiated DBI-treated cells generated reactive oxygen species (ROS), triggering a 3-fold increase of nuclear G4 foci, slowing fork progression and elevated levels of both DNA base damage, 8-oxoguanine, and double-stranded DNA breaks. Consequently, DBI was found to exert significant phototoxic effects (at nanomolar scale) toward cancer cell lines and tumor organoids. Furthermore, in vivo testing reveals that photoactivation of DBI induces not only G4 formation and DNA damage but also apoptosis in zebrafish, specifically in the area where DBI had accumulated. Collectively, this approach shows significant promise for image-guided PDT.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | | | - Pierre Josse
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
| | - Abraha Kahsay
- Department of Integrative Medical Biology, Umeå University, SE-901 87, Umeå, Sweden
| | | | - Korentin Morice
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
| | - Natacha Gillet
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Ranjitha Ravindranath
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
- Indian Institute for Science Education and Research (IISER), Tirupati-517507, India
| | - Ankit Kumar Patel
- Department of Radiation Sciences/Oncology, Umeå University, SE-901 87, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-901 87, Umeå, Sweden
| | - Pallabi Sengupta
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | | | - Lhoussain Khrouz
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Elise Dumont
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| | - Laura Abad Galán
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Magali Allain
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
| | - Bright Walker
- Department of Chemistry, Kyung Hee University, Seoul, 02447, South Korea
| | - Hyun Seo Ahn
- Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, South Korea
| | - Olivier Maury
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | | | - Tangui Le Bahers
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| | - Daniel Öhlund
- Department of Radiation Sciences/Oncology, Umeå University, SE-901 87, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-901 87, Umeå, Sweden
| | - Jonas von Hofsten
- Department of Integrative Medical Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Cyrille Monnereau
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Clément Cabanetos
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
- Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, South Korea
- Building Blocks for FUture Electronics Laboratory (2BFUEL), IRL CNRS 2002, Yonsei University, Seoul, South Korea
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
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6
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Fang J, Xie C, Tao Y, Wei D. An overview of single-molecule techniques and applications in the study of nucleic acid structure and function. Biochimie 2023; 206:1-11. [PMID: 36179939 DOI: 10.1016/j.biochi.2022.09.014] [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: 03/08/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/02/2022]
Abstract
Nucleic acids are an indispensable component in all known life forms. The biological processes are regulated by Nucleic acids, which associate to form special high-order structures. since the high-level structures of nucleic acids are related to gene expression in cancer cells or viruses, it is very likely to become a potential drug target. Traditional biochemical methods are limited to distinguish the conformational distribution and dynamic transition process of single nucleic acid structure. The ligands based on the intermediate and transition states between different conformations are not designed by traditional biochemical methods. The single-molecule techniques enable real-time observation of the individual nucleic acid behavior due to its high resolution. Here, we introduce the application of single-molecule techniques in the study of small molecules to recognize nucleic acid structures, such as single-molecule FRET, magnetic tweezers, optical tweezers and atomic force microscopy. At the same time, we also introduce the specific advantages of single-molecule technology compared with traditional biochemical methods and some problems arisen in current research.
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Affiliation(s)
- Junkang Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Huazhong Agricultural University, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Congbao Xie
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Huazhong Agricultural University, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yanfei Tao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Huazhong Agricultural University, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Huazhong Agricultural University, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
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7
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Pokhrel P, Ren K, Shen H, Mao H. Mechanical Stability of DNA Corona Phase on Gold Nanospheres. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13569-13576. [PMID: 36305083 PMCID: PMC10318588 DOI: 10.1021/acs.langmuir.2c02251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Noncovalent adsorption of biopolymers on the surface of gold nanoparticles (AuNPs) forms a corona phase that drastically diversify AuNP functions. However, mechanical stabilities of such corona phase are still obscure, hindering the application of biopolymer-coated AuNPs. Here, using optical tweezers, we have observed, for the first time, that DNA corona phase adsorbed on a 5 nm AuNP via two (dA)21 strands in proximity can withstand an average desorption force of 40 pN, which is higher than the stall force of DNA/RNA polymerases. This suggests a new role for AuNPs to modulate replications or transcriptions after binding to prevalent poly(dA) segments in eukaryotic genomes. We have also revealed that with increasing AuNP size (1.8-10 nm), DNA corona becomes harder to remove, likely due to the larger surfaces and flatter facets on bigger AuNPs. These findings provide guidance to design AuNP corona that can withstand harsh environments for biological and materials applications.
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Affiliation(s)
- Pravin Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Kehao Ren
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Hao Shen
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
- Advanced materials and liquid crystal institute, Kent State University, Kent, OH 44242, USA
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8
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Chowdhury S, Wang J, Nuccio SP, Mao H, Di Antonio M. Short LNA-modified oligonucleotide probes as efficient disruptors of DNA G-quadruplexes. Nucleic Acids Res 2022; 50:7247-7259. [PMID: 35801856 PMCID: PMC9303293 DOI: 10.1093/nar/gkac569] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/09/2022] [Accepted: 06/18/2022] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (G4s) are well known non-canonical DNA secondary structures that can form in human cells. Most of the tools available to investigate G4-biology rely on small molecule ligands that stabilise these structures. However, the development of probes that disrupt G4s is equally important to study their biology. In this study, we investigated the disruption of G4s using Locked Nucleic Acids (LNA) as invader probes. We demonstrated that strategic positioning of LNA-modifications within short oligonucleotides (10 nts.) can significantly accelerate the rate of G4-disruption. Single-molecule experiments revealed that short LNA-probes can promote disruption of G4s with mechanical stability sufficient to stall polymerases. We corroborated this using a single-step extension assay, revealing that short LNA-probes can relieve replication dependent polymerase-stalling at G4 sites. We further demonstrated the potential of such LNA-based probes to study G4-biology in cells. By using a dual-luciferase assay, we found that short LNA probes can enhance the expression of c-KIT to levels similar to those observed when the c-KIT promoter is mutated to prevent the formation of the c-KIT1 G4. Collectively, our data suggest a potential use of rationally designed LNA-modified oligonucleotides as an accessible chemical-biology tool for disrupting individual G4s and interrogating their biological functions in cells.
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Affiliation(s)
- Souroprobho Chowdhury
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Jiayi Wang
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Sabrina Pia Nuccio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Marco Di Antonio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK.,The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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9
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Jonchhe S, Pandey S, Beneze C, Emura T, Sugiyama H, Endo M, Mao H. Dissection of nanoconfinement and proximity effects on the binding events in DNA origami nanocavity. Nucleic Acids Res 2022; 50:697-703. [PMID: 35037040 PMCID: PMC8789071 DOI: 10.1093/nar/gkab1298] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/06/2021] [Accepted: 01/09/2022] [Indexed: 12/02/2022] Open
Abstract
Both ligand binding and nanocavity can increase the stability of a biomolecular structure. Using mechanical unfolding in optical tweezers, here we found that a DNA origami nanobowl drastically increased the stability of a human telomeric G-quadruplex bound with a pyridostatin (PDS) ligand. Such a stability change is equivalent to >4 orders of magnitude increase (upper limit) in binding affinity (Kd: 490 nM → 10 pM (lower limit)). Since confined space can assist the binding through a proximity effect between the ligand-receptor pair and a nanoconfinement effect that is mediated by water molecules, we named such a binding as mechanochemical binding. After minimizing the proximity effect by using PDS that can enter or leave the DNA nanobowl freely, we attributed the increased affinity to the nanoconfinement effect (22%) and the proximity effect (78%). This represents the first quantification to dissect the effects of proximity and nanoconfinement on binding events in nanocavities. We anticipate these DNA nanoassemblies can deliver both chemical (i.e. ligand) and mechanical (i.e. nanocavity) milieus to facilitate robust mechanochemical binding in various biological systems.
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Affiliation(s)
- Sagun Jonchhe
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Shankar Pandey
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Christian Beneze
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.,Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Osaka 564-8680, Japan
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
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10
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Chen JN, He YD, Liang HT, Cai TT, Chen Q, Zheng KW. Regulation of PDGFR-β gene expression by targeting the G-vacancy bearing G-quadruplex in promoter. Nucleic Acids Res 2021; 49:12634-12643. [PMID: 34850916 PMCID: PMC8682790 DOI: 10.1093/nar/gkab1154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex is an essential element in gene transcription that serves as a promising drug target. Guanine-vacancy-bearing G-quadruplex (GVBQ) is a newly identified G-quadruplex that has distinct structural features from the canonical G-quadruplex. Potential GVBQ-forming motifs are widely distributed in gene promoter regions. However, whether GVBQ can form in genomic DNA and be an effective target for manipulating gene expression is unknown. Using photo-crosslinking, dimethyl sulfate footprinting, exonuclease digestion and in vitro transcription, we demonstrated the formation of a GVBQ in the G-rich nuclease hypersensitivity element within the human PDGFR-β gene promoter region in both single-stranded and double-stranded DNA. The formation of GVBQ in dsDNA could be induced by negative supercoiling created by downstream transcription. We also found that the PDGFR-β GVBQ was specifically recognized and stabilized by a new synthetic porphyrin guanine conjugate (mPG). Targeting the PDGFR-β GVBQ in human cancer cells using the mPG could specifically alter PDGFR-β gene expression. Our work illustrates that targeting GVBQ with mPG in human cells can regulate the expression level of a specific gene, thus indicating a novel strategy for drug development.
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Affiliation(s)
- Juan-Nan Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Yi-de He
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China.,School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Hui-Ting Liang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Ting-Ting Cai
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Qi Chen
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Ke-Wei Zheng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
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11
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Cheng Y, Zhang Y, You H. Characterization of G-Quadruplexes Folding/Unfolding Dynamics and Interactions with Proteins from Single-Molecule Force Spectroscopy. Biomolecules 2021; 11:1579. [PMID: 34827577 PMCID: PMC8615981 DOI: 10.3390/biom11111579] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 12/19/2022] Open
Abstract
G-quadruplexes (G4s) are stable secondary nucleic acid structures that play crucial roles in many fundamental biological processes. The folding/unfolding dynamics of G4 structures are associated with the replication and transcription regulation functions of G4s. However, many DNA G4 sequences can adopt a variety of topologies and have complex folding/unfolding dynamics. Determining the dynamics of G4s and their regulation by proteins remains challenging due to the coexistence of multiple structures in a heterogeneous sample. Here, in this mini-review, we introduce the application of single-molecule force-spectroscopy methods, such as magnetic tweezers, optical tweezers, and atomic force microscopy, to characterize the polymorphism and folding/unfolding dynamics of G4s. We also briefly introduce recent studies using single-molecule force spectroscopy to study the molecular mechanisms of G4-interacting proteins.
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Affiliation(s)
| | | | - Huijuan You
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Y.C.); (Y.Z.)
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12
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Paul R, Dutta D, Das T, Debnath M, Dash J. G4 Sensing Pyridyl-Thiazole Polyamide Represses c-KIT Expression in Leukemia Cells. Chemistry 2021; 27:8590-8599. [PMID: 33851760 DOI: 10.1002/chem.202100907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 12/27/2022]
Abstract
Specific sensing and functional tuning of nucleic acid secondary structures remain less explored to date. Herein, we report a thiazole polyamide TPW that binds specifically to c-KIT1 G-quadruplex (G4) with sub-micromolar affinity and ∼1 : 1 stoichiometry and represses c-KIT proto-oncogene expression. TPW shows up to 10-fold increase in fluorescence upon binding with c-KIT1 G4, but shows weak or no quantifiable binding to other G4s and ds26 DNA. TPW can increase the number of G4-specific antibody (BG4) foci and mark G4 structures in cancer cells. Cell-based assays reveal that TPW can efficiently repress c-KIT expression in leukemia cells via a G4-dependent process. Thus, the polyamide can serve as a promising probe for G-quadruplex recognition with the ability to specifically alter c-KIT oncogene expression.
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Affiliation(s)
- Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Tania Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
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13
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Li X, Wang M, Zheng W, Huang W, Wang Z, Jin K, Liu L, Yu Z. Dynamics of TRF1 organizing a single human telomere. Nucleic Acids Res 2021; 49:760-775. [PMID: 33347580 PMCID: PMC7826288 DOI: 10.1093/nar/gkaa1222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 11/13/2022] Open
Abstract
Chromosome stability is primarily determined by telomere length. TRF1 is the core subunit of shelterin that plays a critical role in telomere organization and replication. However, the dynamics of TRF1 in scenarios of telomere-processing activities remain elusive. Using single-molecule magnetic tweezers, we here investigated the dynamics of TRF1 upon organizing a human telomere and the protein-DNA interactions at a moving telomeric fork. We first developed a method to obtain telomeres from human cells for directly measuring the telomere length by single-molecule force spectroscopy. Next, we examined the compaction and decompaction of a telomere by TRF1 dimers. TRF1 dissociates from a compacted telomere with heterogenous loops in ∼20 s. We also found a negative correlation between the number of telomeric loops and loop sizes. We further characterized the dynamics of TRF1 at a telomeric DNA fork. With binding energies of 11 kBT, TRF1 can modulate the forward and backward steps of DNA fork movements by 2-9 s at a critical force of F1/2, temporarily maintaining the telomeric fork open. Our results shed light on the mechanisms of how TRF1 organizes human telomeres and facilitates the efficient replication of telomeric DNA. Our work will help future research on the chemical biology of telomeres and shelterin-targeted drug discovery.
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Affiliation(s)
- Xu Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 38 Tongyan Road, Tianjin 300350, China
| | - Meijie Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 38 Tongyan Road, Tianjin 300350, China
| | - Wei Zheng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 38 Tongyan Road, Tianjin 300350, China
| | - Wei Huang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 38 Tongyan Road, Tianjin 300350, China
| | - Zeyu Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 38 Tongyan Road, Tianjin 300350, China
| | - Kairang Jin
- State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 38 Tongyan Road, Tianjin 300350, China
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14
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Zhang M, Liang J, Jiang SK, Xu L, Wu YL, Awadasseid A, Zhao XY, Xiong XQ, Sugiyama H, Zhang W. Design, synthesis and anti-cancer activity of pyrrole-imidazole polyamides through target-downregulation of c-kit gene expression. Eur J Med Chem 2020; 207:112704. [DOI: 10.1016/j.ejmech.2020.112704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/12/2020] [Accepted: 07/28/2020] [Indexed: 12/18/2022]
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15
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Tan DJY, Winnerdy FR, Lim KW, Phan AT. Coexistence of two quadruplex-duplex hybrids in the PIM1 gene. Nucleic Acids Res 2020; 48:11162-11171. [PMID: 32976598 PMCID: PMC7641742 DOI: 10.1093/nar/gkaa752] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/31/2022] Open
Abstract
The triple-negative breast cancer (TNBC), a subtype of breast cancer which lacks of targeted therapies, exhibits a poor prognosis. It was shown recently that the PIM1 oncogene is highly related to the proliferation of TNBC cells. A quadruplex-duplex hybrid (QDH) forming sequence was recently found to exist near the transcription start site of PIM1. This structure could be an attractive target for regulation of the PIM1 gene expression and thus the treatment of TNBC. Here, we present the solution structures of two QDHs that could coexist in the human PIM1 gene. Form 1 is a three-G-tetrad-layered (3+1) G-quadruplex containing a propeller loop, a lateral loop and a stem-loop made up of three G•C Watson-Crick base pairs. On the other hand, Form 2 is an anti-parallel G-quadruplex comprising two G-tetrads and a G•C•G•C tetrad; the structure has three lateral loops with the middle stem-loop made up of two Watson-Crick G•C base pairs. These structures provide valuable information for the design of G-quadruplex-specific ligands for PIM1 transcription regulation.
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Affiliation(s)
- Derrick J Y Tan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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16
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Ngoc Nguyen TQ, Lim KW, Phan AT. Duplex formation in a G-quadruplex bulge. Nucleic Acids Res 2020; 48:10567-10575. [PMID: 32960213 PMCID: PMC7544226 DOI: 10.1093/nar/gkaa738] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 01/05/2023] Open
Abstract
Beyond the consensus definition of G-quadruplex-forming motifs with tracts of continuous guanines, G-quadruplexes harboring bulges in the G-tetrad core are prevalent in the human genome. Here, we study the incorporation of a duplex hairpin within a bulge of a G-quadruplex. The NMR solution structure of a G-quadruplex containing a duplex bulge was resolved, revealing the structural details of the junction between the duplex bulge and the G-quadruplex. Unexpectedly, instead of an orthogonal connection the duplex stem was observed to stack below the G-quadruplex forming a unique quadruplex–duplex junction. Breaking up of the immediate base pair step at the junction, coupled with a narrowing of the duplex groove within the context of the bulge, led to a progressive transition between the quadruplex and duplex segments. This study revealed that a duplex bulge can be formed at various positions of a G-quadruplex scaffold. In contrast to a non-structured bulge, the stability of a G-quadruplex slightly increases with an increase in the duplex bulge size. A G-quadruplex structure containing a duplex bulge of up to 33 nt in size was shown to form, which was much larger than the previously reported 7-nt bulge. With G-quadruplexes containing duplex bulges representing new structural motifs with potential biological significance, our findings would broaden the definition of potential G-quadruplex-forming sequences.
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Affiliation(s)
- Thi Quynh Ngoc Nguyen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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17
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Ma TZ, Zhang MJ, Liao TC, Li JH, Zou M, Wang ZM, Zhou CQ. Dimers formed with the mixed-type G-quadruplex binder pyridostatin specifically recognize human telomere G-quadruplex dimers. Org Biomol Chem 2020; 18:920-930. [DOI: 10.1039/c9ob02470k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
By adjusting the length of the polyether linkers, pyridostatin (PDS) dimers displayed higher binding selectivities and thermal stabilization towards human telomere antiparallel and mixed-type G-quadruplex dimers (G2T1).
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Affiliation(s)
- Tian-Zhu Ma
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Meng-Jia Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Ting-Cong Liao
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Jun-Hui Li
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Min Zou
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Zhou-Mo Wang
- Medical School
- Science and Technology College of Hubei University for Nationalities
- Enshi 445000
- P. R. China
| | - Chun-Qiong Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
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18
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Tsvetkov VB, Varizhuk AM, Lizunova SA, Nikolenko TA, Ivanov IA, Severov VV, Belyaev ES, Shitikov EA, Pozmogova GE, Aralov AV. Phenoxazine-based scaffold for designing G4-interacting agents. Org Biomol Chem 2020; 18:6147-6154. [DOI: 10.1039/d0ob00983k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A phenoxazine-based scaffold with one or two positively charged arms for selectively G4 stabilizing was synthesized and probed.
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Affiliation(s)
- Vladimir B. Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
- I.M. Sechenov First Moscow State Medical University
- Moscow 119991
| | - Anna M. Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency
| | - Sofia A. Lizunova
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
- Moscow Institute of Physics and Technology
- Moscow region 141700
| | - Tatiana A. Nikolenko
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
- Moscow Institute of Physics and Technology
- Moscow region 141700
| | - Igor A. Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- Moscow 117997
- Russia
| | - Vjacheslav V. Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
| | - Evgeny S. Belyaev
- Frumkin Institute of Physical Chemistry and Electrochemistry
- Moscow 119071
- Russia
| | - Egor A. Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
| | - Galina E. Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine
- Moscow 119435
- Russia
| | - Andrey V. Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- Moscow 117997
- Russia
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