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D'Errico S, Falanga AP, Greco F, Piccialli G, Oliviero G, Borbone N. State of art in the chemistry of nucleoside-based Pt(II) complexes. Bioorg Chem 2023; 131:106325. [PMID: 36577221 DOI: 10.1016/j.bioorg.2022.106325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/22/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
After the fortuitous discovery of the anticancer properties of cisplatin, many Pt(II) complexes have been synthesized, to obtain less toxic leads which could overcome the resistance phenomena. Given the importance of nucleosides and nucleotides as antimetabolites, studying their coordinating properties towards Pt(II) ions is challenging for bioorganic and medicinal chemistry. This review aims to describe the results achieved so far in the aforementioned field, paying particular attention to the synthetic aspects, the chemical-physical characterization, and the biological activities of the nucleoside-based Pt(II) complexes.
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Affiliation(s)
- Stefano D'Errico
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano, 49, 80131 Naples, Italy.
| | - Andrea Patrizia Falanga
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano, 49, 80131 Naples, Italy.
| | - Francesca Greco
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano, 49, 80131 Naples, Italy.
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano, 49, 80131 Naples, Italy.
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini, 5, 80131 Naples, Italy.
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano, 49, 80131 Naples, Italy.
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2
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Falanga AP, Terracciano M, Oliviero G, Roviello GN, Borbone N. Exploring the Relationship between G-Quadruplex Nucleic Acids and Plants: From Plant G-Quadruplex Function to Phytochemical G4 Ligands with Pharmaceutic Potential. Pharmaceutics 2022; 14:2377. [PMID: 36365194 PMCID: PMC9698481 DOI: 10.3390/pharmaceutics14112377] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/19/2022] [Accepted: 11/01/2022] [Indexed: 10/31/2023] Open
Abstract
G-quadruplex (G4) oligonucleotides are higher-order DNA and RNA secondary structures of enormous relevance due to their implication in several biological processes and pathological states in different organisms. Strategies aiming at modulating human G4 structures and their interrelated functions are first-line approaches in modern research aiming at finding new potential anticancer treatments or G4-based aptamers for various biomedical and biotechnological applications. Plants offer a cornucopia of phytocompounds that, in many cases, are effective in binding and modulating the thermal stability of G4s and, on the other hand, contain almost unexplored G4 motifs in their genome that could inspire new biotechnological strategies. Herein, we describe some G4 structures found in plants, summarizing the existing knowledge of their functions and biological role. Moreover, we review some of the most promising G4 ligands isolated from vegetal sources and report on the known relationships between such phytochemicals and G4-mediated biological processes that make them potential leads in the pharmaceutical sector.
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Affiliation(s)
- Andrea P. Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Giovanni N. Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
- Institute of Applied Sciences and Intelligent Systems, Italian National Council of Research (ISASI-CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
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3
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Exploring the Parallel G-Quadruplex Nucleic Acid World: A Spectroscopic and Computational Investigation on the Binding of the c-myc Oncogene NHE III1 Region by the Phytochemical Polydatin. Molecules 2022; 27:molecules27092997. [PMID: 35566347 PMCID: PMC9099682 DOI: 10.3390/molecules27092997] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 02/04/2023] Open
Abstract
Trans-polydatin (tPD), the 3-β-D-glucoside of the well-known nutraceutical trans-resveratrol, is a natural polyphenol with documented anti-cancer, anti-inflammatory, cardioprotective, and immunoregulatory effects. Considering the anticancer activity of tPD, in this work, we aimed to explore the binding properties of this natural compound with the G-quadruplex (G4) structure formed by the Pu22 [d(TGAGGGTGGGTAGGGTGGGTAA)] DNA sequence by exploiting CD spectroscopy and molecular docking simulations. Pu22 is a mutated and shorter analog of the G4-forming sequence known as Pu27 located in the promoter of the c-myc oncogene, whose overexpression triggers the metabolic changes responsible for cancer cells transformation. The binding of tPD with the parallel Pu22 G4 was confirmed by CD spectroscopy, which showed significant changes in the CD spectrum of the DNA and a slight thermal stabilization of the G4 structure. To gain a deeper insight into the structural features of the tPD-Pu22 complex, we performed an in silico molecular docking study, which indicated that the interaction of tPD with Pu22 G4 may involve partial end-stacking to the terminal G-quartet and H-bonding interactions between the sugar moiety of the ligand and deoxynucleotides not included in the G-tetrads. Finally, we compared the experimental CD profiles of Pu22 G4 with the corresponding theoretical output obtained using DichroCalc, a web-based server normally used for the prediction of proteins’ CD spectra starting from their “.pdb” file. The results indicated a good agreement between the predicted and the experimental CD spectra in terms of the spectral bands’ profile even if with a slight bathochromic shift in the positive band, suggesting the utility of this predictive tool for G4 DNA CD investigations.
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Cadoni E, De Paepe L, Manicardi A, Madder A. Beyond small molecules: targeting G-quadruplex structures with oligonucleotides and their analogues. Nucleic Acids Res 2021; 49:6638-6659. [PMID: 33978760 PMCID: PMC8266634 DOI: 10.1093/nar/gkab334] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022] Open
Abstract
G-Quadruplexes (G4s) are widely studied secondary DNA/RNA structures, naturally occurring when G-rich sequences are present. The strategic localization of G4s in genome areas of crucial importance, such as proto-oncogenes and telomeres, entails fundamental implications in terms of gene expression regulation and other important biological processes. Although thousands of small molecules capable to induce G4 stabilization have been reported over the past 20 years, approaches based on the hybridization of a synthetic probe, allowing sequence-specific G4-recognition and targeting are still rather limited. In this review, after introducing important general notions about G4s, we aim to list, explain and critically analyse in more detail the principal approaches available to target G4s by using oligonucleotides and synthetic analogues such as Locked Nucleic Acids (LNAs) and Peptide Nucleic Acids (PNAs), reporting on the most relevant examples described in literature to date.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
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Virgilio A, Benigno D, Pecoraro A, Russo A, Russo G, Esposito V, Galeone A. Exploring New Potential Anticancer Activities of the G-Quadruplexes Formed by [(GTG 2T(G 3T) 3] and Its Derivatives with an Abasic Site Replacing Single Thymidine. Int J Mol Sci 2021; 22:ijms22137040. [PMID: 34208896 PMCID: PMC8268168 DOI: 10.3390/ijms22137040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 12/27/2022] Open
Abstract
In this paper, we report our investigations on five T30175 analogues, prepared by replacing sequence thymidines with abasic sites (S) one at a time, in comparison to their natural counterpart in order to evaluate their antiproliferative potential and the involvement of the residues not belonging to the central core of stacked guanosines in biological activity. The collected NMR (Nuclear Magnetic Resonance), CD (Circular Dichroism), and PAGE (Polyacrylamide Gel Electrophoresis) data strongly suggest that all of them adopt G-quadruplex (G4) structures strictly similar to that of the parent aptamer with the ability to fold into a dimeric structure composed of two identical G-quadruplexes, each characterized by parallel strands, three all-anti-G-tetrads and four one-thymidine loops (one bulge and three propeller loops). Furthermore, their antiproliferative (MTT assay) and anti-motility (wound healing assay) properties against lung and colorectal cancer cells were tested. Although all of the oligodeoxynucleotides (ODNs) investigated here exhibited anti-proliferative activity, the unmodified T30175 aptamer showed the greatest effect on cell growth, suggesting that both its characteristic folding in dimeric form and its presence in the sequence of all thymidines are crucial elements for antiproliferative activity. This straightforward approach is suitable for understanding the critical requirements of the G-quadruplex structures that affect antiproliferative potential and suggests its application as a starting point to facilitate the reasonable development of G-quadruplexes with improved anticancer properties.
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Promoter G-quadruplex favours epigenetic reprogramming-induced atypical expression of ZEB1 in cancer cells. Biochim Biophys Acta Gen Subj 2021; 1865:129899. [PMID: 33930476 DOI: 10.1016/j.bbagen.2021.129899] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/17/2021] [Accepted: 04/06/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Aberrant expression of Zinc-finger E-box binding homeobox 1 (ZEB1), which remains repressed in normal cells, is frequently associated with cancer aggressiveness. However, transcriptional mechanism underlying such atypical ZEB1 expression in cancer is not yet well-understood. METHODS ZEB1 promoter G-quadruplexes were studied and modeled extensively using circular dichroism, fluorescence spectroscopy, ITC and DMS protection assay. Luciferase assay, qPCR, FAIRE, ChIP, western blotting, confocal microscopy was used to access the regulation of ZEB1 transcription. RESULTS Our study unravels the occupancy of nucleolin to ZEB1 promoter as a crucial determinant which facilitates the binding of SP1 transcription factor to chromatin, by locally remodelling the region. SP1, subsequently, recruits P300 acetyl transferase leading to enriched acetyl-histone H3 at promoter and activates ZEB1 transcription. ZEB1 promoter analysis identifies presence of four putative G-quadruplex (G4) forming motifs within 700 bp of TSS; each quadruplex is characterized structurally in details with an array of biophysical techniques. Surprisingly, stabilization of G4 with cationic porphyrin TMPyP4 represses its transcription and eventually impedes cell invasiveness. CONCLUSIONS TMPyP4 binding to a selected G4 motif (5' -534/-511-3' from TSS), where nucleolin/SP1/P300 co-occupies, prevents the association of nucleolin which consequently hinders SP1 binding, leading to chromatin compactness and transcriptional repression. GENERAL SIGNIFICANCE Our findings demonstrate an epigenetic mechanism of ZEB1 reactivation where dynamic occupancy of transcription regulators encompassing a G4 motif is crucial and thus, small molecule induced G-quadruplex stabilization may act as a potential molecular switch to turn-off gene expression.
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Schult P, Paeschke K. The DEAH helicase DHX36 and its role in G-quadruplex-dependent processes. Biol Chem 2020; 402:581-591. [PMID: 33021960 DOI: 10.1515/hsz-2020-0292] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023]
Abstract
DHX36 is a member of the DExD/H box helicase family, which comprises a large number of proteins involved in various cellular functions. Recently, the function of DHX36 in the regulation of G-quadruplexes (G4s) was demonstrated. G4s are alternative nucleic acid structures, which influence many cellular pathways on a transcriptional and post-transcriptional level. In this review we provide an overview of the current knowledge about DHX36 structure, substrate specificity, and mechanism of action based on the available models and crystal structures. Moreover, we outline its multiple functions in cellular homeostasis, immunity, and disease. Finally, we discuss the open questions and provide potential directions for future research.
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Affiliation(s)
- Philipp Schult
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, D-53127Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, D-53127Bonn, Germany
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8
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Chu B, Zhang D, Paukstelis PJ. A DNA G-quadruplex/i-motif hybrid. Nucleic Acids Res 2020; 47:11921-11930. [PMID: 31724696 PMCID: PMC7145706 DOI: 10.1093/nar/gkz1008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/08/2019] [Accepted: 11/08/2019] [Indexed: 01/23/2023] Open
Abstract
DNA can form many structures beyond the canonical Watson–Crick double helix. It is now clear that noncanonical structures are present in genomic DNA and have biological functions. G-rich G-quadruplexes and C-rich i-motifs are the most well-characterized noncanonical DNA motifs that have been detected in vivo with either proscribed or postulated biological roles. Because of their independent sequence requirements, these structures have largely been considered distinct types of quadruplexes. Here, we describe the crystal structure of the DNA oligonucleotide, d(CCAGGCTGCAA), that self-associates to form a quadruplex structure containing two central antiparallel G-tetrads and six i-motif C–C+ base pairs. Solution studies suggest a robust structural motif capable of assembling as a tetramer of individual strands or as a dimer when composed of tandem repeats. This hybrid structure highlights the growing structural diversity of DNA and suggests that biological systems may harbor many functionally important non-duplex structures.
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Affiliation(s)
- Betty Chu
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Daoning Zhang
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Paul J Paukstelis
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
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Pandith A, Siddappa RG, Seo YJ. Recent developments in novel blue/green/red/NIR small fluorescent probes for in cellulo tracking of RNA/DNA G-quadruplexes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2019. [DOI: 10.1016/j.jphotochemrev.2019.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Ida J, Chan SK, Glökler J, Lim YY, Choong YS, Lim TS. G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing. Molecules 2019; 24:E1079. [PMID: 30893817 PMCID: PMC6471233 DOI: 10.3390/molecules24061079] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/14/2019] [Accepted: 03/16/2019] [Indexed: 12/05/2022] Open
Abstract
G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex architecture as well as the many forms of reporter systems ranging from absorbance to luminescence readouts in various platforms. Furthermore, some challenges and improvements that have been introduced to improve the application of G-quadruplex in diagnostics will be highlighted. As the field of diagnostics has evolved to apply different detection systems, the need for alternative reporter systems such as G-quadruplexes is also paramount.
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Affiliation(s)
- Jeunice Ida
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Jörn Glökler
- Division of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
| | - Yee Ying Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
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Esposito V, Russo A, Vellecco V, Bucci M, Russo G, Mayol L, Virgilio A, Galeone A. Thrombin binding aptamer analogues containing inversion of polarity sites endowed with antiproliferative and anti-motility properties against Calu-6 cells. Biochim Biophys Acta Gen Subj 2018; 1862:2645-2650. [PMID: 30071274 DOI: 10.1016/j.bbagen.2018.07.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/02/2018] [Accepted: 07/27/2018] [Indexed: 11/17/2022]
Abstract
BACKGROUND Although the thrombin binding aptamer (TBA) is endowed with both anticoagulant and antiproliferative properties, it is possible to reduce the first and enhance the second one by suitable chemical modifications. METHODS Two oligonucleotides (TBA353 and TBA535) based on the TBA sequence (GGTTGGTGTGGTTGG) and containing inversion of polarity sites have been investigated by CD, UV and electrophoretic techniques for their ability to form G-quadruplex structures. Furthermore, their anticoagulant (PT assay), antiproliferative (MTT assay) and anti-motility (wound healing assay) properties against Calu-6 cells have been tested and compared with TBA. RESULTS CD, UV and electrophoresis data indicate that both ODNs are able to form G-quadruplex structures. Particularly, results suggest that TBA535 adopts a G-quadruplex structure characterized by a loop arrangement different from that of TBA. Both TBA analogues drop the anticoagulant activity. However, TBA535 is endowed with a significant antiproliferative activity against lung cancer Calu-6 cells. Importantly, both TBA and TBA535 possess a remarkable anti-motility property against the same cell line. CONCLUSIONS Both TBA analogues TBA353 and TBA535 are able to form G-quadruplex structures with no anticoagulant activity. However only TBA535 is endowed with noteworthy antiproliferative and anti-motility properties against lung cancer Calu-6 cells. GENERAL SIGNIFICANCE The switching from the anticoagulant to antiproliferative property can be obtained also in TBA derivatives not adopting the "chair-like" G-quadruplex structure typical of TBA. Furthermore, results have highlighted an unprecedented anti-cell-motility property of TBA and TBA535 reinforcing the potential of these ODNs as anticancer drugs.
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Affiliation(s)
- Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Annapina Russo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Valentina Vellecco
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Mariarosaria Bucci
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Giulia Russo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Luciano Mayol
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy.
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy.
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Virgilio A, Russo A, Amato T, Russo G, Mayol L, Esposito V, Galeone A. Monomolecular G-quadruplex structures with inversion of polarity sites: new topologies and potentiality. Nucleic Acids Res 2017; 45:8156-8166. [PMID: 28666330 PMCID: PMC5737522 DOI: 10.1093/nar/gkx566] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 06/21/2017] [Indexed: 12/11/2022] Open
Abstract
In this paper, we report investigations, based on circular dichroism, nuclear magnetic resonance spectroscopy and electrophoresis methods, on three oligonucleotide sequences, each containing one 3′-3′ and two 5′-5′ inversion of polarity sites, and four G-runs with a variable number of residues, namely two, three and four (mTG2T, mTG3T and mTG4T with sequence 3′-TGnT-5′-5′-TGnT-3′-3′-TGnT-5′-5′-TGnT-3′ in which n = 2, 3 and 4, respectively), in comparison with their canonical counterparts (TGnT)4 (n = 2, 3 and 4). Oligonucleotides mTG3T and mTG4T have been proven to form very stable unprecedented monomolecular parallel G-quadruplex structures, characterized by three side loops containing the inversion of polarity sites. Both G-quadruplexes have shown an all-syn G-tetrad, while the other guanosines adopt anti glycosidic conformations. All oligonucleotides investigated have shown a noteworthy antiproliferative activity against lung cancer cell line Calu 6 and colorectal cancer cell line HCT-116 p53−/−. Interestingly, mTG3T and mTG4T have proven to be mostly resistant to nucleases in a fetal bovine serum assay. The whole of the data suggest the involvement of specific pathways and targets for the biological activity.
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Affiliation(s)
- Antonella Virgilio
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Annapina Russo
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Teresa Amato
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Giulia Russo
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Veronica Esposito
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Aldo Galeone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
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13
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Jackowiak P, Hojka-Osinska A, Gasiorek K, Stelmaszczuk M, Gudanis D, Gdaniec Z, Figlerowicz M. Effects of G-quadruplex topology on translational inhibition by tRNA fragments in mammalian and plant systems in vitro. Int J Biochem Cell Biol 2017; 92:148-154. [PMID: 28989078 DOI: 10.1016/j.biocel.2017.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 09/05/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023]
Abstract
The folding of tRNA fragments (tRFs) into G-quadruplex structures and the implications of G-quadruplexes in translational inhibition have been studied mainly in mammalian systems. To increase our knowledge of these phenomena, we determined the influence of human and plant tRFs and model G-quadruplexes on translation in rabbit reticulocyte lysate and wheat germ extract. The efficiency of translational inhibition in the mammalian system was strongly associated with the type of G-quadruplex topology. In the plant system, the ability of a small RNA to adopt the G-quadruplex conformation was not sufficient to repress translation, indicating the importance of other structural determinants.
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Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Hojka-Osinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Gasiorek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Michal Stelmaszczuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Dorota Gudanis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznan, Poland.
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Bhattacharyya D, Mirihana Arachchilage G, Basu S. Metal Cations in G-Quadruplex Folding and Stability. Front Chem 2016; 4:38. [PMID: 27668212 PMCID: PMC5016522 DOI: 10.3389/fchem.2016.00038] [Citation(s) in RCA: 381] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State UniversityKent, OH, USA
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15
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Esposito V, Pepe A, Filosa R, Mayol L, Virgilio A, Galeone A. A novel pyrimidine tetrad contributing to stabilize tetramolecular G-quadruplex structures. Org Biomol Chem 2016; 14:2938-43. [DOI: 10.1039/c5ob02358k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
5-Amino-2′-deoxyuridine forms an eight hydrogen-bonded tetrad stabilizing a parallel G-quadruplex structure more efficiently than tetrads formed by 5-bromo-2′-deoxyuridine and thymidine.
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Affiliation(s)
- V. Esposito
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Naples
- Italy
| | - A. Pepe
- Department of Science
- University of Basilicata
- Potenza
- Italy
| | - R. Filosa
- Department of Experimental Medicine
- Second University of Naples
- 80138 Napoli
- Italy
| | - L. Mayol
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Naples
- Italy
| | - A. Virgilio
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Naples
- Italy
| | - A. Galeone
- Department of Pharmacy
- University of Naples “Federico II”
- 80131 Naples
- Italy
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16
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Non-Flat Bisbenzylisoquinoline Alkaloid Fangchinoline As a Class of Potent G-Quadruplex Stabilizer with Anti-cancer Activity. CHINESE J CHEM 2015. [DOI: 10.1002/cjoc.201400841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Huang YC, Yu HZ, Sen D. DNA mechatronic devices switched by K+and by Sr2+are structurally, topologically, and electronically distinct. Biopolymers 2015; 103:460-8. [DOI: 10.1002/bip.22595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Yu Chuan Huang
- Department of Molecular Biology & Biochemistry; Simon Fraser University; Burnaby B C V5A 1S6 Canada
| | - Hua-Zhong Yu
- Department of Molecular Biology & Biochemistry; Simon Fraser University; Burnaby B C V5A 1S6 Canada
- Department of Chemistry; Simon Fraser University; Burnaby British Columbia V5A 1S6 Canada
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry; Simon Fraser University; Burnaby B C V5A 1S6 Canada
- Department of Chemistry; Simon Fraser University; Burnaby British Columbia V5A 1S6 Canada
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18
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Jeong JE, Kim B, Woo S, Hwang S, Bazan GC, Woo HY. Principal factors that determine the extension of detection range in molecular beacon aptamer/conjugated polyelectrolyte bioassays. Chem Sci 2015; 6:1887-1894. [PMID: 28706644 PMCID: PMC5494547 DOI: 10.1039/c4sc03258f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 12/22/2014] [Indexed: 01/09/2023] Open
Abstract
A strategy to extend the detection range of weakly-binding targets is reported that takes advantage of fluorescence resonance energy transfer (FRET)-based bioassays based on molecular beacon aptamers (MBAs) and cationic conjugated polyelectrolytes (CPEs). In comparison to other aptamer-target pairs, the aptamer-based adenosine triphosphate (ATP) detection assays are limited by the relatively weak binding between the two partners. In response, a series of MBAs were designed that have different stem stabilities while keeping the constant ATP-specific aptamer sequence in the loop part. The MBAs are labeled with a fluorophore and a quencher at both termini. In the absence of ATP, the hairpin MBAs can be opened by CPEs via a combination of electrostatic and hydrophobic interactions, showing a FRET-sensitized fluorophore signal. In the presence of ATP, the aptamer forms a G-quadruplex and the FRET signal decreases due to tighter contact between the fluorophore and quencher in the ATP/MBA/CPE triplex structure. The FRET-sensitized signal is inversely proportional to [ATP]. The extension of the detection range is determined by the competition between opening of the ATP/MBA G-quadruplex by CPEs and the composite influence by ATP/aptamer binding and the stem interactions. With increasing stem stability, the weak binding of ATP and its aptamer is successfully compensated to show the resistance to disruption by CPEs, resulting in a substantially broadened detection range (from millimolar up to nanomolar concentrations) and a remarkably improved limit of detection. From a general perspective, this strategy has the potential to be extended to other chemical- and biological-assays with low target binding affinity.
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Affiliation(s)
- Ji-Eun Jeong
- Department of Nanofusion Engineering , Department of Cogno-Mechatronics Engineering , Pusan National University , Miryang , Gyeongsangnam-do 627-706 , Republic of Korea .
| | - Boram Kim
- Department of Nanofusion Engineering , Department of Cogno-Mechatronics Engineering , Pusan National University , Miryang , Gyeongsangnam-do 627-706 , Republic of Korea .
| | - Shinjae Woo
- Department of Nanofusion Engineering , Department of Cogno-Mechatronics Engineering , Pusan National University , Miryang , Gyeongsangnam-do 627-706 , Republic of Korea .
| | - Sungu Hwang
- Department of Nanomechatronics Engineering , Pusan National University , Miryang , Gyeongsangnam-do 627-706 , Republic of Korea
| | - Guillermo C Bazan
- Department of Chemistry & Biochemistry , University of California , Santa Barbara , California 93106 , USA .
| | - Han Young Woo
- Department of Nanofusion Engineering , Department of Cogno-Mechatronics Engineering , Pusan National University , Miryang , Gyeongsangnam-do 627-706 , Republic of Korea .
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Sabharwal NC, Savikhin V, Turek-Herman JR, Nicoludis JM, Szalai VA, Yatsunyk LA. N-methylmesoporphyrin IX fluorescence as a reporter of strand orientation in guanine quadruplexes. FEBS J 2014; 281:1726-37. [PMID: 24494857 PMCID: PMC4163640 DOI: 10.1111/febs.12734] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/24/2013] [Accepted: 01/30/2014] [Indexed: 11/30/2022]
Abstract
Guanine quadruplexes (GQ) are four-stranded DNA structures formed by guanine-rich DNA sequences. The formation of GQs inhibits cancer cell growth, although the detection of GQs in vivo has proven difficult, in part because of their structural diversity. The development of GQ-selective fluorescent reporters would enhance our ability to quantify the number and location of GQs, ultimately advancing biological studies of quadruplex relevance and function. N-methylmesoporphyrin IX (NMM) interacts selectively with parallel-stranded GQs; in addition, its fluorescence is sensitive to the presence of DNA, making this ligand a possible candidate for a quadruplex probe. In the present study, we investigated the effect of DNA secondary structure on NMM fluorescence. We found that NMM fluorescence increases by about 60-fold in the presence of parallel-stranded GQs and by about 40-fold in the presence of hybrid GQs. Antiparallel GQs lead to lower than 10-fold increases in NMM fluorescence. Single-stranded DNA, duplex, or i-motif, induce no change in NMM fluorescence. We conclude that NMM shows promise as a 'turn-on' fluorescent probe for detecting quadruplex structures, as well as for differentiating them on the basis of strand orientation.
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Affiliation(s)
- Navin C Sabharwal
- Department of Chemistry and Biochemistry, Swarthmore College, PA, USA
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Virgilio A, Esposito V, Mayol L, Galeone A. More than one non-canonical phosphodiester bond in the G-tract: formation of unusual parallel G-quadruplex structures. Org Biomol Chem 2013; 12:534-40. [PMID: 24287516 DOI: 10.1039/c3ob41712c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this article, we report an investigation, based on NMR and CD spectroscopic and electrophoretic techniques, of 5'TGGGGT3' analogues containing two or three 3'-3' or 5'-5' inversion sites in the G-run, namely 5'TG3'-3'G5'-5'GGT3' (Q350), 5'TG3'-3'GG5'-5'GT3' (Q305), 5'TGG3'-3'G5'-5'GT3' (Q035), 5'TG3'-3'G5'-5'G3'-3'GT5' (Q353) and 3'TG5'-5'G3'-3'G5'-5'GT3' (Q535). Although the sequences investigated contain either no or only one natural 3'-5' linkage in the G-tract, all modified oligodeoxyribonucleotides (ODNs) have been shown to form stable tetramolecular quadruplex structures. The ability of the 3'-3' or 5'-5' inversion sites to affect the glycosidic conformation of guanosines and, consequently, base stacking, has also been investigated. The results of this study allow us to propose some generalizations concerning strand arrangements and the glycosidic conformational preference of residues adjacent to inverted polarity sites. These rules could be of general interest in the design of modified quadruplex structures, in view of their application as G-wires and modified aptamers.
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Affiliation(s)
- Antonella Virgilio
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, 80131 Naples, Italy.
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Do NQ, Phan AT. Monomer-dimer equilibrium for the 5'-5' stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study. Chemistry 2012; 18:14752-9. [PMID: 23019076 DOI: 10.1002/chem.201103295] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Indexed: 01/24/2023]
Abstract
Guanine-rich sequence motifs, which contain tracts of three consecutive guanines connected by single non-guanine nucleotides, are abundant in the human genome and can form a robust G-quadruplex structure with high stability. Herein, by using NMR spectroscopy, we investigate the equilibrium between monomeric and 5'-5' stacked dimeric propeller-type G-quadruplexes that are formed by DNA sequences containing GGGT motifs. We show that the monomer-dimer equilibrium depends on a number of parameters, including the DNA concentration, DNA flanking sequences, the concentration and type of cations, and the temperature. We report on the high-definition structure of a simple monomeric G-quadruplex containing three single-residue loops, which could serve as a reference for propeller-type G-quadruplex structures in solution.
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Affiliation(s)
- Ngoc Quang Do
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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22
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Virgilio A, Esposito V, Citarella G, Pepe A, Mayol L, Galeone A. The insertion of two 8-methyl-2'-deoxyguanosine residues in tetramolecular quadruplex structures: trying to orientate the strands. Nucleic Acids Res 2011; 40:461-75. [PMID: 21908403 PMCID: PMC3245916 DOI: 10.1093/nar/gkr670] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this article, we report a structural study, based on NMR and CD spectroscopies, and molecular modelling of all possible d(TG3T) and d(TG4T) analogues containing two 8-methyl-2′-deoxyguanosine residues (M). Particularly, the potential ability of these modified residues to orientate the strands and then to affect the folding topology of tetramolecular quadruplex structures has been investigated. Oligodeoxynucleotides (ODNs) TMMGT (T12) and TMMGGT (F12) form parallel tetramolecular quadruplexes, characterized by an all-syn M-tetrad at the 5′-side stacked to all-anti M- and G-tetrads. ODNs TMGMT (T13) and TMGGMT (F14) form parallel tetramolecular quadruplexes, in which an all-anti G core is sandwiched between two all-syn M-tetrads at the 5′- and the 3′-side. Notably, the quadruplex formed by T13 corresponds to an unprecedented structure in which the syn residues exceed in number the anti ones. Conversely, ODN TGMGMT (F24) adopts a parallel arrangement in which all-anti G-tetrads alternate with all-syn M-tetrads. Most importantly, all data strongly suggest that ODN TMGMGT (F13) forms an unprecedented anti-parallel tetramolecular quadruplex in which G and M residues adopt anti and syn glycosidic conformations, respectively. This article opens up new understandings and perspectives about the intricate relationship between the quadruplex strands orientation and the glycosidic conformation of the residues.
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Affiliation(s)
- Antonella Virgilio
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, I-80131 Napoli, Italy
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Li Q, Xiang J, Li X, Chen L, Xu X, Tang Y, Zhou Q, Li L, Zhang H, Sun H, Guan A, Yang Q, Yang S, Xu G. Stabilizing parallel G-quadruplex DNA by a new class of ligands: two non-planar alkaloids through interaction in lateral grooves. Biochimie 2009; 91:811-9. [PMID: 19318115 DOI: 10.1016/j.biochi.2009.03.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 03/12/2009] [Indexed: 01/11/2023]
Abstract
Human DNA sequences consisting of tandem guanine (G) nucleotides can fold into a four-stranded structure named G-quadruplex via Hoogsteen hydrogen bonding. As the sequences forming G-quadruplex exist in essential regions of eukaryotic chromosomes and are involved in many important biological processes, the study of their biological functions has currently become a hotspot. Compounds selectively binding and stabilizing G-quadruplex structures have the potential to inhibit telomerase activity or alter oncogene expression levels and thus may act as antitumor agents. Most of reported G-quadruplex ligands generally have planar structures which stabilize G-quadruplex by pi-pi stacking. However, based on a pharmacophore-based virtual screening two non-planar G-quadruplex ligands were found. These two ligands exhibit good capability for G-quadruplex stabilization and prefer binding to paralleled G-quadruplex rather than to duplex DNA. The binding of these ligands to G-quadruplex may result from groove binding at a 2:1 stoichiometry. These results have shown that planar structures are not essential for G-quadruplex stabilizers, which may represent a new class of G-quadruplex-targeted agents as potential antitumor drugs.
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Affiliation(s)
- Qian Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China
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Effects of the introduction of inversion of polarity sites in the quadruplex forming oligonucleotide TGGGT. Bioorg Med Chem 2009; 17:1997-2001. [PMID: 19217303 DOI: 10.1016/j.bmc.2009.01.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 01/13/2009] [Accepted: 01/14/2009] [Indexed: 11/23/2022]
Abstract
Insight into the influence of inversion of polarity sites on the structural features of quadruplex structures is presented. The NMR and CD studies concern modified oligodeoxynucleotides (ODNs) based on the quadruplex forming sequence TGGGT. The presence of inversion of polarity sites not only does not compromise the formation of quadruplexes, but in some cases it increases the thermal stability of modified complexes compared with that of the unmodified one.
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Lane AN, Chaires JB, Gray RD, Trent JO. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res 2008; 36:5482-515. [PMID: 18718931 PMCID: PMC2553573 DOI: 10.1093/nar/gkn517] [Citation(s) in RCA: 571] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 07/26/2008] [Accepted: 07/29/2008] [Indexed: 12/30/2022] Open
Abstract
In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.
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Affiliation(s)
- Andrew N Lane
- Structural Biology Program, JG Brown Cancer Center, University of Louisville, KY 40202, USA.
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