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Andreeva DV, Vedekhina TS, Gostev AS, Dezhenkova LG, Volodina YL, Markova AA, Nguyen MT, Ivanova OM, Dolgusheva VА, Varizhuk AM, Tikhomirov AS, Shchekotikhin AE. Thiadiazole-, selenadiazole- and triazole-fused anthraquinones as G-quadruplex targeting anticancer compounds. Eur J Med Chem 2024; 268:116222. [PMID: 38387333 DOI: 10.1016/j.ejmech.2024.116222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
G-quadruplex (G4) ligands attract considerable attention as potential anticancer therapeutics. In this study we proposed an original scheme for synthesis of azole-fused anthraquinones and prepared a series of G4 ligands carrying amino- or guanidinoalkylamino side chains. The heterocyclic core and structure of the terminal groups strongly affect on binding to G4-forming oligonucleotides, cellular accumulation and antitumor potency of compounds. In particular, thiadiazole- and selenadiazole- but not triazole-based ligands inhibit the proliferation of tumor cells (e.g. K562 leukemia) and stabilize primarily telomeric and c-MYC G4s. Anthraselenadiazole derivative 11a showed a good affinity to c-MYC G4 in vitro and down-regulated expression of c-MYC oncogene in cellular conditions. Further studies revealed that anthraselenadiazole 11a provoked cell cycle arrest and apoptosis in a dose- and time-dependent manner inhibiting K562 cells growth. Taken together, this work gives a valuable example that the closely related heterocycles may cause a significant difference in biological properties of G4 ligands.
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Affiliation(s)
- Daria V Andreeva
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow, 119021, Russia
| | - Tatiana S Vedekhina
- Lopukhin Federal Research and Clinical Center of Physico-Chemical Medicine, Federal Medical Biological Agency, 119435, Moscow, Malaya Pirogovskaya, 1a, Russia; Lomonosov Institute of Fine Chemical Technologies, MIREA - Russian Technological University, 119571, Moscow, Russia
| | - Alexander S Gostev
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow, 119021, Russia; Mendeleev University of Chemical Technology of Russia, 125047, Moscow, Miusskaya square, 9, Russia
| | - Lyubov G Dezhenkova
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow, 119021, Russia
| | - Yulia L Volodina
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow, 119021, Russia; Blokhin National Medical Center of Oncology, 24 Kashirskoye Shosse, Moscow, 115478, Russia
| | - Alina A Markova
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygin Street, 4, Moscow, 119334, Russia
| | - Minh Tuan Nguyen
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygin Street, 4, Moscow, 119334, Russia
| | - Olga M Ivanova
- Lopukhin Federal Research and Clinical Center of Physico-Chemical Medicine, Federal Medical Biological Agency, 119435, Moscow, Malaya Pirogovskaya, 1a, Russia
| | - Vladislava А Dolgusheva
- Lopukhin Federal Research and Clinical Center of Physico-Chemical Medicine, Federal Medical Biological Agency, 119435, Moscow, Malaya Pirogovskaya, 1a, Russia; Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Anna M Varizhuk
- Lopukhin Federal Research and Clinical Center of Physico-Chemical Medicine, Federal Medical Biological Agency, 119435, Moscow, Malaya Pirogovskaya, 1a, Russia; Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
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2
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Monsen RC. Higher-order G-quadruplexes in promoters are untapped drug targets. Front Chem 2023; 11:1211512. [PMID: 37351517 PMCID: PMC10282141 DOI: 10.3389/fchem.2023.1211512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid secondary structures that form within guanine-rich regions of chromatin. G4 motifs are abundant in the genome, with a sizable proportion (∼40%) existing within gene promoter regions. G4s are proven epigenetic features that decorate the promoter landscape as binding centers for transcription factors. Stabilizing or disrupting promoter G4s can directly influence adjacent gene transcription, making G4s attractive as indirect drug targets for hard-to-target proteins, particularly in cancer. However, no G4 ligands have progressed through clinical trials, mostly owing to off targeting effects. A major hurdle in G4 drug discovery is the lack of distinctiveness of the small monomeric G4 structures currently used as receptors. This mini review describes and contrasts monomeric and higher-order G-quadruplex structure and function and provides a rationale for switching focus to the higher-order forms as selective molecular targets. The human telomerase reverse transcriptase (hTERT) core promoter G-quadruplex is then used as a case study that highlights the potential for higher-order G4s as selective indirect inhibitors of hard-to-target proteins in cancer.
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3
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D'Anna L, Rubino S, Pipitone C, Serio G, Gentile C, Palumbo Piccionello A, Giannici F, Barone G, Terenzi A. Salphen metal complexes as potential anticancer agents: interaction profile and selectivity studies toward the three G-quadruplex units in the KIT promoter. Dalton Trans 2023; 52:2966-2975. [PMID: 36444991 DOI: 10.1039/d2dt03229e] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
DNA G-rich sequences can organize in four-stranded structures called G-quadruplexes (G4s). These motifs are enriched in significant sites within the human genomes, including telomeres and promoters of cancer related genes. For instance, KIT proto-oncogene promoter, associated with diverse cancers, contains three adjacent G4 units, namely Kit2, SP, and Kit1. Aiming at finding new and selective G-quadruplex binders, we have synthesized and characterized five non-charged metal complexes of Pt(II), Pd(II), Ni(II), Cu(II) and Zn(II) of a chlorine substituted Salphen ligand. The crystal structure of the Pt(II) and Pd(II) complexes was determined by XRPD. FRET measurements indicated that Pt(II) and Pd(II) compounds stabilize Kit1 and Kit2 G4s but not SP, telomeric and double stranded DNA. Spectroscopic investigations (UV-Vis, circular dichroism and fluorescence) suggested the Cu(II) complex as the most G4-selective compound. Interestingly, docking simulations indicate that the synthesized compounds fit groove binding pockets of both Kit1 and Kit2 G4s. Moreover, they exhibited dose-dependent cytotoxic activity in MCF-7, HepG2 and HeLa cancer cells.
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Affiliation(s)
- Luisa D'Anna
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy.
| | - Simona Rubino
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy.
| | - Candida Pipitone
- Department of Physics and Chemistry "Emilio Segrè", University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy
| | - Graziella Serio
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy.
| | - Carla Gentile
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy.
| | - Antonio Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy.
| | - Francesco Giannici
- Department of Physics and Chemistry "Emilio Segrè", University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy.
| | - Alessio Terenzi
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy.
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4
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Kristoffersen E, Coletta A, Lund L, Schiøtt B, Birkedal V. Inhibited complete folding of consecutive human telomeric G-quadruplexes. Nucleic Acids Res 2023; 51:1571-1582. [PMID: 36715345 PMCID: PMC9976873 DOI: 10.1093/nar/gkad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 12/24/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Noncanonical DNA structures, termed G-quadruplexes, are present in human genomic DNA and are important elements in many DNA metabolic processes. Multiple sites in the human genome have G-rich DNA stretches able to support formation of several consecutive G-quadruplexes. One of those sites is the telomeric overhang region that has multiple repeats of TTAGGG and is tightly associated with both cancer and aging. We investigated the folding of consecutive G-quadruplexes in both potassium- and sodium-containing solutions using single-molecule FRET spectroscopy, circular dichroism, thermal melting and molecular dynamics simulations. Our observations show coexistence of partially and fully folded DNA, the latter consisting of consecutive G-quadruplexes. Following the folding process over hours in sodium-containing buffers revealed fast G-quadruplex folding but slow establishment of thermodynamic equilibrium. We find that full consecutive G-quadruplex formation is inhibited by the many DNA structures randomly nucleating on the DNA, some of which are off-path conformations that need to unfold to allow full folding. Our study allows describing consecutive G-quadruplex formation in both nonequilibrium and equilibrium conditions by a unified picture, where, due to the many possible DNA conformations, full folding with consecutive G-quadruplexes as beads on a string is not necessarily achieved.
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Affiliation(s)
- Emil Laust Kristoffersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Andrea Coletta
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Line Mørkholt Lund
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Birgit Schiøtt
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
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5
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The Promoter Region of the Proto-Oncogene MST1R Contains the Main Features of G-Quadruplexes Formation. Int J Mol Sci 2022; 23:ijms232112905. [PMID: 36361696 PMCID: PMC9653784 DOI: 10.3390/ijms232112905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 11/26/2022] Open
Abstract
MST1R (RON) is a receptor of the MET tyrosine kinase receptor family involved in several cancers such as pancreas, breast, ovary, colon, and stomach. Some studies have shown that overexpression of MST1R increases the migratory and invasive properties of cancer cells. The promoter region of the oncogene MST1R is enriched in guanine residues that can potentially form G-quadruplexes (G4s), as it was observed in other oncogenic promoters such as KRAS and c-MYC. There is abundant literature that links the presence of G4s in promoter regions of oncogenes to diverse gene regulation processes that are not well understood. In this work, we have studied the reverse and forward sequence of MST1R promoter region using the G4Hunter software and performed biophysical studies to characterize the best scored sequences.
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6
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Cozzaglio M, Ceschi S, Groaz E, Sturlese M, Sissi C. G-quadruplexes formation within the promoter of TEAD4 oncogene and their interaction with Vimentin. Front Chem 2022; 10:1008075. [PMID: 36186582 PMCID: PMC9520404 DOI: 10.3389/fchem.2022.1008075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
G-quadruplexes (G4s) are nucleic acid secondary structures detected within human chromosomes, that cluster at gene promoters and enhancers. This suggests that G4s may play specific roles in the regulation of gene expression. Within a distinct subgroup of G-rich domains, the formation of two or more adjacent G4 units (G4-repeats) is feasible. Recently it was shown that Vimentin, a protein highly expressed within mesenchymal cells, selectively recognizes these arrangements. Putative G4-repeats have been searched within the human gene proximal promoters by the bioinformatics tool QPARSE and they resulted to be enriched at genes related to epithelial-to-mesenchymal transition (EMT). This suggested that Vimentin binding at these sites might be relevant for the maintenance of the mesenchymal phenotype. Among all the identified sequences, in the present study we selected the one located within the promoter of the TEAD4 oncogene. TEAD4 codifies for a transcriptional enhancer factor, TEAD4, that actively promotes EMT, supporting, cell proliferation and migration. Moreover, in colorectal cancer cells TEAD4 directly enhances the expression of Vimentin. Thus, the possible interaction of Vimentin with TEAD4 promoter could highlight a positive feedback loop between these two factors, associated to important tumor metastasis related events. Here, we exploited spectroscopic and electrophoretic measurements under different conditions to address the folding behavior of the selected sequence. This allowed us to validate the folding of TEAD4 promoter into a G4-repeat able to interact with Vimentin.
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Affiliation(s)
- Marta Cozzaglio
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Elisabetta Groaz
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
- KU Leuven, Rega Institute for Medical Research, KU Leuven, Medicinal Chemistry, Leuven, Belgium
| | - Mattia Sturlese
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
- *Correspondence: Claudia Sissi,
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7
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Monsen RC, DeLeeuw LW, Dean W, Gray R, Chakravarthy S, Hopkins J, Chaires J, Trent J. Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc, k-Ras and c-Kit promoter sequences. Nucleic Acids Res 2022; 50:4127-4147. [PMID: 35325198 PMCID: PMC9023277 DOI: 10.1093/nar/gkac182] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022] Open
Abstract
We report on higher-order G-quadruplex structures adopted by long promoter sequences obtained by an iterative integrated structural biology approach. Our approach uses quantitative biophysical tools (analytical ultracentrifugation, small-angle X-ray scattering, and circular dichroism spectroscopy) combined with modeling and molecular dynamics simulations, to derive self-consistent structural models. The formal resolution of our approach is 18 angstroms, but in some cases structural features of only a few nucleotides can be discerned. We report here five structures of long (34-70 nt) wild-type sequences selected from three cancer-related promoters: c-Myc, c-Kit and k-Ras. Each sequence studied has a unique structure. Three sequences form structures with two contiguous, stacked, G-quadruplex units. One longer sequence from c-Myc forms a structure with three contiguous stacked quadruplexes. A longer c-Kit sequence forms a quadruplex-hairpin structure. Each structure exhibits interfacial regions between stacked quadruplexes or novel loop geometries that are possible druggable targets. We also report methodological advances in our integrated structural biology approach, which now includes quantitative CD for counting stacked G-tetrads, DNaseI cleavage for hairpin detection and SAXS model refinement. Our results suggest that higher-order quadruplex assemblies may be a common feature within the genome, rather than simple single quadruplex structures.
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Affiliation(s)
- Robert C Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Lynn W DeLeeuw
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - William L Dean
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Robert D Gray
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jonathan B Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
| | - John O Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
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8
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Rigo R, Groaz E, Sissi C. Polymorphic and Higher-Order G-Quadruplexes as Possible Transcription Regulators: Novel Perspectives for Future Anticancer Therapeutic Applications. Pharmaceuticals (Basel) 2022; 15:ph15030373. [PMID: 35337170 PMCID: PMC8950063 DOI: 10.3390/ph15030373] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/06/2023] Open
Abstract
In the past two decades, significant efforts have been put into designing small molecules to target selected genomic sites where DNA conformational rearrangements control gene expression. G-rich sequences at oncogene promoters are considered good points of intervention since, under specific environmental conditions, they can fold into non-canonical tetrahelical structures known as G-quadruplexes. However, emerging evidence points to a frequent lack of correlation between small molecule targeting of G-quadruplexes at gene promoters and the expression of the associated protein, which hampers pharmaceutical applications. The wide genomic localization of G-quadruplexes along with their highly polymorphic behavior may account for this scenario, suggesting the need for more focused drug design strategies. Here, we will summarize the G4 structural features that can be considered to fulfill this goal. In particular, by comparing a telomeric sequence with the well-characterized G-rich domain of the KIT promoter, we will address how multiple secondary structures might cooperate to control genome architecture at a higher level. If this holds true, the link between drug–DNA complex formation and the associated cellular effects will need to be revisited.
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Affiliation(s)
- Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Marzolo 5, 35131 Padova, Italy; (R.R.); (E.G.)
- CEITEC—Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Elisabetta Groaz
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Marzolo 5, 35131 Padova, Italy; (R.R.); (E.G.)
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000 Leuven, Belgium
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Marzolo 5, 35131 Padova, Italy; (R.R.); (E.G.)
- Correspondence:
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9
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Mendes E, Aljnadi IM, Bahls B, Victor BL, Paulo A. Major Achievements in the Design of Quadruplex-Interactive Small Molecules. Pharmaceuticals (Basel) 2022; 15:ph15030300. [PMID: 35337098 PMCID: PMC8953082 DOI: 10.3390/ph15030300] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022] Open
Abstract
Organic small molecules that can recognize and bind to G-quadruplex and i-Motif nucleic acids have great potential as selective drugs or as tools in drug target discovery programs, or even in the development of nanodevices for medical diagnosis. Hundreds of quadruplex-interactive small molecules have been reported, and the challenges in their design vary with the intended application. Herein, we survey the major achievements on the therapeutic potential of such quadruplex ligands, their mode of binding, effects upon interaction with quadruplexes, and consider the opportunities and challenges for their exploitation in drug discovery.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
| | - Israa M. Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bruno L. Victor
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Correspondence:
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10
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Ceschi S, Berselli M, Cozzaglio M, Giantin M, Toppo S, Spolaore B, Sissi C. Vimentin binds to G-quadruplex repeats found at telomeres and gene promoters. Nucleic Acids Res 2022; 50:1370-1381. [PMID: 35100428 PMCID: PMC8860586 DOI: 10.1093/nar/gkab1274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/22/2021] [Accepted: 01/24/2022] [Indexed: 11/15/2022] Open
Abstract
G-quadruplex (G4) structures that can form at guanine-rich genomic sites, including telomeres and gene promoters, are actively involved in genome maintenance, replication, and transcription, through finely tuned interactions with protein networks. In the present study, we identified the intermediate filament protein Vimentin as a binder with nanomolar affinity for those G-rich sequences that give rise to at least two adjacent G4 units, named G4 repeats. This interaction is supported by the N-terminal domains of soluble Vimentin tetramers. The selectivity of Vimentin for G4 repeats versus individual G4s provides an unprecedented result. Based on GO enrichment analysis performed on genes having putative G4 repeats within their core promoters, we suggest that Vimentin recruitment at these sites may contribute to the regulation of gene expression during cell development and migration, possibly by reshaping the local higher-order genome topology, as already reported for lamin B.
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Affiliation(s)
- Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | - Michele Berselli
- Department of Molecular Medicine, University of Padova, Padova 35131, Italy
| | - Marta Cozzaglio
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro 35020, Italy
| | - Stefano Toppo
- CRIBI Biotechnology Center (Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative), University of Padova, Padova 35131, Italy
- Department of Molecular Medicine, University of Padova, Padova 35131, Italy
| | - Barbara Spolaore
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
- CRIBI Biotechnology Center (Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative), University of Padova, Padova 35131, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
- CRIBI Biotechnology Center (Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative), University of Padova, Padova 35131, Italy
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11
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Grün JT, Schwalbe H. Folding dynamics of polymorphic G-quadruplex structures. Biopolymers 2021; 113:e23477. [PMID: 34664713 DOI: 10.1002/bip.23477] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/14/2022]
Abstract
G-quadruplexes (G4), found in numerous places within the human genome, are involved in essential processes of cell regulation. Chromosomal DNA G4s are involved for example, in replication and transcription as first steps of gene expression. Hence, they influence a plethora of downstream processes. G4s possess an intricate structure that differs from canonical B-form DNA. Identical DNA G4 sequences can adopt multiple long-lived conformations, a phenomenon known as G4 polymorphism. A detailed understanding of the molecular mechanisms that drive G4 folding is essential to understand their ambivalent regulatory roles. Disentangling the inherent dynamic and polymorphic nature of G4 structures thus is key to unravel their biological functions and make them amenable as molecular targets in novel therapeutic approaches. We here review recent experimental approaches to monitor G4 folding and discuss structural aspects for possible folding pathways. Substantial progress in the understanding of G4 folding within the recent years now allows drawing comprehensive models of the complex folding energy landscape of G4s that we herein evaluate based on computational and experimental evidence.
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Affiliation(s)
- J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt/M, Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/M, Germany
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12
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Vesco G, Lamperti M, Salerno D, Marrano CA, Cassina V, Rigo R, Buglione E, Bondani M, Nicoletto G, Mantegazza F, Sissi C, Nardo L. Double-stranded flanking ends affect the folding kinetics and conformational equilibrium of G-quadruplexes forming sequences within the promoter of KIT oncogene. Nucleic Acids Res 2021; 49:9724-9737. [PMID: 34478543 PMCID: PMC8464035 DOI: 10.1093/nar/gkab674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/13/2021] [Accepted: 09/01/2021] [Indexed: 12/01/2022] Open
Abstract
G-quadruplexes embedded within promoters play a crucial role in regulating the gene expression. KIT is a widely studied oncogene, whose promoter contains three G-quadruplex forming sequences, c-kit1, c-kit2 and c-kit*. For these sequences available studies cover ensemble and single-molecule analyses, although for kit* the latter were limited to a study on a promoter domain comprising all of them. Recently, c-kit2 has been reported to fold according to a multi-step process involving folding intermediates. Here, by exploiting fluorescence resonance energy transfer, both in ensemble and at the single molecule level, we investigated the folding of expressly designed constructs in which, alike in the physiological context, either c-kit2 or c-kit* are flanked by double stranded DNA segments. To assess whether the presence of flanking ends at the borders of the G-quadruplex affects the folding, we studied under the same protocols oligonucleotides corresponding to the minimal G-quadruplex forming sequences. Data suggest that addition of flanking ends results in biasing both the final equilibrium state and the folding kinetics. A previously unconsidered aspect is thereby unravelled, which ought to be taken into account to achieve a deeper insight of the complex relationships underlying the fine tuning of the gene-regulatory properties of these fascinating DNA structures.
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Affiliation(s)
- Guglielmo Vesco
- Department of Science and High Technology, University of Insubria, 22100 Como, Italy
| | - Marco Lamperti
- Department of Physics, Polytechnic of Milan, 23900 Lecco, Italy
| | - Domenico Salerno
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Claudia Adriana Marrano
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Valeria Cassina
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Enrico Buglione
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Maria Bondani
- Institute for Photonics and Nanotechnology, IFN-CNR, 22100 Como, Italy
| | - Giulia Nicoletto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Francesco Mantegazza
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Luca Nardo
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
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13
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Peterková K, Durník I, Marek R, Plavec J, Podbevšek P. c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry. Nucleic Acids Res 2021; 49:8947-8960. [PMID: 34365512 PMCID: PMC8421218 DOI: 10.1093/nar/gkab659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022] Open
Abstract
Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.
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Affiliation(s)
- Kateřina Peterková
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Ivo Durník
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Radek Marek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Janez Plavec
- Slovenian NMR Centre, 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
| | - Peter Podbevšek
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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14
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Buglione E, Salerno D, Marrano CA, Cassina V, Vesco G, Nardo L, Dacasto M, Rigo R, Sissi C, Mantegazza F. Nanomechanics of G-quadruplexes within the promoter of the KIT oncogene. Nucleic Acids Res 2021; 49:4564-4573. [PMID: 33849064 PMCID: PMC8096272 DOI: 10.1093/nar/gkab079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/07/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes (G4s) are tetrahelical DNA structures stabilized by four guanines paired via Hoogsteen hydrogen bonds into quartets. While their presence within eukaryotic DNA is known to play a key role in regulatory processes, their functional mechanisms are still under investigation. In the present work, we analysed the nanomechanical properties of three G4s present within the promoter of the KIT proto-oncogene from a single-molecule point of view through the use of magnetic tweezers (MTs). The study of DNA extension fluctuations under negative supercoiling allowed us to identify a characteristic fingerprint of G4 folding. We further analysed the energetic contribution of G4 to the double-strand denaturation process in the presence of negative supercoiling, and we observed a reduction in the energy required for strands separation.
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Affiliation(s)
- Enrico Buglione
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Domenico Salerno
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Claudia Adriana Marrano
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Valeria Cassina
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Guglielmo Vesco
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Luca Nardo
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro (PD), Italy
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova (PD), Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova (PD), Italy.,Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, 35121 Padova (PD), Italy
| | - Francesco Mantegazza
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
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15
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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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16
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Cagirici HB, Budak H, Sen TZ. Genome-wide discovery of G-quadruplexes in barley. Sci Rep 2021; 11:7876. [PMID: 33846409 PMCID: PMC8041835 DOI: 10.1038/s41598-021-86838-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/19/2021] [Indexed: 12/04/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.
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Affiliation(s)
- H Busra Cagirici
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA
| | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT, USA.,Agrogen, LLC., Omaha, NE, USA
| | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA.
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17
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Laddachote S, Ishii R, Yoshida W. Effects of CpG methylation on the thermal stability of c-kit2, c-kit*, and c-kit1 G-quadruplex structures. BBA ADVANCES 2021; 1:100007. [PMID: 37082005 PMCID: PMC10074881 DOI: 10.1016/j.bbadva.2021.100007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/24/2021] [Accepted: 03/10/2021] [Indexed: 11/25/2022] Open
Abstract
In genomic DNA, G-quadruplex (G4)-forming DNA can form either a duplex or G4 structure, suggesting that understanding the factors regulating G4 formation is important for revealing the cellular functions controlled by G4 formation. Cytosine DNA methylation in the CpG islands is known to play an important role in transcriptional regulation. Additionally, CpG methylation increases the thermal stability of G4 structures such as BCL2 and VEGF G4. In this study, we evaluated the effects of CpG methylation in three G4 structures (c-kit2, c-kit*, and c-kit1) produced by the c-KIT promoter. Each was analyzed using circular dichroism (CD) melting analysis. The results demonstrate that CpG methylation does not alter the thermal stability of c-kit2 G4 structure when formed in the presence of K+; a single-CpG methylation at C1 or C11 decreases the thermal stability of any c-kit2 G4 structure formed in the presence of Na+ and Mg2+ while methylation at C5 increases the thermal stability; CpG methylation does not alter the thermal stability of c-kit1 or c-kit* G4 structures formed in the presence of K+; and the c-kit1 and c-kit* G4-forming oligonucleotides do not form G4 structures in the presence of Na+ and Mg2+. These results provide important clues for understanding the regulatory mechanisms underlying the formation of CpG methylation-induced G4 structures.
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18
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Da Ros S, Nicoletto G, Rigo R, Ceschi S, Zorzan E, Dacasto M, Giantin M, Sissi C. G-Quadruplex Modulation of SP1 Functional Binding Sites at the KIT Proximal Promoter. Int J Mol Sci 2020; 22:E329. [PMID: 33396937 PMCID: PMC7795597 DOI: 10.3390/ijms22010329] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/27/2020] [Indexed: 11/17/2022] Open
Abstract
The regulation of conformational arrangements of gene promoters is a physiological mechanism that has been associated with the fine control of gene expression. Indeed, it can drive the time and the location for the selective recruitment of proteins of the transcriptional machinery. Here, we address this issue at the KIT proximal promoter where three G-quadruplex forming sites are present (kit1, kit2 and kit*). On this model, we focused on the interplay between G-quadruplex (G4) formation and SP1 recruitment. By site directed mutagenesis, we prepared a library of plasmids containing mutated sequences of the WT KIT promoter that systematically exploited different G4 formation attitudes and SP1 binding properties. Our transfection data showed that the three different G4 sites of the KIT promoter impact on SP1 binding and protein expression at different levels. Notably, kit2 and kit* structural features represent an on-off system for KIT expression through the recruitment of transcription factors. The use of two G4 binders further helps to address kit2-kit* as a reliable target for pharmacological intervention.
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Affiliation(s)
- Silvia Da Ros
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, 35131 Padua, Italy; (S.D.R.); (G.N.); (R.R.); (S.C.)
| | - Giulia Nicoletto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, 35131 Padua, Italy; (S.D.R.); (G.N.); (R.R.); (S.C.)
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, 35131 Padua, Italy; (S.D.R.); (G.N.); (R.R.); (S.C.)
| | - Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, 35131 Padua, Italy; (S.D.R.); (G.N.); (R.R.); (S.C.)
| | - Eleonora Zorzan
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020 Legnaro, Italy; (E.Z.); (M.D.)
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020 Legnaro, Italy; (E.Z.); (M.D.)
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020 Legnaro, Italy; (E.Z.); (M.D.)
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, 35131 Padua, Italy; (S.D.R.); (G.N.); (R.R.); (S.C.)
- CRIBI Biotechnology Center (Centro di Ricerca Interdipartimentale per le Biotecnologie Innovative), University of Padua, 35131 Padua, Italy
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19
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Comez L, Bianchi F, Libera V, Longo M, Petrillo C, Sacchetti F, Sebastiani F, D'Amico F, Rossi B, Gessini A, Masciovecchio C, Amenitsch H, Sissi C, Paciaroni A. Polymorphism of human telomeric quadruplexes with drugs: a multi-technique biophysical study. Phys Chem Chem Phys 2020; 22:11583-11592. [PMID: 32400802 DOI: 10.1039/d0cp01483d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human telomeric G-quadruplex structural motif of DNA has come to be known as a new and stimulating target for anticancer drug discovery. Small molecules that interact with G-quadruplex structures in a selective way have gained impressive interest in recent years as they may serve as potential therapeutic agents. Here, we show how circular dichroism, UV resonance Raman and small angle X-ray scattering spectroscopies can be effectively combined to provide insights into structural and molecular aspects of the interaction between human telomeric quadruplexes and ligands. This study focuses on the ability of berberine and palmatine to bind with human telomeric quadruplexes and provides analysis of the conformational landscape visited by the relevant complexes upon thermal unfolding. With increasing temperature, both free and bound G-quadruplexes undergo melting through a multi-state process, populating different intermediate states. Despite the structural similarity of the two ligands, valuable distinctive features characterising their interaction with the G-quadruplex emerged from our multi-technique approach.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Bianchi
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - V Libera
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - M Longo
- JCNS Forschungszentrum Jülich GmbH at Heinz Maier-Leibnitz Zentrum (MLZ), 85748 Garching, Germany
| | - C Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Sebastiani
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | - F D'Amico
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - B Rossi
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - A Gessini
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - C Masciovecchio
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - H Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - C Sissi
- Dipartimento di Scienze del Farmaco, Via Marzolo 5, 35131 Padova, Italy and Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, University of Padova, Italy
| | - A Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
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20
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Salsbury AM, Dean TJ, Lemkul JA. Polarizable Molecular Dynamics Simulations of Two c-kit Oncogene Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling. J Chem Theory Comput 2020; 16:3430-3444. [PMID: 32307997 DOI: 10.1021/acs.jctc.0c00191] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
G-quadruplexes (GQs) are highly ordered nucleic acid structures that play fundamental roles in regulating gene expression and maintaining genomic stability. GQs are topologically diverse and enriched in promoter sequences of growth regulatory genes and proto-oncogenes, suggesting that they may serve as attractive targets for drug design at the level of transcription rather than inhibiting the activity of the protein products of these genes. The c-kit promoter contains three adjacent GQ-forming sequences that have proposed antagonistic effects on gene expression and thus are promising drug targets for diseases such as gastrointestinal stromal tumors, mast cell disease, and leukemia. Because GQ stability is influenced by primary structure, secondary structure, and ion interactions, a greater understanding of GQ structure, dynamics, and ion binding properties is needed to develop novel, GQ-targeting therapeutics. Here, we performed molecular dynamics simulations to systematically study the c-kit2 and c-kit* GQs, evaluating nonpolarizable and polarizable force fields (FFs) and examining the effects of base substitutions and cation type (K+, Na+, and Li+) on the dynamics of their isolated and linked structures. We found that the Drude polarizable FF outperformed the additive CHARMM36 FF in two- and three-tetrad GQs and solutions of KCl, NaCl, and LiCl. Drude simulations with different cations agreed with the known GQ stabilization preference (K+ > Na+ > Li+) and illustrated that tetrad core-ion coordination differs as a function of cation type. Finally, we showed that differences in primary and secondary structure influence loop sampling, ion binding, and core-ion energetics of GQs.
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Affiliation(s)
- Alexa M Salsbury
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Tanner J Dean
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Justin A Lemkul
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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21
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Gao T, Luo Y, Li W, Cao Y, Pei R. Progress in the isolation of aptamers to light-up the dyes and the applications. Analyst 2020; 145:701-718. [DOI: 10.1039/c9an01825e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The progress in the selection of aptamers to light-up the dyes and the related applications are reviewed.
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Affiliation(s)
- Tian Gao
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Yu Luo
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
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22
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Kotar A, Rigo R, Sissi C, Plavec J. Two-quartet kit* G-quadruplex is formed via double-stranded pre-folded structure. Nucleic Acids Res 2019; 47:2641-2653. [PMID: 30590801 PMCID: PMC6411839 DOI: 10.1093/nar/gky1269] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/16/2018] [Accepted: 12/10/2018] [Indexed: 01/13/2023] Open
Abstract
In the promoter of c-KIT proto-oncogene, whose deregulation has been implicated in many cancers, three G-rich regions (kit1, kit* and kit2) are able to fold into G-quadruplexes. While kit1 and kit2 have been studied in depth, little information is available on kit* folding behavior despite its key role in regulation of c-KIT transcription. Notably, kit* contains consensus sites for SP1 and AP2 transcription factors. Herein, a set of complementary spectroscopic and biophysical methods reveals that kit*, d[GGCGAGGAGGGGCGTGGCCGGC], adopts a chair type antiparallel G-quadruplex with two G-quartets at physiological relevant concentrations of KCl. Heterogeneous ensemble of structures is observed in the presence of Na+ and NH4+ ions, which however stabilize pre-folded structure. In the presence of K+ ions stacking interactions of adenine and thymine residues on the top G-quartet contribute to structural stability together with a G10•C18 base pair and a fold-back motif of the five residues at the 3′-terminal under the bottom G-quartet. The 3′-tail enables formation of a bimolecular pre-folded structure that drives folding of kit* into a single G-quadruplex. Intriguingly, kinetics of kit* G-quadruplex formation matches timescale of transcriptional processes and might demonstrate interplay of kinetic and thermodynamic factors for understanding regulation of c-KIT proto-oncogene expression.
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Affiliation(s)
- Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, 1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.,EN-FIST Center of Excellence, 1000 Ljubljana, Slovenia
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23
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Kolesnikova S, Curtis EA. Structure and Function of Multimeric G-Quadruplexes. Molecules 2019; 24:molecules24173074. [PMID: 31450559 PMCID: PMC6749722 DOI: 10.3390/molecules24173074] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes are noncanonical nucleic acid structures formed from stacked guanine tetrads. They are frequently used as building blocks and functional elements in fields such as synthetic biology and also thought to play widespread biological roles. G-quadruplexes are often studied as monomers, but can also form a variety of higher-order structures. This increases the structural and functional diversity of G-quadruplexes, and recent evidence suggests that it could also be biologically important. In this review, we describe the types of multimeric topologies adopted by G-quadruplexes and highlight what is known about their sequence requirements. We also summarize the limited information available about potential biological roles of multimeric G-quadruplexes and suggest new approaches that could facilitate future studies of these structures.
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Affiliation(s)
- Sofia Kolesnikova
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Edward A Curtis
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic.
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24
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Conserved G-Quadruplexes Regulate the Immediate Early Promoters of Human Alphaherpesviruses. Molecules 2019; 24:molecules24132375. [PMID: 31252527 PMCID: PMC6651000 DOI: 10.3390/molecules24132375] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 01/15/2023] Open
Abstract
Human Alphaherpesviruses comprise three members, herpes simplex virus (HSV) 1 and 2 and varicella zoster virus (VZV). These viruses are characterized by a lytic cycle in epithelial cells and latency in the nervous system, with lifelong infections that may periodically reactivate and lead to serious complications, especially in immunocompromised patients. The mechanisms that regulate viral transcription have not been fully elucidated, but the master role of the immediate early (IE) genes has been established. G-quadruplexes are non-canonical nucleic-acid structures that control transcription, replication, and recombination in many organisms including viruses and that represent attractive antiviral targets. In this work, we investigate the presence, conservation, folding and activity of G-quadruplexes in the IE promoters of the Alphaherpesviruses. Our analysis shows that all IE promoters in the genome of HSV-1, HSV-2 and VZV contain fully conserved G-quadruplex forming sequences. These comprise sequences with long loops and bulges, and thus deviating from the classic G-quadruplex motifs. Moreover, their location is both on the leading and lagging strand and in some instances they contain exuberant G-tracts. Biophysical and biological analysis proved that all sequences actually fold into G-quadruplex under physiological conditions and can be further stabilized by the G-quadruplex ligand BRACO-19, with subsequent impairment of viral IE gene transcription in cells. These results help shed light on the control of viral transcription and indicate new viral targets to design drugs that impair the early steps of Alphaherpesviruses. In addition, they validate the significance of G-quadruplexes in the general regulation of viral cycles.
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25
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Ducani C, Bernardinelli G, Högberg B, Keppler BK, Terenzi A. Interplay of Three G-Quadruplex Units in the KIT Promoter. J Am Chem Soc 2019; 141:10205-10213. [PMID: 31244182 DOI: 10.1021/jacs.8b12753] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proto-oncogene KIT encodes for a tyrosine kinase receptor, which is a clinically validated target for treating gastrointestinal stromal tumors. The KIT promoter contains a G-rich domain within a relatively long sequence potentially able to form three adjacent G-quadruplex (G4) units, namely, K2, SP, and K1. These G4 domains have been studied mainly as single quadruplex units derived from short truncated sequences and are currently considered promising targets for anticancer drugs, alternatively to the encoded protein. Nevertheless, the information reported so far does not contemplate the interplay between those neighboring G4s in the context of the whole promoter, possibly thwarting drug-discovery efforts. Here we report the structural and functional study of the KIT promoter core sequence, in both single- and double-stranded forms, which includes all three predicted G4 units. By preventing the formation of alternatively one or two G4 units and by combining biophysical techniques and biological assays, we show for the first time that these quadruplexes cannot be analyzed independently, but they are correlated to each other. Our data suggest that, while K2 and K1 G-rich sequences retain the ability to fold into parallel G4 motifs within a long sequence, the SP G-rich domain contributes to G4 structure only together with K2. Remarkably, we have found that, in the context of a dynamic equilibrium between the three G4 units, the G4 formed by K1 has the most significant influence on the structure stability and on the biological role of the whole promoter.
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Affiliation(s)
- Cosimo Ducani
- Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm 171 65 , Sweden
| | - Giulio Bernardinelli
- Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm 171 65 , Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm 171 65 , Sweden
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry , University of Vienna , Waehringerstrasse 42 , A-1090 Vienna , Austria
| | - Alessio Terenzi
- Institute of Inorganic Chemistry , University of Vienna , Waehringerstrasse 42 , A-1090 Vienna , Austria
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26
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Distinct biological responses of metastatic castration resistant prostate cancer cells upon exposure to G-quadruplex interacting naphthalenediimide derivatives. Eur J Med Chem 2019; 177:401-413. [PMID: 31158753 DOI: 10.1016/j.ejmech.2019.05.066] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 12/23/2022]
Abstract
Small molecules able to bind non-canonical G-quadruplex DNA structures (G4) have been recently tested as novel potential agents for the treatment of prostate cancer thanks to their repression of aberrant androgen receptor gene. However, metastatic castration-resistant prostate cancer (mCRPC), a letal form of prostate cancer, is still incurable. Here we tested two naphthalenediimide derivatives, previously reported as multitarget agents, on a couple of relevant mCRPC cell models (DU145 and PC-3). We showed that these compounds interfere with the RAS/MEK/ERK and PI3K/AKT pathways. Interestingly, both these two biological processes depend upon Epidermal Growth Factor Receptor (EGFR) activation. By means of biological and analytical tools we showed that our compounds are efficient inducers of the structural transition of the EGFR promoter towards a G-quadruplex conformation, ultimately leading to a reduction of the receptor production. The overall result is an interesting cytotoxic profile for these two derivatives. Thanks to their activity at different steps, these compounds can open the way to novel therapeutic approaches for mCRPC that could contribute to escape resistance to selective treatments.
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27
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Bull GD, Thompson KC. Proton Transfer and Tautomerism in 2-Aminopurine-Thymine and Pyrrolocytosine-Guanine Base Pairs. Biochemistry 2018; 57:4547-4561. [PMID: 30024730 DOI: 10.1021/acs.biochem.8b00521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Pyrrolocytosine (PC) and 2-aminopurine (2AP) are fluorescent nucleobase analogues of the DNA nucleobases cytosine and adenine, respectively, and form base pairs with guanine and thymine. Both fluorescent nucleobases are used extensively as probes for local structure in nucleic acids as the fluorescence properties of PC and 2AP are very sensitive to changes such as helix formation, although the reasons for this sensitivity are not clear. To address this question, ab initio calculations have been used to calculate energies, at the MP2 and CIS level, of three different tautomer pairings of PC-G, and two of 2AP-T, which can potentially be interconverted by double proton transfer between the bases. Potential energy curves linking the different tautomer pairs have been calculated. For both PC-G and 2AP-T, the most stable tautomer pair in the electronic ground state is that analogous to the natural C-G and A-T base pair. In the case of 2AP-T, an alternative, stable, tautomer base pair was located in the first electronically excited state; however, it lies higher in energy than the tautomer pair analogous to A-T, making conversion to the alternative form unlikely. In contrast, in the case of PC-G, an alternative tautomer base pair is found to be the most stable form in the first electronically excited state, and this form is accessible following initial excitation from the ground state tautomer pair, thus suggesting an alternative deactivation route via double proton transfer may be possible when PC is involved in hydrogen bonding, such as occurs in helical conformations.
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Affiliation(s)
- Graham D Bull
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck , University of London , Malet Street , Bloomsbury, London WC1E 7HX , U.K
| | - Katherine C Thompson
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck , University of London , Malet Street , Bloomsbury, London WC1E 7HX , U.K
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